diff --git a/refs/heads/MOP3/.buildinfo b/refs/heads/MOP3/.buildinfo new file mode 100644 index 0000000..fca73bb --- /dev/null +++ b/refs/heads/MOP3/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 4dc3b1b5f2582bb3fc7bd1eb47eda37b +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/refs/heads/MOP3/.doctrees/about.doctree b/refs/heads/MOP3/.doctrees/about.doctree new file mode 100644 index 0000000..a637ceb Binary files /dev/null and b/refs/heads/MOP3/.doctrees/about.doctree differ diff --git a/refs/heads/MOP3/.doctrees/benchmark.doctree b/refs/heads/MOP3/.doctrees/benchmark.doctree new file mode 100644 index 0000000..e632200 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/benchmark.doctree differ diff --git a/refs/heads/MOP3/.doctrees/changelog.doctree b/refs/heads/MOP3/.doctrees/changelog.doctree new file mode 100644 index 0000000..4075bb8 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/changelog.doctree differ diff --git a/refs/heads/MOP3/.doctrees/ci.doctree b/refs/heads/MOP3/.doctrees/ci.doctree new file mode 100644 index 0000000..6fac653 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/ci.doctree differ diff --git a/refs/heads/MOP3/.doctrees/environment.pickle b/refs/heads/MOP3/.doctrees/environment.pickle new file mode 100644 index 0000000..4bbc916 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/environment.pickle differ diff --git a/refs/heads/MOP3/.doctrees/index.doctree b/refs/heads/MOP3/.doctrees/index.doctree new file mode 100644 index 0000000..39314ea Binary files /dev/null and b/refs/heads/MOP3/.doctrees/index.doctree differ diff --git a/refs/heads/MOP3/.doctrees/install.doctree b/refs/heads/MOP3/.doctrees/install.doctree new file mode 100644 index 0000000..fec4769 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/install.doctree differ diff --git a/refs/heads/MOP3/.doctrees/mop_consensus.doctree b/refs/heads/MOP3/.doctrees/mop_consensus.doctree new file mode 100644 index 0000000..1aeb2ab Binary files /dev/null and b/refs/heads/MOP3/.doctrees/mop_consensus.doctree differ diff --git a/refs/heads/MOP3/.doctrees/mop_mod.doctree b/refs/heads/MOP3/.doctrees/mop_mod.doctree new file mode 100644 index 0000000..3ac2c65 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/mop_mod.doctree differ diff --git a/refs/heads/MOP3/.doctrees/mop_preprocess.doctree b/refs/heads/MOP3/.doctrees/mop_preprocess.doctree new file mode 100644 index 0000000..fc9dc87 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/mop_preprocess.doctree differ diff --git a/refs/heads/MOP3/.doctrees/mop_tail.doctree b/refs/heads/MOP3/.doctrees/mop_tail.doctree new file mode 100644 index 0000000..de3045a Binary files /dev/null and b/refs/heads/MOP3/.doctrees/mop_tail.doctree differ diff --git a/refs/heads/MOP3/.doctrees/reporting.doctree b/refs/heads/MOP3/.doctrees/reporting.doctree new file mode 100644 index 0000000..281bdb7 Binary files /dev/null and b/refs/heads/MOP3/.doctrees/reporting.doctree differ diff --git a/refs/heads/MOP3/.doctrees/troubleshooting.doctree b/refs/heads/MOP3/.doctrees/troubleshooting.doctree new file mode 100644 index 0000000..c69b7bf Binary files /dev/null and b/refs/heads/MOP3/.doctrees/troubleshooting.doctree differ diff --git a/refs/heads/MOP3/.nojekyll b/refs/heads/MOP3/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/refs/heads/MOP3/_images/epinano.png b/refs/heads/MOP3/_images/epinano.png new file mode 100644 index 0000000..e505434 Binary files /dev/null and b/refs/heads/MOP3/_images/epinano.png differ diff --git a/refs/heads/MOP3/_images/flow_mod.png b/refs/heads/MOP3/_images/flow_mod.png new file mode 100644 index 0000000..c4fd291 Binary files /dev/null and b/refs/heads/MOP3/_images/flow_mod.png differ diff --git a/refs/heads/MOP3/_images/flow_preproc.png b/refs/heads/MOP3/_images/flow_preproc.png new file mode 100644 index 0000000..ae9ec09 Binary files /dev/null and b/refs/heads/MOP3/_images/flow_preproc.png differ diff --git a/refs/heads/MOP3/_images/flow_tail.png b/refs/heads/MOP3/_images/flow_tail.png new file mode 100644 index 0000000..c134066 Binary files /dev/null and b/refs/heads/MOP3/_images/flow_tail.png differ diff --git a/refs/heads/MOP3/_images/goku3.png b/refs/heads/MOP3/_images/goku3.png new file mode 100644 index 0000000..d227000 Binary files /dev/null and b/refs/heads/MOP3/_images/goku3.png differ diff --git a/refs/heads/MOP3/_images/mod_corr.png b/refs/heads/MOP3/_images/mod_corr.png new file mode 100644 index 0000000..1c9bda9 Binary files /dev/null and b/refs/heads/MOP3/_images/mod_corr.png differ diff --git a/refs/heads/MOP3/_images/nanocons.png b/refs/heads/MOP3/_images/nanocons.png new file mode 100644 index 0000000..3312e6b Binary files /dev/null and b/refs/heads/MOP3/_images/nanocons.png differ diff --git a/refs/heads/MOP3/_images/res_report.png b/refs/heads/MOP3/_images/res_report.png new file mode 100644 index 0000000..68c9d59 Binary files /dev/null and b/refs/heads/MOP3/_images/res_report.png differ diff --git a/refs/heads/MOP3/_images/tower.gif b/refs/heads/MOP3/_images/tower.gif new file mode 100644 index 0000000..c992b6c Binary files /dev/null and b/refs/heads/MOP3/_images/tower.gif differ diff --git a/refs/heads/MOP3/_images/tower.png b/refs/heads/MOP3/_images/tower.png new file mode 100644 index 0000000..7fee909 Binary files /dev/null and b/refs/heads/MOP3/_images/tower.png differ diff --git a/refs/heads/MOP3/_images/tower2.png b/refs/heads/MOP3/_images/tower2.png new file mode 100644 index 0000000..84b7189 Binary files /dev/null and b/refs/heads/MOP3/_images/tower2.png differ diff --git a/refs/heads/MOP3/_images/tower_eli1.png b/refs/heads/MOP3/_images/tower_eli1.png new file mode 100644 index 0000000..2713142 Binary files /dev/null and b/refs/heads/MOP3/_images/tower_eli1.png differ diff --git a/refs/heads/MOP3/_sources/about.rst.txt b/refs/heads/MOP3/_sources/about.rst.txt new file mode 100644 index 0000000..86f016c --- /dev/null +++ b/refs/heads/MOP3/_sources/about.rst.txt @@ -0,0 +1,51 @@ +.. _home-page-about: + +******************* +About Master of Pores 3 +******************* + +.. autosummary:: + :toctree: generated + + +.. |docker| image:: https://img.shields.io/badge/Docker-v20.10.8-blue +.. |status| image:: https://github.com/biocorecrg/master_of_pores/actions/workflows/build.yml/badge.svg +.. |license| image:: https://img.shields.io/badge/License-MIT-yellow.svg +.. |nver| image:: https://img.shields.io/badge/Nextflow-21.04.1-brightgreen +.. |sing| image:: https://img.shields.io/badge/Singularity-v3.2.1-green.svg + +.. list-table:: + :widths: 10 10 10 10 10 + :header-rows: 0 + + * - |docker| + - |status| + - |license| + - |nver| + - |sing| + +`Master of Pores 3 `_ is a collection of pipelines written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc. + +The software is composed by four pipelines: + + - mop_preprocess: preprocessing of input data. Basecalling, demultiplexing, alignment, read counts, and more! + - mop_mod: detecting chemical modifications. It reads the output directly from mop_preprocess + - mop_tail: estimating polyA tail size. It reads the output directly from mop_preprocess + - mop_consensus: it generates a consensus from the predictions from mop_mod. It reads the output directly from mop_mod + +The name is inspired by Metallica's `Master Of Puppets `_ + +.. image:: ../img/goku3.png + :width: 600 + +This is a joint project between `CRG bioinformatics core `_ and `Epitranscriptomics and RNA Dynamics research group `_. + + +Reference +====================== + +If you use this tool, please cite our papers: + +`"Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores" `__ Cozzuto L, Delgado-Tejedor A, Hermoso Pulido T, Novoa EM, Ponomarenko J. N. Methods Mol Biol. 2023;2624:185-205. doi: 10.1007/978-1-0716-2962-8_13. + +`"MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets" `_ Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva Maria Novoa. Front. Genet., 17 March 2020. diff --git a/refs/heads/MOP3/_sources/benchmark.rst.txt b/refs/heads/MOP3/_sources/benchmark.rst.txt new file mode 100644 index 0000000..d16faa7 --- /dev/null +++ b/refs/heads/MOP3/_sources/benchmark.rst.txt @@ -0,0 +1,35 @@ +******************* +Benchmark +******************* + +We tested MoP on two minION runs using the CRG's HPC where we can run up to 100 jobs in parallel (maximum 8 CPUs each) and using up to 10 GPU cards (GeForce RTX 2080 Ti). The test dataset was published at `ENA `_ with the accession `ERR5296640 `__ for pU samples and `ERR5303454 `__ for Nm samples. + + + +.. list-table:: Dataset + + * - + - MOP_PREPROCESS + - MOP_MOD + - MOP_TAIL + - MOP_CONSENSUS + * - Input data + - 95 Gb + - 137 Gb + - 137 Gb + - 14 Mb + * - Execution time + - 10 hours + - 6 hours + - 2.5 hours + - 3 mins + * - Work folder + - 382 Gb + - 595 Gb + - 3 Gb + - 25 Mb + * - Output folder + - 137 Gb + - 14 Mb + - 76 Mb + - 13 Mb diff --git a/refs/heads/MOP3/_sources/changelog.rst.txt b/refs/heads/MOP3/_sources/changelog.rst.txt new file mode 100644 index 0000000..d06a81e --- /dev/null +++ b/refs/heads/MOP3/_sources/changelog.rst.txt @@ -0,0 +1,74 @@ +.. _home-page-changelog: + +************** +CHANGELOG +************** + +.. autosummary:: + :toctree: generated + +Version 3.0 +================ +* mop_preprocess + * We added a custom model for m6A basecalling. It is automatically installed when running INSTALL.sh. For using it you need to indicated ``--pars_tools "drna_tool_splice_m6A_opt.tsv" `` + * We add support to cuda11 for guppy version > 4.4.1. + * Added readucks for improving demultiplexing with guppy (optional). + * New parameter "barcodes" where you can specify a file with barcodes to be kept. Example in **keep_barcodes.txt** + * Adding a `new model for direct RNA basecalling `__. + * Added support to dorado basecalling. Not yet supported the demultiplexing + * Also guppy version >= 6.5.x are supported. No need for indicating different command lines for different guppy versions inside tool_opts. The pipeline will get the version and act accordingly + * pod5 are supported for dorado and guppy >= 6.5.x. No fast5 and stats files will be output. This will limit other pipelines. + +* mop_tail + * we upgraded tailfindR to version 1.3 + * Tailfinder can be used either in standard mode or nano3p mode (chemistry R10 and R9) by specifying the *tailfindr_mode* to: standard, n3ps_r9 or n3ps_r10. + + + +Version 2.0 +================ + +* Completely rewritten using the powerful `DSL2 `__. +* Subworkflows are stored in the independent repository `BioNextflow `__. +* Global nextflow config is broken down to different profiles (cluster, cloud, local...) +* Added the new module **mop_consensus** + +* mop_preprocess (formerly known as nanoPreprocess + nanoPreprocessSimple) + * now can read multiple runs per time using the syntax **"PATH/\*\*/*.fast5"** + * can demultiplex fast5 using guppy too + * deeplexicon can be run on GPU too + * Parameters of each tool are stored in a tsv file. We have different ones already pre-set for cDNA, DNA and dRNA (option **--pars_tools**) + * Added new process **discovery** with bambu / isoquant for discovering and quantifying new transcripts. + * demultiplexing, filtering, mapping, counting and discovery can be switched off by setting "NO" as a parameter + * saveSpace can be set to "YES" to reduce the amount of disk space required. **WARNING This will prevent the possibility to resume!** + * Merged old NanoPreprocess and NanoPreprocessSimple in **mop_preprocess**. Using fastq or fast5 will switch among the two executions. + * Htseq-count now accepts alignments generated by minimap2. https://github.com/htseq/htseq/issues/33 + * We can specify a **final_summary_**.txt** for extracting kit and flowcell info in the params.config file. If not present we should specify those info or a custom model via extra parameters in one of the **\*_opt.tsv** files or guppy will trigger an error. + * This module can be run in AWS BATCH using the profile **awsbatch** + * demultiplexing of fast5 with deeplexicon is now faster thanks to multithreading and parallelization + +* mop_tail (formerly known as nanoTail) + * now you can launch each analysis independently + * Fine tuning of parameter for each step in tools_opt.tsv + +* mop_mod (formerly known as nanoMod) + * coming SOON! + +Version 1.1 +================= + +* Added a new module called NanoPreprocessSimple that starts from fastq files instead of fast5 files. It allows the analysis of multiple files at a time. +* Added support to vbz compressed fast5 https://github.com/nanoporetech/vbz_compression in NanoPreprocess, NanoMod and NanoTail +* NanoPreprocess now outputs also CRAM files and can do downsampling with the parameter --downsampling +* NanoPreprocess allows performing variant calling using medaka (BETA) +* NanoPreprocess allows performing demultiplexing with GUPPY +* Added plots for Epinano output in NanoMod +* Added a conversion of Tombo results in bed format in NanoMod +* Added a INSTALL.sh file for automatically retrieve guppy 3.4.5 from https://mirror.oxfordnanoportal.com/, place it in NanoPreprocess/bin and making the required links +* Added profiles for being used locally and on the CRG SGE cluster + + +Version 1.0 +================ + +This is the original version published in the paper `MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets `__ diff --git a/refs/heads/MOP3/_sources/ci.rst.txt b/refs/heads/MOP3/_sources/ci.rst.txt new file mode 100644 index 0000000..29fa25b --- /dev/null +++ b/refs/heads/MOP3/_sources/ci.rst.txt @@ -0,0 +1,18 @@ +.. _home-page-about: + +******************* +Continuous integration +******************* + +.. autosummary:: + :toctree: generated + +The following pipelines are continuously checked using GitHub actions: + +* mop_preprocess +* mop_mod +* mop_tail + +.. image:: https://github.com/biocorecrg/master_of_pores/actions/workflows/build.yml/badge.svg + :target: https://github.com/biocorecrg/master_of_pores + :alt: pipeline status diff --git a/refs/heads/MOP3/_sources/index.rst.txt b/refs/heads/MOP3/_sources/index.rst.txt new file mode 100644 index 0000000..940d71f --- /dev/null +++ b/refs/heads/MOP3/_sources/index.rst.txt @@ -0,0 +1,43 @@ +.. _home-page-index: + +******************* +Welcome to the documentation of Master Of Pores 3 +******************* + + +.. autosummary:: + :toctree: generated + +.. image:: ../img/goku3.png + :width: 600 + +Master of Pores is a pipeline written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc. + +The pipeline is composed by four modules: + - mop_preprocess: preprocessing + - mop_mod: detecting chemical modifications. It reads the output directly from mop_preprocess + - mop_tail: estimating polyA tail size. It reads the output directly from mop_preprocess + - mop_consensus: it generates a consensus from the predictions from mop_mod. It reads the output directly from mop_mod + +.. MoP3 documentation master file, created by + Luca Cozzuto. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Contents: + +.. toctree:: + :maxdepth: 1 + + about + install + mop_preprocess + mop_mod + mop_consensus + mop_tail + reporting + awsbatch + benchmark + changelog + ci + troubleshooting diff --git a/refs/heads/MOP3/_sources/install.rst.txt b/refs/heads/MOP3/_sources/install.rst.txt new file mode 100644 index 0000000..c00b572 --- /dev/null +++ b/refs/heads/MOP3/_sources/install.rst.txt @@ -0,0 +1,72 @@ +.. _home-page-install: + +************** +Get Started +************** + +.. autosummary:: + :toctree: generated + +Please install nextflow `Nextflow `_ and either `Singularity `_ or `Docker `_ before. + +For installing Nextflow you need a POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and Java 11 (or later, up to 17). Windows system is supported through WSL. For the installation of Nextflow just run: + +.. code-block:: console + + curl -s https://get.nextflow.io | bash + +To install the pipeline you need to download the repo: + +.. code-block:: console + + git clone --depth 1 --recurse-submodules https://github.com/biocorecrg/master_of_pores.git + +Installing Guppy +============ + +You can use **INSTALL.sh** and the version of Guppy you want to download. + +.. note:: + + Please consider that the support of VBZ compression of fast5 started with version 3.4.X. + + +.. code-block:: console + + cd master_of_pores; bash INSTALL.sh 6.0.1 + +or for installing the default 3.4.5 + +.. code-block:: console + + cd master_of_pores; bash INSTALL.sh + +Guppy custom models for RNA basecalling will be downloaded from our repository https://biocore.crg.eu/public/mop3_pub/models.tar and placed automatically within the right path inside the pipeline. + +You can install different versions of Guppy but only one will be run during the pipeline execution. For switching among them you need to run INSTALL.sh with the version you prefer. + +Testing +============ + +.. code-block:: console + + cd mop_preprocess + + nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-singularity -bg -profile local > log + +.. tip:: + + You can replace ```-with-singularity``` with ```-with-docker``` if you want to use the docker engine. + +Profiles +============ +Some nextflow configuration files are stored within the folder **conf** and can be selected using different profiles. Currently, we have: + +- ci: for continuous integration testing (low resources) +- local: for being used in a laptop without GPU support +- m1mac: for running the containers in emulation for being used on M1/M2/M3 Apple processors. +- sge: for being used in an HPC with Sun Grid Engine +- cluster or crg: for being used in the custom HPC environment at CRG +- slurm: for being used in an HPC with SLURM +- awsbatch: for being used in Amazon AWS cloud infrastructure + diff --git a/refs/heads/MOP3/_sources/mop_consensus.rst.txt b/refs/heads/MOP3/_sources/mop_consensus.rst.txt new file mode 100644 index 0000000..8371cfc --- /dev/null +++ b/refs/heads/MOP3/_sources/mop_consensus.rst.txt @@ -0,0 +1,63 @@ +.. _home-page-mopconsensus: + +******************* +MOP_CONSENSUS +******************* + +.. autosummary:: + :toctree: generated + +This pipeline takes as input the output from MOP_MOD with all the four worklows. It outputs the consensus of the diferent predictions running the tool `Nanoconsensus `__ in parallel on each transcript for each comparison. + + +Input Parameters +====================== + +The input parameters are stored in yaml files like the one represented here: + +.. literalinclude:: ../mop_consensus/params.yaml + :language: yaml + + +How to run the pipeline +============================= + +Before launching the pipeline,user should: + +1. Decide which containers to use - either docker or singularity **[-with-docker / -with-singularity]**. +2. Fill in both **params.config** and **tools_opt.tsv** files. + +To launch the pipeline, please use the following command: + +.. code-block:: console + + nextflow run mop_consensus.nf -params-file params.yaml -with-singularity > log.txt + + +You can run the pipeline in the background adding the nextflow parameter **-bg**: + +.. code-block:: console + + nextflow run mop_consensus.nf -params-file params.yaml -with-singularity -bg > log.txt + +You can change the parameters either by changing **params.config** file or by feeding the parameters via command line: + +.. code-block:: console + + nextflow run mop_consensus.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt + + +You can specify a different working directory with temporary files: + +.. code-block:: console + + nextflow run mop_consensus.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt + + +Results +==================== + +Here an example of a result: + +.. image:: ../img/nanocons.png + :width: 800 diff --git a/refs/heads/MOP3/_sources/mop_mod.rst.txt b/refs/heads/MOP3/_sources/mop_mod.rst.txt new file mode 100644 index 0000000..597280c --- /dev/null +++ b/refs/heads/MOP3/_sources/mop_mod.rst.txt @@ -0,0 +1,127 @@ +.. _home-page-mopmod: + +******************* +MOP_MOD +******************* + +.. autosummary:: + :toctree: generated + +This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files and unspliced alignments to the transcriptome . It runs four different RNA detection algorithms (Epinano, Nanopolish, Tombo and Nanocompore) and it outputs the predictions generated by each one of them as individual tab-delimited files. + +.. image:: ../img/flow_mod.png + :width: 600 + :alt: mop_mod graph + +Input Parameters +====================== + +The input parameters are stored in yaml files like the one represented here: + +.. literalinclude:: ../mop_mod/params.yaml + :language: yaml + + + +How to run the pipeline +============================= + +Before launching the pipeline, user should: + +1. Decide which containers to use - either docker or singularity **[-with-docker / -with-singularity]**. +2. Fill in both **params.yaml** and **tools_opt.tsv** files. +3. Fill in **comparison.tsv** file - please see example below: + +.. code-block:: console + + wt_1 ko_1 + wt_2 ko_2 + + +To launch the pipeline, please use the following command: + +.. code-block:: console + + nextflow run mop_mod.nf -params-file params.yaml -with-singularity > log.txt + + +You can run the pipeline in the background adding the nextflow parameter **-bg**: + +.. code-block:: console + + nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg > log.txt + +You can change the parameters either by changing **params.config** file or by feeding the parameters via command line: + +.. code-block:: console + + nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt + + +You can specify a different working directory with temporary files: + +.. code-block:: console + + nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt + + +Results +==================== + +Several folders are created by the pipeline within the output directory specified by the **output** parameter: + +1. **Epinano** results are stored in **epinano_flow** directory. It contains two files per sample: one containing data at position level and the other, at 5-mer level. Different features frequencies as well as quality data are included in the results. See example below: + +.. code-block:: console + + #Ref,pos,base,cov,q_mean,q_median,q_std,mis,ins,del + gene_A,2515,C,45497.0,5.36995,4.00000,3.97797,0.0822032221904741,0.18715519704595907,0.2058377475437941 + gene_A,2516,A,45504.0,5.38207,4.00000,4.71619,0.17128164556962025,0.20497099156118143,0.07733386075949367 + gene_A,2517,C,45529.0,6.92130,5.00000,5.04250,0.06165301236574491,0.1505633771881658,0.13540820136616222 + gene_A,2518,A,45545.0,6.49821,5.00000,5.47485,0.10802503018992206,0.10855198155670216,0.2082775277198375 + gene_A,2519,T,45557.0,6.51247,5.00000,4.81853,0.09386043857145993,0.14792457800118533,0.2033057488421099 + +Here an example of a plot from Epinano: + +.. image:: ../img/epinano.png + :width: 350 + +2. **Tombo** results are stored in **tombo_flow** directory. It contains one file per comparison. It reports the p-value per position, the sum of p-values per 5-mer and coverage in both WT and KO. See example below: + +.. code-block:: console + + "Ref_Position" "Chr" "Position" "Tombo_SiteScore" "Coverage_Sample" "Coverage_IVT" "Tombo_KmerScore" + "gene_A_3" "gene_A" "3" "0.0000" "92" "87" NA + "gene_A_4" "gene_A" "4" "0.0000" "92" "87" NA + "gene_A_5" "gene_A" "5" "0.0000" "92" "87" 0 + "gene_A_6" "gene_A" "6" "0.0000" "93" "88" 0.0014 + "gene_A_7" "gene_A" "7" "0.0000" "95" "89" 0.0027 + "gene_A_8" "gene_A" "8" "0.0014" "95" "89" 0.004 + + +3. **Nanopolish** results are stored in **nanopolish-compore_flow** directory. It contains two files per sample: raw eventalign output (gzipped) and another with the median raw current per position and transcript (**sample_processed_perpos_median.tsv.gz**). See example below: + +.. code-block:: console + + contig position reference_kmer read_name median coverage + gene_A 0 AAATT 1 113.35 433 + gene_A 1 AATTG 1 97.24 506 + gene_A 2 ATTGA 1 70.35 2034 + gene_A 3 TTGAA 1 102.03 416 + gene_A 4 TGAAG 1 115.315 422 + gene_A 5 GAAGA 1 104.25 471 + +4. **Nanocompore** results are stored in **nanopolish-compore_flow** directory. It contains one file per comparison (**wt_1_vs_ko_1_nanocompore_results.tsv**). Default output from Nanocompore (see Nanocompore's repository for a more detailed explanation). + +Encoding of modification information from m6A-aware basecalled data using modPhred +===================================================================================== + +Once the data has been basecalled with our m6A modification-aware basecalling model, modification information data should be encoded for its later downstream analysis. This step is performed by **modPhred**, another software included in the **mop_mod** module. + +To run this software, in the ``params.yaml`` file you should specify ``modphred: "YES"`` and run the code below: + +.. code-block:: console + + cd mop_mod + nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg > yourlog.txt + diff --git a/refs/heads/MOP3/_sources/mop_preprocess.rst.txt b/refs/heads/MOP3/_sources/mop_preprocess.rst.txt new file mode 100644 index 0000000..1dd2273 --- /dev/null +++ b/refs/heads/MOP3/_sources/mop_preprocess.rst.txt @@ -0,0 +1,225 @@ +.. _home-page-moprepr: + +******************* +MOP_PREPROCESS +******************* + +.. autosummary:: + :toctree: generated + +This pipeline takes as input the raw fast5 reads - single or multi - and it produces several outputs (basecalled fast5, sequences in fastq format, aligned reads in BAM format etc). The pre-processing pipeline can perform base-calling, demultiplexing (optional), filtering, quality control, mapping to a reference (either a genome or a transcriptome), feature counting, discovery of novel transcripts, and it generates a final report with the performance and results of each of the steps performed. + +It automatically detects the kind of input fast5 file (single or multi-sequence). It can also support the new pod5 format but it won't output basecalled fastq useful for the other pipelines. The basecalling can be performed with guppy or dorado and the demultiplexing with either guppy, seqtagger, or deeplexicon. Basecalled fastq and Fast5 files can be demultiplexed as well. You can restrict the number of barcodes by indicating a file with barcode list using the **barcodes** parameter. + + +.. image:: ../img/flow_preproc.png + :width: 600 + :alt: mop_preprocess graph + + + +Input Parameters +====================== + +The input parameters are stored in yaml files like the one represented here: + +.. literalinclude:: ../mop_preprocess/params.f5.demrna.yaml + :language: yaml + +You can change them by editing this file or using the command line as explained in the next section. + + +.. tip:: + + In the case of pod5 as input files, you can use them as they were fast5 with dorado or guppy >= 6.5.x. The only limitation is that you cannot obtain basecalled fast5 so you cannot use the other pipelines that need fast5 as input files. + + + +How to run the pipeline +============================= + +Before launching the pipeline, the user can decide which containers to use: either docker or singularity **[-with-docker / -with-singularity]**. + +Then, to launch the pipeline, please use the following command by specifying the path of the yaml parameter file: + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml > log.txt + + +You can run the pipeline in the background by adding the nextflow parameter **-bg**: + +.. code-block:: console + + nextflow run mop_preprocess.nf -params-file params.yaml -with-singularity -bg > log.txt + +You can change the parameters either by changing the yaml config file or by feeding the parameters via command line: + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml -bg --output test2 > log.txt + + +You can specify a different working directory with temporary files: + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml -bg -w /path/working_directory > log.txt + +You can use different profiles for running the pipeline in different environments. We have one set up for HPC using the SGE scheduler: + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile cluster > log.txt + +One for HPC using the slurm scheduler + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile slurm > log.txt + +One for emulating the new M1 processor for Apple: + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile m1mac > log.txt + + +or you can run the pipeline locally: + +.. code-block:: console + + nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile local > log.txt + + +.. note:: + + * In case of errors you can troubleshoot by seeing the log file (log.txt) for more details. Furthermore, if more information is needed, you can also go to the intermediate directory indicated in the log and check both the `.command.log` and `.command.err` files. + +.. tip:: + + Once the error has been solved or if you change a specific parameter, you can resume the execution with the **Netxtlow** parameter **- resume** (only one dash!). If there is an error, the pipeline will resume from the process that had the error and proceed with the rest. If you change a parameter, only the processes affected by this parameter will be re-run. + + +.. code-block:: console + nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml -bg -resume > log_resumed.txt + + To check whether the pipeline has been resumed properly, please check the log file. If previous correctly executed processes are found as *Cached*, the resume worked! + +.. code-block:: console + + ... + + [warm up] executor > crg + [9d/82eeaa] Cached process > checkRef (Checking yeast_rRNA_ref.fa.gz) + [33/b8d053] Submitted process > BASECALL:GUPPY_VERSION:getVersion + [e5/e5c990] Submitted process > BASECALL:GUPPY65_BASECALL:baseCallNew (mod---2) + [b5/0997da] Submitted process > BASECALL:GUPPY65_BASECALL:baseCallNew (wt---1) + [fb/6353d6] Submitted process > SEQFILTER:NANOQ_FILTER:filter (mod---2) + ... + +.. note:: + To resume the execution, temporary files generated previously by the pipeline must be kept. Otherwise, the pipeline will re-start from the beginning. + +tool_opts +==================== + +The command line options for each tool used in the pipeline are stored within specialized tsv files stored within the *tool_opts* folder. Here is an example: + +.. literalinclude:: ../mop_preprocess/tool_opts/drna_tool_m6A_splice_opt.tsv + +The first column indicates the processing step as **basecalling** or **demultiplexing** etc. Some tools such as Guppy can be used for more processing steps. Several pre-compiled tool_opts files are stored within the folder **tool_opts**. + +.. note:: + Readucks is run after guppy demultiplexing. It refines the demultiplexing generating different fastqs + +.. tip:: + You don't need to specify the whole path for the models of seqtagger, just the name of the model will be enough + + +Model libraries for specific tools +==================== +The following folders are available for the respective tools. Some models are already pre-installed- + +* deeplexicon_models + * resnet20-final.h5 + * pAmps-final-actrun_newdata_nanopore_UResNet20v2_model.030.h5 + * pAmps-rep2-4-train1_newdata_nanopore_UResNet20v2_model.039.h5 +* dorado_models + * rna002_70bps_hac@v3 +* seqtagger_models + * b04_RNA002 + * b04_RNA004 + +.. note:: + You need to download the models you want to use in case they are not already available. For instance, if you need another model for dorado you need to do: + +.. code-block:: console + + dorado download --model MODELNAME + + +You also need to add the dedicated parameter within the tool_opts file for the specific tool as: + +.. code-block:: console + + basecalling dorado "rna002_70bps_hac@v3" + demultiplexing seqtagger "-k b100" + demultiplexing deeplexicon "-f multi -m resnet20-final.h5" + +.. note:: + You need to copy the model in the corresponding folder and indicate just the model name. You don't need the absolute path. + + + +Barcodes +=================== + +You can select the barcodes you are interested in by writing them down in a text file as in this example. The format is *samplename---barcodeID* + +.. literalinclude:: ../mop_preprocess/keep_barcodes.txt + +The sample id is given by either the folder containing the fast5 files or the basename of the fastq files. So, if your files are in a folder named **myfiles**, it will be: + +.. code-block:: console + + myfiles---bc_1 + myfiles---bc_2 + myfiles---bc_3 + +.. note:: + + The naming convention of the different barcodes is decided by each tool, so guppy will produce **barcode01**, **barcode02**, while seqtagger will produce bc_1, bc_2, etc. + + +Basecalling with the m6A-aware model +========================================= + +For m6A basecalling in your ``params.f5.yaml`` file you should specify ``basecalling: "guppy"`` and ``pars_tools: "tool_opts/drna_tool_m6A_splice_opt.tsv" `` so that guppy will use the m6A model. In your output folder you will have the ``fast5_files`` folder containing the m6A basecalled fast5 files for downstream analysis. Then run: + +.. code-block:: console + + cd mop_preprocess + nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-singularity -bg > yourlog.txt + + + +Results +==================== + +Several folders are created by the pipeline within the output directory specified by the **output** parameter: + + +* **fast5_files**: Contains the basecalled multifast5 files. Each batch contains 4000 sequences. +* **fastq_files**: Contains one or, in case of demultiplexing, more fastq files. +* **QC_files**: Contains each single QC produced by the pipeline. +* **alignment**: Contains the bam file(s). +* **cram_files**: Contains the cram file(s). +* **counts**: Contains read counts per gene / transcript if counting was performed. +* **assigned**: Contains assignment of each read to a given gene / transcript if counting was performed. +* **report**: Contains the final multiqc report. +* **assembly**: It contains assembled transcripts. + +.. note:: + MOP3 will automatically detect the version of guppy and modify the parameters accordingly. You don't need to add any extra parameter as in MOP2. + diff --git a/refs/heads/MOP3/_sources/mop_tail.rst.txt b/refs/heads/MOP3/_sources/mop_tail.rst.txt new file mode 100644 index 0000000..fa795d6 --- /dev/null +++ b/refs/heads/MOP3/_sources/mop_tail.rst.txt @@ -0,0 +1,81 @@ +.. _home-page-moptail: + +******************* +MOP_TAIL +******************* + +.. autosummary:: + :toctree: generated + +This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files, alignment and assignment read ID to gene/transcript. It outputs the estimation of poly(A) tail length at read level provided by **Tailfindr**, **Nanopolish** or both. Tailfinr can be run using three modes: standard, for Nano3P-seq protocol with R9 chemistry and Nano3P-seq protocol with R10 chemistry. + +.. image:: ../img/flow_tail.png + :width: 600 + :alt: mop_tail graph + + +Input Parameters +====================== + +The input parameters are stored in yaml files like the one represented here: + +.. literalinclude:: ../mop_tail/params.yaml + :language: yaml + + + +How to run the pipeline +============================= +Before launching the pipeline,user should: + +1. Decide which containers to use - either docker or singularity **[-with-docker / -with-singularity]**. +2. Fill in both **params.config** and **tools_opt.tsv** files. + +To launch the pipeline, please use the following command: + +.. code-block:: console + + nextflow run mop_tail.nf -params-file params.yaml -with-singularity > log.txt + + +You can run the pipeline in the background adding the nextflow parameter **-bg**: + +.. code-block:: console + + nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg > log.txt + +You can change the parameters either by changing **params.config** file or by feeding the parameters via command line: + +.. code-block:: console + + nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt + + +You can specify a different working directory with temporary files: + +.. code-block:: console + + nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt + + +Results +==================== + +Several folders are created by the pipeline within the output directory specified by the **output** parameter: + +1. NanoPolish: contains the output of *nanopolish* tool. +2. Tailfindr: contains the output of *tailfindr* tool. +3. PolyA_final: contains the txt files with the combined results (i.e. predicted polyA sizes). Here an example of a test: + +.. code-block:: console + + "Read name" "Tailfindr" "Nanopolish" "Gene Name" + "013a5dde-9c52-4de1-83eb-db70fb2cd130" 52.16 49.39 "YKR072C" + "01119f62-ca68-458d-aa1f-cf8c8c04cd3b" 231.64 274.28 "YDR133C" + "0154ce9c-fe6b-4ebc-bbb1-517fdc524207" 24.05 24.24 "YFL044C" + "020cde28-970d-4710-90a5-977e4b4bbc46" 41.27 56.79 "YGL238W" + +If both programs are run, an additional plot that shows the correlation of their results is generated. + +.. image:: ../img/mod_corr.png + :width: 400 diff --git a/refs/heads/MOP3/_sources/reporting.rst.txt b/refs/heads/MOP3/_sources/reporting.rst.txt new file mode 100644 index 0000000..5d5efc9 --- /dev/null +++ b/refs/heads/MOP3/_sources/reporting.rst.txt @@ -0,0 +1,66 @@ +.. _home-page-reporting: + +************** +Resource reporting +************** + +.. autosummary:: + :toctree: generated + +Since each MOP pipeline is based on `Nextflow `_ we can use its embedded functions for reporting the use of resources as a html file and to have a live reporting. + + +Html report +==================== + +For enabling the generation of a report just run each pipeline with the parameter `-with-report` as in the following example: + +.. code-block:: console + + nextflow run mop_preprocess.nf -profile local -with-docker -bg -with-report + +Once the pipeline is finished you will have a comprehensive report with information about CPU, disk and memory usage for each execution and as a distribution for each process. Here an example: + +.. image:: ../img/res_report.png + :width: 800 + + +Live reporting +==================== + +For having a live reporting your pipeline should run in an environment that has access to internet. Then you have to log-in to the `Tower.nf `_ website that is developed and mantained by the good people at `Seqera Labs `__. + + +.. image:: ../img/tower.png + :width: 800 + + +We suggest you to use either the GitHub or the Google authentication: + +.. image:: ../img/tower_eli1.png + :width: 800 + +You can generate your token at `https://tower.nf/tokens `__ and + +.. image:: ../img/tower2.png + :width: 800 + +then you can export as an environmental variable. + +.. code-block:: console + + export TOWER_ACCESS_TOKEN=*******YOUR***TOKEN*****HERE******* + +.. tip:: + We recommend you to add this line to either your .bashrc or .bash_profile file. + +Finally we can then launch the pipeline adding the parameter `-with-tower`. + +.. code-block:: console + + nextflow run mop_preprocess.nf -profile local -with-docker -bg -with-tower + +Going back to the website you can see now your pipeline running and have a nice looking live reporting. + +.. image:: ../img/tower.gif + :width: 800 diff --git a/refs/heads/MOP3/_sources/troubleshooting.rst.txt b/refs/heads/MOP3/_sources/troubleshooting.rst.txt new file mode 100644 index 0000000..1c76785 --- /dev/null +++ b/refs/heads/MOP3/_sources/troubleshooting.rst.txt @@ -0,0 +1,39 @@ +.. _home-page-troubleshooting: + +***************** +Troubleshooting +***************** + +.. autosummary:: + :toctree: generated + +Demultiplexing with Guppy +================================ +Error: + +.. code-block:: console + + Init time: 2515 ms + + 0% 10 20 30 40 50 60 70 80 90 100% + |----|----|----|----|----|----|----|----|----|----| + *************************************************** + Caller time: 32995 ms, Samples called: 159196780, samples/s: 4.82488e+06 + Finishing up any open output files. + Basecalling completed successfully. + + Command error: + rm: cannot remove '*_out/*/*.fastq': No such file or directory + +Solution: +Check your barcode kit!. You must indicate the **--barcode_kits** in the tool_opts file at the row **demultiplexing guppy**. Example: + +.. code-block:: console + + demultiplexing guppy "--flowcell FLO-MIN114 --kit SQK-LSK114 --barcode_kits SQK-NBD114-24" + + +Memory failures in mop_preprocess and mop_mod +================================================================ + +Sometimes FastQC, Epinano, or other tools can run out of memory because the input data contain low-quality reads. It is always a good idea to double-check it and eventually filter them per size / quality using either **nanoq** or **nanofilt**. diff --git a/refs/heads/MOP3/_static/_sphinx_javascript_frameworks_compat.js b/refs/heads/MOP3/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/refs/heads/MOP3/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/refs/heads/MOP3/_static/basic.css b/refs/heads/MOP3/_static/basic.css new file mode 100644 index 0000000..7ebbd6d --- /dev/null +++ b/refs/heads/MOP3/_static/basic.css @@ -0,0 +1,914 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin-top: 10px; +} + +ul.search li { + padding: 5px 0; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/refs/heads/MOP3/_static/css/badge_only.css b/refs/heads/MOP3/_static/css/badge_only.css new file mode 100644 index 0000000..88ba55b --- /dev/null +++ b/refs/heads/MOP3/_static/css/badge_only.css @@ -0,0 +1 @@ +.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-.8em}ul.fas li .fa{width:.8em}ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before,.icon-book:before{content:"\f02d"}.fa-caret-down:before,.icon-caret-down:before{content:"\f0d7"}.fa-caret-up:before,.icon-caret-up:before{content:"\f0d8"}.fa-caret-left:before,.icon-caret-left:before{content:"\f0d9"}.fa-caret-right:before,.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60}.rst-versions .rst-current-version:after{clear:both;content:"";display:block}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book,.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#f1c40f;color:#000}.rst-versions.shift-up{height:auto;max-height:100%;overflow-y:scroll}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:grey;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:1px solid #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions .rst-other-versions .rtd-current-item{font-weight:700}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px;max-height:90%}.rst-versions.rst-badge .fa-book,.rst-versions.rst-badge .icon-book{float:none;line-height:30px}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book,.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge>.rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width:768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}}#flyout-search-form{padding:6px} \ No newline at end of file diff --git a/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Bold.woff b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Bold.woff new file mode 100644 index 0000000..6cb6000 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Bold.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Bold.woff2 b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Bold.woff2 new file mode 100644 index 0000000..7059e23 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Bold.woff2 differ diff --git a/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Regular.woff b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Regular.woff new file mode 100644 index 0000000..f815f63 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Regular.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Regular.woff2 b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Regular.woff2 new file mode 100644 index 0000000..f2c76e5 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/Roboto-Slab-Regular.woff2 differ diff --git a/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.eot b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.eot new file mode 100644 index 0000000..e9f60ca Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.eot differ diff --git a/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.svg b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.svg new file mode 100644 index 0000000..855c845 --- /dev/null +++ b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.svg @@ -0,0 +1,2671 @@ + + + + +Created by FontForge 20120731 at Mon Oct 24 17:37:40 2016 + By ,,, +Copyright Dave Gandy 2016. All rights reserved. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.ttf b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.ttf new file mode 100644 index 0000000..35acda2 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.ttf differ diff --git a/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.woff b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.woff new file mode 100644 index 0000000..400014a Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.woff2 b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.woff2 new file mode 100644 index 0000000..4d13fc6 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/fontawesome-webfont.woff2 differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-bold-italic.woff b/refs/heads/MOP3/_static/css/fonts/lato-bold-italic.woff new file mode 100644 index 0000000..88ad05b Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-bold-italic.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-bold-italic.woff2 b/refs/heads/MOP3/_static/css/fonts/lato-bold-italic.woff2 new file mode 100644 index 0000000..c4e3d80 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-bold-italic.woff2 differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-bold.woff b/refs/heads/MOP3/_static/css/fonts/lato-bold.woff new file mode 100644 index 0000000..c6dff51 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-bold.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-bold.woff2 b/refs/heads/MOP3/_static/css/fonts/lato-bold.woff2 new file mode 100644 index 0000000..bb19504 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-bold.woff2 differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-normal-italic.woff b/refs/heads/MOP3/_static/css/fonts/lato-normal-italic.woff new file mode 100644 index 0000000..76114bc Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-normal-italic.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-normal-italic.woff2 b/refs/heads/MOP3/_static/css/fonts/lato-normal-italic.woff2 new file mode 100644 index 0000000..3404f37 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-normal-italic.woff2 differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-normal.woff b/refs/heads/MOP3/_static/css/fonts/lato-normal.woff new file mode 100644 index 0000000..ae1307f Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-normal.woff differ diff --git a/refs/heads/MOP3/_static/css/fonts/lato-normal.woff2 b/refs/heads/MOP3/_static/css/fonts/lato-normal.woff2 new file mode 100644 index 0000000..3bf9843 Binary files /dev/null and b/refs/heads/MOP3/_static/css/fonts/lato-normal.woff2 differ diff --git a/refs/heads/MOP3/_static/css/theme.css b/refs/heads/MOP3/_static/css/theme.css new file mode 100644 index 0000000..0f14f10 --- /dev/null +++ b/refs/heads/MOP3/_static/css/theme.css @@ -0,0 +1,4 @@ +html{box-sizing:border-box}*,:after,:before{box-sizing:inherit}article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block}audio,canvas,video{display:inline-block;*display:inline;*zoom:1}[hidden],audio:not([controls]){display:none}*{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}blockquote{margin:0}dfn{font-style:italic}ins{background:#ff9;text-decoration:none}ins,mark{color:#000}mark{background:#ff0;font-style:italic;font-weight:700}.rst-content code,.rst-content tt,code,kbd,pre,samp{font-family:monospace,serif;_font-family:courier new,monospace;font-size:1em}pre{white-space:pre}q{quotes:none}q:after,q:before{content:"";content:none}small{font-size:85%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}dl,ol,ul{margin:0;padding:0;list-style:none;list-style-image:none}li{list-style:none}dd{margin:0}img{border:0;-ms-interpolation-mode:bicubic;vertical-align:middle;max-width:100%}svg:not(:root){overflow:hidden}figure,form{margin:0}label{cursor:pointer}button,input,select,textarea{font-size:100%;margin:0;vertical-align:baseline;*vertical-align:middle}button,input{line-height:normal}button,input[type=button],input[type=reset],input[type=submit]{cursor:pointer;-webkit-appearance:button;*overflow:visible}button[disabled],input[disabled]{cursor:default}input[type=search]{-webkit-appearance:textfield;-moz-box-sizing:content-box;-webkit-box-sizing:content-box;box-sizing:content-box}textarea{resize:vertical}table{border-collapse:collapse;border-spacing:0}td{vertical-align:top}.chromeframe{margin:.2em 0;background:#ccc;color:#000;padding:.2em 0}.ir{display:block;border:0;text-indent:-999em;overflow:hidden;background-color:transparent;background-repeat:no-repeat;text-align:left;direction:ltr;*line-height:0}.ir br{display:none}.hidden{display:none!important;visibility:hidden}.visuallyhidden{border:0;clip:rect(0 0 0 0);height:1px;margin:-1px;overflow:hidden;padding:0;position:absolute;width:1px}.visuallyhidden.focusable:active,.visuallyhidden.focusable:focus{clip:auto;height:auto;margin:0;overflow:visible;position:static;width:auto}.invisible{visibility:hidden}.relative{position:relative}big,small{font-size:100%}@media print{body,html,section{background:none!important}*{box-shadow:none!important;text-shadow:none!important;filter:none!important;-ms-filter:none!important}a,a:visited{text-decoration:underline}.ir a:after,a[href^="#"]:after,a[href^="javascript:"]:after{content:""}blockquote,pre{page-break-inside:avoid}thead{display:table-header-group}img,tr{page-break-inside:avoid}img{max-width:100%!important}@page{margin:.5cm}.rst-content .toctree-wrapper>p.caption,h2,h3,p{orphans:3;widows:3}.rst-content .toctree-wrapper>p.caption,h2,h3{page-break-after:avoid}}.btn,.fa:before,.icon:before,.rst-content .admonition,.rst-content .admonition-title:before,.rst-content .admonition-todo,.rst-content .attention,.rst-content .caution,.rst-content .code-block-caption .headerlink:before,.rst-content .danger,.rst-content .eqno .headerlink:before,.rst-content .error,.rst-content .hint,.rst-content .important,.rst-content .note,.rst-content .seealso,.rst-content .tip,.rst-content .warning,.rst-content code.download span:first-child:before,.rst-content dl dt .headerlink:before,.rst-content h1 .headerlink:before,.rst-content h2 .headerlink:before,.rst-content h3 .headerlink:before,.rst-content h4 .headerlink:before,.rst-content h5 .headerlink:before,.rst-content h6 .headerlink:before,.rst-content p.caption .headerlink:before,.rst-content p .headerlink:before,.rst-content table>caption .headerlink:before,.rst-content tt.download span:first-child:before,.wy-alert,.wy-dropdown .caret:before,.wy-inline-validate.wy-inline-validate-danger .wy-input-context:before,.wy-inline-validate.wy-inline-validate-info .wy-input-context:before,.wy-inline-validate.wy-inline-validate-success .wy-input-context:before,.wy-inline-validate.wy-inline-validate-warning .wy-input-context:before,.wy-menu-vertical li.current>a button.toctree-expand:before,.wy-menu-vertical li.on a button.toctree-expand:before,.wy-menu-vertical li button.toctree-expand:before,input[type=color],input[type=date],input[type=datetime-local],input[type=datetime],input[type=email],input[type=month],input[type=number],input[type=password],input[type=search],input[type=tel],input[type=text],input[type=time],input[type=url],input[type=week],select,textarea{-webkit-font-smoothing:antialiased}.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}/*! + * Font Awesome 4.7.0 by @davegandy - http://fontawesome.io - @fontawesome + * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) + */@font-face{font-family:FontAwesome;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713);src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix&v=4.7.0) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#fontawesomeregular) format("svg");font-weight:400;font-style:normal}.fa,.icon,.rst-content .admonition-title,.rst-content .code-block-caption .headerlink,.rst-content .eqno .headerlink,.rst-content code.download span:first-child,.rst-content dl dt .headerlink,.rst-content h1 .headerlink,.rst-content h2 .headerlink,.rst-content h3 .headerlink,.rst-content h4 .headerlink,.rst-content h5 .headerlink,.rst-content h6 .headerlink,.rst-content p.caption .headerlink,.rst-content p .headerlink,.rst-content table>caption .headerlink,.rst-content tt.download span:first-child,.wy-menu-vertical li.current>a button.toctree-expand,.wy-menu-vertical li.on a button.toctree-expand,.wy-menu-vertical li button.toctree-expand{display:inline-block;font:normal normal normal 14px/1 FontAwesome;font-size:inherit;text-rendering:auto;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}.fa-lg{font-size:1.33333em;line-height:.75em;vertical-align:-15%}.fa-2x{font-size:2em}.fa-3x{font-size:3em}.fa-4x{font-size:4em}.fa-5x{font-size:5em}.fa-fw{width:1.28571em;text-align:center}.fa-ul{padding-left:0;margin-left:2.14286em;list-style-type:none}.fa-ul>li{position:relative}.fa-li{position:absolute;left:-2.14286em;width:2.14286em;top:.14286em;text-align:center}.fa-li.fa-lg{left:-1.85714em}.fa-border{padding:.2em .25em .15em;border:.08em solid #eee;border-radius:.1em}.fa-pull-left{float:left}.fa-pull-right{float:right}.fa-pull-left.icon,.fa.fa-pull-left,.rst-content .code-block-caption .fa-pull-left.headerlink,.rst-content .eqno .fa-pull-left.headerlink,.rst-content .fa-pull-left.admonition-title,.rst-content code.download span.fa-pull-left:first-child,.rst-content dl dt .fa-pull-left.headerlink,.rst-content h1 .fa-pull-left.headerlink,.rst-content h2 .fa-pull-left.headerlink,.rst-content h3 .fa-pull-left.headerlink,.rst-content h4 .fa-pull-left.headerlink,.rst-content h5 .fa-pull-left.headerlink,.rst-content h6 .fa-pull-left.headerlink,.rst-content p .fa-pull-left.headerlink,.rst-content table>caption .fa-pull-left.headerlink,.rst-content tt.download span.fa-pull-left:first-child,.wy-menu-vertical li.current>a button.fa-pull-left.toctree-expand,.wy-menu-vertical li.on a button.fa-pull-left.toctree-expand,.wy-menu-vertical li button.fa-pull-left.toctree-expand{margin-right:.3em}.fa-pull-right.icon,.fa.fa-pull-right,.rst-content .code-block-caption .fa-pull-right.headerlink,.rst-content .eqno .fa-pull-right.headerlink,.rst-content .fa-pull-right.admonition-title,.rst-content code.download span.fa-pull-right:first-child,.rst-content dl dt .fa-pull-right.headerlink,.rst-content h1 .fa-pull-right.headerlink,.rst-content h2 .fa-pull-right.headerlink,.rst-content h3 .fa-pull-right.headerlink,.rst-content h4 .fa-pull-right.headerlink,.rst-content h5 .fa-pull-right.headerlink,.rst-content h6 .fa-pull-right.headerlink,.rst-content p .fa-pull-right.headerlink,.rst-content table>caption .fa-pull-right.headerlink,.rst-content tt.download span.fa-pull-right:first-child,.wy-menu-vertical li.current>a button.fa-pull-right.toctree-expand,.wy-menu-vertical li.on a button.fa-pull-right.toctree-expand,.wy-menu-vertical li button.fa-pull-right.toctree-expand{margin-left:.3em}.pull-right{float:right}.pull-left{float:left}.fa.pull-left,.pull-left.icon,.rst-content .code-block-caption .pull-left.headerlink,.rst-content .eqno .pull-left.headerlink,.rst-content .pull-left.admonition-title,.rst-content code.download span.pull-left:first-child,.rst-content dl dt .pull-left.headerlink,.rst-content h1 .pull-left.headerlink,.rst-content h2 .pull-left.headerlink,.rst-content h3 .pull-left.headerlink,.rst-content h4 .pull-left.headerlink,.rst-content h5 .pull-left.headerlink,.rst-content h6 .pull-left.headerlink,.rst-content p .pull-left.headerlink,.rst-content table>caption .pull-left.headerlink,.rst-content tt.download span.pull-left:first-child,.wy-menu-vertical li.current>a button.pull-left.toctree-expand,.wy-menu-vertical li.on a button.pull-left.toctree-expand,.wy-menu-vertical li button.pull-left.toctree-expand{margin-right:.3em}.fa.pull-right,.pull-right.icon,.rst-content .code-block-caption .pull-right.headerlink,.rst-content .eqno .pull-right.headerlink,.rst-content .pull-right.admonition-title,.rst-content code.download span.pull-right:first-child,.rst-content dl dt .pull-right.headerlink,.rst-content h1 .pull-right.headerlink,.rst-content h2 .pull-right.headerlink,.rst-content h3 .pull-right.headerlink,.rst-content h4 .pull-right.headerlink,.rst-content h5 .pull-right.headerlink,.rst-content h6 .pull-right.headerlink,.rst-content p .pull-right.headerlink,.rst-content table>caption .pull-right.headerlink,.rst-content tt.download span.pull-right:first-child,.wy-menu-vertical li.current>a button.pull-right.toctree-expand,.wy-menu-vertical li.on a button.pull-right.toctree-expand,.wy-menu-vertical li button.pull-right.toctree-expand{margin-left:.3em}.fa-spin{-webkit-animation:fa-spin 2s linear infinite;animation:fa-spin 2s linear infinite}.fa-pulse{-webkit-animation:fa-spin 1s steps(8) infinite;animation:fa-spin 1s steps(8) infinite}@-webkit-keyframes fa-spin{0%{-webkit-transform:rotate(0deg);transform:rotate(0deg)}to{-webkit-transform:rotate(359deg);transform:rotate(359deg)}}@keyframes fa-spin{0%{-webkit-transform:rotate(0deg);transform:rotate(0deg)}to{-webkit-transform:rotate(359deg);transform:rotate(359deg)}}.fa-rotate-90{-ms-filter:"progid:DXImageTransform.Microsoft.BasicImage(rotation=1)";-webkit-transform:rotate(90deg);-ms-transform:rotate(90deg);transform:rotate(90deg)}.fa-rotate-180{-ms-filter:"progid:DXImageTransform.Microsoft.BasicImage(rotation=2)";-webkit-transform:rotate(180deg);-ms-transform:rotate(180deg);transform:rotate(180deg)}.fa-rotate-270{-ms-filter:"progid:DXImageTransform.Microsoft.BasicImage(rotation=3)";-webkit-transform:rotate(270deg);-ms-transform:rotate(270deg);transform:rotate(270deg)}.fa-flip-horizontal{-ms-filter:"progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1)";-webkit-transform:scaleX(-1);-ms-transform:scaleX(-1);transform:scaleX(-1)}.fa-flip-vertical{-ms-filter:"progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1)";-webkit-transform:scaleY(-1);-ms-transform:scaleY(-1);transform:scaleY(-1)}:root .fa-flip-horizontal,:root .fa-flip-vertical,:root .fa-rotate-90,:root .fa-rotate-180,:root .fa-rotate-270{filter:none}.fa-stack{position:relative;display:inline-block;width:2em;height:2em;line-height:2em;vertical-align:middle}.fa-stack-1x,.fa-stack-2x{position:absolute;left:0;width:100%;text-align:center}.fa-stack-1x{line-height:inherit}.fa-stack-2x{font-size:2em}.fa-inverse{color:#fff}.fa-glass:before{content:""}.fa-music:before{content:""}.fa-search:before,.icon-search:before{content:""}.fa-envelope-o:before{content:""}.fa-heart:before{content:""}.fa-star:before{content:""}.fa-star-o:before{content:""}.fa-user:before{content:""}.fa-film:before{content:""}.fa-th-large:before{content:""}.fa-th:before{content:""}.fa-th-list:before{content:""}.fa-check:before{content:""}.fa-close:before,.fa-remove:before,.fa-times:before{content:""}.fa-search-plus:before{content:""}.fa-search-minus:before{content:""}.fa-power-off:before{content:""}.fa-signal:before{content:""}.fa-cog:before,.fa-gear:before{content:""}.fa-trash-o:before{content:""}.fa-home:before,.icon-home:before{content:""}.fa-file-o:before{content:""}.fa-clock-o:before{content:""}.fa-road:before{content:""}.fa-download:before,.rst-content code.download span:first-child:before,.rst-content tt.download span:first-child:before{content:""}.fa-arrow-circle-o-down:before{content:""}.fa-arrow-circle-o-up:before{content:""}.fa-inbox:before{content:""}.fa-play-circle-o:before{content:""}.fa-repeat:before,.fa-rotate-right:before{content:""}.fa-refresh:before{content:""}.fa-list-alt:before{content:""}.fa-lock:before{content:""}.fa-flag:before{content:""}.fa-headphones:before{content:""}.fa-volume-off:before{content:""}.fa-volume-down:before{content:""}.fa-volume-up:before{content:""}.fa-qrcode:before{content:""}.fa-barcode:before{content:""}.fa-tag:before{content:""}.fa-tags:before{content:""}.fa-book:before,.icon-book:before{content:""}.fa-bookmark:before{content:""}.fa-print:before{content:""}.fa-camera:before{content:""}.fa-font:before{content:""}.fa-bold:before{content:""}.fa-italic:before{content:""}.fa-text-height:before{content:""}.fa-text-width:before{content:""}.fa-align-left:before{content:""}.fa-align-center:before{content:""}.fa-align-right:before{content:""}.fa-align-justify:before{content:""}.fa-list:before{content:""}.fa-dedent:before,.fa-outdent:before{content:""}.fa-indent:before{content:""}.fa-video-camera:before{content:""}.fa-image:before,.fa-photo:before,.fa-picture-o:before{content:""}.fa-pencil:before{content:""}.fa-map-marker:before{content:""}.fa-adjust:before{content:""}.fa-tint:before{content:""}.fa-edit:before,.fa-pencil-square-o:before{content:""}.fa-share-square-o:before{content:""}.fa-check-square-o:before{content:""}.fa-arrows:before{content:""}.fa-step-backward:before{content:""}.fa-fast-backward:before{content:""}.fa-backward:before{content:""}.fa-play:before{content:""}.fa-pause:before{content:""}.fa-stop:before{content:""}.fa-forward:before{content:""}.fa-fast-forward:before{content:""}.fa-step-forward:before{content:""}.fa-eject:before{content:""}.fa-chevron-left:before{content:""}.fa-chevron-right:before{content:""}.fa-plus-circle:before{content:""}.fa-minus-circle:before{content:""}.fa-times-circle:before,.wy-inline-validate.wy-inline-validate-danger .wy-input-context:before{content:""}.fa-check-circle:before,.wy-inline-validate.wy-inline-validate-success .wy-input-context:before{content:""}.fa-question-circle:before{content:""}.fa-info-circle:before{content:""}.fa-crosshairs:before{content:""}.fa-times-circle-o:before{content:""}.fa-check-circle-o:before{content:""}.fa-ban:before{content:""}.fa-arrow-left:before{content:""}.fa-arrow-right:before{content:""}.fa-arrow-up:before{content:""}.fa-arrow-down:before{content:""}.fa-mail-forward:before,.fa-share:before{content:""}.fa-expand:before{content:""}.fa-compress:before{content:""}.fa-plus:before{content:""}.fa-minus:before{content:""}.fa-asterisk:before{content:""}.fa-exclamation-circle:before,.rst-content .admonition-title:before,.wy-inline-validate.wy-inline-validate-info .wy-input-context:before,.wy-inline-validate.wy-inline-validate-warning .wy-input-context:before{content:""}.fa-gift:before{content:""}.fa-leaf:before{content:""}.fa-fire:before,.icon-fire:before{content:""}.fa-eye:before{content:""}.fa-eye-slash:before{content:""}.fa-exclamation-triangle:before,.fa-warning:before{content:""}.fa-plane:before{content:""}.fa-calendar:before{content:""}.fa-random:before{content:""}.fa-comment:before{content:""}.fa-magnet:before{content:""}.fa-chevron-up:before{content:""}.fa-chevron-down:before{content:""}.fa-retweet:before{content:""}.fa-shopping-cart:before{content:""}.fa-folder:before{content:""}.fa-folder-open:before{content:""}.fa-arrows-v:before{content:""}.fa-arrows-h:before{content:""}.fa-bar-chart-o:before,.fa-bar-chart:before{content:""}.fa-twitter-square:before{content:""}.fa-facebook-square:before{content:""}.fa-camera-retro:before{content:""}.fa-key:before{content:""}.fa-cogs:before,.fa-gears:before{content:""}.fa-comments:before{content:""}.fa-thumbs-o-up:before{content:""}.fa-thumbs-o-down:before{content:""}.fa-star-half:before{content:""}.fa-heart-o:before{content:""}.fa-sign-out:before{content:""}.fa-linkedin-square:before{content:""}.fa-thumb-tack:before{content:""}.fa-external-link:before{content:""}.fa-sign-in:before{content:""}.fa-trophy:before{content:""}.fa-github-square:before{content:""}.fa-upload:before{content:""}.fa-lemon-o:before{content:""}.fa-phone:before{content:""}.fa-square-o:before{content:""}.fa-bookmark-o:before{content:""}.fa-phone-square:before{content:""}.fa-twitter:before{content:""}.fa-facebook-f:before,.fa-facebook:before{content:""}.fa-github:before,.icon-github:before{content:""}.fa-unlock:before{content:""}.fa-credit-card:before{content:""}.fa-feed:before,.fa-rss:before{content:""}.fa-hdd-o:before{content:""}.fa-bullhorn:before{content:""}.fa-bell:before{content:""}.fa-certificate:before{content:""}.fa-hand-o-right:before{content:""}.fa-hand-o-left:before{content:""}.fa-hand-o-up:before{content:""}.fa-hand-o-down:before{content:""}.fa-arrow-circle-left:before,.icon-circle-arrow-left:before{content:""}.fa-arrow-circle-right:before,.icon-circle-arrow-right:before{content:""}.fa-arrow-circle-up:before{content:""}.fa-arrow-circle-down:before{content:""}.fa-globe:before{content:""}.fa-wrench:before{content:""}.fa-tasks:before{content:""}.fa-filter:before{content:""}.fa-briefcase:before{content:""}.fa-arrows-alt:before{content:""}.fa-group:before,.fa-users:before{content:""}.fa-chain:before,.fa-link:before,.icon-link:before{content:""}.fa-cloud:before{content:""}.fa-flask:before{content:""}.fa-cut:before,.fa-scissors:before{content:""}.fa-copy:before,.fa-files-o:before{content:""}.fa-paperclip:before{content:""}.fa-floppy-o:before,.fa-save:before{content:""}.fa-square:before{content:""}.fa-bars:before,.fa-navicon:before,.fa-reorder:before{content:""}.fa-list-ul:before{content:""}.fa-list-ol:before{content:""}.fa-strikethrough:before{content:""}.fa-underline:before{content:""}.fa-table:before{content:""}.fa-magic:before{content:""}.fa-truck:before{content:""}.fa-pinterest:before{content:""}.fa-pinterest-square:before{content:""}.fa-google-plus-square:before{content:""}.fa-google-plus:before{content:""}.fa-money:before{content:""}.fa-caret-down:before,.icon-caret-down:before,.wy-dropdown .caret:before{content:""}.fa-caret-up:before{content:""}.fa-caret-left:before{content:""}.fa-caret-right:before{content:""}.fa-columns:before{content:""}.fa-sort:before,.fa-unsorted:before{content:""}.fa-sort-desc:before,.fa-sort-down:before{content:""}.fa-sort-asc:before,.fa-sort-up:before{content:""}.fa-envelope:before{content:""}.fa-linkedin:before{content:""}.fa-rotate-left:before,.fa-undo:before{content:""}.fa-gavel:before,.fa-legal:before{content:""}.fa-dashboard:before,.fa-tachometer:before{content:""}.fa-comment-o:before{content:""}.fa-comments-o:before{content:""}.fa-bolt:before,.fa-flash:before{content:""}.fa-sitemap:before{content:""}.fa-umbrella:before{content:""}.fa-clipboard:before,.fa-paste:before{content:""}.fa-lightbulb-o:before{content:""}.fa-exchange:before{content:""}.fa-cloud-download:before{content:""}.fa-cloud-upload:before{content:""}.fa-user-md:before{content:""}.fa-stethoscope:before{content:""}.fa-suitcase:before{content:""}.fa-bell-o:before{content:""}.fa-coffee:before{content:""}.fa-cutlery:before{content:""}.fa-file-text-o:before{content:""}.fa-building-o:before{content:""}.fa-hospital-o:before{content:""}.fa-ambulance:before{content:""}.fa-medkit:before{content:""}.fa-fighter-jet:before{content:""}.fa-beer:before{content:""}.fa-h-square:before{content:""}.fa-plus-square:before{content:""}.fa-angle-double-left:before{content:""}.fa-angle-double-right:before{content:""}.fa-angle-double-up:before{content:""}.fa-angle-double-down:before{content:""}.fa-angle-left:before{content:""}.fa-angle-right:before{content:""}.fa-angle-up:before{content:""}.fa-angle-down:before{content:""}.fa-desktop:before{content:""}.fa-laptop:before{content:""}.fa-tablet:before{content:""}.fa-mobile-phone:before,.fa-mobile:before{content:""}.fa-circle-o:before{content:""}.fa-quote-left:before{content:""}.fa-quote-right:before{content:""}.fa-spinner:before{content:""}.fa-circle:before{content:""}.fa-mail-reply:before,.fa-reply:before{content:""}.fa-github-alt:before{content:""}.fa-folder-o:before{content:""}.fa-folder-open-o:before{content:""}.fa-smile-o:before{content:""}.fa-frown-o:before{content:""}.fa-meh-o:before{content:""}.fa-gamepad:before{content:""}.fa-keyboard-o:before{content:""}.fa-flag-o:before{content:""}.fa-flag-checkered:before{content:""}.fa-terminal:before{content:""}.fa-code:before{content:""}.fa-mail-reply-all:before,.fa-reply-all:before{content:""}.fa-star-half-empty:before,.fa-star-half-full:before,.fa-star-half-o:before{content:""}.fa-location-arrow:before{content:""}.fa-crop:before{content:""}.fa-code-fork:before{content:""}.fa-chain-broken:before,.fa-unlink:before{content:""}.fa-question:before{content:""}.fa-info:before{content:""}.fa-exclamation:before{content:""}.fa-superscript:before{content:""}.fa-subscript:before{content:""}.fa-eraser:before{content:""}.fa-puzzle-piece:before{content:""}.fa-microphone:before{content:""}.fa-microphone-slash:before{content:""}.fa-shield:before{content:""}.fa-calendar-o:before{content:""}.fa-fire-extinguisher:before{content:""}.fa-rocket:before{content:""}.fa-maxcdn:before{content:""}.fa-chevron-circle-left:before{content:""}.fa-chevron-circle-right:before{content:""}.fa-chevron-circle-up:before{content:""}.fa-chevron-circle-down:before{content:""}.fa-html5:before{content:""}.fa-css3:before{content:""}.fa-anchor:before{content:""}.fa-unlock-alt:before{content:""}.fa-bullseye:before{content:""}.fa-ellipsis-h:before{content:""}.fa-ellipsis-v:before{content:""}.fa-rss-square:before{content:""}.fa-play-circle:before{content:""}.fa-ticket:before{content:""}.fa-minus-square:before{content:""}.fa-minus-square-o:before,.wy-menu-vertical li.current>a button.toctree-expand:before,.wy-menu-vertical li.on a button.toctree-expand:before{content:""}.fa-level-up:before{content:""}.fa-level-down:before{content:""}.fa-check-square:before{content:""}.fa-pencil-square:before{content:""}.fa-external-link-square:before{content:""}.fa-share-square:before{content:""}.fa-compass:before{content:""}.fa-caret-square-o-down:before,.fa-toggle-down:before{content:""}.fa-caret-square-o-up:before,.fa-toggle-up:before{content:""}.fa-caret-square-o-right:before,.fa-toggle-right:before{content:""}.fa-eur:before,.fa-euro:before{content:""}.fa-gbp:before{content:""}.fa-dollar:before,.fa-usd:before{content:""}.fa-inr:before,.fa-rupee:before{content:""}.fa-cny:before,.fa-jpy:before,.fa-rmb:before,.fa-yen:before{content:""}.fa-rouble:before,.fa-rub:before,.fa-ruble:before{content:""}.fa-krw:before,.fa-won:before{content:""}.fa-bitcoin:before,.fa-btc:before{content:""}.fa-file:before{content:""}.fa-file-text:before{content:""}.fa-sort-alpha-asc:before{content:""}.fa-sort-alpha-desc:before{content:""}.fa-sort-amount-asc:before{content:""}.fa-sort-amount-desc:before{content:""}.fa-sort-numeric-asc:before{content:""}.fa-sort-numeric-desc:before{content:""}.fa-thumbs-up:before{content:""}.fa-thumbs-down:before{content:""}.fa-youtube-square:before{content:""}.fa-youtube:before{content:""}.fa-xing:before{content:""}.fa-xing-square:before{content:""}.fa-youtube-play:before{content:""}.fa-dropbox:before{content:""}.fa-stack-overflow:before{content:""}.fa-instagram:before{content:""}.fa-flickr:before{content:""}.fa-adn:before{content:""}.fa-bitbucket:before,.icon-bitbucket:before{content:""}.fa-bitbucket-square:before{content:""}.fa-tumblr:before{content:""}.fa-tumblr-square:before{content:""}.fa-long-arrow-down:before{content:""}.fa-long-arrow-up:before{content:""}.fa-long-arrow-left:before{content:""}.fa-long-arrow-right:before{content:""}.fa-apple:before{content:""}.fa-windows:before{content:""}.fa-android:before{content:""}.fa-linux:before{content:""}.fa-dribbble:before{content:""}.fa-skype:before{content:""}.fa-foursquare:before{content:""}.fa-trello:before{content:""}.fa-female:before{content:""}.fa-male:before{content:""}.fa-gittip:before,.fa-gratipay:before{content:""}.fa-sun-o:before{content:""}.fa-moon-o:before{content:""}.fa-archive:before{content:""}.fa-bug:before{content:""}.fa-vk:before{content:""}.fa-weibo:before{content:""}.fa-renren:before{content:""}.fa-pagelines:before{content:""}.fa-stack-exchange:before{content:""}.fa-arrow-circle-o-right:before{content:""}.fa-arrow-circle-o-left:before{content:""}.fa-caret-square-o-left:before,.fa-toggle-left:before{content:""}.fa-dot-circle-o:before{content:""}.fa-wheelchair:before{content:""}.fa-vimeo-square:before{content:""}.fa-try:before,.fa-turkish-lira:before{content:""}.fa-plus-square-o:before,.wy-menu-vertical li button.toctree-expand:before{content:""}.fa-space-shuttle:before{content:""}.fa-slack:before{content:""}.fa-envelope-square:before{content:""}.fa-wordpress:before{content:""}.fa-openid:before{content:""}.fa-bank:before,.fa-institution:before,.fa-university:before{content:""}.fa-graduation-cap:before,.fa-mortar-board:before{content:""}.fa-yahoo:before{content:""}.fa-google:before{content:""}.fa-reddit:before{content:""}.fa-reddit-square:before{content:""}.fa-stumbleupon-circle:before{content:""}.fa-stumbleupon:before{content:""}.fa-delicious:before{content:""}.fa-digg:before{content:""}.fa-pied-piper-pp:before{content:""}.fa-pied-piper-alt:before{content:""}.fa-drupal:before{content:""}.fa-joomla:before{content:""}.fa-language:before{content:""}.fa-fax:before{content:""}.fa-building:before{content:""}.fa-child:before{content:""}.fa-paw:before{content:""}.fa-spoon:before{content:""}.fa-cube:before{content:""}.fa-cubes:before{content:""}.fa-behance:before{content:""}.fa-behance-square:before{content:""}.fa-steam:before{content:""}.fa-steam-square:before{content:""}.fa-recycle:before{content:""}.fa-automobile:before,.fa-car:before{content:""}.fa-cab:before,.fa-taxi:before{content:""}.fa-tree:before{content:""}.fa-spotify:before{content:""}.fa-deviantart:before{content:""}.fa-soundcloud:before{content:""}.fa-database:before{content:""}.fa-file-pdf-o:before{content:""}.fa-file-word-o:before{content:""}.fa-file-excel-o:before{content:""}.fa-file-powerpoint-o:before{content:""}.fa-file-image-o:before,.fa-file-photo-o:before,.fa-file-picture-o:before{content:""}.fa-file-archive-o:before,.fa-file-zip-o:before{content:""}.fa-file-audio-o:before,.fa-file-sound-o:before{content:""}.fa-file-movie-o:before,.fa-file-video-o:before{content:""}.fa-file-code-o:before{content:""}.fa-vine:before{content:""}.fa-codepen:before{content:""}.fa-jsfiddle:before{content:""}.fa-life-bouy:before,.fa-life-buoy:before,.fa-life-ring:before,.fa-life-saver:before,.fa-support:before{content:""}.fa-circle-o-notch:before{content:""}.fa-ra:before,.fa-rebel:before,.fa-resistance:before{content:""}.fa-empire:before,.fa-ge:before{content:""}.fa-git-square:before{content:""}.fa-git:before{content:""}.fa-hacker-news:before,.fa-y-combinator-square:before,.fa-yc-square:before{content:""}.fa-tencent-weibo:before{content:""}.fa-qq:before{content:""}.fa-wechat:before,.fa-weixin:before{content:""}.fa-paper-plane:before,.fa-send:before{content:""}.fa-paper-plane-o:before,.fa-send-o:before{content:""}.fa-history:before{content:""}.fa-circle-thin:before{content:""}.fa-header:before{content:""}.fa-paragraph:before{content:""}.fa-sliders:before{content:""}.fa-share-alt:before{content:""}.fa-share-alt-square:before{content:""}.fa-bomb:before{content:""}.fa-futbol-o:before,.fa-soccer-ball-o:before{content:""}.fa-tty:before{content:""}.fa-binoculars:before{content:""}.fa-plug:before{content:""}.fa-slideshare:before{content:""}.fa-twitch:before{content:""}.fa-yelp:before{content:""}.fa-newspaper-o:before{content:""}.fa-wifi:before{content:""}.fa-calculator:before{content:""}.fa-paypal:before{content:""}.fa-google-wallet:before{content:""}.fa-cc-visa:before{content:""}.fa-cc-mastercard:before{content:""}.fa-cc-discover:before{content:""}.fa-cc-amex:before{content:""}.fa-cc-paypal:before{content:""}.fa-cc-stripe:before{content:""}.fa-bell-slash:before{content:""}.fa-bell-slash-o:before{content:""}.fa-trash:before{content:""}.fa-copyright:before{content:""}.fa-at:before{content:""}.fa-eyedropper:before{content:""}.fa-paint-brush:before{content:""}.fa-birthday-cake:before{content:""}.fa-area-chart:before{content:""}.fa-pie-chart:before{content:""}.fa-line-chart:before{content:""}.fa-lastfm:before{content:""}.fa-lastfm-square:before{content:""}.fa-toggle-off:before{content:""}.fa-toggle-on:before{content:""}.fa-bicycle:before{content:""}.fa-bus:before{content:""}.fa-ioxhost:before{content:""}.fa-angellist:before{content:""}.fa-cc:before{content:""}.fa-ils:before,.fa-shekel:before,.fa-sheqel:before{content:""}.fa-meanpath:before{content:""}.fa-buysellads:before{content:""}.fa-connectdevelop:before{content:""}.fa-dashcube:before{content:""}.fa-forumbee:before{content:""}.fa-leanpub:before{content:""}.fa-sellsy:before{content:""}.fa-shirtsinbulk:before{content:""}.fa-simplybuilt:before{content:""}.fa-skyatlas:before{content:""}.fa-cart-plus:before{content:""}.fa-cart-arrow-down:before{content:""}.fa-diamond:before{content:""}.fa-ship:before{content:""}.fa-user-secret:before{content:""}.fa-motorcycle:before{content:""}.fa-street-view:before{content:""}.fa-heartbeat:before{content:""}.fa-venus:before{content:""}.fa-mars:before{content:""}.fa-mercury:before{content:""}.fa-intersex:before,.fa-transgender:before{content:""}.fa-transgender-alt:before{content:""}.fa-venus-double:before{content:""}.fa-mars-double:before{content:""}.fa-venus-mars:before{content:""}.fa-mars-stroke:before{content:""}.fa-mars-stroke-v:before{content:""}.fa-mars-stroke-h:before{content:""}.fa-neuter:before{content:""}.fa-genderless:before{content:""}.fa-facebook-official:before{content:""}.fa-pinterest-p:before{content:""}.fa-whatsapp:before{content:""}.fa-server:before{content:""}.fa-user-plus:before{content:""}.fa-user-times:before{content:""}.fa-bed:before,.fa-hotel:before{content:""}.fa-viacoin:before{content:""}.fa-train:before{content:""}.fa-subway:before{content:""}.fa-medium:before{content:""}.fa-y-combinator:before,.fa-yc:before{content:""}.fa-optin-monster:before{content:""}.fa-opencart:before{content:""}.fa-expeditedssl:before{content:""}.fa-battery-4:before,.fa-battery-full:before,.fa-battery:before{content:""}.fa-battery-3:before,.fa-battery-three-quarters:before{content:""}.fa-battery-2:before,.fa-battery-half:before{content:""}.fa-battery-1:before,.fa-battery-quarter:before{content:""}.fa-battery-0:before,.fa-battery-empty:before{content:""}.fa-mouse-pointer:before{content:""}.fa-i-cursor:before{content:""}.fa-object-group:before{content:""}.fa-object-ungroup:before{content:""}.fa-sticky-note:before{content:""}.fa-sticky-note-o:before{content:""}.fa-cc-jcb:before{content:""}.fa-cc-diners-club:before{content:""}.fa-clone:before{content:""}.fa-balance-scale:before{content:""}.fa-hourglass-o:before{content:""}.fa-hourglass-1:before,.fa-hourglass-start:before{content:""}.fa-hourglass-2:before,.fa-hourglass-half:before{content:""}.fa-hourglass-3:before,.fa-hourglass-end:before{content:""}.fa-hourglass:before{content:""}.fa-hand-grab-o:before,.fa-hand-rock-o:before{content:""}.fa-hand-paper-o:before,.fa-hand-stop-o:before{content:""}.fa-hand-scissors-o:before{content:""}.fa-hand-lizard-o:before{content:""}.fa-hand-spock-o:before{content:""}.fa-hand-pointer-o:before{content:""}.fa-hand-peace-o:before{content:""}.fa-trademark:before{content:""}.fa-registered:before{content:""}.fa-creative-commons:before{content:""}.fa-gg:before{content:""}.fa-gg-circle:before{content:""}.fa-tripadvisor:before{content:""}.fa-odnoklassniki:before{content:""}.fa-odnoklassniki-square:before{content:""}.fa-get-pocket:before{content:""}.fa-wikipedia-w:before{content:""}.fa-safari:before{content:""}.fa-chrome:before{content:""}.fa-firefox:before{content:""}.fa-opera:before{content:""}.fa-internet-explorer:before{content:""}.fa-television:before,.fa-tv:before{content:""}.fa-contao:before{content:""}.fa-500px:before{content:""}.fa-amazon:before{content:""}.fa-calendar-plus-o:before{content:""}.fa-calendar-minus-o:before{content:""}.fa-calendar-times-o:before{content:""}.fa-calendar-check-o:before{content:""}.fa-industry:before{content:""}.fa-map-pin:before{content:""}.fa-map-signs:before{content:""}.fa-map-o:before{content:""}.fa-map:before{content:""}.fa-commenting:before{content:""}.fa-commenting-o:before{content:""}.fa-houzz:before{content:""}.fa-vimeo:before{content:""}.fa-black-tie:before{content:""}.fa-fonticons:before{content:""}.fa-reddit-alien:before{content:""}.fa-edge:before{content:""}.fa-credit-card-alt:before{content:""}.fa-codiepie:before{content:""}.fa-modx:before{content:""}.fa-fort-awesome:before{content:""}.fa-usb:before{content:""}.fa-product-hunt:before{content:""}.fa-mixcloud:before{content:""}.fa-scribd:before{content:""}.fa-pause-circle:before{content:""}.fa-pause-circle-o:before{content:""}.fa-stop-circle:before{content:""}.fa-stop-circle-o:before{content:""}.fa-shopping-bag:before{content:""}.fa-shopping-basket:before{content:""}.fa-hashtag:before{content:""}.fa-bluetooth:before{content:""}.fa-bluetooth-b:before{content:""}.fa-percent:before{content:""}.fa-gitlab:before,.icon-gitlab:before{content:""}.fa-wpbeginner:before{content:""}.fa-wpforms:before{content:""}.fa-envira:before{content:""}.fa-universal-access:before{content:""}.fa-wheelchair-alt:before{content:""}.fa-question-circle-o:before{content:""}.fa-blind:before{content:""}.fa-audio-description:before{content:""}.fa-volume-control-phone:before{content:""}.fa-braille:before{content:""}.fa-assistive-listening-systems:before{content:""}.fa-american-sign-language-interpreting:before,.fa-asl-interpreting:before{content:""}.fa-deaf:before,.fa-deafness:before,.fa-hard-of-hearing:before{content:""}.fa-glide:before{content:""}.fa-glide-g:before{content:""}.fa-sign-language:before,.fa-signing:before{content:""}.fa-low-vision:before{content:""}.fa-viadeo:before{content:""}.fa-viadeo-square:before{content:""}.fa-snapchat:before{content:""}.fa-snapchat-ghost:before{content:""}.fa-snapchat-square:before{content:""}.fa-pied-piper:before{content:""}.fa-first-order:before{content:""}.fa-yoast:before{content:""}.fa-themeisle:before{content:""}.fa-google-plus-circle:before,.fa-google-plus-official:before{content:""}.fa-fa:before,.fa-font-awesome:before{content:""}.fa-handshake-o:before{content:""}.fa-envelope-open:before{content:""}.fa-envelope-open-o:before{content:""}.fa-linode:before{content:""}.fa-address-book:before{content:""}.fa-address-book-o:before{content:""}.fa-address-card:before,.fa-vcard:before{content:""}.fa-address-card-o:before,.fa-vcard-o:before{content:""}.fa-user-circle:before{content:""}.fa-user-circle-o:before{content:""}.fa-user-o:before{content:""}.fa-id-badge:before{content:""}.fa-drivers-license:before,.fa-id-card:before{content:""}.fa-drivers-license-o:before,.fa-id-card-o:before{content:""}.fa-quora:before{content:""}.fa-free-code-camp:before{content:""}.fa-telegram:before{content:""}.fa-thermometer-4:before,.fa-thermometer-full:before,.fa-thermometer:before{content:""}.fa-thermometer-3:before,.fa-thermometer-three-quarters:before{content:""}.fa-thermometer-2:before,.fa-thermometer-half:before{content:""}.fa-thermometer-1:before,.fa-thermometer-quarter:before{content:""}.fa-thermometer-0:before,.fa-thermometer-empty:before{content:""}.fa-shower:before{content:""}.fa-bath:before,.fa-bathtub:before,.fa-s15:before{content:""}.fa-podcast:before{content:""}.fa-window-maximize:before{content:""}.fa-window-minimize:before{content:""}.fa-window-restore:before{content:""}.fa-times-rectangle:before,.fa-window-close:before{content:""}.fa-times-rectangle-o:before,.fa-window-close-o:before{content:""}.fa-bandcamp:before{content:""}.fa-grav:before{content:""}.fa-etsy:before{content:""}.fa-imdb:before{content:""}.fa-ravelry:before{content:""}.fa-eercast:before{content:""}.fa-microchip:before{content:""}.fa-snowflake-o:before{content:""}.fa-superpowers:before{content:""}.fa-wpexplorer:before{content:""}.fa-meetup:before{content:""}.sr-only{position:absolute;width:1px;height:1px;padding:0;margin:-1px;overflow:hidden;clip:rect(0,0,0,0);border:0}.sr-only-focusable:active,.sr-only-focusable:focus{position:static;width:auto;height:auto;margin:0;overflow:visible;clip:auto}.fa,.icon,.rst-content .admonition-title,.rst-content .code-block-caption .headerlink,.rst-content .eqno .headerlink,.rst-content code.download span:first-child,.rst-content dl dt .headerlink,.rst-content h1 .headerlink,.rst-content h2 .headerlink,.rst-content h3 .headerlink,.rst-content h4 .headerlink,.rst-content h5 .headerlink,.rst-content h6 .headerlink,.rst-content p.caption .headerlink,.rst-content p .headerlink,.rst-content table>caption .headerlink,.rst-content tt.download span:first-child,.wy-dropdown .caret,.wy-inline-validate.wy-inline-validate-danger .wy-input-context,.wy-inline-validate.wy-inline-validate-info .wy-input-context,.wy-inline-validate.wy-inline-validate-success .wy-input-context,.wy-inline-validate.wy-inline-validate-warning .wy-input-context,.wy-menu-vertical li.current>a button.toctree-expand,.wy-menu-vertical li.on a button.toctree-expand,.wy-menu-vertical li button.toctree-expand{font-family:inherit}.fa:before,.icon:before,.rst-content .admonition-title:before,.rst-content .code-block-caption .headerlink:before,.rst-content .eqno .headerlink:before,.rst-content code.download span:first-child:before,.rst-content dl dt .headerlink:before,.rst-content h1 .headerlink:before,.rst-content h2 .headerlink:before,.rst-content h3 .headerlink:before,.rst-content h4 .headerlink:before,.rst-content h5 .headerlink:before,.rst-content h6 .headerlink:before,.rst-content p.caption .headerlink:before,.rst-content p .headerlink:before,.rst-content table>caption .headerlink:before,.rst-content tt.download span:first-child:before,.wy-dropdown .caret:before,.wy-inline-validate.wy-inline-validate-danger .wy-input-context:before,.wy-inline-validate.wy-inline-validate-info .wy-input-context:before,.wy-inline-validate.wy-inline-validate-success .wy-input-context:before,.wy-inline-validate.wy-inline-validate-warning .wy-input-context:before,.wy-menu-vertical li.current>a button.toctree-expand:before,.wy-menu-vertical li.on a button.toctree-expand:before,.wy-menu-vertical li button.toctree-expand:before{font-family:FontAwesome;display:inline-block;font-style:normal;font-weight:400;line-height:1;text-decoration:inherit}.rst-content .code-block-caption a .headerlink,.rst-content .eqno a .headerlink,.rst-content a .admonition-title,.rst-content code.download a span:first-child,.rst-content dl dt a .headerlink,.rst-content h1 a .headerlink,.rst-content h2 a .headerlink,.rst-content h3 a .headerlink,.rst-content h4 a .headerlink,.rst-content h5 a .headerlink,.rst-content h6 a .headerlink,.rst-content p.caption a .headerlink,.rst-content p a .headerlink,.rst-content table>caption a .headerlink,.rst-content tt.download a span:first-child,.wy-menu-vertical li.current>a button.toctree-expand,.wy-menu-vertical li.on a button.toctree-expand,.wy-menu-vertical li a button.toctree-expand,a .fa,a .icon,a .rst-content .admonition-title,a .rst-content .code-block-caption .headerlink,a .rst-content .eqno .headerlink,a .rst-content code.download span:first-child,a .rst-content dl dt .headerlink,a .rst-content h1 .headerlink,a .rst-content h2 .headerlink,a .rst-content h3 .headerlink,a .rst-content h4 .headerlink,a .rst-content h5 .headerlink,a .rst-content h6 .headerlink,a .rst-content p.caption .headerlink,a .rst-content p .headerlink,a .rst-content table>caption .headerlink,a .rst-content tt.download span:first-child,a .wy-menu-vertical li button.toctree-expand{display:inline-block;text-decoration:inherit}.btn .fa,.btn .icon,.btn .rst-content .admonition-title,.btn .rst-content .code-block-caption .headerlink,.btn .rst-content .eqno .headerlink,.btn .rst-content code.download span:first-child,.btn .rst-content dl dt .headerlink,.btn .rst-content h1 .headerlink,.btn .rst-content h2 .headerlink,.btn .rst-content h3 .headerlink,.btn .rst-content h4 .headerlink,.btn .rst-content h5 .headerlink,.btn .rst-content h6 .headerlink,.btn .rst-content p .headerlink,.btn .rst-content table>caption .headerlink,.btn .rst-content tt.download span:first-child,.btn .wy-menu-vertical li.current>a button.toctree-expand,.btn .wy-menu-vertical li.on a button.toctree-expand,.btn .wy-menu-vertical li button.toctree-expand,.nav .fa,.nav .icon,.nav .rst-content .admonition-title,.nav .rst-content .code-block-caption .headerlink,.nav .rst-content .eqno .headerlink,.nav .rst-content code.download span:first-child,.nav .rst-content dl dt .headerlink,.nav .rst-content h1 .headerlink,.nav .rst-content h2 .headerlink,.nav .rst-content h3 .headerlink,.nav .rst-content h4 .headerlink,.nav .rst-content h5 .headerlink,.nav .rst-content h6 .headerlink,.nav .rst-content p .headerlink,.nav .rst-content table>caption .headerlink,.nav .rst-content tt.download span:first-child,.nav .wy-menu-vertical li.current>a button.toctree-expand,.nav .wy-menu-vertical li.on a button.toctree-expand,.nav .wy-menu-vertical li button.toctree-expand,.rst-content .btn .admonition-title,.rst-content .code-block-caption .btn .headerlink,.rst-content .code-block-caption .nav .headerlink,.rst-content .eqno .btn .headerlink,.rst-content .eqno .nav .headerlink,.rst-content .nav .admonition-title,.rst-content code.download .btn span:first-child,.rst-content code.download .nav span:first-child,.rst-content dl dt .btn .headerlink,.rst-content dl dt .nav .headerlink,.rst-content h1 .btn .headerlink,.rst-content h1 .nav .headerlink,.rst-content h2 .btn .headerlink,.rst-content h2 .nav .headerlink,.rst-content h3 .btn .headerlink,.rst-content h3 .nav .headerlink,.rst-content h4 .btn .headerlink,.rst-content h4 .nav .headerlink,.rst-content h5 .btn .headerlink,.rst-content h5 .nav .headerlink,.rst-content h6 .btn .headerlink,.rst-content h6 .nav .headerlink,.rst-content p .btn .headerlink,.rst-content p .nav .headerlink,.rst-content table>caption .btn .headerlink,.rst-content table>caption .nav .headerlink,.rst-content tt.download .btn span:first-child,.rst-content tt.download .nav span:first-child,.wy-menu-vertical li .btn button.toctree-expand,.wy-menu-vertical li.current>a .btn button.toctree-expand,.wy-menu-vertical li.current>a .nav button.toctree-expand,.wy-menu-vertical li .nav button.toctree-expand,.wy-menu-vertical li.on a .btn button.toctree-expand,.wy-menu-vertical li.on a .nav button.toctree-expand{display:inline}.btn .fa-large.icon,.btn .fa.fa-large,.btn .rst-content .code-block-caption .fa-large.headerlink,.btn .rst-content .eqno .fa-large.headerlink,.btn .rst-content .fa-large.admonition-title,.btn .rst-content code.download span.fa-large:first-child,.btn .rst-content dl dt .fa-large.headerlink,.btn .rst-content h1 .fa-large.headerlink,.btn .rst-content h2 .fa-large.headerlink,.btn .rst-content h3 .fa-large.headerlink,.btn .rst-content h4 .fa-large.headerlink,.btn .rst-content h5 .fa-large.headerlink,.btn .rst-content h6 .fa-large.headerlink,.btn .rst-content p .fa-large.headerlink,.btn .rst-content table>caption .fa-large.headerlink,.btn .rst-content tt.download span.fa-large:first-child,.btn .wy-menu-vertical li button.fa-large.toctree-expand,.nav .fa-large.icon,.nav .fa.fa-large,.nav .rst-content .code-block-caption .fa-large.headerlink,.nav .rst-content .eqno .fa-large.headerlink,.nav .rst-content .fa-large.admonition-title,.nav .rst-content code.download span.fa-large:first-child,.nav .rst-content dl dt .fa-large.headerlink,.nav .rst-content h1 .fa-large.headerlink,.nav .rst-content h2 .fa-large.headerlink,.nav .rst-content h3 .fa-large.headerlink,.nav .rst-content h4 .fa-large.headerlink,.nav .rst-content h5 .fa-large.headerlink,.nav .rst-content h6 .fa-large.headerlink,.nav .rst-content p .fa-large.headerlink,.nav .rst-content table>caption .fa-large.headerlink,.nav .rst-content tt.download span.fa-large:first-child,.nav .wy-menu-vertical li button.fa-large.toctree-expand,.rst-content .btn .fa-large.admonition-title,.rst-content .code-block-caption .btn .fa-large.headerlink,.rst-content .code-block-caption .nav .fa-large.headerlink,.rst-content .eqno .btn .fa-large.headerlink,.rst-content .eqno .nav .fa-large.headerlink,.rst-content .nav .fa-large.admonition-title,.rst-content code.download .btn span.fa-large:first-child,.rst-content code.download .nav span.fa-large:first-child,.rst-content dl dt .btn .fa-large.headerlink,.rst-content dl dt .nav .fa-large.headerlink,.rst-content h1 .btn .fa-large.headerlink,.rst-content h1 .nav .fa-large.headerlink,.rst-content h2 .btn .fa-large.headerlink,.rst-content h2 .nav .fa-large.headerlink,.rst-content h3 .btn .fa-large.headerlink,.rst-content h3 .nav .fa-large.headerlink,.rst-content h4 .btn .fa-large.headerlink,.rst-content h4 .nav .fa-large.headerlink,.rst-content h5 .btn .fa-large.headerlink,.rst-content h5 .nav .fa-large.headerlink,.rst-content h6 .btn .fa-large.headerlink,.rst-content h6 .nav .fa-large.headerlink,.rst-content p .btn .fa-large.headerlink,.rst-content p .nav .fa-large.headerlink,.rst-content table>caption .btn .fa-large.headerlink,.rst-content table>caption .nav .fa-large.headerlink,.rst-content tt.download .btn span.fa-large:first-child,.rst-content tt.download .nav span.fa-large:first-child,.wy-menu-vertical li .btn button.fa-large.toctree-expand,.wy-menu-vertical li .nav button.fa-large.toctree-expand{line-height:.9em}.btn .fa-spin.icon,.btn .fa.fa-spin,.btn .rst-content .code-block-caption .fa-spin.headerlink,.btn .rst-content .eqno .fa-spin.headerlink,.btn .rst-content .fa-spin.admonition-title,.btn .rst-content code.download span.fa-spin:first-child,.btn .rst-content dl dt .fa-spin.headerlink,.btn .rst-content h1 .fa-spin.headerlink,.btn .rst-content h2 .fa-spin.headerlink,.btn .rst-content h3 .fa-spin.headerlink,.btn .rst-content h4 .fa-spin.headerlink,.btn .rst-content h5 .fa-spin.headerlink,.btn .rst-content h6 .fa-spin.headerlink,.btn .rst-content p .fa-spin.headerlink,.btn .rst-content table>caption .fa-spin.headerlink,.btn .rst-content tt.download span.fa-spin:first-child,.btn .wy-menu-vertical li button.fa-spin.toctree-expand,.nav .fa-spin.icon,.nav .fa.fa-spin,.nav .rst-content .code-block-caption .fa-spin.headerlink,.nav .rst-content .eqno .fa-spin.headerlink,.nav .rst-content .fa-spin.admonition-title,.nav .rst-content code.download span.fa-spin:first-child,.nav .rst-content dl dt .fa-spin.headerlink,.nav .rst-content h1 .fa-spin.headerlink,.nav .rst-content h2 .fa-spin.headerlink,.nav .rst-content h3 .fa-spin.headerlink,.nav .rst-content h4 .fa-spin.headerlink,.nav .rst-content h5 .fa-spin.headerlink,.nav .rst-content h6 .fa-spin.headerlink,.nav .rst-content p .fa-spin.headerlink,.nav .rst-content table>caption .fa-spin.headerlink,.nav .rst-content tt.download span.fa-spin:first-child,.nav .wy-menu-vertical li button.fa-spin.toctree-expand,.rst-content .btn .fa-spin.admonition-title,.rst-content .code-block-caption .btn .fa-spin.headerlink,.rst-content .code-block-caption .nav .fa-spin.headerlink,.rst-content .eqno .btn .fa-spin.headerlink,.rst-content .eqno .nav .fa-spin.headerlink,.rst-content .nav .fa-spin.admonition-title,.rst-content code.download .btn span.fa-spin:first-child,.rst-content code.download .nav span.fa-spin:first-child,.rst-content dl dt .btn .fa-spin.headerlink,.rst-content dl dt .nav .fa-spin.headerlink,.rst-content h1 .btn .fa-spin.headerlink,.rst-content h1 .nav .fa-spin.headerlink,.rst-content h2 .btn .fa-spin.headerlink,.rst-content h2 .nav .fa-spin.headerlink,.rst-content h3 .btn .fa-spin.headerlink,.rst-content h3 .nav .fa-spin.headerlink,.rst-content h4 .btn .fa-spin.headerlink,.rst-content h4 .nav .fa-spin.headerlink,.rst-content h5 .btn .fa-spin.headerlink,.rst-content h5 .nav .fa-spin.headerlink,.rst-content h6 .btn .fa-spin.headerlink,.rst-content h6 .nav .fa-spin.headerlink,.rst-content p .btn .fa-spin.headerlink,.rst-content p .nav .fa-spin.headerlink,.rst-content table>caption .btn .fa-spin.headerlink,.rst-content table>caption .nav .fa-spin.headerlink,.rst-content tt.download .btn span.fa-spin:first-child,.rst-content tt.download .nav span.fa-spin:first-child,.wy-menu-vertical li .btn button.fa-spin.toctree-expand,.wy-menu-vertical li .nav button.fa-spin.toctree-expand{display:inline-block}.btn.fa:before,.btn.icon:before,.rst-content .btn.admonition-title:before,.rst-content .code-block-caption .btn.headerlink:before,.rst-content .eqno .btn.headerlink:before,.rst-content code.download span.btn:first-child:before,.rst-content dl dt .btn.headerlink:before,.rst-content h1 .btn.headerlink:before,.rst-content h2 .btn.headerlink:before,.rst-content h3 .btn.headerlink:before,.rst-content h4 .btn.headerlink:before,.rst-content h5 .btn.headerlink:before,.rst-content h6 .btn.headerlink:before,.rst-content p .btn.headerlink:before,.rst-content table>caption .btn.headerlink:before,.rst-content tt.download span.btn:first-child:before,.wy-menu-vertical li button.btn.toctree-expand:before{opacity:.5;-webkit-transition:opacity .05s ease-in;-moz-transition:opacity .05s ease-in;transition:opacity .05s ease-in}.btn.fa:hover:before,.btn.icon:hover:before,.rst-content .btn.admonition-title:hover:before,.rst-content .code-block-caption .btn.headerlink:hover:before,.rst-content .eqno .btn.headerlink:hover:before,.rst-content code.download span.btn:first-child:hover:before,.rst-content dl dt .btn.headerlink:hover:before,.rst-content h1 .btn.headerlink:hover:before,.rst-content h2 .btn.headerlink:hover:before,.rst-content h3 .btn.headerlink:hover:before,.rst-content h4 .btn.headerlink:hover:before,.rst-content h5 .btn.headerlink:hover:before,.rst-content h6 .btn.headerlink:hover:before,.rst-content p .btn.headerlink:hover:before,.rst-content table>caption .btn.headerlink:hover:before,.rst-content tt.download span.btn:first-child:hover:before,.wy-menu-vertical li button.btn.toctree-expand:hover:before{opacity:1}.btn-mini .fa:before,.btn-mini .icon:before,.btn-mini .rst-content .admonition-title:before,.btn-mini .rst-content .code-block-caption .headerlink:before,.btn-mini .rst-content .eqno .headerlink:before,.btn-mini .rst-content code.download span:first-child:before,.btn-mini .rst-content dl dt .headerlink:before,.btn-mini .rst-content h1 .headerlink:before,.btn-mini .rst-content h2 .headerlink:before,.btn-mini .rst-content h3 .headerlink:before,.btn-mini .rst-content h4 .headerlink:before,.btn-mini .rst-content h5 .headerlink:before,.btn-mini .rst-content h6 .headerlink:before,.btn-mini .rst-content p .headerlink:before,.btn-mini .rst-content table>caption .headerlink:before,.btn-mini .rst-content tt.download span:first-child:before,.btn-mini .wy-menu-vertical li button.toctree-expand:before,.rst-content .btn-mini .admonition-title:before,.rst-content .code-block-caption .btn-mini .headerlink:before,.rst-content .eqno .btn-mini .headerlink:before,.rst-content code.download .btn-mini span:first-child:before,.rst-content dl dt .btn-mini .headerlink:before,.rst-content h1 .btn-mini .headerlink:before,.rst-content h2 .btn-mini .headerlink:before,.rst-content h3 .btn-mini .headerlink:before,.rst-content h4 .btn-mini .headerlink:before,.rst-content h5 .btn-mini .headerlink:before,.rst-content h6 .btn-mini .headerlink:before,.rst-content p .btn-mini .headerlink:before,.rst-content table>caption .btn-mini .headerlink:before,.rst-content tt.download .btn-mini span:first-child:before,.wy-menu-vertical li .btn-mini button.toctree-expand:before{font-size:14px;vertical-align:-15%}.rst-content .admonition,.rst-content .admonition-todo,.rst-content .attention,.rst-content .caution,.rst-content .danger,.rst-content .error,.rst-content .hint,.rst-content .important,.rst-content .note,.rst-content .seealso,.rst-content .tip,.rst-content .warning,.wy-alert{padding:12px;line-height:24px;margin-bottom:24px;background:#e7f2fa}.rst-content .admonition-title,.wy-alert-title{font-weight:700;display:block;color:#fff;background:#6ab0de;padding:6px 12px;margin:-12px -12px 12px}.rst-content .danger,.rst-content .error,.rst-content .wy-alert-danger.admonition,.rst-content .wy-alert-danger.admonition-todo,.rst-content .wy-alert-danger.attention,.rst-content .wy-alert-danger.caution,.rst-content .wy-alert-danger.hint,.rst-content .wy-alert-danger.important,.rst-content .wy-alert-danger.note,.rst-content .wy-alert-danger.seealso,.rst-content .wy-alert-danger.tip,.rst-content .wy-alert-danger.warning,.wy-alert.wy-alert-danger{background:#fdf3f2}.rst-content .danger .admonition-title,.rst-content .danger .wy-alert-title,.rst-content .error .admonition-title,.rst-content .error .wy-alert-title,.rst-content .wy-alert-danger.admonition-todo .admonition-title,.rst-content .wy-alert-danger.admonition-todo .wy-alert-title,.rst-content .wy-alert-danger.admonition .admonition-title,.rst-content .wy-alert-danger.admonition .wy-alert-title,.rst-content .wy-alert-danger.attention .admonition-title,.rst-content .wy-alert-danger.attention .wy-alert-title,.rst-content .wy-alert-danger.caution .admonition-title,.rst-content .wy-alert-danger.caution .wy-alert-title,.rst-content .wy-alert-danger.hint .admonition-title,.rst-content .wy-alert-danger.hint .wy-alert-title,.rst-content .wy-alert-danger.important .admonition-title,.rst-content .wy-alert-danger.important .wy-alert-title,.rst-content .wy-alert-danger.note .admonition-title,.rst-content .wy-alert-danger.note .wy-alert-title,.rst-content .wy-alert-danger.seealso .admonition-title,.rst-content .wy-alert-danger.seealso .wy-alert-title,.rst-content .wy-alert-danger.tip .admonition-title,.rst-content .wy-alert-danger.tip .wy-alert-title,.rst-content .wy-alert-danger.warning .admonition-title,.rst-content .wy-alert-danger.warning .wy-alert-title,.rst-content .wy-alert.wy-alert-danger .admonition-title,.wy-alert.wy-alert-danger .rst-content .admonition-title,.wy-alert.wy-alert-danger .wy-alert-title{background:#f29f97}.rst-content .admonition-todo,.rst-content .attention,.rst-content .caution,.rst-content .warning,.rst-content .wy-alert-warning.admonition,.rst-content .wy-alert-warning.danger,.rst-content .wy-alert-warning.error,.rst-content .wy-alert-warning.hint,.rst-content .wy-alert-warning.important,.rst-content .wy-alert-warning.note,.rst-content .wy-alert-warning.seealso,.rst-content .wy-alert-warning.tip,.wy-alert.wy-alert-warning{background:#ffedcc}.rst-content .admonition-todo .admonition-title,.rst-content .admonition-todo .wy-alert-title,.rst-content .attention .admonition-title,.rst-content .attention .wy-alert-title,.rst-content .caution .admonition-title,.rst-content .caution .wy-alert-title,.rst-content .warning .admonition-title,.rst-content .warning .wy-alert-title,.rst-content .wy-alert-warning.admonition .admonition-title,.rst-content .wy-alert-warning.admonition .wy-alert-title,.rst-content .wy-alert-warning.danger .admonition-title,.rst-content .wy-alert-warning.danger .wy-alert-title,.rst-content .wy-alert-warning.error .admonition-title,.rst-content .wy-alert-warning.error .wy-alert-title,.rst-content .wy-alert-warning.hint .admonition-title,.rst-content .wy-alert-warning.hint .wy-alert-title,.rst-content .wy-alert-warning.important .admonition-title,.rst-content .wy-alert-warning.important .wy-alert-title,.rst-content .wy-alert-warning.note .admonition-title,.rst-content .wy-alert-warning.note .wy-alert-title,.rst-content .wy-alert-warning.seealso .admonition-title,.rst-content .wy-alert-warning.seealso .wy-alert-title,.rst-content .wy-alert-warning.tip .admonition-title,.rst-content .wy-alert-warning.tip .wy-alert-title,.rst-content .wy-alert.wy-alert-warning .admonition-title,.wy-alert.wy-alert-warning .rst-content .admonition-title,.wy-alert.wy-alert-warning .wy-alert-title{background:#f0b37e}.rst-content .note,.rst-content .seealso,.rst-content .wy-alert-info.admonition,.rst-content .wy-alert-info.admonition-todo,.rst-content .wy-alert-info.attention,.rst-content .wy-alert-info.caution,.rst-content .wy-alert-info.danger,.rst-content .wy-alert-info.error,.rst-content .wy-alert-info.hint,.rst-content .wy-alert-info.important,.rst-content .wy-alert-info.tip,.rst-content .wy-alert-info.warning,.wy-alert.wy-alert-info{background:#e7f2fa}.rst-content .note .admonition-title,.rst-content .note .wy-alert-title,.rst-content .seealso .admonition-title,.rst-content .seealso .wy-alert-title,.rst-content .wy-alert-info.admonition-todo .admonition-title,.rst-content .wy-alert-info.admonition-todo .wy-alert-title,.rst-content .wy-alert-info.admonition .admonition-title,.rst-content .wy-alert-info.admonition .wy-alert-title,.rst-content .wy-alert-info.attention .admonition-title,.rst-content .wy-alert-info.attention .wy-alert-title,.rst-content .wy-alert-info.caution .admonition-title,.rst-content .wy-alert-info.caution .wy-alert-title,.rst-content .wy-alert-info.danger .admonition-title,.rst-content .wy-alert-info.danger .wy-alert-title,.rst-content .wy-alert-info.error .admonition-title,.rst-content .wy-alert-info.error .wy-alert-title,.rst-content .wy-alert-info.hint .admonition-title,.rst-content .wy-alert-info.hint .wy-alert-title,.rst-content .wy-alert-info.important .admonition-title,.rst-content .wy-alert-info.important .wy-alert-title,.rst-content .wy-alert-info.tip .admonition-title,.rst-content .wy-alert-info.tip .wy-alert-title,.rst-content .wy-alert-info.warning .admonition-title,.rst-content .wy-alert-info.warning .wy-alert-title,.rst-content .wy-alert.wy-alert-info .admonition-title,.wy-alert.wy-alert-info .rst-content .admonition-title,.wy-alert.wy-alert-info .wy-alert-title{background:#6ab0de}.rst-content .hint,.rst-content .important,.rst-content .tip,.rst-content .wy-alert-success.admonition,.rst-content .wy-alert-success.admonition-todo,.rst-content .wy-alert-success.attention,.rst-content .wy-alert-success.caution,.rst-content .wy-alert-success.danger,.rst-content .wy-alert-success.error,.rst-content .wy-alert-success.note,.rst-content .wy-alert-success.seealso,.rst-content .wy-alert-success.warning,.wy-alert.wy-alert-success{background:#dbfaf4}.rst-content .hint .admonition-title,.rst-content .hint .wy-alert-title,.rst-content .important .admonition-title,.rst-content .important .wy-alert-title,.rst-content .tip .admonition-title,.rst-content .tip .wy-alert-title,.rst-content .wy-alert-success.admonition-todo .admonition-title,.rst-content .wy-alert-success.admonition-todo .wy-alert-title,.rst-content .wy-alert-success.admonition .admonition-title,.rst-content .wy-alert-success.admonition .wy-alert-title,.rst-content .wy-alert-success.attention .admonition-title,.rst-content .wy-alert-success.attention .wy-alert-title,.rst-content .wy-alert-success.caution .admonition-title,.rst-content .wy-alert-success.caution .wy-alert-title,.rst-content .wy-alert-success.danger .admonition-title,.rst-content .wy-alert-success.danger .wy-alert-title,.rst-content .wy-alert-success.error .admonition-title,.rst-content .wy-alert-success.error .wy-alert-title,.rst-content .wy-alert-success.note .admonition-title,.rst-content .wy-alert-success.note .wy-alert-title,.rst-content .wy-alert-success.seealso .admonition-title,.rst-content .wy-alert-success.seealso .wy-alert-title,.rst-content .wy-alert-success.warning .admonition-title,.rst-content .wy-alert-success.warning .wy-alert-title,.rst-content .wy-alert.wy-alert-success .admonition-title,.wy-alert.wy-alert-success .rst-content .admonition-title,.wy-alert.wy-alert-success .wy-alert-title{background:#1abc9c}.rst-content .wy-alert-neutral.admonition,.rst-content .wy-alert-neutral.admonition-todo,.rst-content .wy-alert-neutral.attention,.rst-content .wy-alert-neutral.caution,.rst-content .wy-alert-neutral.danger,.rst-content .wy-alert-neutral.error,.rst-content .wy-alert-neutral.hint,.rst-content .wy-alert-neutral.important,.rst-content .wy-alert-neutral.note,.rst-content .wy-alert-neutral.seealso,.rst-content .wy-alert-neutral.tip,.rst-content .wy-alert-neutral.warning,.wy-alert.wy-alert-neutral{background:#f3f6f6}.rst-content .wy-alert-neutral.admonition-todo .admonition-title,.rst-content .wy-alert-neutral.admonition-todo .wy-alert-title,.rst-content .wy-alert-neutral.admonition .admonition-title,.rst-content .wy-alert-neutral.admonition .wy-alert-title,.rst-content .wy-alert-neutral.attention .admonition-title,.rst-content .wy-alert-neutral.attention .wy-alert-title,.rst-content .wy-alert-neutral.caution .admonition-title,.rst-content .wy-alert-neutral.caution .wy-alert-title,.rst-content .wy-alert-neutral.danger .admonition-title,.rst-content .wy-alert-neutral.danger .wy-alert-title,.rst-content .wy-alert-neutral.error .admonition-title,.rst-content .wy-alert-neutral.error .wy-alert-title,.rst-content .wy-alert-neutral.hint .admonition-title,.rst-content .wy-alert-neutral.hint .wy-alert-title,.rst-content .wy-alert-neutral.important .admonition-title,.rst-content .wy-alert-neutral.important .wy-alert-title,.rst-content .wy-alert-neutral.note .admonition-title,.rst-content .wy-alert-neutral.note .wy-alert-title,.rst-content .wy-alert-neutral.seealso .admonition-title,.rst-content .wy-alert-neutral.seealso .wy-alert-title,.rst-content .wy-alert-neutral.tip .admonition-title,.rst-content .wy-alert-neutral.tip .wy-alert-title,.rst-content .wy-alert-neutral.warning .admonition-title,.rst-content .wy-alert-neutral.warning .wy-alert-title,.rst-content .wy-alert.wy-alert-neutral .admonition-title,.wy-alert.wy-alert-neutral .rst-content .admonition-title,.wy-alert.wy-alert-neutral .wy-alert-title{color:#404040;background:#e1e4e5}.rst-content .wy-alert-neutral.admonition-todo a,.rst-content .wy-alert-neutral.admonition a,.rst-content .wy-alert-neutral.attention a,.rst-content .wy-alert-neutral.caution a,.rst-content .wy-alert-neutral.danger a,.rst-content .wy-alert-neutral.error a,.rst-content .wy-alert-neutral.hint a,.rst-content .wy-alert-neutral.important a,.rst-content .wy-alert-neutral.note a,.rst-content .wy-alert-neutral.seealso a,.rst-content .wy-alert-neutral.tip a,.rst-content .wy-alert-neutral.warning a,.wy-alert.wy-alert-neutral a{color:#2980b9}.rst-content .admonition-todo p:last-child,.rst-content .admonition p:last-child,.rst-content .attention p:last-child,.rst-content .caution p:last-child,.rst-content .danger p:last-child,.rst-content .error p:last-child,.rst-content .hint p:last-child,.rst-content .important p:last-child,.rst-content .note p:last-child,.rst-content .seealso p:last-child,.rst-content .tip p:last-child,.rst-content .warning p:last-child,.wy-alert p:last-child{margin-bottom:0}.wy-tray-container{position:fixed;bottom:0;left:0;z-index:600}.wy-tray-container li{display:block;width:300px;background:transparent;color:#fff;text-align:center;box-shadow:0 5px 5px 0 rgba(0,0,0,.1);padding:0 24px;min-width:20%;opacity:0;height:0;line-height:56px;overflow:hidden;-webkit-transition:all .3s ease-in;-moz-transition:all .3s ease-in;transition:all .3s ease-in}.wy-tray-container li.wy-tray-item-success{background:#27ae60}.wy-tray-container li.wy-tray-item-info{background:#2980b9}.wy-tray-container li.wy-tray-item-warning{background:#e67e22}.wy-tray-container li.wy-tray-item-danger{background:#e74c3c}.wy-tray-container li.on{opacity:1;height:56px}@media screen and (max-width:768px){.wy-tray-container{bottom:auto;top:0;width:100%}.wy-tray-container li{width:100%}}button{font-size:100%;margin:0;vertical-align:baseline;*vertical-align:middle;cursor:pointer;line-height:normal;-webkit-appearance:button;*overflow:visible}button::-moz-focus-inner,input::-moz-focus-inner{border:0;padding:0}button[disabled]{cursor:default}.btn{display:inline-block;border-radius:2px;line-height:normal;white-space:nowrap;text-align:center;cursor:pointer;font-size:100%;padding:6px 12px 8px;color:#fff;border:1px solid rgba(0,0,0,.1);background-color:#27ae60;text-decoration:none;font-weight:400;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;box-shadow:inset 0 1px 2px -1px hsla(0,0%,100%,.5),inset 0 -2px 0 0 rgba(0,0,0,.1);outline-none:false;vertical-align:middle;*display:inline;zoom:1;-webkit-user-drag:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none;-webkit-transition:all .1s linear;-moz-transition:all .1s linear;transition:all .1s linear}.btn-hover{background:#2e8ece;color:#fff}.btn:hover{background:#2cc36b;color:#fff}.btn:focus{background:#2cc36b;outline:0}.btn:active{box-shadow:inset 0 -1px 0 0 rgba(0,0,0,.05),inset 0 2px 0 0 rgba(0,0,0,.1);padding:8px 12px 6px}.btn:visited{color:#fff}.btn-disabled,.btn-disabled:active,.btn-disabled:focus,.btn-disabled:hover,.btn:disabled{background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:alpha(opacity=40);opacity:.4;cursor:not-allowed;box-shadow:none}.btn::-moz-focus-inner{padding:0;border:0}.btn-small{font-size:80%}.btn-info{background-color:#2980b9!important}.btn-info:hover{background-color:#2e8ece!important}.btn-neutral{background-color:#f3f6f6!important;color:#404040!important}.btn-neutral:hover{background-color:#e5ebeb!important;color:#404040}.btn-neutral:visited{color:#404040!important}.btn-success{background-color:#27ae60!important}.btn-success:hover{background-color:#295!important}.btn-danger{background-color:#e74c3c!important}.btn-danger:hover{background-color:#ea6153!important}.btn-warning{background-color:#e67e22!important}.btn-warning:hover{background-color:#e98b39!important}.btn-invert{background-color:#222}.btn-invert:hover{background-color:#2f2f2f!important}.btn-link{background-color:transparent!important;color:#2980b9;box-shadow:none;border-color:transparent!important}.btn-link:active,.btn-link:hover{background-color:transparent!important;color:#409ad5!important;box-shadow:none}.btn-link:visited{color:#9b59b6}.wy-btn-group .btn,.wy-control .btn{vertical-align:middle}.wy-btn-group{margin-bottom:24px;*zoom:1}.wy-btn-group:after,.wy-btn-group:before{display:table;content:""}.wy-btn-group:after{clear:both}.wy-dropdown{position:relative;display:inline-block}.wy-dropdown-active .wy-dropdown-menu{display:block}.wy-dropdown-menu{position:absolute;left:0;display:none;float:left;top:100%;min-width:100%;background:#fcfcfc;z-index:100;border:1px solid #cfd7dd;box-shadow:0 2px 2px 0 rgba(0,0,0,.1);padding:12px}.wy-dropdown-menu>dd>a{display:block;clear:both;color:#404040;white-space:nowrap;font-size:90%;padding:0 12px;cursor:pointer}.wy-dropdown-menu>dd>a:hover{background:#2980b9;color:#fff}.wy-dropdown-menu>dd.divider{border-top:1px solid #cfd7dd;margin:6px 0}.wy-dropdown-menu>dd.search{padding-bottom:12px}.wy-dropdown-menu>dd.search input[type=search]{width:100%}.wy-dropdown-menu>dd.call-to-action{background:#e3e3e3;text-transform:uppercase;font-weight:500;font-size:80%}.wy-dropdown-menu>dd.call-to-action:hover{background:#e3e3e3}.wy-dropdown-menu>dd.call-to-action .btn{color:#fff}.wy-dropdown.wy-dropdown-up .wy-dropdown-menu{bottom:100%;top:auto;left:auto;right:0}.wy-dropdown.wy-dropdown-bubble .wy-dropdown-menu{background:#fcfcfc;margin-top:2px}.wy-dropdown.wy-dropdown-bubble .wy-dropdown-menu a{padding:6px 12px}.wy-dropdown.wy-dropdown-bubble .wy-dropdown-menu a:hover{background:#2980b9;color:#fff}.wy-dropdown.wy-dropdown-left .wy-dropdown-menu{right:0;left:auto;text-align:right}.wy-dropdown-arrow:before{content:" ";border-bottom:5px solid #f5f5f5;border-left:5px solid transparent;border-right:5px solid transparent;position:absolute;display:block;top:-4px;left:50%;margin-left:-3px}.wy-dropdown-arrow.wy-dropdown-arrow-left:before{left:11px}.wy-form-stacked select{display:block}.wy-form-aligned .wy-help-inline,.wy-form-aligned input,.wy-form-aligned label,.wy-form-aligned select,.wy-form-aligned textarea{display:inline-block;*display:inline;*zoom:1;vertical-align:middle}.wy-form-aligned .wy-control-group>label{display:inline-block;vertical-align:middle;width:10em;margin:6px 12px 0 0;float:left}.wy-form-aligned .wy-control{float:left}.wy-form-aligned .wy-control label{display:block}.wy-form-aligned .wy-control select{margin-top:6px}fieldset{margin:0}fieldset,legend{border:0;padding:0}legend{width:100%;white-space:normal;margin-bottom:24px;font-size:150%;*margin-left:-7px}label,legend{display:block}label{margin:0 0 .3125em;color:#333;font-size:90%}input,select,textarea{font-size:100%;margin:0;vertical-align:baseline;*vertical-align:middle}.wy-control-group{margin-bottom:24px;max-width:1200px;margin-left:auto;margin-right:auto;*zoom:1}.wy-control-group:after,.wy-control-group:before{display:table;content:""}.wy-control-group:after{clear:both}.wy-control-group.wy-control-group-required>label:after{content:" *";color:#e74c3c}.wy-control-group .wy-form-full,.wy-control-group .wy-form-halves,.wy-control-group .wy-form-thirds{padding-bottom:12px}.wy-control-group .wy-form-full input[type=color],.wy-control-group .wy-form-full input[type=date],.wy-control-group .wy-form-full input[type=datetime-local],.wy-control-group .wy-form-full input[type=datetime],.wy-control-group .wy-form-full input[type=email],.wy-control-group .wy-form-full input[type=month],.wy-control-group .wy-form-full input[type=number],.wy-control-group .wy-form-full input[type=password],.wy-control-group .wy-form-full input[type=search],.wy-control-group .wy-form-full input[type=tel],.wy-control-group .wy-form-full input[type=text],.wy-control-group .wy-form-full input[type=time],.wy-control-group .wy-form-full input[type=url],.wy-control-group .wy-form-full input[type=week],.wy-control-group .wy-form-full select,.wy-control-group .wy-form-halves input[type=color],.wy-control-group .wy-form-halves input[type=date],.wy-control-group .wy-form-halves input[type=datetime-local],.wy-control-group .wy-form-halves input[type=datetime],.wy-control-group .wy-form-halves input[type=email],.wy-control-group .wy-form-halves input[type=month],.wy-control-group .wy-form-halves input[type=number],.wy-control-group .wy-form-halves input[type=password],.wy-control-group .wy-form-halves input[type=search],.wy-control-group .wy-form-halves input[type=tel],.wy-control-group .wy-form-halves input[type=text],.wy-control-group .wy-form-halves input[type=time],.wy-control-group .wy-form-halves input[type=url],.wy-control-group .wy-form-halves input[type=week],.wy-control-group .wy-form-halves select,.wy-control-group .wy-form-thirds input[type=color],.wy-control-group .wy-form-thirds input[type=date],.wy-control-group .wy-form-thirds input[type=datetime-local],.wy-control-group .wy-form-thirds input[type=datetime],.wy-control-group .wy-form-thirds input[type=email],.wy-control-group .wy-form-thirds input[type=month],.wy-control-group .wy-form-thirds input[type=number],.wy-control-group .wy-form-thirds input[type=password],.wy-control-group .wy-form-thirds input[type=search],.wy-control-group .wy-form-thirds input[type=tel],.wy-control-group .wy-form-thirds input[type=text],.wy-control-group .wy-form-thirds input[type=time],.wy-control-group .wy-form-thirds input[type=url],.wy-control-group .wy-form-thirds input[type=week],.wy-control-group .wy-form-thirds select{width:100%}.wy-control-group .wy-form-full{float:left;display:block;width:100%;margin-right:0}.wy-control-group .wy-form-full:last-child{margin-right:0}.wy-control-group .wy-form-halves{float:left;display:block;margin-right:2.35765%;width:48.82117%}.wy-control-group .wy-form-halves:last-child,.wy-control-group .wy-form-halves:nth-of-type(2n){margin-right:0}.wy-control-group .wy-form-halves:nth-of-type(odd){clear:left}.wy-control-group .wy-form-thirds{float:left;display:block;margin-right:2.35765%;width:31.76157%}.wy-control-group .wy-form-thirds:last-child,.wy-control-group .wy-form-thirds:nth-of-type(3n){margin-right:0}.wy-control-group .wy-form-thirds:nth-of-type(3n+1){clear:left}.wy-control-group.wy-control-group-no-input .wy-control,.wy-control-no-input{margin:6px 0 0;font-size:90%}.wy-control-no-input{display:inline-block}.wy-control-group.fluid-input input[type=color],.wy-control-group.fluid-input input[type=date],.wy-control-group.fluid-input input[type=datetime-local],.wy-control-group.fluid-input input[type=datetime],.wy-control-group.fluid-input input[type=email],.wy-control-group.fluid-input input[type=month],.wy-control-group.fluid-input input[type=number],.wy-control-group.fluid-input input[type=password],.wy-control-group.fluid-input input[type=search],.wy-control-group.fluid-input input[type=tel],.wy-control-group.fluid-input input[type=text],.wy-control-group.fluid-input input[type=time],.wy-control-group.fluid-input input[type=url],.wy-control-group.fluid-input input[type=week]{width:100%}.wy-form-message-inline{padding-left:.3em;color:#666;font-size:90%}.wy-form-message{display:block;color:#999;font-size:70%;margin-top:.3125em;font-style:italic}.wy-form-message p{font-size:inherit;font-style:italic;margin-bottom:6px}.wy-form-message p:last-child{margin-bottom:0}input{line-height:normal}input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;*overflow:visible}input[type=color],input[type=date],input[type=datetime-local],input[type=datetime],input[type=email],input[type=month],input[type=number],input[type=password],input[type=search],input[type=tel],input[type=text],input[type=time],input[type=url],input[type=week]{-webkit-appearance:none;padding:6px;display:inline-block;border:1px solid #ccc;font-size:80%;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;box-shadow:inset 0 1px 3px #ddd;border-radius:0;-webkit-transition:border .3s linear;-moz-transition:border .3s linear;transition:border .3s linear}input[type=datetime-local]{padding:.34375em .625em}input[disabled]{cursor:default}input[type=checkbox],input[type=radio]{padding:0;margin-right:.3125em;*height:13px;*width:13px}input[type=checkbox],input[type=radio],input[type=search]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}input[type=color]:focus,input[type=date]:focus,input[type=datetime-local]:focus,input[type=datetime]:focus,input[type=email]:focus,input[type=month]:focus,input[type=number]:focus,input[type=password]:focus,input[type=search]:focus,input[type=tel]:focus,input[type=text]:focus,input[type=time]:focus,input[type=url]:focus,input[type=week]:focus{outline:0;outline:thin dotted\9;border-color:#333}input.no-focus:focus{border-color:#ccc!important}input[type=checkbox]:focus,input[type=file]:focus,input[type=radio]:focus{outline:thin dotted #333;outline:1px auto #129fea}input[type=color][disabled],input[type=date][disabled],input[type=datetime-local][disabled],input[type=datetime][disabled],input[type=email][disabled],input[type=month][disabled],input[type=number][disabled],input[type=password][disabled],input[type=search][disabled],input[type=tel][disabled],input[type=text][disabled],input[type=time][disabled],input[type=url][disabled],input[type=week][disabled]{cursor:not-allowed;background-color:#fafafa}input:focus:invalid,select:focus:invalid,textarea:focus:invalid{color:#e74c3c;border:1px solid #e74c3c}input:focus:invalid:focus,select:focus:invalid:focus,textarea:focus:invalid:focus{border-color:#e74c3c}input[type=checkbox]:focus:invalid:focus,input[type=file]:focus:invalid:focus,input[type=radio]:focus:invalid:focus{outline-color:#e74c3c}input.wy-input-large{padding:12px;font-size:100%}textarea{overflow:auto;vertical-align:top;width:100%;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif}select,textarea{padding:.5em .625em;display:inline-block;border:1px solid #ccc;font-size:80%;box-shadow:inset 0 1px 3px #ddd;-webkit-transition:border .3s linear;-moz-transition:border .3s linear;transition:border .3s linear}select{border:1px solid #ccc;background-color:#fff}select[multiple]{height:auto}select:focus,textarea:focus{outline:0}input[readonly],select[disabled],select[readonly],textarea[disabled],textarea[readonly]{cursor:not-allowed;background-color:#fafafa}input[type=checkbox][disabled],input[type=radio][disabled]{cursor:not-allowed}.wy-checkbox,.wy-radio{margin:6px 0;color:#404040;display:block}.wy-checkbox input,.wy-radio input{vertical-align:baseline}.wy-form-message-inline{display:inline-block;*display:inline;*zoom:1;vertical-align:middle}.wy-input-prefix,.wy-input-suffix{white-space:nowrap;padding:6px}.wy-input-prefix .wy-input-context,.wy-input-suffix .wy-input-context{line-height:27px;padding:0 8px;display:inline-block;font-size:80%;background-color:#f3f6f6;border:1px solid #ccc;color:#999}.wy-input-suffix .wy-input-context{border-left:0}.wy-input-prefix .wy-input-context{border-right:0}.wy-switch{position:relative;display:block;height:24px;margin-top:12px;cursor:pointer}.wy-switch:before{left:0;top:0;width:36px;height:12px;background:#ccc}.wy-switch:after,.wy-switch:before{position:absolute;content:"";display:block;border-radius:4px;-webkit-transition:all .2s ease-in-out;-moz-transition:all .2s ease-in-out;transition:all .2s ease-in-out}.wy-switch:after{width:18px;height:18px;background:#999;left:-3px;top:-3px}.wy-switch span{position:absolute;left:48px;display:block;font-size:12px;color:#ccc;line-height:1}.wy-switch.active:before{background:#1e8449}.wy-switch.active:after{left:24px;background:#27ae60}.wy-switch.disabled{cursor:not-allowed;opacity:.8}.wy-control-group.wy-control-group-error .wy-form-message,.wy-control-group.wy-control-group-error>label{color:#e74c3c}.wy-control-group.wy-control-group-error input[type=color],.wy-control-group.wy-control-group-error input[type=date],.wy-control-group.wy-control-group-error input[type=datetime-local],.wy-control-group.wy-control-group-error input[type=datetime],.wy-control-group.wy-control-group-error input[type=email],.wy-control-group.wy-control-group-error input[type=month],.wy-control-group.wy-control-group-error input[type=number],.wy-control-group.wy-control-group-error input[type=password],.wy-control-group.wy-control-group-error input[type=search],.wy-control-group.wy-control-group-error input[type=tel],.wy-control-group.wy-control-group-error input[type=text],.wy-control-group.wy-control-group-error input[type=time],.wy-control-group.wy-control-group-error input[type=url],.wy-control-group.wy-control-group-error input[type=week],.wy-control-group.wy-control-group-error textarea{border:1px solid #e74c3c}.wy-inline-validate{white-space:nowrap}.wy-inline-validate .wy-input-context{padding:.5em .625em;display:inline-block;font-size:80%}.wy-inline-validate.wy-inline-validate-success .wy-input-context{color:#27ae60}.wy-inline-validate.wy-inline-validate-danger .wy-input-context{color:#e74c3c}.wy-inline-validate.wy-inline-validate-warning .wy-input-context{color:#e67e22}.wy-inline-validate.wy-inline-validate-info .wy-input-context{color:#2980b9}.rotate-90{-webkit-transform:rotate(90deg);-moz-transform:rotate(90deg);-ms-transform:rotate(90deg);-o-transform:rotate(90deg);transform:rotate(90deg)}.rotate-180{-webkit-transform:rotate(180deg);-moz-transform:rotate(180deg);-ms-transform:rotate(180deg);-o-transform:rotate(180deg);transform:rotate(180deg)}.rotate-270{-webkit-transform:rotate(270deg);-moz-transform:rotate(270deg);-ms-transform:rotate(270deg);-o-transform:rotate(270deg);transform:rotate(270deg)}.mirror{-webkit-transform:scaleX(-1);-moz-transform:scaleX(-1);-ms-transform:scaleX(-1);-o-transform:scaleX(-1);transform:scaleX(-1)}.mirror.rotate-90{-webkit-transform:scaleX(-1) rotate(90deg);-moz-transform:scaleX(-1) rotate(90deg);-ms-transform:scaleX(-1) rotate(90deg);-o-transform:scaleX(-1) rotate(90deg);transform:scaleX(-1) rotate(90deg)}.mirror.rotate-180{-webkit-transform:scaleX(-1) rotate(180deg);-moz-transform:scaleX(-1) rotate(180deg);-ms-transform:scaleX(-1) rotate(180deg);-o-transform:scaleX(-1) rotate(180deg);transform:scaleX(-1) rotate(180deg)}.mirror.rotate-270{-webkit-transform:scaleX(-1) rotate(270deg);-moz-transform:scaleX(-1) rotate(270deg);-ms-transform:scaleX(-1) rotate(270deg);-o-transform:scaleX(-1) rotate(270deg);transform:scaleX(-1) rotate(270deg)}@media only screen and (max-width:480px){.wy-form button[type=submit]{margin:.7em 0 0}.wy-form input[type=color],.wy-form input[type=date],.wy-form input[type=datetime-local],.wy-form input[type=datetime],.wy-form input[type=email],.wy-form input[type=month],.wy-form input[type=number],.wy-form input[type=password],.wy-form input[type=search],.wy-form input[type=tel],.wy-form input[type=text],.wy-form input[type=time],.wy-form input[type=url],.wy-form input[type=week],.wy-form label{margin-bottom:.3em;display:block}.wy-form input[type=color],.wy-form input[type=date],.wy-form input[type=datetime-local],.wy-form input[type=datetime],.wy-form input[type=email],.wy-form input[type=month],.wy-form input[type=number],.wy-form input[type=password],.wy-form input[type=search],.wy-form input[type=tel],.wy-form input[type=time],.wy-form input[type=url],.wy-form input[type=week]{margin-bottom:0}.wy-form-aligned .wy-control-group label{margin-bottom:.3em;text-align:left;display:block;width:100%}.wy-form-aligned .wy-control{margin:1.5em 0 0}.wy-form-message,.wy-form-message-inline,.wy-form .wy-help-inline{display:block;font-size:80%;padding:6px 0}}@media screen and (max-width:768px){.tablet-hide{display:none}}@media screen and (max-width:480px){.mobile-hide{display:none}}.float-left{float:left}.float-right{float:right}.full-width{width:100%}.rst-content table.docutils,.rst-content table.field-list,.wy-table{border-collapse:collapse;border-spacing:0;empty-cells:show;margin-bottom:24px}.rst-content table.docutils caption,.rst-content table.field-list caption,.wy-table caption{color:#000;font:italic 85%/1 arial,sans-serif;padding:1em 0;text-align:center}.rst-content table.docutils td,.rst-content table.docutils th,.rst-content table.field-list td,.rst-content table.field-list th,.wy-table td,.wy-table th{font-size:90%;margin:0;overflow:visible;padding:8px 16px}.rst-content table.docutils td:first-child,.rst-content table.docutils th:first-child,.rst-content table.field-list td:first-child,.rst-content table.field-list th:first-child,.wy-table td:first-child,.wy-table th:first-child{border-left-width:0}.rst-content table.docutils thead,.rst-content table.field-list thead,.wy-table thead{color:#000;text-align:left;vertical-align:bottom;white-space:nowrap}.rst-content table.docutils thead th,.rst-content table.field-list thead th,.wy-table thead th{font-weight:700;border-bottom:2px solid #e1e4e5}.rst-content table.docutils td,.rst-content table.field-list td,.wy-table td{background-color:transparent;vertical-align:middle}.rst-content table.docutils td p,.rst-content table.field-list td p,.wy-table td p{line-height:18px}.rst-content table.docutils td p:last-child,.rst-content table.field-list td p:last-child,.wy-table td p:last-child{margin-bottom:0}.rst-content table.docutils .wy-table-cell-min,.rst-content table.field-list .wy-table-cell-min,.wy-table .wy-table-cell-min{width:1%;padding-right:0}.rst-content table.docutils .wy-table-cell-min input[type=checkbox],.rst-content table.field-list .wy-table-cell-min input[type=checkbox],.wy-table .wy-table-cell-min input[type=checkbox]{margin:0}.wy-table-secondary{color:grey;font-size:90%}.wy-table-tertiary{color:grey;font-size:80%}.rst-content table.docutils:not(.field-list) tr:nth-child(2n-1) td,.wy-table-backed,.wy-table-odd td,.wy-table-striped tr:nth-child(2n-1) td{background-color:#f3f6f6}.rst-content table.docutils,.wy-table-bordered-all{border:1px solid #e1e4e5}.rst-content table.docutils td,.wy-table-bordered-all td{border-bottom:1px solid #e1e4e5;border-left:1px solid #e1e4e5}.rst-content table.docutils tbody>tr:last-child td,.wy-table-bordered-all tbody>tr:last-child td{border-bottom-width:0}.wy-table-bordered{border:1px solid #e1e4e5}.wy-table-bordered-rows td{border-bottom:1px solid #e1e4e5}.wy-table-bordered-rows tbody>tr:last-child td{border-bottom-width:0}.wy-table-horizontal td,.wy-table-horizontal th{border-width:0 0 1px;border-bottom:1px solid #e1e4e5}.wy-table-horizontal tbody>tr:last-child td{border-bottom-width:0}.wy-table-responsive{margin-bottom:24px;max-width:100%;overflow:auto}.wy-table-responsive table{margin-bottom:0!important}.wy-table-responsive table td,.wy-table-responsive table th{white-space:nowrap}a{color:#2980b9;text-decoration:none;cursor:pointer}a:hover{color:#3091d1}a:visited{color:#9b59b6}html{height:100%}body,html{overflow-x:hidden}body{font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;font-weight:400;color:#404040;min-height:100%;background:#edf0f2}.wy-text-left{text-align:left}.wy-text-center{text-align:center}.wy-text-right{text-align:right}.wy-text-large{font-size:120%}.wy-text-normal{font-size:100%}.wy-text-small,small{font-size:80%}.wy-text-strike{text-decoration:line-through}.wy-text-warning{color:#e67e22!important}a.wy-text-warning:hover{color:#eb9950!important}.wy-text-info{color:#2980b9!important}a.wy-text-info:hover{color:#409ad5!important}.wy-text-success{color:#27ae60!important}a.wy-text-success:hover{color:#36d278!important}.wy-text-danger{color:#e74c3c!important}a.wy-text-danger:hover{color:#ed7669!important}.wy-text-neutral{color:#404040!important}a.wy-text-neutral:hover{color:#595959!important}.rst-content .toctree-wrapper>p.caption,h1,h2,h3,h4,h5,h6,legend{margin-top:0;font-weight:700;font-family:Roboto Slab,ff-tisa-web-pro,Georgia,Arial,sans-serif}p{line-height:24px;font-size:16px;margin:0 0 24px}h1{font-size:175%}.rst-content .toctree-wrapper>p.caption,h2{font-size:150%}h3{font-size:125%}h4{font-size:115%}h5{font-size:110%}h6{font-size:100%}hr{display:block;height:1px;border:0;border-top:1px solid #e1e4e5;margin:24px 0;padding:0}.rst-content code,.rst-content tt,code{white-space:nowrap;max-width:100%;background:#fff;border:1px solid #e1e4e5;font-size:75%;padding:0 5px;font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;color:#e74c3c;overflow-x:auto}.rst-content tt.code-large,code.code-large{font-size:90%}.rst-content .section ul,.rst-content .toctree-wrapper ul,.rst-content section ul,.wy-plain-list-disc,article ul{list-style:disc;line-height:24px;margin-bottom:24px}.rst-content .section ul li,.rst-content .toctree-wrapper ul li,.rst-content section ul li,.wy-plain-list-disc li,article ul li{list-style:disc;margin-left:24px}.rst-content .section ul li p:last-child,.rst-content .section ul li ul,.rst-content .toctree-wrapper ul li p:last-child,.rst-content .toctree-wrapper ul li ul,.rst-content section ul li p:last-child,.rst-content section ul li ul,.wy-plain-list-disc li p:last-child,.wy-plain-list-disc li ul,article ul li p:last-child,article ul li ul{margin-bottom:0}.rst-content .section ul li li,.rst-content .toctree-wrapper ul li li,.rst-content section ul li li,.wy-plain-list-disc li li,article ul li li{list-style:circle}.rst-content .section ul li li li,.rst-content .toctree-wrapper ul li li li,.rst-content section ul li li li,.wy-plain-list-disc li li li,article ul li li li{list-style:square}.rst-content .section ul li ol li,.rst-content .toctree-wrapper ul li ol li,.rst-content section ul li ol li,.wy-plain-list-disc li ol li,article ul li ol li{list-style:decimal}.rst-content .section ol,.rst-content .section ol.arabic,.rst-content .toctree-wrapper ol,.rst-content .toctree-wrapper ol.arabic,.rst-content section ol,.rst-content section ol.arabic,.wy-plain-list-decimal,article ol{list-style:decimal;line-height:24px;margin-bottom:24px}.rst-content .section ol.arabic li,.rst-content .section ol li,.rst-content .toctree-wrapper ol.arabic li,.rst-content .toctree-wrapper ol li,.rst-content section ol.arabic li,.rst-content section ol li,.wy-plain-list-decimal li,article ol li{list-style:decimal;margin-left:24px}.rst-content .section ol.arabic li ul,.rst-content .section ol li p:last-child,.rst-content .section ol li ul,.rst-content .toctree-wrapper ol.arabic li ul,.rst-content .toctree-wrapper ol li p:last-child,.rst-content .toctree-wrapper ol li ul,.rst-content section ol.arabic li ul,.rst-content section ol li p:last-child,.rst-content section ol li ul,.wy-plain-list-decimal li p:last-child,.wy-plain-list-decimal li ul,article ol li p:last-child,article ol li ul{margin-bottom:0}.rst-content .section ol.arabic li ul li,.rst-content .section ol li ul li,.rst-content .toctree-wrapper ol.arabic li ul li,.rst-content .toctree-wrapper ol li ul li,.rst-content section ol.arabic li ul li,.rst-content section ol li ul li,.wy-plain-list-decimal li ul li,article ol li ul li{list-style:disc}.wy-breadcrumbs{*zoom:1}.wy-breadcrumbs:after,.wy-breadcrumbs:before{display:table;content:""}.wy-breadcrumbs:after{clear:both}.wy-breadcrumbs>li{display:inline-block;padding-top:5px}.wy-breadcrumbs>li.wy-breadcrumbs-aside{float:right}.rst-content .wy-breadcrumbs>li code,.rst-content .wy-breadcrumbs>li tt,.wy-breadcrumbs>li .rst-content tt,.wy-breadcrumbs>li code{all:inherit;color:inherit}.breadcrumb-item:before{content:"/";color:#bbb;font-size:13px;padding:0 6px 0 3px}.wy-breadcrumbs-extra{margin-bottom:0;color:#b3b3b3;font-size:80%;display:inline-block}@media screen and (max-width:480px){.wy-breadcrumbs-extra,.wy-breadcrumbs li.wy-breadcrumbs-aside{display:none}}@media print{.wy-breadcrumbs li.wy-breadcrumbs-aside{display:none}}html{font-size:16px}.wy-affix{position:fixed;top:1.618em}.wy-menu a:hover{text-decoration:none}.wy-menu-horiz{*zoom:1}.wy-menu-horiz:after,.wy-menu-horiz:before{display:table;content:""}.wy-menu-horiz:after{clear:both}.wy-menu-horiz li,.wy-menu-horiz ul{display:inline-block}.wy-menu-horiz li:hover{background:hsla(0,0%,100%,.1)}.wy-menu-horiz li.divide-left{border-left:1px solid #404040}.wy-menu-horiz li.divide-right{border-right:1px solid #404040}.wy-menu-horiz a{height:32px;display:inline-block;line-height:32px;padding:0 16px}.wy-menu-vertical{width:300px}.wy-menu-vertical header,.wy-menu-vertical p.caption{color:#55a5d9;height:32px;line-height:32px;padding:0 1.618em;margin:12px 0 0;display:block;font-weight:700;text-transform:uppercase;font-size:85%;white-space:nowrap}.wy-menu-vertical ul{margin-bottom:0}.wy-menu-vertical li.divide-top{border-top:1px solid #404040}.wy-menu-vertical li.divide-bottom{border-bottom:1px solid #404040}.wy-menu-vertical li.current{background:#e3e3e3}.wy-menu-vertical li.current a{color:grey;border-right:1px solid #c9c9c9;padding:.4045em 2.427em}.wy-menu-vertical li.current a:hover{background:#d6d6d6}.rst-content .wy-menu-vertical li tt,.wy-menu-vertical li .rst-content tt,.wy-menu-vertical li code{border:none;background:inherit;color:inherit;padding-left:0;padding-right:0}.wy-menu-vertical li button.toctree-expand{display:block;float:left;margin-left:-1.2em;line-height:18px;color:#4d4d4d;border:none;background:none;padding:0}.wy-menu-vertical li.current>a,.wy-menu-vertical li.on a{color:#404040;font-weight:700;position:relative;background:#fcfcfc;border:none;padding:.4045em 1.618em}.wy-menu-vertical li.current>a:hover,.wy-menu-vertical li.on a:hover{background:#fcfcfc}.wy-menu-vertical li.current>a:hover button.toctree-expand,.wy-menu-vertical li.on a:hover button.toctree-expand{color:grey}.wy-menu-vertical li.current>a button.toctree-expand,.wy-menu-vertical li.on a button.toctree-expand{display:block;line-height:18px;color:#333}.wy-menu-vertical li.toctree-l1.current>a{border-bottom:1px solid #c9c9c9;border-top:1px solid #c9c9c9}.wy-menu-vertical .toctree-l1.current .toctree-l2>ul,.wy-menu-vertical .toctree-l2.current .toctree-l3>ul,.wy-menu-vertical .toctree-l3.current .toctree-l4>ul,.wy-menu-vertical .toctree-l4.current .toctree-l5>ul,.wy-menu-vertical .toctree-l5.current .toctree-l6>ul,.wy-menu-vertical .toctree-l6.current .toctree-l7>ul,.wy-menu-vertical .toctree-l7.current .toctree-l8>ul,.wy-menu-vertical .toctree-l8.current .toctree-l9>ul,.wy-menu-vertical .toctree-l9.current .toctree-l10>ul,.wy-menu-vertical .toctree-l10.current .toctree-l11>ul{display:none}.wy-menu-vertical .toctree-l1.current .current.toctree-l2>ul,.wy-menu-vertical .toctree-l2.current .current.toctree-l3>ul,.wy-menu-vertical .toctree-l3.current .current.toctree-l4>ul,.wy-menu-vertical .toctree-l4.current .current.toctree-l5>ul,.wy-menu-vertical .toctree-l5.current .current.toctree-l6>ul,.wy-menu-vertical .toctree-l6.current .current.toctree-l7>ul,.wy-menu-vertical .toctree-l7.current .current.toctree-l8>ul,.wy-menu-vertical .toctree-l8.current .current.toctree-l9>ul,.wy-menu-vertical .toctree-l9.current .current.toctree-l10>ul,.wy-menu-vertical .toctree-l10.current .current.toctree-l11>ul{display:block}.wy-menu-vertical li.toctree-l3,.wy-menu-vertical li.toctree-l4{font-size:.9em}.wy-menu-vertical li.toctree-l2 a,.wy-menu-vertical li.toctree-l3 a,.wy-menu-vertical li.toctree-l4 a,.wy-menu-vertical li.toctree-l5 a,.wy-menu-vertical li.toctree-l6 a,.wy-menu-vertical li.toctree-l7 a,.wy-menu-vertical li.toctree-l8 a,.wy-menu-vertical li.toctree-l9 a,.wy-menu-vertical li.toctree-l10 a{color:#404040}.wy-menu-vertical li.toctree-l2 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l3 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l4 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l5 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l6 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l7 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l8 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l9 a:hover button.toctree-expand,.wy-menu-vertical li.toctree-l10 a:hover button.toctree-expand{color:grey}.wy-menu-vertical li.toctree-l2.current li.toctree-l3>a,.wy-menu-vertical li.toctree-l3.current li.toctree-l4>a,.wy-menu-vertical li.toctree-l4.current li.toctree-l5>a,.wy-menu-vertical li.toctree-l5.current li.toctree-l6>a,.wy-menu-vertical li.toctree-l6.current li.toctree-l7>a,.wy-menu-vertical li.toctree-l7.current li.toctree-l8>a,.wy-menu-vertical li.toctree-l8.current li.toctree-l9>a,.wy-menu-vertical li.toctree-l9.current li.toctree-l10>a,.wy-menu-vertical li.toctree-l10.current li.toctree-l11>a{display:block}.wy-menu-vertical li.toctree-l2.current>a{padding:.4045em 2.427em}.wy-menu-vertical li.toctree-l2.current li.toctree-l3>a{padding:.4045em 1.618em .4045em 4.045em}.wy-menu-vertical li.toctree-l3.current>a{padding:.4045em 4.045em}.wy-menu-vertical li.toctree-l3.current li.toctree-l4>a{padding:.4045em 1.618em .4045em 5.663em}.wy-menu-vertical li.toctree-l4.current>a{padding:.4045em 5.663em}.wy-menu-vertical li.toctree-l4.current li.toctree-l5>a{padding:.4045em 1.618em .4045em 7.281em}.wy-menu-vertical li.toctree-l5.current>a{padding:.4045em 7.281em}.wy-menu-vertical li.toctree-l5.current li.toctree-l6>a{padding:.4045em 1.618em .4045em 8.899em}.wy-menu-vertical li.toctree-l6.current>a{padding:.4045em 8.899em}.wy-menu-vertical li.toctree-l6.current li.toctree-l7>a{padding:.4045em 1.618em .4045em 10.517em}.wy-menu-vertical li.toctree-l7.current>a{padding:.4045em 10.517em}.wy-menu-vertical li.toctree-l7.current li.toctree-l8>a{padding:.4045em 1.618em .4045em 12.135em}.wy-menu-vertical li.toctree-l8.current>a{padding:.4045em 12.135em}.wy-menu-vertical li.toctree-l8.current li.toctree-l9>a{padding:.4045em 1.618em .4045em 13.753em}.wy-menu-vertical li.toctree-l9.current>a{padding:.4045em 13.753em}.wy-menu-vertical li.toctree-l9.current li.toctree-l10>a{padding:.4045em 1.618em .4045em 15.371em}.wy-menu-vertical li.toctree-l10.current>a{padding:.4045em 15.371em}.wy-menu-vertical li.toctree-l10.current li.toctree-l11>a{padding:.4045em 1.618em .4045em 16.989em}.wy-menu-vertical li.toctree-l2.current>a,.wy-menu-vertical li.toctree-l2.current li.toctree-l3>a{background:#c9c9c9}.wy-menu-vertical li.toctree-l2 button.toctree-expand{color:#a3a3a3}.wy-menu-vertical li.toctree-l3.current>a,.wy-menu-vertical li.toctree-l3.current li.toctree-l4>a{background:#bdbdbd}.wy-menu-vertical li.toctree-l3 button.toctree-expand{color:#969696}.wy-menu-vertical li.current ul{display:block}.wy-menu-vertical li ul{margin-bottom:0;display:none}.wy-menu-vertical li ul li a{margin-bottom:0;color:#d9d9d9;font-weight:400}.wy-menu-vertical a{line-height:18px;padding:.4045em 1.618em;display:block;position:relative;font-size:90%;color:#d9d9d9}.wy-menu-vertical a:hover{background-color:#4e4a4a;cursor:pointer}.wy-menu-vertical a:hover button.toctree-expand{color:#d9d9d9}.wy-menu-vertical a:active{background-color:#2980b9;cursor:pointer;color:#fff}.wy-menu-vertical a:active button.toctree-expand{color:#fff}.wy-side-nav-search{display:block;width:300px;padding:.809em;margin-bottom:.809em;z-index:200;background-color:#2980b9;text-align:center;color:#fcfcfc}.wy-side-nav-search input[type=text]{width:100%;border-radius:50px;padding:6px 12px;border-color:#2472a4}.wy-side-nav-search img{display:block;margin:auto auto .809em;height:45px;width:45px;background-color:#2980b9;padding:5px;border-radius:100%}.wy-side-nav-search .wy-dropdown>a,.wy-side-nav-search>a{color:#fcfcfc;font-size:100%;font-weight:700;display:inline-block;padding:4px 6px;margin-bottom:.809em;max-width:100%}.wy-side-nav-search .wy-dropdown>a:hover,.wy-side-nav-search .wy-dropdown>aactive,.wy-side-nav-search .wy-dropdown>afocus,.wy-side-nav-search>a:hover,.wy-side-nav-search>aactive,.wy-side-nav-search>afocus{background:hsla(0,0%,100%,.1)}.wy-side-nav-search .wy-dropdown>a img.logo,.wy-side-nav-search>a img.logo{display:block;margin:0 auto;height:auto;width:auto;border-radius:0;max-width:100%;background:transparent}.wy-side-nav-search .wy-dropdown>a.icon,.wy-side-nav-search>a.icon{display:block}.wy-side-nav-search .wy-dropdown>a.icon img.logo,.wy-side-nav-search>a.icon img.logo{margin-top:.85em}.wy-side-nav-search>div.switch-menus{position:relative;display:block;margin-top:-.4045em;margin-bottom:.809em;font-weight:400;color:hsla(0,0%,100%,.3)}.wy-side-nav-search>div.switch-menus>div.language-switch,.wy-side-nav-search>div.switch-menus>div.version-switch{display:inline-block;padding:.2em}.wy-side-nav-search>div.switch-menus>div.language-switch select,.wy-side-nav-search>div.switch-menus>div.version-switch select{display:inline-block;margin-right:-2rem;padding-right:2rem;max-width:240px;text-align-last:center;background:none;border:none;border-radius:0;box-shadow:none;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;font-size:1em;font-weight:400;color:hsla(0,0%,100%,.3);cursor:pointer;appearance:none;-webkit-appearance:none;-moz-appearance:none}.wy-side-nav-search>div.switch-menus>div.language-switch select:active,.wy-side-nav-search>div.switch-menus>div.language-switch select:focus,.wy-side-nav-search>div.switch-menus>div.language-switch select:hover,.wy-side-nav-search>div.switch-menus>div.version-switch select:active,.wy-side-nav-search>div.switch-menus>div.version-switch select:focus,.wy-side-nav-search>div.switch-menus>div.version-switch select:hover{background:hsla(0,0%,100%,.1);color:hsla(0,0%,100%,.5)}.wy-side-nav-search>div.switch-menus>div.language-switch select option,.wy-side-nav-search>div.switch-menus>div.version-switch select option{color:#000}.wy-side-nav-search>div.switch-menus>div.language-switch:has(>select):after,.wy-side-nav-search>div.switch-menus>div.version-switch:has(>select):after{display:inline-block;width:1.5em;height:100%;padding:.1em;content:"\f0d7";font-size:1em;line-height:1.2em;font-family:FontAwesome;text-align:center;pointer-events:none;box-sizing:border-box}.wy-nav .wy-menu-vertical header{color:#2980b9}.wy-nav .wy-menu-vertical a{color:#b3b3b3}.wy-nav .wy-menu-vertical a:hover{background-color:#2980b9;color:#fff}[data-menu-wrap]{-webkit-transition:all .2s ease-in;-moz-transition:all .2s ease-in;transition:all .2s ease-in;position:absolute;opacity:1;width:100%;opacity:0}[data-menu-wrap].move-center{left:0;right:auto;opacity:1}[data-menu-wrap].move-left{right:auto;left:-100%;opacity:0}[data-menu-wrap].move-right{right:-100%;left:auto;opacity:0}.wy-body-for-nav{background:#fcfcfc}.wy-grid-for-nav{position:absolute;width:100%;height:100%}.wy-nav-side{position:fixed;top:0;bottom:0;left:0;padding-bottom:2em;width:300px;overflow-x:hidden;overflow-y:hidden;min-height:100%;color:#9b9b9b;background:#343131;z-index:200}.wy-side-scroll{width:320px;position:relative;overflow-x:hidden;overflow-y:scroll;height:100%}.wy-nav-top{display:none;background:#2980b9;color:#fff;padding:.4045em .809em;position:relative;line-height:50px;text-align:center;font-size:100%;*zoom:1}.wy-nav-top:after,.wy-nav-top:before{display:table;content:""}.wy-nav-top:after{clear:both}.wy-nav-top a{color:#fff;font-weight:700}.wy-nav-top img{margin-right:12px;height:45px;width:45px;background-color:#2980b9;padding:5px;border-radius:100%}.wy-nav-top i{font-size:30px;float:left;cursor:pointer;padding-top:inherit}.wy-nav-content-wrap{margin-left:300px;background:#fcfcfc;min-height:100%}.wy-nav-content{padding:1.618em 3.236em;height:100%;max-width:800px;margin:auto}.wy-body-mask{position:fixed;width:100%;height:100%;background:rgba(0,0,0,.2);display:none;z-index:499}.wy-body-mask.on{display:block}footer{color:grey}footer p{margin-bottom:12px}.rst-content footer span.commit tt,footer span.commit .rst-content tt,footer span.commit code{padding:0;font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;font-size:1em;background:none;border:none;color:grey}.rst-footer-buttons{*zoom:1}.rst-footer-buttons:after,.rst-footer-buttons:before{width:100%;display:table;content:""}.rst-footer-buttons:after{clear:both}.rst-breadcrumbs-buttons{margin-top:12px;*zoom:1}.rst-breadcrumbs-buttons:after,.rst-breadcrumbs-buttons:before{display:table;content:""}.rst-breadcrumbs-buttons:after{clear:both}#search-results .search li{margin-bottom:24px;border-bottom:1px solid #e1e4e5;padding-bottom:24px}#search-results .search li:first-child{border-top:1px solid #e1e4e5;padding-top:24px}#search-results .search li a{font-size:120%;margin-bottom:12px;display:inline-block}#search-results .context{color:grey;font-size:90%}.genindextable li>ul{margin-left:24px}@media screen and (max-width:768px){.wy-body-for-nav{background:#fcfcfc}.wy-nav-top{display:block}.wy-nav-side{left:-300px}.wy-nav-side.shift{width:85%;left:0}.wy-menu.wy-menu-vertical,.wy-side-nav-search,.wy-side-scroll{width:auto}.wy-nav-content-wrap{margin-left:0}.wy-nav-content-wrap .wy-nav-content{padding:1.618em}.wy-nav-content-wrap.shift{position:fixed;min-width:100%;left:85%;top:0;height:100%;overflow:hidden}}@media screen and (min-width:1100px){.wy-nav-content-wrap{background:rgba(0,0,0,.05)}.wy-nav-content{margin:0;background:#fcfcfc}}@media print{.rst-versions,.wy-nav-side,footer{display:none}.wy-nav-content-wrap{margin-left:0}}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60;*zoom:1}.rst-versions .rst-current-version:after,.rst-versions .rst-current-version:before{display:table;content:""}.rst-versions .rst-current-version:after{clear:both}.rst-content .code-block-caption .rst-versions .rst-current-version .headerlink,.rst-content .eqno .rst-versions .rst-current-version .headerlink,.rst-content .rst-versions .rst-current-version .admonition-title,.rst-content code.download .rst-versions .rst-current-version span:first-child,.rst-content dl dt .rst-versions .rst-current-version .headerlink,.rst-content h1 .rst-versions .rst-current-version .headerlink,.rst-content h2 .rst-versions .rst-current-version .headerlink,.rst-content h3 .rst-versions .rst-current-version .headerlink,.rst-content h4 .rst-versions .rst-current-version .headerlink,.rst-content h5 .rst-versions .rst-current-version .headerlink,.rst-content h6 .rst-versions .rst-current-version .headerlink,.rst-content p .rst-versions .rst-current-version .headerlink,.rst-content table>caption .rst-versions .rst-current-version .headerlink,.rst-content tt.download .rst-versions .rst-current-version span:first-child,.rst-versions .rst-current-version .fa,.rst-versions .rst-current-version .icon,.rst-versions .rst-current-version .rst-content .admonition-title,.rst-versions .rst-current-version .rst-content .code-block-caption .headerlink,.rst-versions .rst-current-version .rst-content .eqno .headerlink,.rst-versions .rst-current-version .rst-content code.download span:first-child,.rst-versions .rst-current-version .rst-content dl dt .headerlink,.rst-versions .rst-current-version .rst-content h1 .headerlink,.rst-versions .rst-current-version .rst-content h2 .headerlink,.rst-versions .rst-current-version .rst-content h3 .headerlink,.rst-versions .rst-current-version .rst-content h4 .headerlink,.rst-versions .rst-current-version .rst-content h5 .headerlink,.rst-versions .rst-current-version .rst-content h6 .headerlink,.rst-versions .rst-current-version .rst-content p .headerlink,.rst-versions .rst-current-version .rst-content table>caption .headerlink,.rst-versions .rst-current-version .rst-content tt.download span:first-child,.rst-versions .rst-current-version .wy-menu-vertical li button.toctree-expand,.wy-menu-vertical li .rst-versions .rst-current-version button.toctree-expand{color:#fcfcfc}.rst-versions .rst-current-version .fa-book,.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#f1c40f;color:#000}.rst-versions.shift-up{height:auto;max-height:100%;overflow-y:scroll}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:grey;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:1px solid #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions .rst-other-versions .rtd-current-item{font-weight:700}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px;max-height:90%}.rst-versions.rst-badge .fa-book,.rst-versions.rst-badge .icon-book{float:none;line-height:30px}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book,.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge>.rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width:768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}}#flyout-search-form{padding:6px}.rst-content .toctree-wrapper>p.caption,.rst-content h1,.rst-content h2,.rst-content h3,.rst-content h4,.rst-content h5,.rst-content h6{margin-bottom:24px}.rst-content img{max-width:100%;height:auto}.rst-content div.figure,.rst-content figure{margin-bottom:24px}.rst-content div.figure .caption-text,.rst-content figure .caption-text{font-style:italic}.rst-content div.figure p:last-child.caption,.rst-content figure p:last-child.caption{margin-bottom:0}.rst-content div.figure.align-center,.rst-content figure.align-center{text-align:center}.rst-content .section>a>img,.rst-content .section>img,.rst-content section>a>img,.rst-content section>img{margin-bottom:24px}.rst-content abbr[title]{text-decoration:none}.rst-content.style-external-links a.reference.external:after{font-family:FontAwesome;content:"\f08e";color:#b3b3b3;vertical-align:super;font-size:60%;margin:0 .2em}.rst-content blockquote{margin-left:24px;line-height:24px;margin-bottom:24px}.rst-content pre.literal-block{white-space:pre;margin:0;padding:12px;font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;display:block;overflow:auto}.rst-content div[class^=highlight],.rst-content pre.literal-block{border:1px solid #e1e4e5;overflow-x:auto;margin:1px 0 24px}.rst-content div[class^=highlight] div[class^=highlight],.rst-content pre.literal-block div[class^=highlight]{padding:0;border:none;margin:0}.rst-content div[class^=highlight] td.code{width:100%}.rst-content .linenodiv pre{border-right:1px solid #e6e9ea;margin:0;padding:12px;font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;user-select:none;pointer-events:none}.rst-content div[class^=highlight] pre{white-space:pre;margin:0;padding:12px;display:block;overflow:auto}.rst-content div[class^=highlight] pre .hll{display:block;margin:0 -12px;padding:0 12px}.rst-content .linenodiv pre,.rst-content div[class^=highlight] pre,.rst-content pre.literal-block{font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;font-size:12px;line-height:1.4}.rst-content div.highlight .gp,.rst-content div.highlight span.linenos{user-select:none;pointer-events:none}.rst-content div.highlight span.linenos{display:inline-block;padding-left:0;padding-right:12px;margin-right:12px;border-right:1px solid #e6e9ea}.rst-content .code-block-caption{font-style:italic;font-size:85%;line-height:1;padding:1em 0;text-align:center}@media print{.rst-content .codeblock,.rst-content div[class^=highlight],.rst-content div[class^=highlight] pre{white-space:pre-wrap}}.rst-content .admonition,.rst-content .admonition-todo,.rst-content .attention,.rst-content .caution,.rst-content .danger,.rst-content .error,.rst-content .hint,.rst-content .important,.rst-content .note,.rst-content .seealso,.rst-content .tip,.rst-content .warning{clear:both}.rst-content .admonition-todo .last,.rst-content .admonition-todo>:last-child,.rst-content .admonition .last,.rst-content .admonition>:last-child,.rst-content .attention .last,.rst-content .attention>:last-child,.rst-content .caution .last,.rst-content .caution>:last-child,.rst-content .danger .last,.rst-content .danger>:last-child,.rst-content .error .last,.rst-content .error>:last-child,.rst-content .hint .last,.rst-content .hint>:last-child,.rst-content .important .last,.rst-content .important>:last-child,.rst-content .note .last,.rst-content .note>:last-child,.rst-content .seealso .last,.rst-content .seealso>:last-child,.rst-content .tip .last,.rst-content .tip>:last-child,.rst-content .warning .last,.rst-content .warning>:last-child{margin-bottom:0}.rst-content .admonition-title:before{margin-right:4px}.rst-content .admonition table{border-color:rgba(0,0,0,.1)}.rst-content .admonition table td,.rst-content .admonition table th{background:transparent!important;border-color:rgba(0,0,0,.1)!important}.rst-content .section ol.loweralpha,.rst-content .section ol.loweralpha>li,.rst-content .toctree-wrapper ol.loweralpha,.rst-content .toctree-wrapper ol.loweralpha>li,.rst-content section ol.loweralpha,.rst-content section ol.loweralpha>li{list-style:lower-alpha}.rst-content .section ol.upperalpha,.rst-content .section ol.upperalpha>li,.rst-content .toctree-wrapper ol.upperalpha,.rst-content .toctree-wrapper ol.upperalpha>li,.rst-content section ol.upperalpha,.rst-content section ol.upperalpha>li{list-style:upper-alpha}.rst-content .section ol li>*,.rst-content .section ul li>*,.rst-content .toctree-wrapper ol li>*,.rst-content .toctree-wrapper ul li>*,.rst-content section ol li>*,.rst-content section ul li>*{margin-top:12px;margin-bottom:12px}.rst-content .section ol li>:first-child,.rst-content .section ul li>:first-child,.rst-content .toctree-wrapper ol li>:first-child,.rst-content .toctree-wrapper ul li>:first-child,.rst-content section ol li>:first-child,.rst-content section ul li>:first-child{margin-top:0}.rst-content .section ol li>p,.rst-content .section ol li>p:last-child,.rst-content .section ul li>p,.rst-content .section ul li>p:last-child,.rst-content .toctree-wrapper ol li>p,.rst-content .toctree-wrapper ol li>p:last-child,.rst-content .toctree-wrapper ul li>p,.rst-content .toctree-wrapper ul li>p:last-child,.rst-content section ol li>p,.rst-content section ol li>p:last-child,.rst-content section ul li>p,.rst-content section ul li>p:last-child{margin-bottom:12px}.rst-content .section ol li>p:only-child,.rst-content .section ol li>p:only-child:last-child,.rst-content .section ul li>p:only-child,.rst-content .section ul li>p:only-child:last-child,.rst-content .toctree-wrapper ol li>p:only-child,.rst-content .toctree-wrapper ol li>p:only-child:last-child,.rst-content .toctree-wrapper ul li>p:only-child,.rst-content .toctree-wrapper ul li>p:only-child:last-child,.rst-content section ol li>p:only-child,.rst-content section ol li>p:only-child:last-child,.rst-content section ul li>p:only-child,.rst-content section ul li>p:only-child:last-child{margin-bottom:0}.rst-content .section ol li>ol,.rst-content .section ol li>ul,.rst-content .section ul li>ol,.rst-content .section ul li>ul,.rst-content .toctree-wrapper ol li>ol,.rst-content .toctree-wrapper ol li>ul,.rst-content .toctree-wrapper ul li>ol,.rst-content .toctree-wrapper ul li>ul,.rst-content section ol li>ol,.rst-content section ol li>ul,.rst-content section ul li>ol,.rst-content section ul li>ul{margin-bottom:12px}.rst-content .section ol.simple li>*,.rst-content .section ol.simple li ol,.rst-content .section ol.simple li ul,.rst-content .section ul.simple li>*,.rst-content .section ul.simple li ol,.rst-content .section ul.simple li ul,.rst-content .toctree-wrapper ol.simple li>*,.rst-content .toctree-wrapper ol.simple li ol,.rst-content .toctree-wrapper ol.simple li ul,.rst-content .toctree-wrapper ul.simple li>*,.rst-content .toctree-wrapper ul.simple li ol,.rst-content .toctree-wrapper ul.simple li ul,.rst-content section ol.simple li>*,.rst-content section ol.simple li ol,.rst-content section ol.simple li ul,.rst-content section ul.simple li>*,.rst-content section ul.simple li ol,.rst-content section ul.simple li ul{margin-top:0;margin-bottom:0}.rst-content .line-block{margin-left:0;margin-bottom:24px;line-height:24px}.rst-content .line-block .line-block{margin-left:24px;margin-bottom:0}.rst-content .topic-title{font-weight:700;margin-bottom:12px}.rst-content .toc-backref{color:#404040}.rst-content .align-right{float:right;margin:0 0 24px 24px}.rst-content .align-left{float:left;margin:0 24px 24px 0}.rst-content .align-center{margin:auto}.rst-content .align-center:not(table){display:block}.rst-content .code-block-caption .headerlink,.rst-content .eqno .headerlink,.rst-content .toctree-wrapper>p.caption .headerlink,.rst-content dl dt .headerlink,.rst-content h1 .headerlink,.rst-content h2 .headerlink,.rst-content h3 .headerlink,.rst-content h4 .headerlink,.rst-content h5 .headerlink,.rst-content h6 .headerlink,.rst-content p.caption .headerlink,.rst-content p .headerlink,.rst-content table>caption .headerlink{opacity:0;font-size:14px;font-family:FontAwesome;margin-left:.5em}.rst-content .code-block-caption .headerlink:focus,.rst-content .code-block-caption:hover .headerlink,.rst-content .eqno .headerlink:focus,.rst-content .eqno:hover .headerlink,.rst-content .toctree-wrapper>p.caption .headerlink:focus,.rst-content .toctree-wrapper>p.caption:hover .headerlink,.rst-content dl dt .headerlink:focus,.rst-content dl dt:hover .headerlink,.rst-content h1 .headerlink:focus,.rst-content h1:hover .headerlink,.rst-content h2 .headerlink:focus,.rst-content h2:hover .headerlink,.rst-content h3 .headerlink:focus,.rst-content h3:hover .headerlink,.rst-content h4 .headerlink:focus,.rst-content h4:hover .headerlink,.rst-content h5 .headerlink:focus,.rst-content h5:hover .headerlink,.rst-content h6 .headerlink:focus,.rst-content h6:hover .headerlink,.rst-content p.caption .headerlink:focus,.rst-content p.caption:hover .headerlink,.rst-content p .headerlink:focus,.rst-content p:hover .headerlink,.rst-content table>caption .headerlink:focus,.rst-content table>caption:hover .headerlink{opacity:1}.rst-content p a{overflow-wrap:anywhere}.rst-content .wy-table td p,.rst-content .wy-table td ul,.rst-content .wy-table th p,.rst-content .wy-table th ul,.rst-content table.docutils td p,.rst-content table.docutils td ul,.rst-content table.docutils th p,.rst-content table.docutils th ul,.rst-content table.field-list td p,.rst-content table.field-list td ul,.rst-content table.field-list th p,.rst-content table.field-list th ul{font-size:inherit}.rst-content .btn:focus{outline:2px solid}.rst-content table>caption .headerlink:after{font-size:12px}.rst-content .centered{text-align:center}.rst-content .sidebar{float:right;width:40%;display:block;margin:0 0 24px 24px;padding:24px;background:#f3f6f6;border:1px solid #e1e4e5}.rst-content .sidebar dl,.rst-content .sidebar p,.rst-content .sidebar ul{font-size:90%}.rst-content .sidebar .last,.rst-content .sidebar>:last-child{margin-bottom:0}.rst-content .sidebar .sidebar-title{display:block;font-family:Roboto Slab,ff-tisa-web-pro,Georgia,Arial,sans-serif;font-weight:700;background:#e1e4e5;padding:6px 12px;margin:-24px -24px 24px;font-size:100%}.rst-content .highlighted{background:#f1c40f;box-shadow:0 0 0 2px #f1c40f;display:inline;font-weight:700}.rst-content .citation-reference,.rst-content .footnote-reference{vertical-align:baseline;position:relative;top:-.4em;line-height:0;font-size:90%}.rst-content .citation-reference>span.fn-bracket,.rst-content .footnote-reference>span.fn-bracket{display:none}.rst-content .hlist{width:100%}.rst-content dl dt span.classifier:before{content:" : "}.rst-content dl dt span.classifier-delimiter{display:none!important}html.writer-html4 .rst-content table.docutils.citation,html.writer-html4 .rst-content table.docutils.footnote{background:none;border:none}html.writer-html4 .rst-content table.docutils.citation td,html.writer-html4 .rst-content table.docutils.citation tr,html.writer-html4 .rst-content table.docutils.footnote td,html.writer-html4 .rst-content table.docutils.footnote tr{border:none;background-color:transparent!important;white-space:normal}html.writer-html4 .rst-content table.docutils.citation td.label,html.writer-html4 .rst-content table.docutils.footnote td.label{padding-left:0;padding-right:0;vertical-align:top}html.writer-html5 .rst-content dl.citation,html.writer-html5 .rst-content dl.field-list,html.writer-html5 .rst-content dl.footnote{display:grid;grid-template-columns:auto minmax(80%,95%)}html.writer-html5 .rst-content dl.citation>dt,html.writer-html5 .rst-content dl.field-list>dt,html.writer-html5 .rst-content dl.footnote>dt{display:inline-grid;grid-template-columns:max-content auto}html.writer-html5 .rst-content aside.citation,html.writer-html5 .rst-content aside.footnote,html.writer-html5 .rst-content div.citation{display:grid;grid-template-columns:auto auto minmax(.65rem,auto) minmax(40%,95%)}html.writer-html5 .rst-content aside.citation>span.label,html.writer-html5 .rst-content aside.footnote>span.label,html.writer-html5 .rst-content div.citation>span.label{grid-column-start:1;grid-column-end:2}html.writer-html5 .rst-content aside.citation>span.backrefs,html.writer-html5 .rst-content aside.footnote>span.backrefs,html.writer-html5 .rst-content div.citation>span.backrefs{grid-column-start:2;grid-column-end:3;grid-row-start:1;grid-row-end:3}html.writer-html5 .rst-content aside.citation>p,html.writer-html5 .rst-content aside.footnote>p,html.writer-html5 .rst-content div.citation>p{grid-column-start:4;grid-column-end:5}html.writer-html5 .rst-content dl.citation,html.writer-html5 .rst-content dl.field-list,html.writer-html5 .rst-content dl.footnote{margin-bottom:24px}html.writer-html5 .rst-content dl.citation>dt,html.writer-html5 .rst-content dl.field-list>dt,html.writer-html5 .rst-content dl.footnote>dt{padding-left:1rem}html.writer-html5 .rst-content dl.citation>dd,html.writer-html5 .rst-content dl.citation>dt,html.writer-html5 .rst-content dl.field-list>dd,html.writer-html5 .rst-content dl.field-list>dt,html.writer-html5 .rst-content dl.footnote>dd,html.writer-html5 .rst-content dl.footnote>dt{margin-bottom:0}html.writer-html5 .rst-content dl.citation,html.writer-html5 .rst-content dl.footnote{font-size:.9rem}html.writer-html5 .rst-content dl.citation>dt,html.writer-html5 .rst-content dl.footnote>dt{margin:0 .5rem .5rem 0;line-height:1.2rem;word-break:break-all;font-weight:400}html.writer-html5 .rst-content dl.citation>dt>span.brackets:before,html.writer-html5 .rst-content dl.footnote>dt>span.brackets:before{content:"["}html.writer-html5 .rst-content dl.citation>dt>span.brackets:after,html.writer-html5 .rst-content dl.footnote>dt>span.brackets:after{content:"]"}html.writer-html5 .rst-content dl.citation>dt>span.fn-backref,html.writer-html5 .rst-content dl.footnote>dt>span.fn-backref{text-align:left;font-style:italic;margin-left:.65rem;word-break:break-word;word-spacing:-.1rem;max-width:5rem}html.writer-html5 .rst-content dl.citation>dt>span.fn-backref>a,html.writer-html5 .rst-content dl.footnote>dt>span.fn-backref>a{word-break:keep-all}html.writer-html5 .rst-content dl.citation>dt>span.fn-backref>a:not(:first-child):before,html.writer-html5 .rst-content dl.footnote>dt>span.fn-backref>a:not(:first-child):before{content:" "}html.writer-html5 .rst-content dl.citation>dd,html.writer-html5 .rst-content dl.footnote>dd{margin:0 0 .5rem;line-height:1.2rem}html.writer-html5 .rst-content dl.citation>dd p,html.writer-html5 .rst-content dl.footnote>dd p{font-size:.9rem}html.writer-html5 .rst-content aside.citation,html.writer-html5 .rst-content aside.footnote,html.writer-html5 .rst-content div.citation{padding-left:1rem;padding-right:1rem;font-size:.9rem;line-height:1.2rem}html.writer-html5 .rst-content aside.citation p,html.writer-html5 .rst-content aside.footnote p,html.writer-html5 .rst-content div.citation p{font-size:.9rem;line-height:1.2rem;margin-bottom:12px}html.writer-html5 .rst-content aside.citation span.backrefs,html.writer-html5 .rst-content aside.footnote span.backrefs,html.writer-html5 .rst-content div.citation span.backrefs{text-align:left;font-style:italic;margin-left:.65rem;word-break:break-word;word-spacing:-.1rem;max-width:5rem}html.writer-html5 .rst-content aside.citation span.backrefs>a,html.writer-html5 .rst-content aside.footnote span.backrefs>a,html.writer-html5 .rst-content div.citation span.backrefs>a{word-break:keep-all}html.writer-html5 .rst-content aside.citation span.backrefs>a:not(:first-child):before,html.writer-html5 .rst-content aside.footnote span.backrefs>a:not(:first-child):before,html.writer-html5 .rst-content div.citation span.backrefs>a:not(:first-child):before{content:" "}html.writer-html5 .rst-content aside.citation span.label,html.writer-html5 .rst-content aside.footnote span.label,html.writer-html5 .rst-content div.citation span.label{line-height:1.2rem}html.writer-html5 .rst-content aside.citation-list,html.writer-html5 .rst-content aside.footnote-list,html.writer-html5 .rst-content div.citation-list{margin-bottom:24px}html.writer-html5 .rst-content dl.option-list kbd{font-size:.9rem}.rst-content table.docutils.footnote,html.writer-html4 .rst-content table.docutils.citation,html.writer-html5 .rst-content aside.footnote,html.writer-html5 .rst-content aside.footnote-list aside.footnote,html.writer-html5 .rst-content div.citation-list>div.citation,html.writer-html5 .rst-content dl.citation,html.writer-html5 .rst-content dl.footnote{color:grey}.rst-content table.docutils.footnote code,.rst-content table.docutils.footnote tt,html.writer-html4 .rst-content table.docutils.citation code,html.writer-html4 .rst-content table.docutils.citation tt,html.writer-html5 .rst-content aside.footnote-list aside.footnote code,html.writer-html5 .rst-content aside.footnote-list aside.footnote tt,html.writer-html5 .rst-content aside.footnote code,html.writer-html5 .rst-content aside.footnote tt,html.writer-html5 .rst-content div.citation-list>div.citation code,html.writer-html5 .rst-content div.citation-list>div.citation tt,html.writer-html5 .rst-content dl.citation code,html.writer-html5 .rst-content dl.citation tt,html.writer-html5 .rst-content dl.footnote code,html.writer-html5 .rst-content dl.footnote tt{color:#555}.rst-content .wy-table-responsive.citation,.rst-content .wy-table-responsive.footnote{margin-bottom:0}.rst-content .wy-table-responsive.citation+:not(.citation),.rst-content .wy-table-responsive.footnote+:not(.footnote){margin-top:24px}.rst-content .wy-table-responsive.citation:last-child,.rst-content .wy-table-responsive.footnote:last-child{margin-bottom:24px}.rst-content table.docutils th{border-color:#e1e4e5}html.writer-html5 .rst-content table.docutils th{border:1px solid #e1e4e5}html.writer-html5 .rst-content table.docutils td>p,html.writer-html5 .rst-content table.docutils th>p{line-height:1rem;margin-bottom:0;font-size:.9rem}.rst-content table.docutils td .last,.rst-content table.docutils td .last>:last-child{margin-bottom:0}.rst-content table.field-list,.rst-content table.field-list td{border:none}.rst-content table.field-list td p{line-height:inherit}.rst-content table.field-list td>strong{display:inline-block}.rst-content table.field-list .field-name{padding-right:10px;text-align:left;white-space:nowrap}.rst-content table.field-list .field-body{text-align:left}.rst-content code,.rst-content tt{color:#000;font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;padding:2px 5px}.rst-content code big,.rst-content code em,.rst-content tt big,.rst-content tt em{font-size:100%!important;line-height:normal}.rst-content code.literal,.rst-content tt.literal{color:#e74c3c;white-space:normal}.rst-content code.xref,.rst-content tt.xref,a .rst-content code,a .rst-content tt{font-weight:700;color:#404040;overflow-wrap:normal}.rst-content kbd,.rst-content pre,.rst-content samp{font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace}.rst-content a code,.rst-content a tt{color:#2980b9}.rst-content dl{margin-bottom:24px}.rst-content dl dt{font-weight:700;margin-bottom:12px}.rst-content dl ol,.rst-content dl p,.rst-content dl table,.rst-content dl ul{margin-bottom:12px}.rst-content dl dd{margin:0 0 12px 24px;line-height:24px}.rst-content dl dd>ol:last-child,.rst-content dl dd>p:last-child,.rst-content dl dd>table:last-child,.rst-content dl dd>ul:last-child{margin-bottom:0}html.writer-html4 .rst-content dl:not(.docutils),html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple){margin-bottom:24px}html.writer-html4 .rst-content dl:not(.docutils)>dt,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt{display:table;margin:6px 0;font-size:90%;line-height:normal;background:#e7f2fa;color:#2980b9;border-top:3px solid #6ab0de;padding:6px;position:relative}html.writer-html4 .rst-content dl:not(.docutils)>dt:before,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt:before{color:#6ab0de}html.writer-html4 .rst-content dl:not(.docutils)>dt .headerlink,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt .headerlink{color:#404040;font-size:100%!important}html.writer-html4 .rst-content dl:not(.docutils) dl:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) dl:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt{margin-bottom:6px;border:none;border-left:3px solid #ccc;background:#f0f0f0;color:#555}html.writer-html4 .rst-content dl:not(.docutils) dl:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt .headerlink,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) dl:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt .headerlink{color:#404040;font-size:100%!important}html.writer-html4 .rst-content dl:not(.docutils)>dt:first-child,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple)>dt:first-child{margin-top:0}html.writer-html4 .rst-content dl:not(.docutils) code.descclassname,html.writer-html4 .rst-content dl:not(.docutils) code.descname,html.writer-html4 .rst-content dl:not(.docutils) tt.descclassname,html.writer-html4 .rst-content dl:not(.docutils) tt.descname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) code.descclassname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) code.descname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) tt.descclassname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) tt.descname{background-color:transparent;border:none;padding:0;font-size:100%!important}html.writer-html4 .rst-content dl:not(.docutils) code.descname,html.writer-html4 .rst-content dl:not(.docutils) tt.descname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) code.descname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) tt.descname{font-weight:700}html.writer-html4 .rst-content dl:not(.docutils) .optional,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) .optional{display:inline-block;padding:0 4px;color:#000;font-weight:700}html.writer-html4 .rst-content dl:not(.docutils) .property,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) .property{display:inline-block;padding-right:8px;max-width:100%}html.writer-html4 .rst-content dl:not(.docutils) .k,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) .k{font-style:italic}html.writer-html4 .rst-content dl:not(.docutils) .descclassname,html.writer-html4 .rst-content dl:not(.docutils) .descname,html.writer-html4 .rst-content dl:not(.docutils) .sig-name,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) .descclassname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) .descname,html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.citation):not(.glossary):not(.simple) .sig-name{font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,Courier,monospace;color:#000}.rst-content .viewcode-back,.rst-content .viewcode-link{display:inline-block;color:#27ae60;font-size:80%;padding-left:24px}.rst-content .viewcode-back{display:block;float:right}.rst-content p.rubric{margin-bottom:12px;font-weight:700}.rst-content code.download,.rst-content tt.download{background:inherit;padding:inherit;font-weight:400;font-family:inherit;font-size:inherit;color:inherit;border:inherit;white-space:inherit}.rst-content code.download span:first-child,.rst-content tt.download span:first-child{-webkit-font-smoothing:subpixel-antialiased}.rst-content code.download span:first-child:before,.rst-content tt.download span:first-child:before{margin-right:4px}.rst-content .guilabel,.rst-content .menuselection{font-size:80%;font-weight:700;border-radius:4px;padding:2.4px 6px;margin:auto 2px}.rst-content .guilabel,.rst-content .menuselection{border:1px solid #7fbbe3;background:#e7f2fa}.rst-content :not(dl.option-list)>:not(dt):not(kbd):not(.kbd)>.kbd,.rst-content :not(dl.option-list)>:not(dt):not(kbd):not(.kbd)>kbd{color:inherit;font-size:80%;background-color:#fff;border:1px solid #a6a6a6;border-radius:4px;box-shadow:0 2px grey;padding:2.4px 6px;margin:auto 0}.rst-content .versionmodified{font-style:italic}@media screen and (max-width:480px){.rst-content .sidebar{width:100%}}span[id*=MathJax-Span]{color:#404040}.math{text-align:center}@font-face{font-family:Lato;src:url(fonts/lato-normal.woff2?bd03a2cc277bbbc338d464e679fe9942) format("woff2"),url(fonts/lato-normal.woff?27bd77b9162d388cb8d4c4217c7c5e2a) format("woff");font-weight:400;font-style:normal;font-display:block}@font-face{font-family:Lato;src:url(fonts/lato-bold.woff2?cccb897485813c7c256901dbca54ecf2) format("woff2"),url(fonts/lato-bold.woff?d878b6c29b10beca227e9eef4246111b) format("woff");font-weight:700;font-style:normal;font-display:block}@font-face{font-family:Lato;src:url(fonts/lato-bold-italic.woff2?0b6bb6725576b072c5d0b02ecdd1900d) format("woff2"),url(fonts/lato-bold-italic.woff?9c7e4e9eb485b4a121c760e61bc3707c) format("woff");font-weight:700;font-style:italic;font-display:block}@font-face{font-family:Lato;src:url(fonts/lato-normal-italic.woff2?4eb103b4d12be57cb1d040ed5e162e9d) format("woff2"),url(fonts/lato-normal-italic.woff?f28f2d6482446544ef1ea1ccc6dd5892) format("woff");font-weight:400;font-style:italic;font-display:block}@font-face{font-family:Roboto Slab;font-style:normal;font-weight:400;src:url(fonts/Roboto-Slab-Regular.woff2?7abf5b8d04d26a2cafea937019bca958) format("woff2"),url(fonts/Roboto-Slab-Regular.woff?c1be9284088d487c5e3ff0a10a92e58c) format("woff");font-display:block}@font-face{font-family:Roboto Slab;font-style:normal;font-weight:700;src:url(fonts/Roboto-Slab-Bold.woff2?9984f4a9bda09be08e83f2506954adbe) format("woff2"),url(fonts/Roboto-Slab-Bold.woff?bed5564a116b05148e3b3bea6fb1162a) format("woff");font-display:block} \ No newline at end of file diff --git a/refs/heads/MOP3/_static/doctools.js b/refs/heads/MOP3/_static/doctools.js new file mode 100644 index 0000000..0398ebb --- /dev/null +++ b/refs/heads/MOP3/_static/doctools.js @@ -0,0 +1,149 @@ +/* + * Base JavaScript utilities for all Sphinx HTML documentation. + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/refs/heads/MOP3/_static/documentation_options.js b/refs/heads/MOP3/_static/documentation_options.js new file mode 100644 index 0000000..7e4c114 --- /dev/null +++ b/refs/heads/MOP3/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/refs/heads/MOP3/_static/file.png b/refs/heads/MOP3/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/refs/heads/MOP3/_static/file.png differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bold.eot b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.eot new file mode 100644 index 0000000..3361183 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.eot differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bold.ttf b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.ttf new file mode 100644 index 0000000..29f691d Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.ttf differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bold.woff b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.woff new file mode 100644 index 0000000..c6dff51 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.woff differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bold.woff2 b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.woff2 new file mode 100644 index 0000000..bb19504 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bold.woff2 differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.eot b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.eot new file mode 100644 index 0000000..3d41549 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.eot differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.ttf b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.ttf new file mode 100644 index 0000000..f402040 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.ttf differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.woff b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.woff new file mode 100644 index 0000000..88ad05b Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.woff differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.woff2 b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.woff2 new file mode 100644 index 0000000..c4e3d80 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-bolditalic.woff2 differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-italic.eot b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.eot new file mode 100644 index 0000000..3f82642 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.eot differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-italic.ttf b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.ttf new file mode 100644 index 0000000..b4bfc9b Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.ttf differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-italic.woff b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.woff new file mode 100644 index 0000000..76114bc Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.woff differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-italic.woff2 b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.woff2 new file mode 100644 index 0000000..3404f37 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-italic.woff2 differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-regular.eot b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.eot new file mode 100644 index 0000000..11e3f2a Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.eot differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-regular.ttf b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.ttf new file mode 100644 index 0000000..74decd9 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.ttf differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-regular.woff b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.woff new file mode 100644 index 0000000..ae1307f Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.woff differ diff --git a/refs/heads/MOP3/_static/fonts/Lato/lato-regular.woff2 b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.woff2 new file mode 100644 index 0000000..3bf9843 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/Lato/lato-regular.woff2 differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot new file mode 100644 index 0000000..79dc8ef Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf new file mode 100644 index 0000000..df5d1df Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff new file mode 100644 index 0000000..6cb6000 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 new file mode 100644 index 0000000..7059e23 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot new file mode 100644 index 0000000..2f7ca78 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf new file mode 100644 index 0000000..eb52a79 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff new file mode 100644 index 0000000..f815f63 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff differ diff --git a/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 new file mode 100644 index 0000000..f2c76e5 Binary files /dev/null and b/refs/heads/MOP3/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 differ diff --git a/refs/heads/MOP3/_static/jquery.js b/refs/heads/MOP3/_static/jquery.js new file mode 100644 index 0000000..c4c6022 --- /dev/null +++ b/refs/heads/MOP3/_static/jquery.js @@ -0,0 +1,2 @@ +/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */ +!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return t.concat.apply([],e)},u=t.push,i=t.indexOf,n={},o=n.toString,v=n.hasOwnProperty,a=v.toString,l=a.call(Object),y={},m=function(e){return"function"==typeof e&&"number"!=typeof e.nodeType&&"function"!=typeof e.item},x=function(e){return null!=e&&e===e.window},E=C.document,c={type:!0,src:!0,nonce:!0,noModule:!0};function b(e,t,n){var r,i,o=(n=n||E).createElement("script");if(o.text=e,t)for(r in c)(i=t[r]||t.getAttribute&&t.getAttribute(r))&&o.setAttribute(r,i);n.head.appendChild(o).parentNode.removeChild(o)}function w(e){return null==e?e+"":"object"==typeof e||"function"==typeof e?n[o.call(e)]||"object":typeof e}var f="3.6.0",S=function(e,t){return new S.fn.init(e,t)};function p(e){var t=!!e&&"length"in e&&e.length,n=w(e);return!m(e)&&!x(e)&&("array"===n||0===t||"number"==typeof t&&0+~]|"+M+")"+M+"*"),U=new RegExp(M+"|>"),X=new RegExp(F),V=new RegExp("^"+I+"$"),G={ID:new RegExp("^#("+I+")"),CLASS:new RegExp("^\\.("+I+")"),TAG:new RegExp("^("+I+"|[*])"),ATTR:new RegExp("^"+W),PSEUDO:new RegExp("^"+F),CHILD:new RegExp("^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\("+M+"*(even|odd|(([+-]|)(\\d*)n|)"+M+"*(?:([+-]|)"+M+"*(\\d+)|))"+M+"*\\)|)","i"),bool:new RegExp("^(?:"+R+")$","i"),needsContext:new RegExp("^"+M+"*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\("+M+"*((?:-\\d)?\\d*)"+M+"*\\)|)(?=[^-]|$)","i")},Y=/HTML$/i,Q=/^(?:input|select|textarea|button)$/i,J=/^h\d$/i,K=/^[^{]+\{\s*\[native \w/,Z=/^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,ee=/[+~]/,te=new RegExp("\\\\[\\da-fA-F]{1,6}"+M+"?|\\\\([^\\r\\n\\f])","g"),ne=function(e,t){var n="0x"+e.slice(1)-65536;return t||(n<0?String.fromCharCode(n+65536):String.fromCharCode(n>>10|55296,1023&n|56320))},re=/([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,ie=function(e,t){return t?"\0"===e?"\ufffd":e.slice(0,-1)+"\\"+e.charCodeAt(e.length-1).toString(16)+" ":"\\"+e},oe=function(){T()},ae=be(function(e){return!0===e.disabled&&"fieldset"===e.nodeName.toLowerCase()},{dir:"parentNode",next:"legend"});try{H.apply(t=O.call(p.childNodes),p.childNodes),t[p.childNodes.length].nodeType}catch(e){H={apply:t.length?function(e,t){L.apply(e,O.call(t))}:function(e,t){var n=e.length,r=0;while(e[n++]=t[r++]);e.length=n-1}}}function se(t,e,n,r){var i,o,a,s,u,l,c,f=e&&e.ownerDocument,p=e?e.nodeType:9;if(n=n||[],"string"!=typeof t||!t||1!==p&&9!==p&&11!==p)return n;if(!r&&(T(e),e=e||C,E)){if(11!==p&&(u=Z.exec(t)))if(i=u[1]){if(9===p){if(!(a=e.getElementById(i)))return n;if(a.id===i)return n.push(a),n}else if(f&&(a=f.getElementById(i))&&y(e,a)&&a.id===i)return n.push(a),n}else{if(u[2])return H.apply(n,e.getElementsByTagName(t)),n;if((i=u[3])&&d.getElementsByClassName&&e.getElementsByClassName)return H.apply(n,e.getElementsByClassName(i)),n}if(d.qsa&&!N[t+" "]&&(!v||!v.test(t))&&(1!==p||"object"!==e.nodeName.toLowerCase())){if(c=t,f=e,1===p&&(U.test(t)||z.test(t))){(f=ee.test(t)&&ye(e.parentNode)||e)===e&&d.scope||((s=e.getAttribute("id"))?s=s.replace(re,ie):e.setAttribute("id",s=S)),o=(l=h(t)).length;while(o--)l[o]=(s?"#"+s:":scope")+" "+xe(l[o]);c=l.join(",")}try{return H.apply(n,f.querySelectorAll(c)),n}catch(e){N(t,!0)}finally{s===S&&e.removeAttribute("id")}}}return g(t.replace($,"$1"),e,n,r)}function ue(){var r=[];return function e(t,n){return r.push(t+" ")>b.cacheLength&&delete e[r.shift()],e[t+" "]=n}}function le(e){return e[S]=!0,e}function ce(e){var t=C.createElement("fieldset");try{return!!e(t)}catch(e){return!1}finally{t.parentNode&&t.parentNode.removeChild(t),t=null}}function fe(e,t){var n=e.split("|"),r=n.length;while(r--)b.attrHandle[n[r]]=t}function pe(e,t){var n=t&&e,r=n&&1===e.nodeType&&1===t.nodeType&&e.sourceIndex-t.sourceIndex;if(r)return r;if(n)while(n=n.nextSibling)if(n===t)return-1;return e?1:-1}function de(t){return function(e){return"input"===e.nodeName.toLowerCase()&&e.type===t}}function he(n){return function(e){var t=e.nodeName.toLowerCase();return("input"===t||"button"===t)&&e.type===n}}function ge(t){return function(e){return"form"in e?e.parentNode&&!1===e.disabled?"label"in e?"label"in e.parentNode?e.parentNode.disabled===t:e.disabled===t:e.isDisabled===t||e.isDisabled!==!t&&ae(e)===t:e.disabled===t:"label"in e&&e.disabled===t}}function ve(a){return le(function(o){return o=+o,le(function(e,t){var n,r=a([],e.length,o),i=r.length;while(i--)e[n=r[i]]&&(e[n]=!(t[n]=e[n]))})})}function ye(e){return e&&"undefined"!=typeof e.getElementsByTagName&&e}for(e in d=se.support={},i=se.isXML=function(e){var t=e&&e.namespaceURI,n=e&&(e.ownerDocument||e).documentElement;return!Y.test(t||n&&n.nodeName||"HTML")},T=se.setDocument=function(e){var t,n,r=e?e.ownerDocument||e:p;return r!=C&&9===r.nodeType&&r.documentElement&&(a=(C=r).documentElement,E=!i(C),p!=C&&(n=C.defaultView)&&n.top!==n&&(n.addEventListener?n.addEventListener("unload",oe,!1):n.attachEvent&&n.attachEvent("onunload",oe)),d.scope=ce(function(e){return a.appendChild(e).appendChild(C.createElement("div")),"undefined"!=typeof e.querySelectorAll&&!e.querySelectorAll(":scope fieldset div").length}),d.attributes=ce(function(e){return e.className="i",!e.getAttribute("className")}),d.getElementsByTagName=ce(function(e){return e.appendChild(C.createComment("")),!e.getElementsByTagName("*").length}),d.getElementsByClassName=K.test(C.getElementsByClassName),d.getById=ce(function(e){return a.appendChild(e).id=S,!C.getElementsByName||!C.getElementsByName(S).length}),d.getById?(b.filter.ID=function(e){var t=e.replace(te,ne);return function(e){return e.getAttribute("id")===t}},b.find.ID=function(e,t){if("undefined"!=typeof t.getElementById&&E){var n=t.getElementById(e);return n?[n]:[]}}):(b.filter.ID=function(e){var n=e.replace(te,ne);return function(e){var t="undefined"!=typeof e.getAttributeNode&&e.getAttributeNode("id");return t&&t.value===n}},b.find.ID=function(e,t){if("undefined"!=typeof t.getElementById&&E){var n,r,i,o=t.getElementById(e);if(o){if((n=o.getAttributeNode("id"))&&n.value===e)return[o];i=t.getElementsByName(e),r=0;while(o=i[r++])if((n=o.getAttributeNode("id"))&&n.value===e)return[o]}return[]}}),b.find.TAG=d.getElementsByTagName?function(e,t){return"undefined"!=typeof t.getElementsByTagName?t.getElementsByTagName(e):d.qsa?t.querySelectorAll(e):void 0}:function(e,t){var n,r=[],i=0,o=t.getElementsByTagName(e);if("*"===e){while(n=o[i++])1===n.nodeType&&r.push(n);return r}return o},b.find.CLASS=d.getElementsByClassName&&function(e,t){if("undefined"!=typeof t.getElementsByClassName&&E)return t.getElementsByClassName(e)},s=[],v=[],(d.qsa=K.test(C.querySelectorAll))&&(ce(function(e){var t;a.appendChild(e).innerHTML="",e.querySelectorAll("[msallowcapture^='']").length&&v.push("[*^$]="+M+"*(?:''|\"\")"),e.querySelectorAll("[selected]").length||v.push("\\["+M+"*(?:value|"+R+")"),e.querySelectorAll("[id~="+S+"-]").length||v.push("~="),(t=C.createElement("input")).setAttribute("name",""),e.appendChild(t),e.querySelectorAll("[name='']").length||v.push("\\["+M+"*name"+M+"*="+M+"*(?:''|\"\")"),e.querySelectorAll(":checked").length||v.push(":checked"),e.querySelectorAll("a#"+S+"+*").length||v.push(".#.+[+~]"),e.querySelectorAll("\\\f"),v.push("[\\r\\n\\f]")}),ce(function(e){e.innerHTML="";var t=C.createElement("input");t.setAttribute("type","hidden"),e.appendChild(t).setAttribute("name","D"),e.querySelectorAll("[name=d]").length&&v.push("name"+M+"*[*^$|!~]?="),2!==e.querySelectorAll(":enabled").length&&v.push(":enabled",":disabled"),a.appendChild(e).disabled=!0,2!==e.querySelectorAll(":disabled").length&&v.push(":enabled",":disabled"),e.querySelectorAll("*,:x"),v.push(",.*:")})),(d.matchesSelector=K.test(c=a.matches||a.webkitMatchesSelector||a.mozMatchesSelector||a.oMatchesSelector||a.msMatchesSelector))&&ce(function(e){d.disconnectedMatch=c.call(e,"*"),c.call(e,"[s!='']:x"),s.push("!=",F)}),v=v.length&&new RegExp(v.join("|")),s=s.length&&new RegExp(s.join("|")),t=K.test(a.compareDocumentPosition),y=t||K.test(a.contains)?function(e,t){var n=9===e.nodeType?e.documentElement:e,r=t&&t.parentNode;return e===r||!(!r||1!==r.nodeType||!(n.contains?n.contains(r):e.compareDocumentPosition&&16&e.compareDocumentPosition(r)))}:function(e,t){if(t)while(t=t.parentNode)if(t===e)return!0;return!1},j=t?function(e,t){if(e===t)return l=!0,0;var n=!e.compareDocumentPosition-!t.compareDocumentPosition;return n||(1&(n=(e.ownerDocument||e)==(t.ownerDocument||t)?e.compareDocumentPosition(t):1)||!d.sortDetached&&t.compareDocumentPosition(e)===n?e==C||e.ownerDocument==p&&y(p,e)?-1:t==C||t.ownerDocument==p&&y(p,t)?1:u?P(u,e)-P(u,t):0:4&n?-1:1)}:function(e,t){if(e===t)return l=!0,0;var n,r=0,i=e.parentNode,o=t.parentNode,a=[e],s=[t];if(!i||!o)return e==C?-1:t==C?1:i?-1:o?1:u?P(u,e)-P(u,t):0;if(i===o)return pe(e,t);n=e;while(n=n.parentNode)a.unshift(n);n=t;while(n=n.parentNode)s.unshift(n);while(a[r]===s[r])r++;return r?pe(a[r],s[r]):a[r]==p?-1:s[r]==p?1:0}),C},se.matches=function(e,t){return se(e,null,null,t)},se.matchesSelector=function(e,t){if(T(e),d.matchesSelector&&E&&!N[t+" "]&&(!s||!s.test(t))&&(!v||!v.test(t)))try{var n=c.call(e,t);if(n||d.disconnectedMatch||e.document&&11!==e.document.nodeType)return n}catch(e){N(t,!0)}return 0":{dir:"parentNode",first:!0}," ":{dir:"parentNode"},"+":{dir:"previousSibling",first:!0},"~":{dir:"previousSibling"}},preFilter:{ATTR:function(e){return e[1]=e[1].replace(te,ne),e[3]=(e[3]||e[4]||e[5]||"").replace(te,ne),"~="===e[2]&&(e[3]=" "+e[3]+" "),e.slice(0,4)},CHILD:function(e){return e[1]=e[1].toLowerCase(),"nth"===e[1].slice(0,3)?(e[3]||se.error(e[0]),e[4]=+(e[4]?e[5]+(e[6]||1):2*("even"===e[3]||"odd"===e[3])),e[5]=+(e[7]+e[8]||"odd"===e[3])):e[3]&&se.error(e[0]),e},PSEUDO:function(e){var t,n=!e[6]&&e[2];return G.CHILD.test(e[0])?null:(e[3]?e[2]=e[4]||e[5]||"":n&&X.test(n)&&(t=h(n,!0))&&(t=n.indexOf(")",n.length-t)-n.length)&&(e[0]=e[0].slice(0,t),e[2]=n.slice(0,t)),e.slice(0,3))}},filter:{TAG:function(e){var t=e.replace(te,ne).toLowerCase();return"*"===e?function(){return!0}:function(e){return e.nodeName&&e.nodeName.toLowerCase()===t}},CLASS:function(e){var t=m[e+" "];return t||(t=new RegExp("(^|"+M+")"+e+"("+M+"|$)"))&&m(e,function(e){return t.test("string"==typeof e.className&&e.className||"undefined"!=typeof e.getAttribute&&e.getAttribute("class")||"")})},ATTR:function(n,r,i){return function(e){var t=se.attr(e,n);return null==t?"!="===r:!r||(t+="","="===r?t===i:"!="===r?t!==i:"^="===r?i&&0===t.indexOf(i):"*="===r?i&&-1:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i;function j(e,n,r){return m(n)?S.grep(e,function(e,t){return!!n.call(e,t,e)!==r}):n.nodeType?S.grep(e,function(e){return e===n!==r}):"string"!=typeof n?S.grep(e,function(e){return-1)[^>]*|#([\w-]+))$/;(S.fn.init=function(e,t,n){var r,i;if(!e)return this;if(n=n||D,"string"==typeof e){if(!(r="<"===e[0]&&">"===e[e.length-1]&&3<=e.length?[null,e,null]:q.exec(e))||!r[1]&&t)return!t||t.jquery?(t||n).find(e):this.constructor(t).find(e);if(r[1]){if(t=t instanceof S?t[0]:t,S.merge(this,S.parseHTML(r[1],t&&t.nodeType?t.ownerDocument||t:E,!0)),N.test(r[1])&&S.isPlainObject(t))for(r in t)m(this[r])?this[r](t[r]):this.attr(r,t[r]);return this}return(i=E.getElementById(r[2]))&&(this[0]=i,this.length=1),this}return e.nodeType?(this[0]=e,this.length=1,this):m(e)?void 0!==n.ready?n.ready(e):e(S):S.makeArray(e,this)}).prototype=S.fn,D=S(E);var L=/^(?:parents|prev(?:Until|All))/,H={children:!0,contents:!0,next:!0,prev:!0};function O(e,t){while((e=e[t])&&1!==e.nodeType);return e}S.fn.extend({has:function(e){var t=S(e,this),n=t.length;return this.filter(function(){for(var e=0;e\x20\t\r\n\f]*)/i,he=/^$|^module$|\/(?:java|ecma)script/i;ce=E.createDocumentFragment().appendChild(E.createElement("div")),(fe=E.createElement("input")).setAttribute("type","radio"),fe.setAttribute("checked","checked"),fe.setAttribute("name","t"),ce.appendChild(fe),y.checkClone=ce.cloneNode(!0).cloneNode(!0).lastChild.checked,ce.innerHTML="",y.noCloneChecked=!!ce.cloneNode(!0).lastChild.defaultValue,ce.innerHTML="",y.option=!!ce.lastChild;var ge={thead:[1,"","
"],col:[2,"","
"],tr:[2,"","
"],td:[3,"","
"],_default:[0,"",""]};function ve(e,t){var n;return n="undefined"!=typeof e.getElementsByTagName?e.getElementsByTagName(t||"*"):"undefined"!=typeof e.querySelectorAll?e.querySelectorAll(t||"*"):[],void 0===t||t&&A(e,t)?S.merge([e],n):n}function ye(e,t){for(var n=0,r=e.length;n",""]);var me=/<|&#?\w+;/;function xe(e,t,n,r,i){for(var o,a,s,u,l,c,f=t.createDocumentFragment(),p=[],d=0,h=e.length;d\s*$/g;function je(e,t){return A(e,"table")&&A(11!==t.nodeType?t:t.firstChild,"tr")&&S(e).children("tbody")[0]||e}function De(e){return e.type=(null!==e.getAttribute("type"))+"/"+e.type,e}function qe(e){return"true/"===(e.type||"").slice(0,5)?e.type=e.type.slice(5):e.removeAttribute("type"),e}function Le(e,t){var n,r,i,o,a,s;if(1===t.nodeType){if(Y.hasData(e)&&(s=Y.get(e).events))for(i in Y.remove(t,"handle events"),s)for(n=0,r=s[i].length;n").attr(n.scriptAttrs||{}).prop({charset:n.scriptCharset,src:n.url}).on("load error",i=function(e){r.remove(),i=null,e&&t("error"===e.type?404:200,e.type)}),E.head.appendChild(r[0])},abort:function(){i&&i()}}});var _t,zt=[],Ut=/(=)\?(?=&|$)|\?\?/;S.ajaxSetup({jsonp:"callback",jsonpCallback:function(){var e=zt.pop()||S.expando+"_"+wt.guid++;return this[e]=!0,e}}),S.ajaxPrefilter("json jsonp",function(e,t,n){var r,i,o,a=!1!==e.jsonp&&(Ut.test(e.url)?"url":"string"==typeof e.data&&0===(e.contentType||"").indexOf("application/x-www-form-urlencoded")&&Ut.test(e.data)&&"data");if(a||"jsonp"===e.dataTypes[0])return r=e.jsonpCallback=m(e.jsonpCallback)?e.jsonpCallback():e.jsonpCallback,a?e[a]=e[a].replace(Ut,"$1"+r):!1!==e.jsonp&&(e.url+=(Tt.test(e.url)?"&":"?")+e.jsonp+"="+r),e.converters["script json"]=function(){return o||S.error(r+" was not called"),o[0]},e.dataTypes[0]="json",i=C[r],C[r]=function(){o=arguments},n.always(function(){void 0===i?S(C).removeProp(r):C[r]=i,e[r]&&(e.jsonpCallback=t.jsonpCallback,zt.push(r)),o&&m(i)&&i(o[0]),o=i=void 0}),"script"}),y.createHTMLDocument=((_t=E.implementation.createHTMLDocument("").body).innerHTML="
",2===_t.childNodes.length),S.parseHTML=function(e,t,n){return"string"!=typeof e?[]:("boolean"==typeof t&&(n=t,t=!1),t||(y.createHTMLDocument?((r=(t=E.implementation.createHTMLDocument("")).createElement("base")).href=E.location.href,t.head.appendChild(r)):t=E),o=!n&&[],(i=N.exec(e))?[t.createElement(i[1])]:(i=xe([e],t,o),o&&o.length&&S(o).remove(),S.merge([],i.childNodes)));var r,i,o},S.fn.load=function(e,t,n){var r,i,o,a=this,s=e.indexOf(" ");return-1").append(S.parseHTML(e)).find(r):e)}).always(n&&function(e,t){a.each(function(){n.apply(this,o||[e.responseText,t,e])})}),this},S.expr.pseudos.animated=function(t){return S.grep(S.timers,function(e){return t===e.elem}).length},S.offset={setOffset:function(e,t,n){var r,i,o,a,s,u,l=S.css(e,"position"),c=S(e),f={};"static"===l&&(e.style.position="relative"),s=c.offset(),o=S.css(e,"top"),u=S.css(e,"left"),("absolute"===l||"fixed"===l)&&-1<(o+u).indexOf("auto")?(a=(r=c.position()).top,i=r.left):(a=parseFloat(o)||0,i=parseFloat(u)||0),m(t)&&(t=t.call(e,n,S.extend({},s))),null!=t.top&&(f.top=t.top-s.top+a),null!=t.left&&(f.left=t.left-s.left+i),"using"in t?t.using.call(e,f):c.css(f)}},S.fn.extend({offset:function(t){if(arguments.length)return void 0===t?this:this.each(function(e){S.offset.setOffset(this,t,e)});var e,n,r=this[0];return r?r.getClientRects().length?(e=r.getBoundingClientRect(),n=r.ownerDocument.defaultView,{top:e.top+n.pageYOffset,left:e.left+n.pageXOffset}):{top:0,left:0}:void 0},position:function(){if(this[0]){var e,t,n,r=this[0],i={top:0,left:0};if("fixed"===S.css(r,"position"))t=r.getBoundingClientRect();else{t=this.offset(),n=r.ownerDocument,e=r.offsetParent||n.documentElement;while(e&&(e===n.body||e===n.documentElement)&&"static"===S.css(e,"position"))e=e.parentNode;e&&e!==r&&1===e.nodeType&&((i=S(e).offset()).top+=S.css(e,"borderTopWidth",!0),i.left+=S.css(e,"borderLeftWidth",!0))}return{top:t.top-i.top-S.css(r,"marginTop",!0),left:t.left-i.left-S.css(r,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var e=this.offsetParent;while(e&&"static"===S.css(e,"position"))e=e.offsetParent;return e||re})}}),S.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(t,i){var o="pageYOffset"===i;S.fn[t]=function(e){return $(this,function(e,t,n){var r;if(x(e)?r=e:9===e.nodeType&&(r=e.defaultView),void 0===n)return r?r[i]:e[t];r?r.scrollTo(o?r.pageXOffset:n,o?n:r.pageYOffset):e[t]=n},t,e,arguments.length)}}),S.each(["top","left"],function(e,n){S.cssHooks[n]=Fe(y.pixelPosition,function(e,t){if(t)return t=We(e,n),Pe.test(t)?S(e).position()[n]+"px":t})}),S.each({Height:"height",Width:"width"},function(a,s){S.each({padding:"inner"+a,content:s,"":"outer"+a},function(r,o){S.fn[o]=function(e,t){var n=arguments.length&&(r||"boolean"!=typeof e),i=r||(!0===e||!0===t?"margin":"border");return $(this,function(e,t,n){var r;return x(e)?0===o.indexOf("outer")?e["inner"+a]:e.document.documentElement["client"+a]:9===e.nodeType?(r=e.documentElement,Math.max(e.body["scroll"+a],r["scroll"+a],e.body["offset"+a],r["offset"+a],r["client"+a])):void 0===n?S.css(e,t,i):S.style(e,t,n,i)},s,n?e:void 0,n)}})}),S.each(["ajaxStart","ajaxStop","ajaxComplete","ajaxError","ajaxSuccess","ajaxSend"],function(e,t){S.fn[t]=function(e){return this.on(t,e)}}),S.fn.extend({bind:function(e,t,n){return this.on(e,null,t,n)},unbind:function(e,t){return this.off(e,null,t)},delegate:function(e,t,n,r){return this.on(t,e,n,r)},undelegate:function(e,t,n){return 1===arguments.length?this.off(e,"**"):this.off(t,e||"**",n)},hover:function(e,t){return this.mouseenter(e).mouseleave(t||e)}}),S.each("blur focus focusin focusout resize scroll click dblclick mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave change select submit keydown keypress keyup contextmenu".split(" "),function(e,n){S.fn[n]=function(e,t){return 0"),n("table.docutils.footnote").wrap("
"),n("table.docutils.citation").wrap("
"),n(".wy-menu-vertical ul").not(".simple").siblings("a").each((function(){var t=n(this);expand=n(''),expand.on("click",(function(n){return e.toggleCurrent(t),n.stopPropagation(),!1})),t.prepend(expand)}))},reset:function(){var n=encodeURI(window.location.hash)||"#";try{var e=$(".wy-menu-vertical"),t=e.find('[href="'+n+'"]');if(0===t.length){var i=$('.document [id="'+n.substring(1)+'"]').closest("div.section");0===(t=e.find('[href="#'+i.attr("id")+'"]')).length&&(t=e.find('[href="#"]'))}if(t.length>0){$(".wy-menu-vertical .current").removeClass("current").attr("aria-expanded","false"),t.addClass("current").attr("aria-expanded","true"),t.closest("li.toctree-l1").parent().addClass("current").attr("aria-expanded","true");for(let n=1;n<=10;n++)t.closest("li.toctree-l"+n).addClass("current").attr("aria-expanded","true");t[0].scrollIntoView()}}catch(n){console.log("Error expanding nav for anchor",n)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,t=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(t),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",(function(){this.linkScroll=!1}))},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current").attr("aria-expanded","false"),e.siblings().find("li.current").removeClass("current").attr("aria-expanded","false");var t=e.find("> ul li");t.length&&(t.removeClass("current").attr("aria-expanded","false"),e.toggleClass("current").attr("aria-expanded",(function(n,e){return"true"==e?"false":"true"})))}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:n.exports.ThemeNav,StickyNav:n.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],t=0;t a.language.name.localeCompare(b.language.name)); + + const languagesHTML = ` +
+
Languages
+ ${languages + .map( + (translation) => ` +
+ ${translation.language.code} +
+ `, + ) + .join("\n")} +
+ `; + return languagesHTML; + } + + function renderVersions(config) { + if (!config.versions.active.length) { + return ""; + } + const versionsHTML = ` +
+
Versions
+ ${config.versions.active + .map( + (version) => ` +
+ ${version.slug} +
+ `, + ) + .join("\n")} +
+ `; + return versionsHTML; + } + + function renderDownloads(config) { + if (!Object.keys(config.versions.current.downloads).length) { + return ""; + } + const downloadsNameDisplay = { + pdf: "PDF", + epub: "Epub", + htmlzip: "HTML", + }; + + const downloadsHTML = ` +
+
Downloads
+ ${Object.entries(config.versions.current.downloads) + .map( + ([name, url]) => ` +
+ ${downloadsNameDisplay[name]} +
+ `, + ) + .join("\n")} +
+ `; + return downloadsHTML; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const flyout = ` +
+ + Read the Docs + v: ${config.versions.current.slug} + + +
+
+ ${renderLanguages(config)} + ${renderVersions(config)} + ${renderDownloads(config)} +
+
On Read the Docs
+
+ Project Home +
+
+ Builds +
+
+ Downloads +
+
+
+
Search
+
+
+ +
+
+
+
+ + Hosted by Read the Docs + +
+
+ `; + + // Inject the generated flyout into the body HTML element. + document.body.insertAdjacentHTML("beforeend", flyout); + + // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout. + document + .querySelector("#flyout-search-form") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); + }) +} + +if (themeLanguageSelector || themeVersionSelector) { + function onSelectorSwitch(event) { + const option = event.target.selectedIndex; + const item = event.target.options[option]; + window.location.href = item.dataset.url; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const versionSwitch = document.querySelector( + "div.switch-menus > div.version-switch", + ); + if (themeVersionSelector) { + let versions = config.versions.active; + if (config.versions.current.hidden || config.versions.current.type === "external") { + versions.unshift(config.versions.current); + } + const versionSelect = ` + + `; + + versionSwitch.innerHTML = versionSelect; + versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + + const languageSwitch = document.querySelector( + "div.switch-menus > div.language-switch", + ); + + if (themeLanguageSelector) { + if (config.projects.translations.length) { + // Add the current language to the options on the selector + let languages = config.projects.translations.concat( + config.projects.current, + ); + languages = languages.sort((a, b) => + a.language.name.localeCompare(b.language.name), + ); + + const languageSelect = ` + + `; + + languageSwitch.innerHTML = languageSelect; + languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + else { + languageSwitch.remove(); + } + } + }); +} + +document.addEventListener("readthedocs-addons-data-ready", function (event) { + // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav. + document + .querySelector("[role='search'] input") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/refs/heads/MOP3/_static/language_data.js b/refs/heads/MOP3/_static/language_data.js new file mode 100644 index 0000000..c7fe6c6 --- /dev/null +++ b/refs/heads/MOP3/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/refs/heads/MOP3/_static/minus.png b/refs/heads/MOP3/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/refs/heads/MOP3/_static/minus.png differ diff --git a/refs/heads/MOP3/_static/plus.png b/refs/heads/MOP3/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/refs/heads/MOP3/_static/plus.png differ diff --git a/refs/heads/MOP3/_static/pygments.css b/refs/heads/MOP3/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/refs/heads/MOP3/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ +.highlight .gr { color: #E40000 } /* Generic.Error */ +.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ +.highlight .gi { color: #008400 } /* Generic.Inserted */ +.highlight .go { color: #717171 } /* Generic.Output */ +.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */ +.highlight .gs { font-weight: bold } /* Generic.Strong */ +.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ +.highlight .gt { color: #0044DD } /* Generic.Traceback */ +.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */ +.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */ +.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */ +.highlight .kp { color: #008000 } /* Keyword.Pseudo */ +.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */ +.highlight .kt { color: #B00040 } /* Keyword.Type */ +.highlight .m { color: #666666 } /* Literal.Number */ +.highlight .s { color: #BA2121 } /* Literal.String */ +.highlight .na { color: #687822 } /* Name.Attribute */ +.highlight .nb { color: #008000 } /* Name.Builtin */ +.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */ +.highlight .no { color: #880000 } /* Name.Constant */ +.highlight .nd { color: #AA22FF } /* Name.Decorator */ +.highlight .ni { color: #717171; font-weight: bold } /* Name.Entity */ +.highlight .ne { color: #CB3F38; font-weight: bold } /* Name.Exception */ +.highlight .nf { color: #0000FF } /* Name.Function */ +.highlight .nl { color: #767600 } /* Name.Label */ +.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */ +.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */ +.highlight .nv { color: #19177C } /* Name.Variable */ +.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */ +.highlight .w { color: #bbbbbb } /* Text.Whitespace */ +.highlight .mb { color: #666666 } /* Literal.Number.Bin */ +.highlight .mf { color: #666666 } /* Literal.Number.Float */ +.highlight .mh { color: #666666 } /* Literal.Number.Hex */ +.highlight .mi { color: #666666 } /* Literal.Number.Integer */ +.highlight .mo { color: #666666 } /* Literal.Number.Oct */ +.highlight .sa { color: #BA2121 } /* Literal.String.Affix */ +.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */ +.highlight .sc { color: #BA2121 } /* Literal.String.Char */ +.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */ +.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #BA2121 } /* Literal.String.Double */ +.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/refs/heads/MOP3/_static/searchtools.js b/refs/heads/MOP3/_static/searchtools.js new file mode 100644 index 0000000..2c774d1 --- /dev/null +++ b/refs/heads/MOP3/_static/searchtools.js @@ -0,0 +1,632 @@ +/* + * Sphinx JavaScript utilities for the full-text search. + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/refs/heads/MOP3/_static/sphinx_highlight.js b/refs/heads/MOP3/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/refs/heads/MOP3/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/refs/heads/MOP3/about.html b/refs/heads/MOP3/about.html new file mode 100644 index 0000000..1108b26 --- /dev/null +++ b/refs/heads/MOP3/about.html @@ -0,0 +1,160 @@ + + + + + + + + + About Master of Pores 3 — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

About Master of Pores 3

+ +++++++ + + + + + + + + +

docker

status

license

nver

sing

+

Master of Pores 3 is a collection of pipelines written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc.

+

The software is composed by four pipelines:

+
+
    +

  • mop_preprocess: preprocessing of input data. Basecalling, demultiplexing, alignment, read counts, and more!

    • +

  • mop_mod: detecting chemical modifications. It reads the output directly from mop_preprocess

    • +

  • mop_tail: estimating polyA tail size. It reads the output directly from mop_preprocess

    • +

  • mop_consensus: it generates a consensus from the predictions from mop_mod. It reads the output directly from mop_mod

    • +
+
+

The name is inspired by Metallica’s Master Of Puppets

+_images/goku3.png + +

This is a joint project between CRG bioinformatics core and Epitranscriptomics and RNA Dynamics research group.

+
+

Reference

+

If you use this tool, please cite our papers:

+

“Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores” Cozzuto L, Delgado-Tejedor A, Hermoso Pulido T, Novoa EM, Ponomarenko J. N. Methods Mol Biol. 2023;2624:185-205. doi: 10.1007/978-1-0716-2962-8_13.

+

“MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets” Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva Maria Novoa. Front. Genet., 17 March 2020.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/benchmark.html b/refs/heads/MOP3/benchmark.html new file mode 100644 index 0000000..1072647 --- /dev/null +++ b/refs/heads/MOP3/benchmark.html @@ -0,0 +1,156 @@ + + + + + + + + + Benchmark — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Benchmark

+

We tested MoP on two minION runs using the CRG’s HPC where we can run up to 100 jobs in parallel (maximum 8 CPUs each) and using up to 10 GPU cards (GeForce RTX 2080 Ti). The test dataset was published at ENA with the accession ERR5296640 for pU samples and ERR5303454 for Nm samples.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Dataset

MOP_PREPROCESS

MOP_MOD

MOP_TAIL

MOP_CONSENSUS

Input data

95 Gb

137 Gb

137 Gb

14 Mb

Execution time

10 hours

6 hours

2.5 hours

3 mins

Work folder

382 Gb

595 Gb

3 Gb

25 Mb

Output folder

137 Gb

14 Mb

76 Mb

13 Mb

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/changelog.html b/refs/heads/MOP3/changelog.html new file mode 100644 index 0000000..0228565 --- /dev/null +++ b/refs/heads/MOP3/changelog.html @@ -0,0 +1,213 @@ + + + + + + + + + CHANGELOG — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

CHANGELOG

+
+

Version 3.0

+
    +
  • +
    mop_preprocess
      +

    • We added a custom model for m6A basecalling. It is automatically installed when running INSTALL.sh. For using it you need to indicated ``–pars_tools “drna_tool_splice_m6A_opt.tsv” ``

      • +

    • We add support to cuda11 for guppy version > 4.4.1.

      • +

    • Added readucks for improving demultiplexing with guppy (optional).

      • +

    • New parameter “barcodes” where you can specify a file with barcodes to be kept. Example in keep_barcodes.txt

      • +

    • Adding a new model for direct RNA basecalling.

      • +

    • Added support to dorado basecalling. Not yet supported the demultiplexing

      • +

    • Also guppy version >= 6.5.x are supported. No need for indicating different command lines for different guppy versions inside tool_opts. The pipeline will get the version and act accordingly

      • +

    • pod5 are supported for dorado and guppy >= 6.5.x. No fast5 and stats files will be output. This will limit other pipelines.

      • +
    +
    +
    +
    • +
  • +
    mop_tail
      +

    • we upgraded tailfindR to version 1.3

      • +

    • Tailfinder can be used either in standard mode or nano3p mode (chemistry R10 and R9) by specifying the tailfindr_mode to: standard, n3ps_r9 or n3ps_r10.

      • +
    +
    +
    +
    • +
+
+
+

Version 2.0

+
    +

  • Completely rewritten using the powerful DSL2.

    • +

  • Subworkflows are stored in the independent repository BioNextflow.

    • +

  • Global nextflow config is broken down to different profiles (cluster, cloud, local…)

    • +

  • Added the new module mop_consensus

    • +
  • +
    mop_preprocess (formerly known as nanoPreprocess + nanoPreprocessSimple)
      +

    • now can read multiple runs per time using the syntax “PATH/**/*.fast5”

      • +

    • can demultiplex fast5 using guppy too

      • +

    • deeplexicon can be run on GPU too

      • +

    • Parameters of each tool are stored in a tsv file. We have different ones already pre-set for cDNA, DNA and dRNA (option –pars_tools)

      • +

    • Added new process discovery with bambu / isoquant for discovering and quantifying new transcripts.

      • +

    • demultiplexing, filtering, mapping, counting and discovery can be switched off by setting “NO” as a parameter

      • +

    • saveSpace can be set to “YES” to reduce the amount of disk space required. WARNING This will prevent the possibility to resume!

      • +

    • Merged old NanoPreprocess and NanoPreprocessSimple in mop_preprocess. Using fastq or fast5 will switch among the two executions.

      • +

    • Htseq-count now accepts alignments generated by minimap2. https://github.com/htseq/htseq/issues/33

      • +

    • We can specify a final_summary_.txt** for extracting kit and flowcell info in the params.config file. If not present we should specify those info or a custom model via extra parameters in one of the *_opt.tsv files or guppy will trigger an error.

      • +

    • This module can be run in AWS BATCH using the profile awsbatch

      • +

    • demultiplexing of fast5 with deeplexicon is now faster thanks to multithreading and parallelization

      • +
    +
    +
    +
    • +
  • +
    mop_tail (formerly known as nanoTail)
      +

    • now you can launch each analysis independently

      • +

    • Fine tuning of parameter for each step in tools_opt.tsv

      • +
    +
    +
    +
    • +
  • +
    mop_mod (formerly known as nanoMod)
      +

    • coming SOON!

      • +
    +
    +
    +
    • +
+
+
+

Version 1.1

+
    +

  • Added a new module called NanoPreprocessSimple that starts from fastq files instead of fast5 files. It allows the analysis of multiple files at a time.

    • +

  • Added support to vbz compressed fast5 https://github.com/nanoporetech/vbz_compression in NanoPreprocess, NanoMod and NanoTail

    • +

  • NanoPreprocess now outputs also CRAM files and can do downsampling with the parameter –downsampling

    • +

  • NanoPreprocess allows performing variant calling using medaka (BETA)

    • +

  • NanoPreprocess allows performing demultiplexing with GUPPY

    • +

  • Added plots for Epinano output in NanoMod

    • +

  • Added a conversion of Tombo results in bed format in NanoMod

    • +

  • Added a INSTALL.sh file for automatically retrieve guppy 3.4.5 from https://mirror.oxfordnanoportal.com/, place it in NanoPreprocess/bin and making the required links

    • +

  • Added profiles for being used locally and on the CRG SGE cluster

    • +
+
+
+

Version 1.0

+

This is the original version published in the paper MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/ci.html b/refs/heads/MOP3/ci.html new file mode 100644 index 0000000..59b830c --- /dev/null +++ b/refs/heads/MOP3/ci.html @@ -0,0 +1,128 @@ + + + + + + + + + Continuous integration — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Continuous integration

+

The following pipelines are continuously checked using GitHub actions:

+
    +

  • mop_preprocess

    • +

  • mop_mod

    • +

  • mop_tail

    • +
+pipeline status + +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/genindex.html b/refs/heads/MOP3/genindex.html new file mode 100644 index 0000000..fa2362d --- /dev/null +++ b/refs/heads/MOP3/genindex.html @@ -0,0 +1,116 @@ + + + + + + + + Index — MoP3 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/index.html b/refs/heads/MOP3/index.html new file mode 100644 index 0000000..ea2e95b --- /dev/null +++ b/refs/heads/MOP3/index.html @@ -0,0 +1,146 @@ + + + + + + + + + Welcome to the documentation of Master Of Pores 3 — MoP3 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Welcome to the documentation of Master Of Pores 3

+_images/goku3.png + +

Master of Pores is a pipeline written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc.

+
+
The pipeline is composed by four modules:
    +

  • mop_preprocess: preprocessing

    • +

  • mop_mod: detecting chemical modifications. It reads the output directly from mop_preprocess

    • +

  • mop_tail: estimating polyA tail size. It reads the output directly from mop_preprocess

    • +

  • mop_consensus: it generates a consensus from the predictions from mop_mod. It reads the output directly from mop_mod

    • +
+
+
+

Contents:

+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/install.html b/refs/heads/MOP3/install.html new file mode 100644 index 0000000..6fcdc06 --- /dev/null +++ b/refs/heads/MOP3/install.html @@ -0,0 +1,176 @@ + + + + + + + + + Get Started — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Get Started

+

Please install nextflow Nextflow and either Singularity or Docker before.

+

For installing Nextflow you need a POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and Java 11 (or later, up to 17). Windows system is supported through WSL. For the installation of Nextflow just run:

+
curl -s https://get.nextflow.io | bash
+
+
+

To install the pipeline you need to download the repo:

+
git clone --depth 1 --recurse-submodules https://github.com/biocorecrg/master_of_pores.git
+
+
+
+

Installing Guppy

+

You can use INSTALL.sh and the version of Guppy you want to download.

+
+

Note

+

Please consider that the support of VBZ compression of fast5 started with version 3.4.X.

+
+
cd master_of_pores; bash INSTALL.sh 6.0.1
+
+
+

or for installing the default 3.4.5

+
cd master_of_pores; bash INSTALL.sh
+
+
+

Guppy custom models for RNA basecalling will be downloaded from our repository https://biocore.crg.eu/public/mop3_pub/models.tar and placed automatically within the right path inside the pipeline.

+

You can install different versions of Guppy but only one will be run during the pipeline execution. For switching among them you need to run INSTALL.sh with the version you prefer.

+
+
+

Testing

+
cd mop_preprocess
+
+nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-singularity -bg -profile local > log
+
+
+
+

Tip

+

You can replace `-with-singularity` with `-with-docker` if you want to use the docker engine.

+
+
+
+

Profiles

+

Some nextflow configuration files are stored within the folder conf and can be selected using different profiles. Currently, we have:

+
    +

  • ci: for continuous integration testing (low resources)

    • +

  • local: for being used in a laptop without GPU support

    • +

  • m1mac: for running the containers in emulation for being used on M1/M2/M3 Apple processors.

    • +

  • sge: for being used in an HPC with Sun Grid Engine

    • +

  • cluster or crg: for being used in the custom HPC environment at CRG

    • +

  • slurm: for being used in an HPC with SLURM

    • +

  • awsbatch: for being used in Amazon AWS cloud infrastructure

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/mop_consensus.html b/refs/heads/MOP3/mop_consensus.html new file mode 100644 index 0000000..7200be5 --- /dev/null +++ b/refs/heads/MOP3/mop_consensus.html @@ -0,0 +1,171 @@ + + + + + + + + + MOP_CONSENSUS — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

MOP_CONSENSUS

+

This pipeline takes as input the output from MOP_MOD with all the four worklows. It outputs the consensus of the diferent predictions running the tool Nanoconsensus in parallel on each transcript for each comparison.

+
+

Input Parameters

+

The input parameters are stored in yaml files like the one represented here:

+
input_path: "${projectDir}/../mop_mod/output_mod"
+reference:  "/path/to/reference.fa"
+
+comparison: "comparison.tsv"
+padsize:    50
+output:     "${projectDir}/output"
+
+extraparams: ""
+email: ""
+
+
+
+
+

How to run the pipeline

+

Before launching the pipeline,user should:

+
    +

  1. Decide which containers to use - either docker or singularity [-with-docker / -with-singularity].

    2. +

  2. Fill in both params.config and tools_opt.tsv files.

    3. +
+

To launch the pipeline, please use the following command:

+
nextflow run mop_consensus.nf -params-file params.yaml  -with-singularity > log.txt
+
+
+

You can run the pipeline in the background adding the nextflow parameter -bg:

+
nextflow run mop_consensus.nf -params-file params.yaml -with-singularity -bg > log.txt
+
+
+

You can change the parameters either by changing params.config file or by feeding the parameters via command line:

+
nextflow run mop_consensus.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt
+
+
+

You can specify a different working directory with temporary files:

+
nextflow run mop_consensus.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt
+
+
+
+
+

Results

+

Here an example of a result:

+_images/nanocons.png + +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/mop_mod.html b/refs/heads/MOP3/mop_mod.html new file mode 100644 index 0000000..f97189a --- /dev/null +++ b/refs/heads/MOP3/mop_mod.html @@ -0,0 +1,235 @@ + + + + + + + + + MOP_MOD — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

MOP_MOD

+

This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files and unspliced alignments to the transcriptome . It runs four different RNA detection algorithms (Epinano, Nanopolish, Tombo and Nanocompore) and it outputs the predictions generated by each one of them as individual tab-delimited files.

+mop_mod graph + +
+

Input Parameters

+

The input parameters are stored in yaml files like the one represented here:

+
input_path: "${projectDir}/../mop_preprocess/outfolder/"
+comparison: "${projectDir}/comparison.tsv"
+
+reference: "${projectDir}/../anno/yeast_rRNA_ref.fa.gz"
+output: "${projectDir}/output_mod"
+pars_tools: "${projectDir}/tools_opt.tsv"
+
+# flows
+epinano: "YES"
+nanocompore: "NO"
+tombo_lsc: "YES"
+tombo_msc: "YES"
+modphred: "NO"
+
+# epinano plots
+epinano_plots: "YES"
+email: ""
+
+
+
+
+

How to run the pipeline

+

Before launching the pipeline, user should:

+
    +

  1. Decide which containers to use - either docker or singularity [-with-docker / -with-singularity].

    2. +

  2. Fill in both params.yaml and tools_opt.tsv files.

    3. +

  3. Fill in comparison.tsv file - please see example below:

    4. +
+
wt_1 ko_1
+wt_2 ko_2
+
+
+

To launch the pipeline, please use the following command:

+
nextflow run mop_mod.nf -params-file params.yaml -with-singularity > log.txt
+
+
+

You can run the pipeline in the background adding the nextflow parameter -bg:

+
nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg > log.txt
+
+
+

You can change the parameters either by changing params.config file or by feeding the parameters via command line:

+
nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt
+
+
+

You can specify a different working directory with temporary files:

+
nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt
+
+
+
+
+

Results

+

Several folders are created by the pipeline within the output directory specified by the output parameter:

+
    +

  1. Epinano results are stored in epinano_flow directory. It contains two files per sample: one containing data at position level and the other, at 5-mer level. Different features frequencies as well as quality data are included in the results. See example below:

    2. +
+
#Ref,pos,base,cov,q_mean,q_median,q_std,mis,ins,del
+gene_A,2515,C,45497.0,5.36995,4.00000,3.97797,0.0822032221904741,0.18715519704595907,0.2058377475437941
+gene_A,2516,A,45504.0,5.38207,4.00000,4.71619,0.17128164556962025,0.20497099156118143,0.07733386075949367
+gene_A,2517,C,45529.0,6.92130,5.00000,5.04250,0.06165301236574491,0.1505633771881658,0.13540820136616222
+gene_A,2518,A,45545.0,6.49821,5.00000,5.47485,0.10802503018992206,0.10855198155670216,0.2082775277198375
+gene_A,2519,T,45557.0,6.51247,5.00000,4.81853,0.09386043857145993,0.14792457800118533,0.2033057488421099
+
+
+

Here an example of a plot from Epinano:

+_images/epinano.png + +
    +

  1. Tombo results are stored in tombo_flow directory. It contains one file per comparison. It reports the p-value per position, the sum of p-values per 5-mer and coverage in both WT and KO. See example below:

    2. +
+
"Ref_Position"       "Chr"   "Position"      "Tombo_SiteScore"       "Coverage_Sample"       "Coverage_IVT"  "Tombo_KmerScore"
+"gene_A_3"   "gene_A"        "3"     "0.0000"        "92"    "87"    NA
+"gene_A_4"   "gene_A"        "4"     "0.0000"        "92"    "87"    NA
+"gene_A_5"   "gene_A"        "5"     "0.0000"        "92"    "87"    0
+"gene_A_6"   "gene_A"        "6"     "0.0000"        "93"    "88"    0.0014
+"gene_A_7"   "gene_A"        "7"     "0.0000"        "95"    "89"    0.0027
+"gene_A_8"   "gene_A"        "8"     "0.0014"        "95"    "89"    0.004
+
+
+
    +

  1. Nanopolish results are stored in nanopolish-compore_flow directory. It contains two files per sample: raw eventalign output (gzipped) and another with the median raw current per position and transcript (sample_processed_perpos_median.tsv.gz). See example below:

    2. +
+
contig       position        reference_kmer  read_name       median  coverage
+gene_A       0       AAATT   1       113.35  433
+gene_A       1       AATTG   1       97.24   506
+gene_A       2       ATTGA   1       70.35   2034
+gene_A       3       TTGAA   1       102.03  416
+gene_A       4       TGAAG   1       115.315 422
+gene_A       5       GAAGA   1       104.25  471
+
+
+
    +

  1. Nanocompore results are stored in nanopolish-compore_flow directory. It contains one file per comparison (wt_1_vs_ko_1_nanocompore_results.tsv). Default output from Nanocompore (see Nanocompore’s repository for a more detailed explanation).

    2. +
+
+
+

Encoding of modification information from m6A-aware basecalled data using modPhred

+

Once the data has been basecalled with our m6A modification-aware basecalling model, modification information data should be encoded for its later downstream analysis. This step is performed by modPhred, another software included in the mop_mod module.

+

To run this software, in the params.yaml file you should specify modphred: "YES" and run the code below:

+
cd mop_mod
+nextflow run mop_mod.nf -params-file params.yaml -with-singularity -bg > yourlog.txt
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/mop_preprocess.html b/refs/heads/MOP3/mop_preprocess.html new file mode 100644 index 0000000..d7a8548 --- /dev/null +++ b/refs/heads/MOP3/mop_preprocess.html @@ -0,0 +1,325 @@ + + + + + + + + + MOP_PREPROCESS — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

MOP_PREPROCESS

+

This pipeline takes as input the raw fast5 reads - single or multi - and it produces several outputs (basecalled fast5, sequences in fastq format, aligned reads in BAM format etc). The pre-processing pipeline can perform base-calling, demultiplexing (optional), filtering, quality control, mapping to a reference (either a genome or a transcriptome), feature counting, discovery of novel transcripts, and it generates a final report with the performance and results of each of the steps performed.

+

It automatically detects the kind of input fast5 file (single or multi-sequence). It can also support the new pod5 format but it won’t output basecalled fastq useful for the other pipelines. The basecalling can be performed with guppy or dorado and the demultiplexing with either guppy, seqtagger, or deeplexicon. Basecalled fastq and Fast5 files can be demultiplexed as well. You can restrict the number of barcodes by indicating a file with barcode list using the barcodes parameter.

+mop_preprocess graph + +
+

Input Parameters

+

The input parameters are stored in yaml files like the one represented here:

+

You can change them by editing this file or using the command line as explained in the next section.

+
+

Tip

+

In the case of pod5 as input files, you can use them as they were fast5 with dorado or guppy >= 6.5.x. The only limitation is that you cannot obtain basecalled fast5 so you cannot use the other pipelines that need fast5 as input files.

+
+
+
+

How to run the pipeline

+

Before launching the pipeline, the user can decide which containers to use: either docker or singularity [-with-docker / -with-singularity].

+

Then, to launch the pipeline, please use the following command by specifying the path of the yaml parameter file:

+
nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml > log.txt
+
+
+

You can run the pipeline in the background by adding the nextflow parameter -bg:

+
nextflow run mop_preprocess.nf -params-file params.yaml -with-singularity -bg > log.txt
+
+
+

You can change the parameters either by changing the yaml config file or by feeding the parameters via command line:

+
nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml -bg --output test2 > log.txt
+
+
+

You can specify a different working directory with temporary files:

+
nextflow run mop_preprocess.nf -with-singularity -params-file params.yaml -bg -w /path/working_directory > log.txt
+
+
+

You can use different profiles for running the pipeline in different environments. We have one set up for HPC using the SGE scheduler:

+
nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile cluster > log.txt
+
+
+

One for HPC using the slurm scheduler

+
nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile slurm > log.txt
+
+
+

One for emulating the new M1 processor for Apple:

+
nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile m1mac > log.txt
+
+
+

or you can run the pipeline locally:

+
nextflow run mop_preprocess.nf -with-singularity -bg -params-file params.yaml -w /path/working_directory -profile local > log.txt
+
+
+
+

Note

+
    +

  • In case of errors you can troubleshoot by seeing the log file (log.txt) for more details. Furthermore, if more information is needed, you can also go to the intermediate directory indicated in the log and check both the .command.log and .command.err files.

    • +
+
+
+

Tip

+

Once the error has been solved or if you change a specific parameter, you can resume the execution with the Netxtlow parameter - resume (only one dash!). If there is an error, the pipeline will resume from the process that had the error and proceed with the rest. If you change a parameter, only the processes affected by this parameter will be re-run.

+
+
...
+
+[warm up] executor > crg
+[9d/82eeaa] Cached process > checkRef (Checking yeast_rRNA_ref.fa.gz)
+[33/b8d053] Submitted process > BASECALL:GUPPY_VERSION:getVersion
+[e5/e5c990] Submitted process > BASECALL:GUPPY65_BASECALL:baseCallNew (mod---2)
+[b5/0997da] Submitted process > BASECALL:GUPPY65_BASECALL:baseCallNew (wt---1)
+[fb/6353d6] Submitted process > SEQFILTER:NANOQ_FILTER:filter (mod---2)
+...
+
+
+
+

Note

+

To resume the execution, temporary files generated previously by the pipeline must be kept. Otherwise, the pipeline will re-start from the beginning.

+
+
+
+

tool_opts

+

The command line options for each tool used in the pipeline are stored within specialized tsv files stored within the tool_opts folder. Here is an example:

+
#step	tool	extrapars
+basecalling	dorado	"rna002_70bps_hac@v3"
+basecalling	guppy	"-c rna_r9.4.1_70bps_m6A_hac.cfg"
+demultiplexing	deeplexicon	""
+demultiplexing	guppy	""
+demultiplexing	seqtagger	""
+filtering	nanofilt	""
+filtering	nanoq	""
+mapping	graphmap	""
+mapping	graphmap2	"-x rnaseq"
+mapping	minimap2	"-uf -ax splice -k14"
+mapping	bwa	""
+counting	htseq	"-a 0"
+counting	nanocount	""
+discovery	bambu	""
+
+
+

The first column indicates the processing step as basecalling or demultiplexing etc. Some tools such as Guppy can be used for more processing steps. Several pre-compiled tool_opts files are stored within the folder tool_opts.

+
+

Note

+

Readucks is run after guppy demultiplexing. It refines the demultiplexing generating different fastqs

+
+
+

Tip

+

You don’t need to specify the whole path for the models of seqtagger, just the name of the model will be enough

+
+
+
+

Model libraries for specific tools

+

The following folders are available for the respective tools. Some models are already pre-installed-

+
    +
  • +
    deeplexicon_models
      +

    • resnet20-final.h5

      • +

    • pAmps-final-actrun_newdata_nanopore_UResNet20v2_model.030.h5

      • +

    • pAmps-rep2-4-train1_newdata_nanopore_UResNet20v2_model.039.h5

      • +
    +
    +
    +
    • +
  • +
    dorado_models
    +
    +
    +
    • +
  • +
    seqtagger_models
      +

    • b04_RNA002

      • +

    • b04_RNA004

      • +
    +
    +
    +
    • +
+
+

Note

+

You need to download the models you want to use in case they are not already available. For instance, if you need another model for dorado you need to do:

+
+
dorado download --model MODELNAME
+
+
+

You also need to add the dedicated parameter within the tool_opts file for the specific tool as:

+
basecalling dorado   "rna002_70bps_hac@v3"
+demultiplexing       seqtagger   "-k b100"
+demultiplexing       deeplexicon   "-f multi -m resnet20-final.h5"
+
+
+
+

Note

+

You need to copy the model in the corresponding folder and indicate just the model name. You don’t need the absolute path.

+
+
+
+

Barcodes

+

You can select the barcodes you are interested in by writing them down in a text file as in this example. The format is samplename—barcodeID

+
anna---bc_104
+anna---bc_102
+
+
+

The sample id is given by either the folder containing the fast5 files or the basename of the fastq files. So, if your files are in a folder named myfiles, it will be:

+
myfiles---bc_1
+myfiles---bc_2
+myfiles---bc_3
+
+
+
+

Note

+

The naming convention of the different barcodes is decided by each tool, so guppy will produce barcode01, barcode02, while seqtagger will produce bc_1, bc_2, etc.

+
+
+
+

Basecalling with the m6A-aware model

+

For m6A basecalling in your params.f5.yaml file you should specify basecalling: "guppy" and pars_tools: "tool_opts/drna_tool_m6A_splice_opt.tsv" `` so that guppy will use the m6A model. In your output folder you will have the ``fast5_files folder containing the m6A basecalled fast5 files for downstream analysis. Then run:

+
cd mop_preprocess
+nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-singularity -bg > yourlog.txt
+
+
+
+
+

Results

+

Several folders are created by the pipeline within the output directory specified by the output parameter:

+
    +

  • fast5_files: Contains the basecalled multifast5 files. Each batch contains 4000 sequences.

    • +

  • fastq_files: Contains one or, in case of demultiplexing, more fastq files.

    • +

  • QC_files: Contains each single QC produced by the pipeline.

    • +

  • alignment: Contains the bam file(s).

    • +

  • cram_files: Contains the cram file(s).

    • +

  • counts: Contains read counts per gene / transcript if counting was performed.

    • +

  • assigned: Contains assignment of each read to a given gene / transcript if counting was performed.

    • +

  • report: Contains the final multiqc report.

    • +

  • assembly: It contains assembled transcripts.

    • +
+
+

Note

+

MOP3 will automatically detect the version of guppy and modify the parameters accordingly. You don’t need to add any extra parameter as in MOP2.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/mop_tail.html b/refs/heads/MOP3/mop_tail.html new file mode 100644 index 0000000..32b7e0d --- /dev/null +++ b/refs/heads/MOP3/mop_tail.html @@ -0,0 +1,192 @@ + + + + + + + + + MOP_TAIL — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

MOP_TAIL

+

This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files, alignment and assignment read ID to gene/transcript. It outputs the estimation of poly(A) tail length at read level provided by Tailfindr, Nanopolish or both. Tailfinr can be run using three modes: standard, for Nano3P-seq protocol with R9 chemistry and Nano3P-seq protocol with R10 chemistry.

+mop_tail graph + +
+

Input Parameters

+

The input parameters are stored in yaml files like the one represented here:

+
input_path: "${projectDir}/../mop_preprocess/outfolder/"
+reference: "${projectDir}/../anno/yeast_rRNA_ref.fa.gz"
+
+pars_tools: "${projectDir}/tools_opt.tsv"
+
+output: "${projectDir}/outputPoly"
+
+tailfindr: "YES"
+
+# Different modes: standard, n3ps_r9 or n3ps_r10
+tailfindr_mode: "standard"
+
+nanopolish: "YES"
+
+email: "yourname@yourdomain"
+
+
+
+
+

How to run the pipeline

+

Before launching the pipeline,user should:

+
    +

  1. Decide which containers to use - either docker or singularity [-with-docker / -with-singularity].

    2. +

  2. Fill in both params.config and tools_opt.tsv files.

    3. +
+

To launch the pipeline, please use the following command:

+
nextflow run mop_tail.nf -params-file params.yaml  -with-singularity > log.txt
+
+
+

You can run the pipeline in the background adding the nextflow parameter -bg:

+
nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg > log.txt
+
+
+

You can change the parameters either by changing params.config file or by feeding the parameters via command line:

+
nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt
+
+
+

You can specify a different working directory with temporary files:

+
nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt
+
+
+
+
+

Results

+

Several folders are created by the pipeline within the output directory specified by the output parameter:

+
    +

  1. NanoPolish: contains the output of nanopolish tool.

    2. +

  2. Tailfindr: contains the output of tailfindr tool.

    3. +

  3. PolyA_final: contains the txt files with the combined results (i.e. predicted polyA sizes). Here an example of a test:

    4. +
+
"Read name"  "Tailfindr"     "Nanopolish"    "Gene Name"
+"013a5dde-9c52-4de1-83eb-db70fb2cd130"       52.16   49.39   "YKR072C"
+"01119f62-ca68-458d-aa1f-cf8c8c04cd3b"       231.64  274.28  "YDR133C"
+"0154ce9c-fe6b-4ebc-bbb1-517fdc524207"       24.05   24.24   "YFL044C"
+"020cde28-970d-4710-90a5-977e4b4bbc46"       41.27   56.79   "YGL238W"
+
+
+

If both programs are run, an additional plot that shows the correlation of their results is generated.

+_images/mod_corr.png + +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/objects.inv b/refs/heads/MOP3/objects.inv new file mode 100644 index 0000000..570545a Binary files /dev/null and b/refs/heads/MOP3/objects.inv differ diff --git a/refs/heads/MOP3/reporting.html b/refs/heads/MOP3/reporting.html new file mode 100644 index 0000000..86763fa --- /dev/null +++ b/refs/heads/MOP3/reporting.html @@ -0,0 +1,162 @@ + + + + + + + + + Resource reporting — MoP3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Resource reporting

+

Since each MOP pipeline is based on Nextflow we can use its embedded functions for reporting the use of resources as a html file and to have a live reporting.

+
+

Html report

+

For enabling the generation of a report just run each pipeline with the parameter -with-report as in the following example:

+
nextflow run mop_preprocess.nf -profile local -with-docker -bg -with-report
+
+
+

Once the pipeline is finished you will have a comprehensive report with information about CPU, disk and memory usage for each execution and as a distribution for each process. Here an example:

+_images/res_report.png + +
+
+

Live reporting

+

For having a live reporting your pipeline should run in an environment that has access to internet. Then you have to log-in to the Tower.nf website that is developed and mantained by the good people at Seqera Labs.

+_images/tower.png + +

We suggest you to use either the GitHub or the Google authentication:

+_images/tower_eli1.png + +

You can generate your token at https://tower.nf/tokens and

+_images/tower2.png + +

then you can export as an environmental variable.

+
export TOWER_ACCESS_TOKEN=*******YOUR***TOKEN*****HERE*******
+
+
+
+

Tip

+

We recommend you to add this line to either your .bashrc or .bash_profile file.

+
+

Finally we can then launch the pipeline adding the parameter -with-tower.

+
nextflow run mop_preprocess.nf -profile local -with-docker -bg -with-tower
+
+
+

Going back to the website you can see now your pipeline running and have a nice looking live reporting.

+_images/tower.gif + +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refs/heads/MOP3/search.html b/refs/heads/MOP3/search.html new file mode 100644 index 0000000..49ea0b7 --- /dev/null +++ b/refs/heads/MOP3/search.html @@ -0,0 +1,131 @@ + + + + + + + + Search — MoP3 documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/refs/heads/MOP3/searchindex.js b/refs/heads/MOP3/searchindex.js new file mode 100644 index 0000000..eb7dd38 --- /dev/null +++ b/refs/heads/MOP3/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"About Master of Pores 3": [[0, null]], "Barcodes": [[8, "barcodes"]], "Basecalling with the m6A-aware model": [[8, "basecalling-with-the-m6a-aware-model"]], "Benchmark": [[1, null]], "CHANGELOG": [[2, null]], "Continuous integration": [[3, null]], "Dataset": [[1, "id1"]], "Demultiplexing with Guppy": [[11, "demultiplexing-with-guppy"]], "Encoding of modification information from m6A-aware basecalled data using modPhred": [[7, "encoding-of-modification-information-from-m6a-aware-basecalled-data-using-modphred"]], "Get Started": [[5, null]], "How to run the pipeline": [[6, "how-to-run-the-pipeline"], [7, "how-to-run-the-pipeline"], [8, "how-to-run-the-pipeline"], [9, "how-to-run-the-pipeline"]], "Html report": [[10, "html-report"]], "Input Parameters": [[6, "input-parameters"], [7, "input-parameters"], [8, "input-parameters"], [9, "input-parameters"]], "Installing Guppy": [[5, "installing-guppy"]], "Live reporting": [[10, "live-reporting"]], "MOP_CONSENSUS": [[6, null]], "MOP_MOD": [[7, null]], "MOP_PREPROCESS": [[8, null]], "MOP_TAIL": [[9, null]], "Memory failures in mop_preprocess and mop_mod": [[11, "memory-failures-in-mop-preprocess-and-mop-mod"]], "Model libraries for specific tools": [[8, "model-libraries-for-specific-tools"]], "Profiles": [[5, "profiles"]], "Reference": [[0, "reference"]], "Resource reporting": [[10, null]], "Results": [[6, "results"], [7, "results"], [8, "results"], [9, "results"]], "Testing": [[5, "testing"]], "Troubleshooting": [[11, null]], "Version 1.0": [[2, "version-1-0"]], "Version 1.1": [[2, "version-1-1"]], "Version 2.0": [[2, "version-2-0"]], "Version 3.0": [[2, "version-3-0"]], "Welcome to the documentation of Master Of Pores 3": [[4, null]], "tool_opts": [[8, "tool-opts"]]}, "docnames": ["about", "benchmark", "changelog", "ci", "index", "install", "mop_consensus", "mop_mod", "mop_preprocess", "mop_tail", "reporting", "troubleshooting"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.rst", "benchmark.rst", "changelog.rst", "ci.rst", "index.rst", "install.rst", "mop_consensus.rst", "mop_mod.rst", "mop_preprocess.rst", "mop_tail.rst", "reporting.rst", "troubleshooting.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [0, 1, 5, 7, 8, 11], "0": [5, 7, 8, 11], "0000": 7, "00000": 7, "0014": 7, "0027": 7, "004": 7, "01119f62": 9, "013a5dd": 9, "0154ce9c": 9, "020cde28": 9, "03": 7, "030": 8, "039": 8, "04250": 7, "05": 9, "06": 11, "06165301236574491": 7, "0716": 0, "07733386075949367": 7, "0822032221904741": 7, "09386043857145993": 7, "0997da": 8, "1": [0, 5, 7, 8], "10": [0, 1, 11], "100": [1, 11], "1007": 0, "102": 7, "104": 7, "10802503018992206": 7, "10855198155670216": 7, "11": 5, "113": 7, "115": 7, "13": 1, "13540820136616222": 7, "137": 1, "14": 1, "14792457800118533": 7, "1505633771881658": 7, "159196780": 11, "16": 9, "17": [0, 5], "17128164556962025": 7, "185": 0, "18715519704595907": 7, "1_70bps_m6a_hac": 8, "2": [1, 5, 7, 8], "20": 11, "2020": 0, "2023": 0, "2033057488421099": 7, "2034": 7, "20497099156118143": 7, "205": 0, "2058377475437941": 7, "2080": 1, "2082775277198375": 7, "231": 9, "24": [7, 9, 11], "25": [1, 7], "2515": [7, 11], "2516": 7, "2517": 7, "2518": 7, "2519": 7, "2624": 0, "27": 9, "274": 9, "28": 9, "2962": 0, "3": [1, 5, 7], "30": 11, "315": 7, "32995": 11, "33": [2, 8], "35": 7, "36995": 7, "382": 1, "38207": 7, "39": 9, "4": [2, 5, 7, 8, 11], "40": 11, "4000": 8, "41": 9, "416": 7, "422": 7, "433": 7, "45497": 7, "45504": 7, "45529": 7, "45545": 7, "45557": 7, "458d": 9, "471": 7, "4710": 9, "47485": 7, "49": 9, "49821": 7, "4de1": 9, "4ebc": 9, "5": [1, 2, 5, 7, 8], "50": [6, 11], "506": 7, "51247": 7, "517fdc524207": 9, "52": 9, "56": 9, "595": 1, "6": [1, 2, 5, 7, 8], "60": 11, "6353d6": 8, "64": 9, "7": 7, "70": [7, 11], "71619": 7, "76": 1, "79": 9, "8": [1, 7], "80": 11, "81853": 7, "82488e": 11, "82eeaa": 8, "83eb": 9, "87": 7, "88": 7, "89": 7, "8_13": 0, "90": 11, "90a5": 9, "92": 7, "92130": 7, "93": 7, "95": [1, 7], "97": 7, "970d": 9, "97797": 7, "977e4b4bbc46": 9, "978": 0, "9c52": 9, "9d": 8, "A": [0, 2, 7, 9], "For": [2, 5, 8, 10], "If": [0, 2, 8, 9], "In": 8, "It": [0, 2, 4, 5, 6, 7, 8, 9, 11], "NO": [2, 7], "No": [2, 11], "Not": 2, "Of": 0, "One": 8, "The": [0, 1, 2, 3, 4, 6, 7, 8, 9], "Then": [8, 10], "To": [5, 6, 7, 8, 9], "_opt": 2, "_out": 11, "aa1f": 9, "aaatt": 7, "aattg": 7, "about": [4, 10], "absolut": 8, "accept": 2, "access": [1, 10], "accordingli": [2, 8], "act": 2, "action": 3, "actrun_newdata_nanopore_uresnet20v2_model": 8, "ad": [2, 6, 7, 8, 9, 10], "add": [2, 8, 10], "addit": 9, "affect": 8, "after": 8, "algorithm": 7, "align": [0, 2, 7, 8, 9], "all": 6, "allow": 2, "alreadi": [2, 8], "also": [2, 8], "alwai": 11, "amazon": 5, "among": [2, 5], "amount": 2, "an": [2, 5, 6, 7, 8, 9, 10], "analysi": [0, 2, 4, 7, 8], "ani": [8, 11], "anna": [0, 8], "anno": [7, 9], "anoth": [7, 8], "appl": [5, 8], "ar": [2, 3, 5, 6, 7, 8, 9], "assembl": 8, "assembli": 8, "assign": [8, 9], "attga": 7, "authent": 10, "automat": [2, 5, 8], "avail": 8, "aw": [2, 5], "awsbatch": [2, 5], "ax": 8, "b04_rna002": 8, "b04_rna004": 8, "b100": 8, "b5": 8, "b8d053": 8, "back": 10, "background": [6, 7, 8, 9], "bam": 8, "bambu": [2, 8], "barcod": [2, 11], "barcode01": 8, "barcode02": 8, "barcode_kit": 11, "barcodeid": 8, "base": [7, 8, 10], "basecal": [0, 2, 5, 9, 11], "basecallnew": 8, "basenam": 8, "bash": 5, "bash_profil": 10, "bashrc": 10, "batch": [2, 8], "bbb1": 9, "bc_1": 8, "bc_102": 8, "bc_104": 8, "bc_2": 8, "bc_3": 8, "becaus": 11, "bed": 2, "been": [7, 8], "befor": [5, 6, 7, 8, 9], "begin": 8, "being": [2, 5], "below": 7, "benchmark": 4, "beta": 2, "between": 0, "bg": [5, 6, 7, 8, 9, 10], "bin": 2, "biocor": 5, "biocorecrg": 5, "bioinformat": 0, "biol": 0, "bionextflow": 2, "both": [6, 7, 8, 9], "broken": 2, "bwa": 8, "c": [7, 8], "ca68": 9, "cach": 8, "call": [2, 8, 11], "caller": 11, "can": [0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11], "cannot": [8, 11], "card": 1, "case": 8, "cd": [5, 7, 8], "cdna": 2, "cdnaseq": [0, 4], "cf8c8c04cd3b": 9, "cfg": 8, "chang": [6, 7, 8, 9], "changelog": 4, "check": [3, 8, 11], "checkref": 8, "chemic": [0, 4], "chemistri": [2, 9], "chr": 7, "ci": 5, "cite": 0, "clone": 5, "cloud": [2, 5], "cluster": [2, 5, 8], "code": 7, "collect": 0, "column": 8, "com": [2, 5], "combin": 9, "come": 2, "command": [2, 6, 7, 8, 9, 11], "comparison": [6, 7], "compat": 5, "compil": 8, "complet": [2, 11], "compore_flow": 7, "compos": [0, 4], "comprehens": 10, "compress": [2, 5], "conf": 5, "config": [2, 6, 7, 8, 9], "configur": 5, "consensu": [0, 4, 6], "consid": 5, "contain": [5, 6, 7, 8, 9, 11], "content": 4, "contig": 7, "continu": [4, 5], "control": 8, "convent": 8, "convers": 2, "copi": 8, "core": 0, "correl": 9, "correspond": 8, "count": [0, 2, 8], "cov": 7, "coverag": 7, "coverage_ivt": 7, "coverage_sampl": 7, "cozzuto": 0, "cpu": [1, 10], "cram": [2, 8], "cram_fil": 8, "creat": [7, 8, 9], "crg": [0, 1, 2, 5, 8], "cuda11": 2, "curl": 5, "current": [5, 7], "custom": [2, 5], "dash": 8, "data": [0, 1, 4, 11], "dataset": [0, 2], "db70fb2cd130": 9, "decid": [6, 7, 8, 9], "dedic": 8, "deeplexicon": [2, 8], "deeplexicon_model": 8, "default": [5, 7], "del": 7, "delgado": 0, "delimit": 7, "demultiplex": [0, 2, 8], "depth": 5, "detail": [7, 8], "detect": [0, 4, 7, 8], "develop": 10, "difer": 6, "differ": [2, 5, 6, 7, 8, 9], "direct": [0, 2, 4], "directli": [0, 4], "directori": [6, 7, 8, 9, 11], "discov": 2, "discoveri": [2, 8], "disk": [2, 10], "distribut": 10, "dna": 2, "dnaseq": [0, 4], "do": [2, 8], "docker": [5, 6, 7, 8, 9, 10], "doi": 0, "don": 8, "dorado": [2, 8], "dorado_model": 8, "doubl": 11, "down": [2, 8], "download": [5, 8], "downsampl": 2, "downstream": [7, 8], "drna": 2, "drna_tool_m6a_splice_opt": 8, "drna_tool_splice_m6a_opt": 2, "dsl2": [0, 2, 4], "dure": 5, "dynam": 0, "e": 9, "e5": 8, "e5c990": 8, "each": [1, 2, 6, 7, 8, 10], "edit": 8, "either": [2, 5, 6, 7, 8, 9, 10, 11], "em": 0, "email": [6, 7, 9], "embed": 10, "emul": [5, 8], "ena": 1, "enabl": 10, "engin": 5, "enough": 8, "environ": [5, 8, 10], "environment": 10, "epinano": [2, 7, 11], "epinano_flow": 7, "epinano_plot": 7, "epitranscriptom": 0, "err": 8, "err5296640": 1, "err5303454": 1, "error": [2, 8, 11], "estim": [0, 4, 9], "etc": [0, 4, 5, 8], "eu": 5, "eva": 0, "eventalign": 7, "eventu": 11, "exampl": [2, 6, 7, 8, 9, 10, 11], "execut": [1, 2, 5, 8, 10], "executor": 8, "explain": 8, "explan": 7, "export": 10, "extra": [2, 8], "extract": 2, "extrapar": 8, "extraparam": 6, "f": 8, "f5": [5, 8], "fa": [6, 7, 8, 9], "fast5": [2, 5, 7, 8, 9], "fast5_fil": 8, "faster": 2, "fastq": [2, 7, 8, 9, 11], "fastq_fil": 8, "fastqc": 11, "fb": 8, "fe6b": 9, "featur": [7, 8], "feed": [6, 7, 8, 9], "file": [2, 5, 6, 7, 8, 9, 10, 11], "fill": [6, 7, 9], "filter": [2, 8, 11], "final": [8, 10], "final_summary_": 2, "fine": 2, "finish": [10, 11], "first": 8, "flo": 11, "flow": 7, "flowcel": [2, 11], "folder": [1, 5, 7, 8, 9], "follow": [3, 6, 7, 8, 9, 10], "format": [2, 8], "formerli": 2, "four": [0, 4, 6, 7], "frequenc": 7, "from": [0, 2, 4, 5, 6, 8, 9], "front": 0, "function": 10, "furthermor": 8, "gaaga": 7, "gb": 1, "geforc": 1, "gene": [8, 9], "gene_a": 7, "gene_a_3": 7, "gene_a_4": 7, "gene_a_5": 7, "gene_a_6": 7, "gene_a_7": 7, "gene_a_8": 7, "gener": [0, 2, 4, 7, 8, 9, 10], "genet": 0, "genom": 8, "get": [2, 4], "getvers": 8, "git": 5, "github": [2, 3, 5, 10], "given": 8, "global": 2, "go": [8, 10], "good": [10, 11], "googl": 10, "gpu": [1, 2, 5], "graphmap": 8, "graphmap2": 8, "grid": 5, "group": 0, "guppi": [2, 8], "guppy65_basecal": 8, "guppy_vers": 8, "gz": [7, 8, 9], "gzip": 7, "h5": 8, "ha": [7, 8, 10], "had": 8, "handl": [0, 4], "have": [2, 5, 8, 10], "here": [6, 7, 8, 9, 10], "hermoso": 0, "hour": 1, "hpc": [1, 5, 8], "htseq": [2, 8], "http": [2, 5, 10], "huanl": 0, "i": [0, 2, 4, 5, 7, 8, 9, 10, 11], "id": [8, 9], "idea": 11, "improv": 2, "includ": 7, "independ": 2, "indic": [2, 8, 11], "individu": 7, "info": 2, "inform": [8, 10], "infrastructur": 5, "init": 11, "input": [0, 1, 11], "input_path": [6, 7, 9], "ins": 7, "insid": [2, 5], "inspir": 0, "instal": [2, 8], "instanc": 8, "instead": 2, "integr": [4, 5], "interest": 8, "intermedi": 8, "internet": 10, "io": 5, "isoqu": 2, "issu": 2, "its": [7, 10], "j": 0, "java": 5, "job": 1, "joint": 0, "julia": 0, "just": [5, 8, 10], "k": 8, "k14": 8, "keep_barcod": 2, "kept": [2, 8], "kind": 8, "kit": [2, 11], "known": 2, "ko": 7, "ko_1": 7, "ko_2": 7, "l": 0, "lab": 10, "laptop": 5, "later": [5, 7], "launch": [2, 6, 7, 8, 9, 10], "length": 9, "leszek": 0, "level": [7, 9], "like": [6, 7, 8, 9], "limit": [2, 8], "line": [2, 6, 7, 8, 9, 10], "link": 2, "linux": 5, "list": 8, "liu": 0, "local": [2, 5, 8, 10], "log": [5, 6, 7, 8, 9, 10], "look": 10, "low": [5, 11], "lsk114": 11, "luca": 0, "m": [8, 11], "m1": [5, 8], "m1mac": [5, 8], "m2": 5, "m3": 5, "m6a": 2, "make": 2, "mantain": 10, "map": [2, 8], "march": 0, "maria": 0, "master_of_por": 5, "masterofpor": [0, 2], "maximum": 1, "mb": 1, "medaka": 2, "median": 7, "memori": 10, "mer": 7, "merg": 2, "metallica": 0, "method": 0, "mi": 7, "min": 1, "min114": 11, "minimap2": [2, 8], "minion": 1, "mirror": 2, "mod": 8, "mode": [2, 9], "model": [2, 5, 7], "modelnam": 8, "modif": [0, 4], "modifi": 8, "modul": [2, 4, 7], "mol": 0, "mop": [1, 10], "mop2": 8, "mop3": 8, "mop3_pub": 5, "mop_consensu": [0, 1, 2, 4], "mop_mod": [0, 1, 2, 3, 4, 6], "mop_preprocess": [0, 1, 2, 3, 4, 5, 7, 9, 10], "mop_tail": [0, 1, 2, 3, 4], "more": [0, 7, 8], "multi": 8, "multifast5": 8, "multipl": 2, "multiqc": 8, "multithread": 2, "must": [8, 11], "myfil": 8, "n": 0, "n3ps_r10": [2, 9], "n3ps_r9": [2, 9], "na": 7, "name": [0, 8, 9], "nano3p": [2, 9], "nanocompor": 7, "nanoconsensu": 6, "nanocount": 8, "nanofilt": [8, 11], "nanomod": 2, "nanopolish": [7, 9], "nanopor": [0, 2, 4], "nanoporetech": 2, "nanopreprocess": 2, "nanopreprocesssimpl": 2, "nanoq": [8, 11], "nanoq_filt": 8, "nanotail": 2, "nbd114": 11, "need": [2, 5, 8], "netxtlow": 8, "new": [2, 8], "next": 8, "nextflow": [0, 2, 4, 5, 6, 7, 8, 9, 10], "nf": [5, 6, 7, 8, 9, 10], "nice": 10, "nm": 1, "novel": 8, "novoa": 0, "now": [2, 10], "number": 8, "o": 5, "obtain": 8, "off": 2, "old": 2, "onc": [7, 8, 10], "one": [2, 5, 6, 7, 8, 9], "ones": 2, "onli": [5, 8], "open": 11, "option": [2, 8], "origin": 2, "other": [2, 7, 8, 11], "otherwis": 8, "our": [0, 5, 7], "out": 11, "outfold": [7, 9], "output": [0, 1, 2, 4, 6, 7, 8, 9, 11], "output_mod": [6, 7], "outputpoli": 9, "oxford": [0, 2], "oxfordnanoport": 2, "p": [0, 7], "padsiz": 6, "pamp": 8, "paper": [0, 2], "parallel": [1, 2, 6], "param": [2, 5, 6, 7, 8, 9], "paramet": [2, 10], "pars_tool": [2, 7, 8, 9], "path": [2, 5, 6, 7, 8, 9], "peopl": 10, "per": [2, 7, 8, 11], "perform": [2, 7, 8], "pipelin": [0, 2, 3, 4, 5, 10], "place": [2, 5], "pleas": [0, 5, 6, 7, 8, 9], "plot": [2, 7, 9], "po": 7, "pod5": [2, 8], "poli": 9, "polya": [0, 4, 9], "polya_fin": 9, "ponomarenko": 0, "posit": 7, "posix": 5, "possibl": 2, "power": 2, "pre": [2, 8], "predict": [0, 4, 6, 7, 9], "prefer": 5, "preprocess": [0, 4], "present": 2, "prevent": 2, "previous": 8, "proce": 8, "process": [0, 2, 8, 10], "processor": [5, 8], "produc": 8, "profil": [2, 8, 10], "program": 9, "project": 0, "projectdir": [6, 7, 9], "protocol": 9, "provid": 9, "pryszcz": 0, "pu": 1, "public": 5, "publish": [1, 2], "pulido": 0, "puppet": 0, "q_mean": 7, "q_median": 7, "q_std": 7, "qc": 8, "qc_file": 8, "qualiti": [7, 8, 11], "quantifi": 2, "r10": [2, 9], "r9": [2, 9], "raw": [7, 8], "re": 8, "read": [0, 2, 4, 7, 8, 9, 11], "read_nam": 7, "readuck": [2, 8], "recommend": 10, "recurs": 5, "reduc": 2, "ref": 7, "ref_posit": 7, "refer": [6, 7, 8, 9], "reference_km": 7, "refin": 8, "remov": 11, "rep2": 8, "replac": 5, "repo": 5, "report": [4, 7, 8], "repositori": [2, 5, 7], "repres": [6, 7, 8, 9], "requir": [2, 5], "research": 0, "resnet20": 8, "resourc": [4, 5], "respect": [7, 8, 9], "rest": 8, "restrict": 8, "result": 2, "resum": [2, 8], "retriev": 2, "rewritten": 2, "right": 5, "rm": 11, "rna": [0, 2, 5, 7], "rna002_70bps_hac": 8, "rna_r9": 8, "rnaseq": [0, 4, 8], "row": 11, "rtx": 1, "run": [1, 2, 5, 10, 11], "sampl": [1, 7, 8, 11], "sample_processed_perpos_median": 7, "samplenam": 8, "savespac": 2, "schedul": 8, "section": 8, "see": [7, 8, 10], "select": [5, 8], "seq": 9, "seqera": 10, "seqfilt": 8, "seqtagg": 8, "seqtagger_model": 8, "sequenc": [0, 2, 8], "set": [2, 8], "sever": [7, 8, 9], "sge": [2, 5, 8], "sh": [2, 5], "should": [2, 6, 7, 8, 9, 10], "show": 9, "sinc": 10, "singl": 8, "singular": [5, 6, 7, 8, 9], "size": [0, 4, 9, 11], "slurm": [5, 8], "so": 8, "softwar": [0, 7], "solut": 11, "solv": 8, "some": [5, 8], "sometim": 11, "soon": 2, "space": 2, "special": 8, "specifi": [2, 6, 7, 8, 9], "splice": 8, "sqk": 11, "standard": [2, 9], "start": [2, 4, 8], "stat": 2, "step": [2, 7, 8], "store": [2, 5, 6, 7, 8, 9], "submit": 8, "submodul": 5, "subworkflow": 2, "successfulli": 11, "suggest": 10, "sum": 7, "sun": 5, "support": [2, 5, 8], "switch": [2, 5], "syntax": 2, "system": 5, "t": [0, 7, 8], "tab": 7, "tail": [0, 4, 9], "tailfind": 2, "tailfindr": [2, 9], "tailfindr_mod": [2, 9], "tailfinr": 9, "take": [6, 7, 8, 9], "tar": 5, "tejedor": 0, "temporari": [6, 7, 8, 9], "test": [1, 9], "test2": [6, 7, 8, 9], "text": 8, "tgaag": 7, "thank": 2, "thei": 8, "them": [5, 7, 8, 11], "thi": [0, 2, 6, 7, 8, 9, 10], "those": 2, "three": 9, "through": 5, "ti": 1, "time": [1, 2, 11], "togeth": [7, 9], "token": 10, "tombo": [2, 7], "tombo_flow": 7, "tombo_kmerscor": 7, "tombo_lsc": 7, "tombo_msc": 7, "tombo_sitescor": 7, "toni": 0, "too": 2, "tool": [0, 2, 6, 9, 11], "tool_opt": [2, 11], "tools_opt": [2, 6, 7, 9], "tower": 10, "tower_access_token": 10, "train1_newdata_nanopore_uresnet20v2_model": 8, "transcript": [2, 6, 7, 8, 9], "transcriptom": [7, 8], "trigger": 2, "troubleshoot": [4, 8], "tsv": [2, 6, 7, 8, 9], "ttgaa": 7, "tune": 2, "two": [1, 2, 7], "txt": [2, 6, 7, 8, 9], "uf": 8, "unsplic": 7, "up": [1, 5, 8, 11], "upgrad": 2, "us": [0, 1, 2, 3, 5, 6, 8, 9, 10, 11], "usag": 10, "user": [6, 7, 8, 9], "v3": 8, "valu": 7, "variabl": 10, "variant": 2, "vbz": [2, 5], "vbz_compress": 2, "version": [5, 8], "via": [2, 6, 7, 8, 9], "w": [6, 7, 8, 9], "wa": [1, 8], "want": [5, 8], "warm": 8, "warn": 2, "we": [1, 2, 5, 8, 10], "websit": 10, "well": [7, 8], "were": 8, "when": 2, "where": [1, 2], "which": [6, 7, 8, 9], "while": 8, "whole": 8, "window": 5, "within": [5, 7, 8, 9], "without": 5, "won": 8, "work": [1, 6, 7, 8, 9], "workflow": [0, 2], "working_directori": [6, 7, 8, 9], "worklow": 6, "write": 8, "written": [0, 4], "wsl": 5, "wt": [7, 8], "wt_1": 7, "wt_1_vs_ko_1_nanocompore_result": 7, "wt_2": 7, "x": [2, 5, 8], "yaml": [5, 6, 7, 8, 9], "ydr133c": 9, "ye": [2, 7, 9], "yeast_rrna_ref": [7, 8, 9], "yet": 2, "yfl044c": 9, "ygl238w": 9, "ykr072c": 9, "you": [0, 2, 5, 6, 7, 8, 9, 10, 11], "your": [8, 10, 11], "yourdomain": 9, "yourlog": [7, 8], "yournam": 9}, "titles": ["About Master of Pores 3", "Benchmark", "CHANGELOG", "Continuous integration", "Welcome to the documentation of Master Of Pores 3", "Get Started", "MOP_CONSENSUS", "MOP_MOD", "MOP_PREPROCESS", "MOP_TAIL", "Resource reporting", "Troubleshooting"], "titleterms": {"0": 2, "1": 2, "2": 2, "3": [0, 2, 4], "Of": 4, "about": 0, "awar": [7, 8], "barcod": 8, "basecal": [7, 8], "benchmark": 1, "changelog": 2, "continu": 3, "data": 7, "dataset": 1, "demultiplex": 11, "document": 4, "encod": 7, "failur": 11, "from": 7, "get": 5, "guppi": [5, 11], "how": [6, 7, 8, 9], "html": 10, "inform": 7, "input": [6, 7, 8, 9], "instal": 5, "integr": 3, "librari": 8, "live": 10, "m6a": [7, 8], "master": [0, 4], "memori": 11, "model": 8, "modif": 7, "modphr": 7, "mop_consensu": 6, "mop_mod": [7, 11], "mop_preprocess": [8, 11], "mop_tail": 9, "paramet": [6, 7, 8, 9], "pipelin": [6, 7, 8, 9], "pore": [0, 4], "profil": 5, "refer": 0, "report": 10, "resourc": 10, "result": [6, 7, 8, 9], "run": [6, 7, 8, 9], "specif": 8, "start": 5, "test": 5, "tool": 8, "tool_opt": 8, "troubleshoot": 11, "us": 7, "version": 2, "welcom": 4}}) \ No newline at end of file diff --git a/refs/heads/MOP3/troubleshooting.html b/refs/heads/MOP3/troubleshooting.html new file mode 100644 index 0000000..485db3b --- /dev/null +++ b/refs/heads/MOP3/troubleshooting.html @@ -0,0 +1,148 @@ + + + + + + + + + Troubleshooting — MoP3 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Troubleshooting

+
+

Demultiplexing with Guppy

+

Error:

+
Init time: 2515 ms
+
+0%   10   20   30   40   50   60   70   80   90   100%
+|----|----|----|----|----|----|----|----|----|----|
+***************************************************
+Caller time: 32995 ms, Samples called: 159196780, samples/s: 4.82488e+06
+Finishing up any open output files.
+Basecalling completed successfully.
+
+Command error:
+rm: cannot remove '*_out/*/*.fastq': No such file or directory
+
+
+

Solution: +Check your barcode kit!. You must indicate the –barcode_kits in the tool_opts file at the row demultiplexing guppy. Example:

+
demultiplexing guppy  "--flowcell FLO-MIN114 --kit SQK-LSK114 --barcode_kits SQK-NBD114-24"
+
+
+
+
+

Memory failures in mop_preprocess and mop_mod

+

Sometimes FastQC, Epinano, or other tools can run out of memory because the input data contain low-quality reads. It is always a good idea to double-check it and eventually filter them per size / quality using either nanoq or nanofilt.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file