Feat docs

.github/workflows/gh-pages.yml

@@ -0,0 +1,61 @@
+# workflow's name
+name: "Build and deploy Github pages"
+
+# This event triggers the workflow
+on:
+  push:         # <- on push
+    branches:
+      - master  # <- ... on the branch "master"
+
+jobs:
+
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    # Set custom default shell to enable proper activation of conda env
+    #  see: https://github.com/conda-incubator/setup-miniconda#important
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    # Tasks to do:
+    steps:
+
+      # 1. Retrieving repository
+
+      - name: "Checkout"
+        uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+
+      # 2. Setting up conda env
+
+      - name: "Set up conda environment"
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-activate-base: false
+          activate-environment: rptools-dev
+          environment-file: environment.yaml
+
+      # 3. Installing Python dependencies (Sphinx)
+
+      - name: "Install Python dependencies"
+        run: |
+          conda install -c conda-forge sphinx sphinx_rtd_theme myst-parser
+
+      # 4. Building doc
+
+      - name: "Build Sphinx Doc"
+        run: |
+          cd docsource
+          make html
+
+      # 5. Deploying doc on Github Pages
+
+      - name: "Deploy Github Pages"
+        uses: JamesIves/github-pages-deploy-action@3.7.1
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages
+          FOLDER: docsource/_build/html/

.gitignore

@@ -8,4 +8,5 @@ node_modules
 *.code-workspace
 .coverage*
 .vscode
-_exclude
+_exclude
+/docsource/_build/

ci/Makefile

@@ -66,10 +66,4 @@ conda-create-run_env: ## Make an conda environment to run program
 	@$(MAKE_CMD) -f conda.mk check-environment-test env=${PACKAGE}_test
 
 doc-pdoc:
-	cd .. ; rm -rf chemlite/__pycache__ ; pdoc --force --html -o docs chemlite
-
-doc-sphinx:
-	cd .. ; sphinx-apidoc -f -o docs/source chemlite
-
-doc-sphinx-html:
-	cd ../docs ; make html
+	cd .. ; rm -rf chemlite/__pycache__ ; pdoc --force --html -o docs chemlite

docsource/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docsource/_autosummary/rptools.Args.build_args_parser.rst

@@ -0,0 +1,6 @@
+rptools.Args.build\_args\_parser
+================================
+
+.. currentmodule:: rptools.Args
+
+.. autofunction:: build_args_parser

docsource/_autosummary/rptools.Args.rst

@@ -0,0 +1,32 @@
+rptools.Args
+============
+
+.. automodule:: rptools.Args
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      build_args_parser
+
+
+
+
+
+
+
+
+
+
+
+
+
+

docsource/_autosummary/rptools.rpcompletion.Args.add_arguments.rst

@@ -0,0 +1,6 @@
+rptools.rpcompletion.Args.add\_arguments
+========================================
+
+.. currentmodule:: rptools.rpcompletion.Args
+
+.. autofunction:: add_arguments

docsource/_autosummary/rptools.rpcompletion.Args.rst

@@ -0,0 +1,32 @@
+rptools.rpcompletion.Args
+=========================
+
+.. automodule:: rptools.rpcompletion.Args
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      add_arguments
+
+
+
+
+
+
+
+
+
+
+
+
+
+

docsource/_autosummary/rptools.rpcompletion.rpCompletion.rp_completion.rst

@@ -0,0 +1,6 @@
+rptools.rpcompletion.rpCompletion.rp\_completion
+================================================
+
+.. currentmodule:: rptools.rpcompletion.rpCompletion
+
+.. autofunction:: rp_completion

docsource/_autosummary/rptools.rpcompletion.rpCompletion.rst

@@ -0,0 +1,32 @@
+rptools.rpcompletion.rpCompletion
+=================================
+
+.. automodule:: rptools.rpcompletion.rpCompletion
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      rp_completion
+
+
+
+
+
+
+
+
+
+
+
+
+
+

docsource/_autosummary/rptools.rpcompletion.rst

@@ -0,0 +1,32 @@
+rptools.rpcompletion
+====================
+
+.. automodule:: rptools.rpcompletion
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+
+   rptools.rpcompletion.Args
+   rptools.rpcompletion.rpCompletion
+
+

docsource/_autosummary/rptools.rpextractsink.Args.add_arguments.rst

@@ -0,0 +1,6 @@
+rptools.rpextractsink.Args.add\_arguments
+=========================================
+
+.. currentmodule:: rptools.rpextractsink.Args
+
+.. autofunction:: add_arguments

docsource/_autosummary/rptools.rpextractsink.Args.rst

@@ -0,0 +1,32 @@
+rptools.rpextractsink.Args
+==========================
+
+.. automodule:: rptools.rpextractsink.Args
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      add_arguments
+
+
+
+
+
+
+
+
+
+
+
+
+
+

docsource/_autosummary/rptools.rpextractsink.rpextractsink.genSink.rst

@@ -0,0 +1,6 @@
+rptools.rpextractsink.rpextractsink.genSink
+===========================================
+
+.. currentmodule:: rptools.rpextractsink.rpextractsink
+
+.. autofunction:: genSink

docsource/_autosummary/rptools.rpextractsink.rpextractsink.rst

@@ -0,0 +1,33 @@
+rptools.rpextractsink.rpextractsink
+===================================
+
+.. automodule:: rptools.rpextractsink.rpextractsink
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      genSink
+      write
+
+
+
+
+
+
+
+
+
+
+
+
+
+

docsource/_autosummary/rptools.rpextractsink.rpextractsink.write.rst

@@ -0,0 +1,6 @@
+rptools.rpextractsink.rpextractsink.write
+=========================================
+
+.. currentmodule:: rptools.rpextractsink.rpextractsink
+
+.. autofunction:: write

docsource/_autosummary/rptools.rpextractsink.rst

@@ -0,0 +1,32 @@
+rptools.rpextractsink
+=====================
+
+.. automodule:: rptools.rpextractsink
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+
+   rptools.rpextractsink.Args
+   rptools.rpextractsink.rpextractsink
+
+

docsource/_autosummary/rptools.rpfba.Args.add_arguments.rst

@@ -0,0 +1,6 @@
+rptools.rpfba.Args.add\_arguments
+=================================
+
+.. currentmodule:: rptools.rpfba.Args
+
+.. autofunction:: add_arguments