Eac/docs

.gitignore

@@ -37,6 +37,11 @@ MANIFEST
 pip-log.txt
 pip-delete-this-directory.txt
 
+# docs stuff
+docs/_build
+docs/api
+docs/examples
+
 # Unit test / coverage reports
 htmlcov/
 .tox/
@@ -51,6 +56,9 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+tests/ci_test.tgz
+tests/temp_data
+
 
 # backups
 *~

.readthedocs.yaml

@@ -0,0 +1,31 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .
+     extra_requirements:
+       - dev
+       - docs

docs/Makefile

@@ -0,0 +1,21 @@
+# 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
+SPHINXPROJ    = RAIL_PROJECT
+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)

docs/_static/css/notebooks.css

@@ -0,0 +1,32 @@
+/* Hide the title of each notebook -- otherwise we get a redundancy with the  
+   required rst title. Choosing to keep the rst title because it allows users
+   to use Read The Docs' heading link feature */
+
+div.jp-RenderedHTMLCommon > h1 {
+    display: none;
+}
+
+section:not(:first-child) > h2 {
+    padding-top: 30px;
+}
+
+/* nbconvert overrides link color */
+
+p.notebook-link {
+    margin-bottom: 20px;
+    font-weight: bold;
+}
+
+p.notebook-link > a {
+    margin-left: 6px;
+    color: rgb(25, 118, 210);
+    font-family: sans-serif;
+    font-weight: bold;
+}
+
+/* Keeps the bottom of the sidebar from overlapping and becoming unscrollable
+   all the way down, hiding reference > API Documentation */
+
+div.wy-menu-vertical {
+    padding-bottom: 4em;
+}

docs/conf.py

@@ -0,0 +1,193 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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 subprocess
+import sys
+import pkgutil
+import rail.projects
+import rail.plotting
+
+sys.path.insert(0, os.path.abspath('..'))
+
+print(sys.path)
+
+
+# Use unittest mock module to shield some modules away from docs building.
+# This way one does not need to install them when dealing with the doc.
+from unittest.mock import MagicMock
+
+MOCK_MODULES = [
+    'qp',
+    'tables_io',
+]
+for mod_name in MOCK_MODULES:
+    if mod_name in sys.modules:
+        sys.modules[mod_name] = MagicMock()
+
+
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'RAIL_Projects'
+copyright = '2025, LSST DESC RAIL Contributors'
+author = 'LSST DESC RAIL Contributors'
+
+# The short X.Y version
+from rail.projects import _version
+version = "%i.%i" % (_version.version_tuple[0], _version.version_tuple[1])
+# The full version, including alpha/beta/rc tags
+release = _version.version
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.mathjax',
+    'nbsphinx',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosectionlabel',
+    'sphinx_tabs.tabs',
+]
+
+# 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'
+
+# 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 pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'setup.rst', 'api/.*.rst']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# Allow NB to fail
+nbsphinx_allow_errors = True
+
+# By default, tabs can be closed by selecting the open tab. This
+# functionality can be disabled using the sphinx_tabs_disable_tab_closing
+# configuration option:
+sphinx_tabs_disable_tab_closing = 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 = '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 = {}
+html_theme_options = {'prev_next_buttons_location': None,
+                      'collapse_navigation': False,
+                      'titles_only': False}
+
+# 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']
+
+# These paths are either relative to html_static_path
+# or fully qualified paths (eg. https://...)
+html_css_files = [
+    'css/notebooks.css',
+]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'rail_projects_doc'
+
+
+# -- Options for Autodoc--------------------------------------------------
+# Autodoc collects docstrings and builds API pages
+# from sphinxcontrib.apidoc import main as apidoc_main
+
+def run_apidoc(_):
+
+    if not os.path.exists('examples'):
+        os.system('ln -s ../examples')
+
+
+    from sphinx.ext.apidoc import main as apidoc_main
+    cur_dir = os.path.normpath(os.path.dirname(__file__))
+    output_path = os.path.join(cur_dir, 'api')
+
+    top_dir = os.path.abspath(os.path.join(os.path.dirname(rail.projects.__file__), '..'))
+
+    #paramlist = ['--separate', '--implicit-namespaces', '--no-toc', '-M', '-o', output_path, '-f', top_dir]
+    paramlist = ['--separate', '--implicit-namespaces', '-M', '-o', output_path, '-f', top_dir]
+    print(f"running {paramlist}")
+    apidoc_main(paramlist)
+
+
+def setup(app):
+    app.connect('builder-inited', run_apidoc)
+
+

docs/demos.rst

@@ -0,0 +1,46 @@
+
+*****************
+Example Notebooks
+*****************
+
+`rail_projects` comes with several notebooks that demonstrate how to use it to analyze data in a number of different ways.
+
+Here we describe the various notebooks and suggest other ways in which you might study the data.
+
+
+Demos
+=====
+
+We recommend starting with notebook this this notebook,
+which demonstrates top-level rail project functionality, such as how to create a project from an example
+configuration, and how to do simple things with such as reducing the input data, sub-selecting data to
+make training and tests data sets and how to run simple analysis pipelines on those.
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Creating and using a RailProject
+
+   examples/rail_project_example.ipynb
+
+
+This notebook shows how to manage the library of components that make up a `RailProject`
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: The rail project component library
+
+   examples/rail_project_library.ipynb
+
+
+This notebook shows how to use the `rail.plotting.control` module to
+make plots from a `RailProject`
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Making plots
+
+   examples/rail_plotting_control.ipynb
+
+