Sbachmei/mic 5643/publish docs (#129)

.github/workflows/build.yml

@@ -1,6 +1,11 @@
 # -----------------------------------------------------------------------------
 #   - invoked on push, pull_request, or manual trigger
-#   - test under at least 3 versions of python
+#   - tests under multiple versions of python
+#   - only quick tests are run here
+#
+#   NOTE: We do not run tests marked as slow nor do we schedule runs here.
+#   Slow tests and scheduled runs are handled via Jenkins because that has 
+#   access to the cluster which is required for some tests.
 # -----------------------------------------------------------------------------
 name: build
 on: [push, pull_request, workflow_dispatch]
@@ -35,3 +40,7 @@ jobs:
       - name: Test
         run: |
           pytest ./tests
+      - name: Build Docs
+        run: |
+          make html -C docs/ SPHINXOPTS="-W --keep-going -n"
+          

.github/workflows/deploy.yml

@@ -21,6 +21,9 @@ jobs:
           python -m pip install --upgrade pip
           pip install setuptools wheel build
       - name: Test
+        # NOTE: We only run tests not marked as `slow` here since github actions
+        # does not have access to the cluster (which is required for some tests). 
+        # This means that we may inadvertenlly deploy code that has failing tests!
         run: |
           pip install .[test]
           pytest ./tests

.readthedocs.yml

@@ -0,0 +1,21 @@
+# This is the version for the readthedocs configuration. Version 2 ignores
+# web-based configuration and uses everything from this file.
+version: 2
+
+# Configure the python version and environment construction run before
+# docs are built.
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+python:
+  install:
+      # This runs pip install .[docs] from the project root.
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+# Doc builds will fail if there are any warnings
+sphinx:
+  fail_on_warning: true

CHANGELOG.rst

@@ -1,6 +1,7 @@
 **0.1.2 - 12/16/24**
 
  - Add optional arg to pass allowable schemas to the Config constructor
+ - Initial documentation publication
 
 **0.1.1 - 12/10/24**
 

Jenkinsfile

@@ -148,7 +148,7 @@ pipeline {
       }
     }
 
-    stage("Test") {
+    stage("Test and Build Docs") {
       parallel {
         stage("Run End-to-End Tests") {
           steps {
@@ -194,6 +194,12 @@ pipeline {
             ])
           }
         }
+
+        stage("Build Docs") {
+          steps {
+            sh "${ACTIVATE} && make build-doc"
+          }
+        }
       }
     }
   }

docs/Makefile

@@ -0,0 +1,22 @@
+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = easylink
+SOURCEDIR     = source
+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)
+
+clean:
+	rm -rf build/*

docs/source/_static/style.css

@@ -0,0 +1,3 @@
+.wy-nav-content {
+    max-width: 1000px !important;
+}

docs/source/_templates/layout.html

@@ -0,0 +1,4 @@
+{% extends "!layout.html" %}
+{% block extrahead %}
+    <link href="{{ pathto("_static/style.css", True) }}" rel="stylesheet" type="text/css">
+{% endblock %}

docs/source/api_reference/cli.rst

@@ -0,0 +1 @@
+.. automodule:: easylink.cli

docs/source/api_reference/index.rst

@@ -0,0 +1,10 @@
+API Reference
+=============
+
+.. automodule:: easylink
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   *

docs/source/concepts/index.rst

@@ -0,0 +1,10 @@
+.. _concepts_main:
+
+========
+Concepts
+========
+Here we cover several core conceptual topics related using EasyLink.
+
+.. todo::
+
+   Everything

docs/source/conf.py

@@ -0,0 +1,233 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+
+# 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.
+from pathlib import Path
+
+import easylink
+
+base_dir = Path(easylink.__file__).parent
+
+about = {}
+with (base_dir / "__about__.py").open() as f:
+    exec(f.read(), about)
+
+sys.path.insert(0, str(Path("..").resolve()))
+
+# -- Project information -----------------------------------------------------
+
+project = about["__title__"]
+copyright = f'2024, {about["__author__"]}'
+author = about["__author__"]
+
+# The short X.Y version.
+version = easylink.__version__
+# The full version, including alpha/beta/rc tags.
+release = easylink.__version__
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+
+needs_sphinx = "4.0"
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_click.ext",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- 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_path = ["_theme"]
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    "**": [
+        "globaltoc.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = f'{about["__title__"]}doc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        f'{about["__title__"]}.tex',
+        f'{about["__title__"]} Documentation',
+        about["__author__"],
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, f'{about["__title__"]}', f'{about["__title__"]} Documentation', [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        f'{about["__title__"]}',
+        f'{about["__title__"]} Documentation',
+        author,
+        f'{about["__title__"]}',
+        about["__summary__"],
+        "Miscellaneous",
+    ),
+]
+
+# Other docs we can link to
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "tables": ("https://www.pytables.org/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+    "layered_config_tree": ("https://layered-config-tree.readthedocs.io/en/latest/", None),
+}
+
+
+# -- Autodoc configuration ------------------------------------------------
+
+autodoc_default_options = {
+    # Automatically document members (e.g. classes in a module,
+    # methods in a class, etc.)
+    "members": True,
+    # Order of items documented is determined by the order
+    # of appearance in the source code
+    "member-order": "bysource",
+    # Generate docs even if an item has no docstring.
+    "undoc-members": True,
+    # Don't document things with a leading underscore.
+    "private-members": False,
+}
+# Display type hints in the description instead of the signature.
+autodoc_typehints = "description"
+
+
+# -- nitpicky mode --------------------------------------------------------
+# Ensures that all references in the docs resolve.
+
+nitpicky = True
+
+nitpick_ignore = []
+for line in open("../nitpick-exceptions"):
+    if line.strip() == "" or line.startswith("#"):
+        continue
+    dtype, target = line.split(None, 1)
+    target = target.strip()
+    nitpick_ignore.append((dtype, target))

docs/source/glossary.rst

@@ -0,0 +1,11 @@
+.. _glossary:
+
+========
+Glossary
+========
+
+tbd
+
+
+
+