DEV: add documentation pages

.github/workflows/pages.yml

@@ -0,0 +1,65 @@
+name: GitHub Pages
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: "3.11"
+          conda-channels: anaconda, conda-forge
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -r doc/pages_requirements.txt
+          python -m pip install .
+
+      - name: Build documentation
+        run: |
+          # cp examples/*.ipynb docs
+          cd doc
+          make clean
+          make html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'doc/build/html'
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main'
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -1,3 +1,5 @@
 *.pyc
 *.egg-info
-build/
+build/
+doc/build/
+doc/source/api/

README.rst

@@ -4,6 +4,34 @@ Backend agnostic astropy-like cosmology
 The primary intention for this package is for use with :code:`GWPopulation`
 but the main functionality can be used externally.
 
+Installation and contribution
+-----------------------------
+
+Currently installation is only available from source
+
+.. code-block:: console
+
+    $ pip install git+https://github.com/ColmTalbot/wcosmo.git
+
+for development you should follow a standard fork-and-pull workflow.
+
+- First create a new fork at :code:`github.com/UserName/wcosmo`.
+- Clone your fork
+
+  .. code-block:: console
+
+    $ git clone git@github.com:UserName/wcosmo.git
+
+  or use a GitHub codespace.
+- Install the local version with
+
+  .. code-block:: console
+
+    $ python -m pip install .
+
+- Make any desired edits and push to your fork.
+- Open a pull request into :code:`git@github.com:ColmTalbot/wcosmo.git`.
+
 Basic usage
 -----------
 
@@ -14,21 +42,9 @@ To import an astropy-like cosmology (without units)
     from wcosmo import FlatwCDM
     cosmology = FlatwCDM(H0=70, Om0=0.3, w0=-1)
 
-To use this in :code:`GWPopulation`
-
-.. code-block:: python
-
-    import gwpopulation as gwpop
-    from wcosmo.models import CosmoModel, PowerLawRedshift
-
-    model = CosmoModel(
-        model_functions=[
-            gwpop.models.mass.two_component_primary_mass_ratio,
-            gwpop.models.spin.iid_spin,
-            PowerLawRedshift(cosmo_model="FlatwCDM"),
-        ],
-        cosmo_model="FlatwCDM",
-    )
+This code is automatically used in :code:`GWPopulation` when using either
+:code:`gwpopulation.experimental.cosmo_models.CosmoModel` and/or
+:code:`PowerLawRedshift`
 
 Changing backend
 ----------------
@@ -47,6 +63,7 @@ Manual backend setting can be done as follows:
     import jax.numpy as jnp
     from jax.scipy.linalg.toeplitz import toeplitz
 
-    from wcosmo import wcosmo
+    from wcosmo import wcosmo, utils
     wcosmo.xp = jnp
-    wcosmo.toeplitz = toeplitz
+    utils.xp = jnp
+    utils.toeplitz = toeplitz

doc/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     = 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)

doc/index.rst

@@ -0,0 +1,8 @@
+.. currentmodule:: wcosmo
+
+.. include:: ../README.rst
+
+.. autosummary::
+
+   wcosmo.wcosmo
+   wcosmo.utils

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/pages_requirements.txt

@@ -0,0 +1,9 @@
+ipython_genutils
+jinja2
+nbsphinx
+numpydoc
+pandoc
+pygments
+sphinx
+sphinx_rtd_theme
+sphinx-nefertiti

doc/source/_templates/custom-class-template.rst

@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

doc/source/_templates/custom-module-template.rst

@@ -0,0 +1,68 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ fullname }}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

doc/source/conf.py

@@ -0,0 +1,39 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'wcosmo'
+copyright = '2024, Colm Talbot, Amanda Farah'
+author = 'Colm Talbot, Amanda Farah'
+release = '0.0.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.autosummary',
+    'numpydoc',
+    'nbsphinx',
+    'sphinx.ext.viewcode',
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+root_doc = 'index'
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_nefertiti'
+html_static_path = ['_static']
+
+autosummary_generate = True

doc/source/index.rst

@@ -0,0 +1,25 @@
+.. currentmodule:: wcosmo
+
+.. include:: ../../README.rst
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+.. autosummary::
+   :toctree: api
+   :template: custom-module-template.rst
+   :caption: API
+   :recursive:
+
+   wcosmo
+   utils
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

pyproject.toml

@@ -27,7 +27,7 @@ packages = ["wcosmo"]
 
 [project.entry-points."gwpopulation.xp"]
 wcosmo = "wcosmo.wcosmo"
-wcosmo-models = "wcosmo.models"
+wcosmo-utils = "wcosmo.utils"
 
 [project.entry-points."gwpopulation.other"]
-wcosmo = "wcosmo.wcosmo:scipy.linalg.toeplitz"
+wcosmo-utils = "wcosmo.utils:scipy.linalg.toeplitz"