first draft of unified docs for PySAP

.github/workflows/cd-build.yml

@@ -41,3 +41,59 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml
           flags: unittests
+
+api:
+  name: Deploy API Documentation
+  needs: coverage
+  runs-on: ubuntu-latest
+  if: success()
+
+  env:
+    root: https://github.com/CEA-COSMIC/
+    tag: /archive/refs/tags/
+    vastro: 0.0.1
+    vetomo: 0.0.1
+    vmri: 0.4.0
+
+  steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Set up Conda with Python 3.8
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+        auto-activate-base: false
+
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        conda install -c conda-forge pandoc
+        python -m pip install --upgrade pip
+        python -m pip install -r docs/requirements.txt
+        python -m pip install .
+
+    - name: Download plug-ins
+      shell: bash -l {0}
+      run: |
+        wget ${root}pysap-astro${tag}v${vastro}.tar.gz -O pysap-astro.tar.gz
+        wget ${root}pysap-etomo${tag}v${vetomo}.tar.gz -O pysap-etomo.tar.gz
+        wget ${root}pysap-mri${tag}v${vmri}.tar.gz -O pysap-mri.tar.gz
+        for file in *.tar.gz; do tar xzf "$file"; done
+        rm *.tar.gz
+
+    - name: Build API documentation
+      shell: bash -l {0}
+      run: |
+        sphinx-apidoc -t docs/_templates -feTMo docs/source pysap
+        sphinx-apidoc -t docs/_templates -feTMo docs/source pysap-astro-${vastro}/astro
+        sphinx-apidoc -t docs/_templates -feTMo docs/source pysap-astro-${vetomo}/etomo
+        sphinx-apidoc -t docs/_templates -feTMo docs/source pysap-astro-${vmri}/mri
+        sphinx-build -E docs/source docs/_build
+
+    - name: Deploy API documentation
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/_build

.gitignore

@@ -1,19 +1,149 @@
-# Compiled source #
-###################
-*.o
-*.so
-*.pyc
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Logs and temporaries #
-########################
-*.log
-*~
-.coverage
+# C extensions
+*.so
 
-# Folders #
-###########
+# Distribution / packaging
+.Python
 build/
+develop-eggs/
 dist/
-python_pySAP.egg-info/
-__pycache__/
+downloads/
+eggs/
 .eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+pytest.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/fortuna.*
+docs/source/scripts.*
+docs/source/*.nblink
+docs/source/*astro*
+docs/source/*etomo*
+docs/source/*mri*
+docs/source/*pysap*
+pysap-astro*
+pysap-etomo*
+pysap-mri*
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/