Merge pull request #29 from TimVanMourik/setup_ci

Setup continuous integrations, misc doc fixes
TimVanMourik · Jan 12, 2018 · 30e1663 · 30e1663
2 parents 69d9db3 + e9a9425
commit 30e1663
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diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,21 @@
+language: python
+sudo: required
+
+branches:
+  only:
+    - master
+    - setup_ci
+
+python:
+  - '3.6'
+
+before_install:
+- sudo apt-get update && sudo apt-get install -y --no-install-recommends build-essential
+- sudo add-apt-repository --yes ppa:beineri/opt-qt571-trusty
+- sudo apt-get update && sudo apt-get install -qq qt57-meta-full
+install:
+- source /opt/qt57/bin/qt57-env.sh
+
+script:
+- qmake
+- make
diff --git a/README.md b/README.md
@@ -1,4 +1,9 @@
 # PORcupine Creates Ur PipelINE
+
+[![Build status](https://ci.appveyor.com/api/projects/status/2451r3j95fngau7r?svg=true)](https://ci.appveyor.com/project/lukassnoek/porcupine)
+[![Build Status](https://travis-ci.org/TimVanMourik/Porcupine.svg?branch=master)](https://travis-ci.org/TimVanMourik/Porcupine)
+
+
 “PORcupine Creates Ur PipelINE, the worst recursive acronym with bad capitalisation and annoying use of slang.”
 Please find all documentation, examples, and much more on https://timvanmourik.github.io/Porcupine
 
@@ -12,4 +17,3 @@ After pulling this repository, it should readily compile with Qt Creator, provid
 Porcupine features interfaces to
 * My own fMRI analysis toolbox, including laminar fMRI https://github.com/TimVanMourik/OpenFmriAnalysis
 * NiPype https://github.com/nipy/nipype
-
diff --git a/appveyor.yml b/appveyor.yml
@@ -0,0 +1,22 @@
+build: false
+
+environment:
+  matrix:
+    - PYTHON: "C:\\Python35"
+      PYTHON_VERSION: "3.5.1"
+      PYTHON_ARCH: "32"
+      MINICONDA: C:\Miniconda35
+
+init:
+  - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH% %MINICONDA%"
+
+install:
+  - set QTDIR=C:\Qt\5.5\mingw492_32
+  - set PATH=%PATH%;%QTDIR%\bin;C:\MinGW\bin
+build_script:
+  - qmake Porcupine.pro
+  - mingw32-make
+
+#test_script:
+  #- In the future: test integrity of workflow creation
+
diff --git a/docs/_documentation/1_basics_7_building_dockerfiles.md b/docs/_documentation/1_basics_7_building_dockerfiles.md
@@ -75,6 +75,12 @@ $ docker build -t skullstripimage -f Dockerfile .
 Here, the `-t` flag specifies the name of your image and the `-f` flag specifies
 the Dockerfile that you want to use to build your image.
 
+**Beware**: Installing FSL in Docker images causes the image to become very large
+(>10GB), which may cause an error on Mac OS and Windows due to size restrictions
+("No space left on device" error). Check [this post](https://forums.docker.com/t/increase-docker-container-disk-space-on-os-x/26725/2)
+ on how to increase disk space for the Docker container.
+{: .notice--warning}
+
 ### Running your docker-image!
 Once you've built your docker-image, it's easy to actually run it. To do so,
 run the following in your terminal:

diff --git a/docs/_examples/1_simple_example.md b/docs/_examples/1_simple_example.md
@@ -46,5 +46,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/2_iterables_example.md b/docs/_examples/2_iterables_example.md
@@ -45,5 +45,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/3_mapnode_example.md b/docs/_examples/3_mapnode_example.md
@@ -58,5 +58,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/4_skullstrip_example.md b/docs/_examples/4_skullstrip_example.md
@@ -12,7 +12,7 @@ permalink: /examples/skullstrip-example
 {% assign caption = 'Skullstripping workflow including bias field correction and intensity harmonization' %}
 
 This example pipeline reconstructs the skullstripping-pipeline originally
-defined in the [niworkflows] Python package](https://github.com/poldracklab/niworkflows)
+defined in the [niworkflows Python package](https://github.com/poldracklab/niworkflows)
 from the [Poldrack-lab](https://poldracklab.stanford.edu/). This pipeline
 loads a T1-weighted structural scan, applies bias field correction (using ANTs)
 and intensity harmonization (using AFNI), skullstrips the image, and finally
@@ -35,5 +35,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/5_rsfmri_example.md b/docs/_examples/5_rsfmri_example.md
@@ -34,5 +34,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/6_firstlevel_example.md b/docs/_examples/6_firstlevel_example.md
@@ -38,5 +38,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/7_FEAT_example.md b/docs/_examples/7_FEAT_example.md
@@ -30,5 +30,5 @@ associated Dockerfile in our [Github repository](https://github.com/TimVanMourik
 [<i class="fa fa-download"></i> Download Dockerfile][3]{: .btn}
 
 [1]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_pipeline.pork
-[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_workflow.py
+[2]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/porcupine_generated_pipeline.py
 [3]:{{ site.url }}{{ site.baseurl }}/{{ example_path }}/Dockerfile
diff --git a/docs/_examples/example_pipelines/FEAT_fsl_complete_firstlevel_and_secondlevel/Dockerfile b/docs/_examples/example_pipelines/FEAT_fsl_complete_firstlevel_and_secondlevel/Dockerfile
@@ -69,6 +69,6 @@ ENV FSLDIR=/opt/fsl \
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD ./porcupine_generated_workflow.py /run.py
+ADD ./porcupine_generated_pipeline.py /run.py
 ADD ./firstlevelhelpers.py /firstlevelhelpers.py
-CMD ["python", "/run.py"]
+CMD ["python", "/run.py"]
diff --git a/...condlevel/porcupine_generated_workflow.py → ...condlevel/porcupine_generated_pipeline.py b/...condlevel/porcupine_generated_workflow.py → ...condlevel/porcupine_generated_pipeline.py
diff --git a/docs/_examples/example_pipelines/firstlevel_fsl_and_custom_modules_example/Dockerfile b/docs/_examples/example_pipelines/firstlevel_fsl_and_custom_modules_example/Dockerfile
@@ -69,6 +69,6 @@ ENV FSLDIR=/opt/fsl \
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD ./porcupine_generated_workflow.py /run.py
+ADD ./porcupine_generated_pipeline.py /run.py
 ADD ./firstlevelhelpers.py /firstlevelhelpers.py
-CMD ["python", "/run.py"]
+CMD ["python", "/run.py"]
diff --git a/...s_example/porcupine_generated_workflow.py → ...s_example/porcupine_generated_pipeline.py b/...s_example/porcupine_generated_workflow.py → ...s_example/porcupine_generated_pipeline.py
diff --git a/docs/_examples/example_pipelines/iterable_example/Dockerfile b/docs/_examples/example_pipelines/iterable_example/Dockerfile
@@ -69,5 +69,5 @@ ENV FSLDIR=/opt/fsl \
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD ./porcupine_generated_workflow.py /run.py
+ADD ./porcupine_generated_pipeline.py /run.py
 CMD ["python", "/run.py"]
diff --git a/...e_example/porcupine_generated_workflow.py → ...e_example/porcupine_generated_pipeline.py b/...e_example/porcupine_generated_workflow.py → ...e_example/porcupine_generated_pipeline.py
diff --git a/docs/_examples/example_pipelines/multirun_mapnode_example/Dockerfile b/docs/_examples/example_pipelines/multirun_mapnode_example/Dockerfile
@@ -87,5 +87,5 @@ RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD ./porcupine_generated_workflow.py /run.py
-CMD ["python", "/run.py"]
+ADD ./porcupine_generated_pipeline.py /run.py
+CMD ["python", "/run.py"]
diff --git a/...e_example/porcupine_generated_workflow.py → ...e_example/porcupine_generated_pipeline.py b/...e_example/porcupine_generated_workflow.py → ...e_example/porcupine_generated_pipeline.py
diff --git a/docs/_examples/example_pipelines/resting_preproc_fsl_example/Dockerfile b/docs/_examples/example_pipelines/resting_preproc_fsl_example/Dockerfile
@@ -69,5 +69,5 @@ ENV FSLDIR=/opt/fsl \
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD ./porcupine_generated_workflow.py /run.py
-CMD ["python", "/run.py"]
+ADD ./porcupine_generated_pipeline.py /run.py
+CMD ["python", "/run.py"]
diff --git a/...l_example/porcupine_generated_workflow.py → ...l_example/porcupine_generated_pipeline.py b/...l_example/porcupine_generated_workflow.py → ...l_example/porcupine_generated_pipeline.py
diff --git a/docs/_examples/example_pipelines/simple_example/Dockerfile b/docs/_examples/example_pipelines/simple_example/Dockerfile
@@ -67,5 +67,5 @@ ENV FSLDIR=/opt/fsl \
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD porcupine_generated_workflow.py /run.py
+ADD porcupine_generated_pipeline.py /run.py
 CMD ["python", "/run.py"]
diff --git a/...e_example/porcupine_generated_workflow.py → ...e_example/porcupine_generated_pipeline.py b/...e_example/porcupine_generated_workflow.py → ...e_example/porcupine_generated_pipeline.py
diff --git a/docs/_examples/example_pipelines/skullstrip_afni_ants_example/Dockerfile b/docs/_examples/example_pipelines/skullstrip_afni_ants_example/Dockerfile
@@ -113,5 +113,5 @@ ENV FSLDIR=/opt/fsl \
 #--------------------------------
 # Add custom analysis file as CMD
 #--------------------------------
-ADD ./porcupine_generated_workflow.py /run.py
+ADD ./porcupine_generated_pipeline.py /run.py
 CMD ["python", "/run.py"]
diff --git a/docs/_examples/zzz_your_example_here.md b/docs/_examples/zzz_your_example_here.md
@@ -7,5 +7,5 @@ layout: single
 permalink: /examples/a-short-name-of-your-workflow
 ---
 
-Follow the instructions on the [examples](/Porcupine/examples/) page to add your pipeline
-to our example gallery!
+Follow the instructions in the [Contributing](/Porcupine/documentation/advanced/contributing)
+section in our documentation on how to add your pipeline to our example gallery!