Initial commit

.github/workflows/sphinx.yml

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+# From: https://github.com/rkdarst/sphinx-actions-test/blob/master/.github/workflows/sphinx-build.yml
+
+name: sphinx
+on: [push, pull_request]
+
+env:
+  DEFAULT_BRANCH: "main"
+  #SPHINXOPTS: "-W --keep-going -T"
+  # ^-- If these SPHINXOPTS are enabled, then be strict about the builds and fail on any warnings
+
+jobs:
+  build-and-deploy:
+    name: Build and gh-pages
+    runs-on: ubuntu-latest
+    steps:
+      # https://github.com/marketplace/actions/checkout
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          lfs: true
+      # https://github.com/marketplace/actions/setup-python
+      # ^-- This gives info on matrix testing.
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      # https://docs.github.com/en/actions/guides/building-and-testing-python#caching-dependencies
+      # ^-- How to set up caching for pip on Ubuntu
+      - name: Cache pip
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+            ${{ runner.os }}-
+      # https://docs.github.com/en/actions/guides/building-and-testing-python#installing-dependencies
+      # ^-- This gives info on installing dependencies with pip
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: Debugging information
+        run: |
+          echo "github.ref:" ${{github.ref}}
+          echo "github.event_name:" ${{github.event_name}}
+          echo "github.head_ref:" ${{github.head_ref}}
+          echo "github.base_ref:" ${{github.base_ref}}
+          set -x
+          git rev-parse --abbrev-ref HEAD
+          git branch
+          git branch -a
+          git remote -v
+          python -V
+          pip list --not-required
+          pip list
+
+
+      # Build
+      - uses: ammaraskar/sphinx-problem-matcher@master
+      - name: Build Sphinx docs
+        run: |
+          make dirhtml
+          # This fixes broken copy button icons, as explained in
+          #   https://github.com/coderefinery/sphinx-lesson/issues/50
+          #   https://github.com/executablebooks/sphinx-copybutton/issues/110
+          # This can be removed once these PRs are accepted (but the
+          # fixes also need to propagate to other themes):
+          #   https://github.com/sphinx-doc/sphinx/pull/8524
+          #   https://github.com/readthedocs/sphinx_rtd_theme/pull/1025
+          sed -i 's/url_root="#"/url_root=""/' _build/dirhtml/index.html || true
+
+
+      # The following supports building all branches and combining on
+      # gh-pages
+
+      # Clone and set up the old gh-pages branch
+      - name: Clone old gh-pages
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          git fetch
+          ( git branch gh-pages remotes/origin/gh-pages && git clone . --branch=gh-pages _gh-pages/ ) || mkdir _gh-pages
+          rm -rf _gh-pages/.git/
+          mkdir -p _gh-pages/branch/
+      # If a push and default branch, copy build to _gh-pages/ as the "main"
+      # deployment.
+      - name: Copy new build (default branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          # Delete everything under _gh-pages/ that is from the
+          # primary branch deployment.  Eicludes the other branches
+          # _gh-pages/branch-* paths, and not including
+          # _gh-pages itself.
+          find _gh-pages/ -mindepth 1 ! -path '_gh-pages/branch*' -delete
+          rsync -a _build/dirhtml/ _gh-pages/
+      # If a push and not on default branch, then copy the build to
+      # _gh-pages/branch/$brname (transforming '/' into '--')
+      - name: Copy new build (branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          !contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          #brname=$(git rev-parse --abbrev-ref HEAD)
+          brname="${{github.ref}}"
+          brname="${brname##refs/heads/}"
+          brdir=${brname//\//--}   # replace '/' with '--'
+          rm -rf   _gh-pages/branch/${brdir}
+          rsync -a _build/dirhtml/ _gh-pages/branch/${brdir}
+      # Go through each branch in _gh-pages/branch/, if it's not a
+      # ref, then delete it.
+      - name: Delete old feature branches
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          for brdir in `ls _gh-pages/branch/` ; do
+              brname=${brdir//--/\/}   # replace '--' with '/'
+              if ! git show-ref remotes/origin/$brname ; then
+                  echo "Removing $brdir"
+                  rm -r _gh-pages/branch/$brdir/
+              fi
+          done
+
+      # Add the .nojekyll file
+      - name: nojekyll
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          touch _gh-pages/.nojekyll
+
+      # Deploy
+      # https://github.com/peaceiris/actions-gh-pages
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' }}
+        #if: ${{ success() && github.event_name == 'push' && github.ref == 'refs/heads/$defaultBranch' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _gh-pages/
+          force_orphan: true

.gitignore

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+/_build
+.ipynb_checkpoints
+/venv*
+.jupyter_cache
+jupyter_execute

Makefile

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+# 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     = content
+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) $(O)
+
+# Live reload site documents for local development
+livehtml:
+	sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

content/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "Real-life compute cluster workflows"
+copyright = "2022-, The contributors"
+author = "The contributors"
+github_user = "coderefinery"
+github_repo_name = ""  # auto-detected from dirname if blank
+github_version = "main"
+conf_py_path = "/content/"  # with leading and trailing slash
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    # githubpages just adds a .nojekyll file
+    "sphinx.ext.githubpages",
+    "sphinx_lesson",
+    # remove once sphinx_rtd_theme updated for contrast and accessibility:
+    "sphinx_rtd_theme_ext_color_contrast",
+    "sphinx_coderefinery_branding",
+]
+
+# Settings for myst_nb:
+# https://myst-nb.readthedocs.io/en/latest/use/execute.html#triggering-notebook-execution
+# jupyter_execute_notebooks = "off"
+# jupyter_execute_notebooks = "auto"   # *only* execute if at least one output is missing.
+# jupyter_execute_notebooks = "force"
+nb_execution_mode = "cache"
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    "README*",
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "jupyter_execute",
+    "*venv*",
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+
+# HTML context:
+from os.path import basename, dirname, realpath
+
+html_context = {
+    "display_github": True,
+    "github_user": github_user,
+    # Auto-detect directory name.  This can break, but
+    # useful as a default.
+    "github_repo": github_repo_name or basename(dirname(realpath(__file__))),
+    "github_version": github_version,
+    "conf_py_path": conf_py_path,
+}
+
+# Intersphinx mapping.  For example, with this you can use
+# :py:mod:`multiprocessing` to link straight to the Python docs of that module.
+# List all available references:
+#   python -msphinx.ext.intersphinx https://docs.python.org/3/objects.inv
+# extensions.append('sphinx.ext.intersphinx')
+# intersphinx_mapping = {
+#    #'python': ('https://docs.python.org/3', None),
+#    #'sphinx': ('https://www.sphinx-doc.org/', None),
+#    #'numpy': ('https://numpy.org/doc/stable/', None),
+#    #'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+#    #'pandas': ('https://pandas.pydata.org/docs/', None),
+#    #'matplotlib': ('https://matplotlib.org/', None),
+#    'seaborn': ('https://seaborn.pydata.org/', None),
+# }