Merge pull request #65 from Medical-Image-Analysis-Laboratory/64_doc_…

…singularity_v2.0.1-dev [DOC] Update documentation
Medical-Image-Analysis-Laboratory · Dec 21, 2020 · a6fbea4 · a6fbea4
2 parents 6bbcaed + 5870837
commit a6fbea4
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Showing 20 changed files with 463 additions and 1,085 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -63,7 +63,7 @@ jobs:
             # Build CMP BIDS App docker image
             ls -la ./docker/bidsapp
             e=1 && for i in {1..5}; do
-              docker build --cache-from sebastientourbier/mialsuperresolutiontoolkit-bidsapp --rm=false --build-arg MAIN_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04" --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" -t sebastientourbier/mialsuperresolutiontoolkit-bidsapp ./docker/bidsapp \
+              docker build --cache-from sebastientourbier/mialsuperresolutiontoolkit --rm=false --build-arg MAIN_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04" --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" -t sebastientourbier/mialsuperresolutiontoolkit ./docker/bidsapp \
               && e=0 && break || sleep 15
             done && [ "$e" -eq "0" ]
       - run:
@@ -73,7 +73,7 @@ jobs:
             # Get version, update files.
             THISVERSION=$( python get_version.py )
             mkdir -p /tmp/cache
-            docker save sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04 sebastientourbier/mialsuperresolutiontoolkit-bidsapp \
+            docker save sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04 sebastientourbier/mialsuperresolutiontoolkit \
             | pigz -8 -p 3 > /tmp/cache/docker.tar.gz
       - persist_to_workspace:
           root: /tmp
@@ -121,16 +121,16 @@ jobs:
       - run:
           name: "Building Singularity image from Docker image"
           command: |
-            docker tag sebastientourbier/mialsuperresolutiontoolkit-bidsapp localhost:5000/sebastientourbier/mialsuperresolutiontoolkit-bidsapp:latest
-            docker push localhost:5000/sebastientourbier/mialsuperresolutiontoolkit-bidsapp:latest
-            SINGULARITY_NOHTTPS=1 singularity build /tmp/cache/mialsuperrresolutiontoolkit-bidsapp.simg docker://localhost:5000/sebastientourbier/mialsuperresolutiontoolkit-bidsapp:latest
+            docker tag sebastientourbier/mialsuperresolutiontoolkit localhost:5000/sebastientourbier/mialsuperresolutiontoolkit:latest
+            docker push localhost:5000/sebastientourbier/mialsuperresolutiontoolkit:latest
+            SINGULARITY_NOHTTPS=1 singularity build /tmp/cache/mialsuperresolutiontoolkit.simg docker://localhost:5000/sebastientourbier/mialsuperresolutiontoolkit:latest
           no_output_timeout: 5h
       - persist_to_workspace:
           root: /tmp
           paths:
-            - cache/mialsuperrresolutiontoolkit-bidsapp.simg
+            - cache/mialsuperresolutiontoolkit.simg
       - store_artifacts:
-          path: /tmp/cache/mialsuperrresolutiontoolkit-bidsapp.simg
+          path: /tmp/cache/mialsuperresolutiontoolkit.simg
 
   test-docker:
     machine:
@@ -188,7 +188,7 @@ jobs:
             docker run -it --rm --entrypoint /app/run_srr_coverage.sh \
                 -v /tmp/src/mialsuperresolutiontoolkit/data:/bids_dir \
                 -v /tmp/src/mialsuperresolutiontoolkit/data/derivatives:/output_dir \
-                sebastientourbier/mialsuperresolutiontoolkit-bidsapp \
+                sebastientourbier/mialsuperresolutiontoolkit \
                 /bids_dir /output_dir participant --participant_label 01 \
                 --param_file /bids_dir/code/participants_params.json \
                 --openmp_nb_of_cores 1 \
@@ -229,7 +229,7 @@ jobs:
             docker run -it --rm --entrypoint /app/run_srr_coverage.sh \
                 -v /tmp/src/mialsuperresolutiontoolkit/data:/bids_dir \
                 -v /tmp/src/mialsuperresolutiontoolkit/data/derivatives:/output_dir \
-                sebastientourbier/mialsuperresolutiontoolkit-bidsapp \
+                sebastientourbier/mialsuperresolutiontoolkit \
                 /bids_dir /output_dir participant --participant_label 01 \
                 --param_file /bids_dir/code/participants_params.json \
                 --openmp_nb_of_cores 1 \
@@ -323,7 +323,7 @@ jobs:
             singularity run --containall \
                 --bind /tmp/src/mialsuperresolutiontoolkit/data:/bids_dir \
                 --bind /tmp/src/mialsuperresolutiontoolkit/data/singularity-derivatives:/output_dir \
-                /tmp/cache/mialsuperrresolutiontoolkit-bidsapp.simg \
+                /tmp/cache/mialsuperresolutiontoolkit.simg \
                 /bids_dir /output_dir participant --participant_label 01 \
                 --param_file /bids_dir/code/participants_params.json \
                 --openmp_nb_of_cores 1 \
@@ -354,7 +354,7 @@ jobs:
             singularity run --containall \
                 --bind /tmp/src/mialsuperresolutiontoolkit/data:/bids_dir \
                 --bind /tmp/src/mialsuperresolutiontoolkit/data/singularity-derivatives:/output_dir \
-                /tmp/cache/mialsuperrresolutiontoolkit-bidsapp.simg \
+                /tmp/cache/mialsuperresolutiontoolkit.simg \
                 /bids_dir /output_dir participant --participant_label 01 \
                 --param_file /bids_dir/code/participants_params.json \
                 --openmp_nb_of_cores 1 \
@@ -525,8 +525,8 @@ jobs:
             if [[ -n "$DOCKER_PASS" ]]; then
               docker login -u $DOCKER_USER -p $DOCKER_PASS
               if [[ -n "$CIRCLE_TAG" ]]; then
-                docker tag sebastientourbier/mialsuperresolutiontoolkit-bidsapp sebastientourbier/mialsuperresolutiontoolkit-bidsapp:$CIRCLE_TAG
-                docker push sebastientourbier/mialsuperresolutiontoolkit-bidsapp:$CIRCLE_TAG
+                docker tag sebastientourbier/mialsuperresolutiontoolkit sebastientourbier/mialsuperresolutiontoolkit:$CIRCLE_TAG
+                docker push sebastientourbier/mialsuperresolutiontoolkit:$CIRCLE_TAG
               fi
             fi
 
@@ -563,8 +563,8 @@ jobs:
 
             if [[ -n "$DOCKER_PASS" ]]; then
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker tag sebastientourbier/mialsuperresolutiontoolkit-bidsapp sebastientourbier/mialsuperresolutiontoolkit-bidsapp:latest
-              docker push sebastientourbier/mialsuperresolutiontoolkit-bidsapp:latest
+              docker tag sebastientourbier/mialsuperresolutiontoolkit sebastientourbier/mialsuperresolutiontoolkit:latest
+              docker push sebastientourbier/mialsuperresolutiontoolkit:latest
             fi
 
   deploy-singularity-latest:
@@ -597,7 +597,7 @@ jobs:
       - run:
           name: 'Deploy simg with latest tag to Sylabs.io'
           command: |
-            singularity push -U /tmp/cache/mialsuperrresolutiontoolkit-bidsapp.simg library://tourbier/default/mialsuperrresolutiontoolkit-bidsapp:latest
+            singularity push -U /tmp/cache/mialsuperresolutiontoolkit.simg library://tourbier/default/mialsuperresolutiontoolkit:latest
 
   deploy-singularity-release:
     machine:
@@ -633,7 +633,7 @@ jobs:
             THISVERSION=v$( python /home/circleci/src/mialsuperresolutiontoolkit/get_version.py )
             echo "THISVERSION : ${THISVERSION}"
             echo "CIRCLE_TAG : ${CIRCLE_TAG}"
-            singularity push -U tmp/cache/mialsuperrresolutiontoolkit-bidsapp.simg library://tourbier/default/mialsuperrresolutiontoolkit-bidsapp:"${CIRCLE_TAG}"
+            singularity push -U tmp/cache/mialsuperresolutiontoolkit.simg library://tourbier/default/mialsuperresolutiontoolkit:"${CIRCLE_TAG}"
 
 workflows:
   version: 2

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@ Copyright © 2016-2020 Medical Image Analysis Laboratory, University Hospital Ce
 This software is distributed under the open-source BSD 3-Clause License. See [LICENSE](LICENSE.txt) file for details.
 
 ---
-![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit?include_prereleases) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4290209.svg)](https://doi.org/10.5281/zenodo.4290209) [![Docker Pulls (BIDS App)](https://img.shields.io/docker/pulls/sebastientourbier/mialsuperresolutiontoolkit-bidsapp?label=docker%20pulls%20%28BIDS%20App%29)](https://hub.docker.com/repository/docker/sebastientourbier/mialsuperresolutiontoolkit-bidsapp) [![Docker Pulls (v1)](https://img.shields.io/docker/pulls/sebastientourbier/mialsuperresolutiontoolkit?label=docker%20pulls%20%28v1%29)](https://hub.docker.com/repository/docker/sebastientourbier/mialsuperresolutiontoolkit) [![Build Status](https://travis-ci.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit.svg?branch=master)](https://travis-ci.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit) [![CircleCI](https://circleci.com/gh/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit.svg?style=shield)](https://app.circleci.com/pipelines/github/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit) [![Code Coverage](https://app.codacy.com/project/badge/Coverage/a27593d6fae7436eb2cd65b80f3342c3)](https://www.codacy.com/gh/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit?utm_source=github.com&utm_medium=referral&utm_content=Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit&utm_campaign=Badge_Coverage) [![Documentation Status](https://readthedocs.org/projects/mialsrtk/badge/?version=latest)](https://mialsrtk.readthedocs.io/en/latest/?badge=latest) [![Code Quality](https://app.codacy.com/project/badge/Grade/a27593d6fae7436eb2cd65b80f3342c3)](https://www.codacy.com/gh/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit&amp;utm_campaign=Badge_Grade) [![Github All Contributors](https://img.shields.io/github/all-contributors/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit)](#credits-) 
+![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit?include_prereleases) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4290209.svg)](https://doi.org/10.5281/zenodo.4290209) [![Docker Pulls](https://img.shields.io/docker/pulls/sebastientourbier/mialsuperresolutiontoolkit?label=docker%20pulls%20%28v1%29)](https://hub.docker.com/repository/docker/sebastientourbier/mialsuperresolutiontoolkit) [![Build Status](https://travis-ci.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit.svg?branch=master)](https://travis-ci.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit) [![CircleCI](https://circleci.com/gh/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit.svg?style=shield)](https://app.circleci.com/pipelines/github/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit) [![Code Coverage](https://app.codacy.com/project/badge/Coverage/a27593d6fae7436eb2cd65b80f3342c3)](https://www.codacy.com/gh/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit?utm_source=github.com&utm_medium=referral&utm_content=Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit&utm_campaign=Badge_Coverage) [![Documentation Status](https://readthedocs.org/projects/mialsrtk/badge/?version=latest)](https://mialsrtk.readthedocs.io/en/latest/?badge=latest) [![Code Quality](https://app.codacy.com/project/badge/Grade/a27593d6fae7436eb2cd65b80f3342c3)](https://www.codacy.com/gh/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit&amp;utm_campaign=Badge_Grade) [![Github All Contributors](https://img.shields.io/github/all-contributors/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit)](#credits-) 
 
 The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) provides a set of C++ and Python tools necessary to perform motion-robust super-resolution fetal MRI reconstruction. 
 

diff --git a/documentation/api_commandlineinterface.rst b/documentation/api_commandlineinterface.rst
@@ -4,5 +4,12 @@
 Command-line interface (CLI) module
 ************************************
 
-.. automodule:: pymialsrtk.cli.mialsuperresolutiontoolkit_bidsapp
-   :members:
+.. automodule:: pymialsrtk.cli.mialsuperresolutiontoolkit_docker
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: pymialsrtk.cli.mialsuperresolutiontoolkit_singularity
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api_pipelines.rst b/documentation/api_pipelines.rst
@@ -5,4 +5,6 @@ Pipelines module
 ******************
 
 .. automodule:: pymialsrtk.pipelines.anatomical.srr
-   :members:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api_postprocess.rst b/documentation/api_postprocess.rst
@@ -5,4 +5,6 @@ Postprocess module
 *******************
 
 .. automodule:: pymialsrtk.interfaces.postprocess
-   :members:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api_preprocess.rst b/documentation/api_preprocess.rst
@@ -6,3 +6,6 @@ Preprocess module
 
 .. automodule:: pymialsrtk.interfaces.preprocess
    :members:
+   :undoc-members:
+   :show-inheritance:
+
diff --git a/documentation/api_reconstruction.rst b/documentation/api_reconstruction.rst
@@ -5,4 +5,6 @@ Reconstruction module
 **********************
 
 .. automodule:: pymialsrtk.interfaces.reconstruction
-   :members:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/api_utils.rst b/documentation/api_utils.rst
@@ -5,4 +5,6 @@ Utility (utils) module
 ***********************
 
 .. automodule:: pymialsrtk.interfaces.utils
-   :members:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/documentation/conf.py b/documentation/conf.py
@@ -51,17 +51,22 @@ def visit_document(self, node):
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autosectionlabel',
               'sphinx.ext.autodoc',
-              'sphinx.ext.napoleon',
               'sphinx.ext.mathjax',
               'sphinx.ext.viewcode',
               'sphinxarg.ext',
-              'nbsphinx']
+              'sphinx.ext.inheritance_diagram',
+              'sphinxcontrib.apidoc',
+              'nbsphinx',
+              'nipype.sphinxext.plot_workflow',
+              'nipype.sphinxext.apidoc',
+              'nipype.sphinxext.documenter',
+              ]
 
 # autodoc_default_options = {
 #    'autosummary': True,
 # }
 
-autodoc_mock_imports = ['nipype','cv2', 'skimage']
+autodoc_mock_imports = ['cv2', 'skimage']
 
 # Allow errors in notebooks for doc
 nbsphinx_allow_errors = True

diff --git a/documentation/index.rst b/documentation/index.rst
@@ -15,12 +15,9 @@ This neuroimaging processing pipeline software is developed by the Medical Image
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4290209.svg
   :target: https://doi.org/10.5281/zenodo.4290209
   :alt: Digital Object Identifier
-.. image:: https://img.shields.io/docker/pulls/sebastientourbier/mialsuperresolutiontoolkit-bidsapp?label=docker%20pulls%20%28BIDS%20App%29
-  :target: https://hub.docker.com/repository/docker/sebastientourbier/mialsuperresolutiontoolkit-bidsapp
-  :alt: Docker Pulls (BIDS App)
 .. image:: https://img.shields.io/docker/pulls/sebastientourbier/mialsuperresolutiontoolkit?label=docker%20pulls%20%28v1%29
   :target: https://hub.docker.com/repository/docker/sebastientourbier/mialsuperresolutiontoolkit
-  :alt: Docker Pulls (v1)
+  :alt: Docker Pulls
 .. image:: https://travis-ci.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit.svg?branch=master
   :target: https://travis-ci.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit
   :alt: TravisCI Status (C++)