From 0552065dbc4f883a8f2cae9c5a452b505b20d31e Mon Sep 17 00:00:00 2001 From: Samuel Farrens Date: Thu, 22 Apr 2021 18:12:08 +0200 Subject: [PATCH 1/4] updated readme --- README.rst | 101 ++++++++++++++++++++++++++++++++++++++++------------- 1 file changed, 76 insertions(+), 25 deletions(-) diff --git a/README.rst b/README.rst index 392c6fb3..9a7a70e2 100644 --- a/README.rst +++ b/README.rst @@ -1,14 +1,11 @@ -|Travis|_ |Coveralls|_ |Python35|_ |Python36|_ |Python37|_ |Python38|_ |PyPi|_ |Doc|_ |CircleCI|_ +|CI|_ |Codecov|_ |Python36|_ |Python37|_ |Python38|_ |Python39|_ |PyPi|_ |Doc|_ -.. |Travis| image:: https://travis-ci.org/CEA-COSMIC/pysap.svg?branch=master -.. _Travis: https://travis-ci.org/CEA-COSMIC/pysap +.. |CI| image:: https://github.com/CEA-COSMIC/pysap/workflows/CI/badge.svg +.. _CI: https://github.com/CEA-COSMIC/modopt/actions?query=workflow%3ACI -.. |Coveralls| image:: https://coveralls.io/repos/CEA-COSMIC/pysap/badge.svg?branch=master&service=github -.. _Coveralls: https://coveralls.io/github/CEA-COSMIC/pysap - -.. |Python35| image:: https://img.shields.io/badge/python-3.5-blue.svg -.. _Python35: https://badge.fury.io/py/python-pySAP +.. |Codecov| image:: https://codecov.io/gh/CEA-COSMIC/pysap/branch/master/graph/badge.svg?token=XHJIQXV7AX +.. _Codecov: https://codecov.io/gh/CEA-COSMIC/pysap .. |Python36| image:: https://img.shields.io/badge/python-3.6-blue.svg .. _Python36: https://badge.fury.io/py/python-pySAP @@ -19,15 +16,15 @@ .. |Python38| image:: https://img.shields.io/badge/python-3.8-blue.svg .. _Python38: https://badge.fury.io/py/python-pySAP +.. |Python39| image:: https://img.shields.io/badge/python-3.9-blue.svg +.. _Python39: https://badge.fury.io/py/python-pySAP + .. |PyPi| image:: https://badge.fury.io/py/python-pySAP.svg .. _PyPi: https://badge.fury.io/py/python-pySAP .. |Doc| image:: https://readthedocs.org/projects/python-pysap/badge/?version=latest .. _Doc: https://python-pysap.readthedocs.io/en/latest/?badge=latest -.. |CircleCI| image:: https://circleci.com/gh/CEA-COSMIC/pysap.svg?style=svg -.. _CircleCI: https://circleci.com/gh/CEA-COSMIC/pysap - PySAP ====== @@ -35,7 +32,7 @@ PySAP (Python Sparse data Analysis Package) is a Python module for **sparse data * A common API for astronomical and neuroimaging datasets. * Access to |link-to-sparse2d| executables with both wrappers and bindings. -* Access to application specific plugins. +* Access to application specific plug-ins. * A graphical user interface to play with the provided functions. .. |link-to-sparse2d| raw:: html @@ -50,7 +47,6 @@ PySAP (Python Sparse data Analysis Package) is a Python module for **sparse data This package is the result of the COSMIC project, which is a collaboration between the CEA Neurospin UNATI and CEA CosmoStat laboratories. - Important links =============== @@ -58,7 +54,6 @@ Important links - API documentation (last stable release): https://python-pysap.readthedocs.io/ - PySAP paper: https://arxiv.org/abs/1910.08465 - Dependencies ============ @@ -76,26 +71,46 @@ new issue. 2. PySAP also requires the installation of the following third party software packages: -* astropy -* matplotlib -* nibabel -* numpy -* scipy -* progressbar2 -* pyqtgraph -* PyWavelets -* scikit-learn +* scipy [==1.5.4] +* numpy [==1.19.5] +* matplotlib [==3.3.4] +* astropy [==4.1] +* nibabel [==3.2.1] +* pyqtgraph [==0.11.1] +* progressbar2 [==3.53.1] +* scikit-learn [==0.24.1] +* pybind11 [==2.6.2] +* pyqt5 [==5.15.4] +* PyWavelets [==1.1.1] + +Plug-Ins +======== + +PySAP currently supports the following plug-ins: + +* |link-to-pysap-astro| [==0.0.1] +* |link-to-pysap-mri| [==0.3.0] +.. |link-to-pysap-astro| raw:: html + + PySAP-Astro + +.. |link-to-pysap-mri| raw:: html + + PySAP-MRI Installation ============ The installation of PySAP has been extensively tested on Ubuntu and macOS, however -we cannot guarantee it will work on every operating system (e.g. Windows). +we cannot guarantee it will work on every operating system (e.g. Windows). A Docker +image is available (see below) for those unable to install PySAP directly. If you encounter any installation issues be sure to go through the following steps before opening a new issue: -1. Check that that all of the installed all the dependencies listed above have been installed. +1. Check that that all of the installed all the dependencies listed above have been correctly installed. 2. Read through all of the documentation provided, including the troubleshooting suggestions. 3. Check if you problem has already been addressed in a previous issue. @@ -144,6 +159,42 @@ or: As before, use the ``--user`` option if needed. +Conda Environment +----------------- + +A a conda ``environment.yml`` file is provided to facilitate the installation of +the required PySAP dependencies along with some optional dependencies that +provide additional features. To build the environment run: + +.. code-block:: bash + + $ conda env create -f environment.yml + +Then to activate the environment run: + +.. code-block:: bash + + $ conda activate pysap + +Finally, install PySAP following the previous instructions. + +Docker Image +------------ + +A PySAP Docker image is available via DockerHub that includes the latest stable +version of PySAP pre-installed. To install the image run: + +.. code-block:: bash + + $ docker pull ... + +A Jupyter notebook can be launched using the Docker image as a backend and with +access to the users current working directory as follows: + +.. code-block:: bash + + $ docker run -p 8888:8888 -v ${PWD}:/home pysap + macOS ----- From 73b802eedda52a07ab116594a151b28cf2a8bf32 Mon Sep 17 00:00:00 2001 From: Samuel Farrens Date: Thu, 22 Apr 2021 20:03:10 +0200 Subject: [PATCH 2/4] fixed typos --- README.rst | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 9a7a70e2..c56dc61c 100644 --- a/README.rst +++ b/README.rst @@ -2,7 +2,7 @@ |CI|_ |Codecov|_ |Python36|_ |Python37|_ |Python38|_ |Python39|_ |PyPi|_ |Doc|_ .. |CI| image:: https://github.com/CEA-COSMIC/pysap/workflows/CI/badge.svg -.. _CI: https://github.com/CEA-COSMIC/modopt/actions?query=workflow%3ACI +.. _CI: https://github.com/CEA-COSMIC/pysap/actions?query=workflow%3ACI .. |Codecov| image:: https://codecov.io/gh/CEA-COSMIC/pysap/branch/master/graph/badge.svg?token=XHJIQXV7AX .. _Codecov: https://codecov.io/gh/CEA-COSMIC/pysap @@ -44,9 +44,14 @@ PySAP (Python Sparse data Analysis Package) is a Python module for **sparse data -This package is the result of the COSMIC project, which is a collaboration between +This package is the result of the |link-to-cosmic| project, which is a collaboration between the CEA Neurospin UNATI and CEA CosmoStat laboratories. +.. |link-to-cosmic| raw:: html + + COSMIC + Important links =============== @@ -110,9 +115,9 @@ image is available (see below) for those unable to install PySAP directly. If you encounter any installation issues be sure to go through the following steps before opening a new issue: -1. Check that that all of the installed all the dependencies listed above have been correctly installed. +1. Check that that all the dependencies listed above have been correctly installed. 2. Read through all of the documentation provided, including the troubleshooting suggestions. -3. Check if you problem has already been addressed in a previous issue. +3. Check if your problem has already been addressed in a previous issue. Further instructions are available |link-to-install|. @@ -176,7 +181,7 @@ Then to activate the environment run: $ conda activate pysap -Finally, install PySAP following the previous instructions. +Finally, install PySAP following the instructions above. Docker Image ------------ From 1157a9486c5251cc6de84686431d95c855cf955b Mon Sep 17 00:00:00 2001 From: Samuel Farrens Date: Thu, 22 Apr 2021 20:47:29 +0200 Subject: [PATCH 3/4] updated docker instructions --- Dockerfile | 5 +++-- README.rst | 4 ++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 86bffadd..bbdfb354 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,8 +16,9 @@ RUN apt-get update && \ apt-get install -y cmake && \ apt-get clean -RUN git clone https://github.com/CEA-COSMIC/pysap.git && \ - cd pysap && \ +RUN git clone https://github.com/CEA-COSMIC/pysap.git + +RUN cd pysap && \ conda env create -f environment.yml ENV PATH /opt/conda/envs/pysap/bin:$PATH diff --git a/README.rst b/README.rst index c56dc61c..e811ed93 100644 --- a/README.rst +++ b/README.rst @@ -191,14 +191,14 @@ version of PySAP pre-installed. To install the image run: .. code-block:: bash - $ docker pull ... + $ docker pull ceacosmic/pysap A Jupyter notebook can be launched using the Docker image as a backend and with access to the users current working directory as follows: .. code-block:: bash - $ docker run -p 8888:8888 -v ${PWD}:/home pysap + $ docker run -p 8888:8888 -v ${PWD}:/home ceacosmic/pysap macOS ----- From 1fa449cf1246f60399481ece336e0572b108e2d6 Mon Sep 17 00:00:00 2001 From: Samuel Farrens Date: Fri, 23 Apr 2021 13:53:34 +0200 Subject: [PATCH 4/4] updated readthedocs to use conda env --- .readthedocs.yml | 6 ++---- doc/requirements.txt | 15 --------------- 2 files changed, 2 insertions(+), 19 deletions(-) delete mode 100644 doc/requirements.txt diff --git a/.readthedocs.yml b/.readthedocs.yml index 7ad39b3d..c15cd26f 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,7 +12,5 @@ sphinx: formats: [] -python: - version: 3.6 - install: - - requirements: doc/requirements.txt +conda: + environment: environment.yml diff --git a/doc/requirements.txt b/doc/requirements.txt deleted file mode 100644 index 5930f4f3..00000000 --- a/doc/requirements.txt +++ /dev/null @@ -1,15 +0,0 @@ -git+https://github.com/AGrigis/pysphinxdoc.git -scipy>=1.3.0 -numpy>=1.16.4 -matplotlib>=3.0.0 -astropy>=3.0.0 -nibabel>=2.3.2 -pyqtgraph>=0.10.0 -progressbar2>=3.34.3 -modopt>=1.4.0 -scikit-learn>=0.19.1 -PyWavelets>=1.0.0 -pybind11>=2.3.0 -pyqt5>=5.12.2 -sphinx==1.3.6 -scikit-image