Add doc with GitHub actions

.github/workflows/check_on_PR.yml

@@ -21,9 +21,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-            pip install codecov pytest pytest-cov
-            pip install -e .
-            pip install flake8
+            pip install -e .[test]
             sudo apt-get install build-essential  graphviz libgraphviz-dev
             pip install --upgrade pygraphviz graphviz
 

.github/workflows/test_doc.yml

@@ -0,0 +1,44 @@
+name: "Test and deploy"
+
+on:
+  push:
+    branches: [ master ]
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python  3.10.5
+        uses: actions/setup-python@v2
+        with:
+          python-version:  3.10.5
+
+      - name: Install dependencies
+        run: |
+            pip install -e .[doc]
+            sudo apt-get install build-essential  graphviz libgraphviz-dev
+            pip install --upgrade pygraphviz graphviz
+
+      - name: Test with pytest
+        run:
+            py.test --cov macapype --ignore=examples/ --ignore=run_examples/
+
+
+      - name: Build the Doc 🔧
+        run: |
+          cd docs
+          make clean
+          make html
+          touch build/html/.nojekyll
+
+      - name: Deploy Github Pages 🚀
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: docs/build/html/
+          clean: true
+          ssh-key: ${{ secrets.DEPLOY_KEY }}

docs/Makefile

@@ -0,0 +1,139 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html-noplot to make standalone HTML files, without plotting anything"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  install    to make the html and push it online"
+
+.PHONY: clean
+
+clean:
+	rm -rf $(BUILDDIR)/*
+	rm -rf auto_examples/
+	rm -rf generated/*
+	rm -rf modules/*
+
+clean_no_plot:
+	rm -rf $(BUILDDIR)/*
+	rm -rf generated/*
+	rm -rf modules/*
+
+
+html-noplot:
+	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+		  ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+		  ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/macapype.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/macapype.qhc"
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+		  "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+		  "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+		  "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+		  "results in $(BUILDDIR)/coverage/python.txt."
+

requirements.txt

@@ -0,0 +1,8 @@
+nipype
+nilearn
+networkx
+pybids
+scikit-image
+nibabel
+numpy
+brain-slam

setup.py

@@ -4,17 +4,11 @@
 import re
 from setuptools import find_packages, setup
 
-
-required_packages = [
-    "nipype", "nilearn", "networkx",
-    "pybids", "scikit-image", "nibabel",
-    "numpy", "brain-slam"]
-
 verstr = "unknown"
 try:
     verstrline = open('macapype/_version.py', "rt").read()
 except EnvironmentError:
-    pass # Okay, there is no version file.
+    pass  # Okay, there is no version file.
 else:
     VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
     mo = re.search(VSRE, verstrline, re.M)
@@ -25,6 +19,13 @@
 
 print("Will not build conda module")
 
+test_deps = ['codecov', 'pytest', 'pytest-cov']
+flake_deps = ['flake8']
+doc_deps = ['sphinx', 'sphinx-gallery']
+
+with open('requirements.txt') as f:
+    requirements = f.read().splitlines()
+
 setup(
     name="macapype",
     version=verstr,
@@ -36,5 +37,9 @@
     license='BSD 3',
     entry_points={
         'console_scripts': ['segment_pnh = workflows.segment_pnh:main']},
-    install_requires=required_packages,
+    install_requires=requirements,
+    extras_require={
+        'test': test_deps + flake_deps,
+        'doc': flake_deps + test_deps + doc_deps
+    },
     include_package_data=True)