Merge pull request #44 from pyt-team/nina-docs-deploy

Deploy doc website from upstream after ssh clone

.github/workflows/docs.yml

@@ -0,0 +1,45 @@
+name: "Docs: Check and Deploy"
+
+on:
+  push:
+    branches: [main, github-actions-test]
+  pull_request:
+    branches: [main]
+permissions:
+  contents: write
+
+jobs:
+  build:
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.10.11]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.python-version}}
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+      - name: Install dependencies [pip]
+        run: |
+          pip install --upgrade pip setuptools wheel
+          pip install -e .[doc]
+      - name: Install Pandoc [apt-get]
+        run: |
+          sudo apt-get -y install pandoc
+      - name: Generate Docs [Sphinx]
+        run: |
+          sphinx-build  -b html -D version=latest -D release=latest docs docs/_build
+      - name: Deploy Docs
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: main
+          folder: docs/_build
+          token: ${{ secrets.DOCUMENTATION_KEY }}
+          repository-name: pyt-team/pyt-team.github.io
+          target-folder: topomodelx
+          clean: true

docs/Makefile

@@ -1,12 +1,11 @@
 # 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     = source
-BUILDDIR      = build
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/api/base.rst

@@ -0,0 +1,12 @@
+****
+Base
+****
+
+.. automodule:: topomodelx.base.aggregation
+    :members:
+
+.. automodule:: topomodelx.base.conv
+    :members:
+
+.. automodule:: topomodelx.base.message_passing
+    :members:

docs/api/index.rst

@@ -0,0 +1,18 @@
+=============
+API Reference
+=============
+
+The API reference gives an overview of `TopoModelX`, which consists of several modules:
+
+- `base` implements the core mathematical concepts of the package, such as the concept of message passing.
+- `nn` implements neural network layers, organized by topological domains.
+- `utils` implements utilities such as computing with sparse tensors.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Packages & Modules
+
+   base
+   nn
+   utils

docs/api/nn.rst

@@ -0,0 +1,15 @@
+***************
+Neural Networks
+***************
+
+Simplicial Complex Neural Networks
+================================
+
+.. automodule:: topomodelx.nn.simplicial
+   :members:
+
+Cellular Complex Neural Networks
+================================
+
+.. automodule:: topomodelx.nn.cellular
+   :members:

docs/api/utils.rst

@@ -0,0 +1,6 @@
+*****
+Utils
+*****
+
+.. automodule:: topomodelx.utils.scatter
+    :members:

docs/conf.py

@@ -0,0 +1,94 @@
+"""Sphinx configuration file."""
+
+project = "TopoModelX"
+copyright = "2022-2023, PyT-Team, Inc."
+author = "PyT-Team Authors"
+
+extensions = [
+    "nbsphinx",
+    "nbsphinx_link",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_gallery.load_style",
+]
+
+# Configure napoleon for numpy docstring
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_use_param = False
+napoleon_use_ivar = False
+napoleon_use_rtype = False
+napoleon_include_init_with_doc = False
+
+# Configure nbsphinx for notebooks execution
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', 'pdf'}",
+    "--InlineBackend.rc={'figure.dpi': 96}",
+]
+
+nbsphinx_execute = "never"
+
+# To get a prompt similar to the Classic Notebook, use
+nbsphinx_input_prompt = " In [%s]:"
+nbsphinx_output_prompt = " Out [%s]:"
+
+nbsphinx_allow_errors = True
+
+templates_path = ["_templates"]
+
+source_suffix = [".rst"]
+
+master_doc = "index"
+
+language = None
+
+nbsphinx_prolog = r"""
+{% set docname = env.doc2path(env.docname, base=None) %}
+
+.. raw:: latex
+    \nbsphinxstartnotebook{\scriptsize\noindent\strut
+    \textcolor{gray}{The following section was generated from
+    \sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
+    """
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+pygments_style = None
+
+html_baseurl = "pyt-team.github.io"
+htmlhelp_basename = "pyt-teamdoc"
+html_last_updated_fmt = "%c"
+
+latex_elements = {}
+
+
+latex_documents = [
+    (
+        master_doc,
+        "topomodelx.tex",
+        "TopoModelX Documentation",
+        "PyT-Team",
+        "manual",
+    ),
+]
+
+man_pages = [(master_doc, "topomodelx", "TopoModelX Documentation", [author], 1)]
+
+texinfo_documents = [
+    (
+        master_doc,
+        "topomodelx",
+        "TopoModelX Documentation",
+        author,
+        "topomodelx",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+epub_title = project
+epub_exclude_files = ["search.html"]