attempt 1 at sphinx docs

lanl · Sep 26, 2024 · 431128f · 431128f
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
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+name: Build and Deploy docs
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  release:
+    types:
+      - created
+
+jobs:
+    docs:
+      name: build and deploy docs
+      runs-on: ubuntu-latest
+
+      steps:      
+        - name: Checkout code
+          uses: actions/checkout@v2
+          with:
+            fetch-depth: 0
+        - name: Set system to non-interactive mode
+          run: export DEBIAN_FRONTEND=noninteractive
+        - name: install dependencies
+          run: |
+            pip install sphinx
+            pip install sphinx-rtd-theme
+            pip install sphinx-multiversion
+        - name: build docs
+          run: |
+            echo "Repo = ${GITHUB_REPOSITORY}"
+            cd doc/sphinx
+            # throw warnings as error to make sure docs properly build
+            make multiversion SPHINXOPTS="-W --keep-going -n"
+        - name: Deploy
+          if: ${{ (github.event.pull_request.head.repo.full_name == github.repository) || (github.ref == 'refs/heads/main') }}
+          uses: peaceiris/[email protected]
+          with:
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            publish_dir: ./doc/sphinx/_build/html
+            force_orphan: true
diff --git a/doc/index.html b/doc/index.html
@@ -0,0 +1,10 @@
+<!DOCTYPE html>
+<!-- This is needed to redirect to the main version when building docs -->
+<html>
+  <head>
+    <title>Redirecting to develop branch</title>
+    <meta charset="utf-8">
+    <meta http-equiv="refresh" content="0; url=./develop/index.html">
+    <link rel="canonical" href="https://parthenon-hpc-lab.github.io/parthenon/develop/index.html">
+  </head>
+</html>
diff --git a/doc/sphinx/.gitignore b/doc/sphinx/.gitignore
@@ -0,0 +1 @@
+_build
diff --git a/doc/sphinx/Makefile b/doc/sphinx/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(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) $(O)
diff --git a/doc/sphinx/conf.py b/doc/sphinx/conf.py
@@ -0,0 +1,43 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Phoebus'
+copyright = '2024, Triad National Security'
+author = 'The Phoebus Team'
+release = '1.0.0'
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["sphinx_multiversion"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# configuration for sphinx_multiversion
+smv_remote_whitelist = r"^(origin)$"
diff --git a/doc/sphinx/index.rst b/doc/sphinx/index.rst
@@ -0,0 +1,31 @@
+.. Phoebus documentation master file, created by
+   sphinx-quickstart on Thu Sep 26 15:18:20 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Phoebus: Performance portable GRRMHD for supernovae, mergers, and more
+======================================================================
+
+`Phoebus`_ is a performance portable general relativistic neutrino radiation magnetohydrodynamics code built upon the `Parthenon`_ adaptive mesh refinement framework.
+
+.. _Parthenon: https://github.com/parthenon-hpc-lab/parthenon
+.. _Phoebus: https://github.com/lanl/phoebus
+
+Key Features
+^^^^^^^^^^^^^
+
+* Finite volume GRMHD
+* Neutrino transport
+* GR...
+* fill out
+
+.. note::
+
+   These docs are under active development.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+   :glob:
+
+   src/*
diff --git a/doc/sphinx/make.bat b/doc/sphinx/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+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
diff --git a/doc/sphinx/src/code_of_conduct.rst b/doc/sphinx/src/code_of_conduct.rst
@@ -0,0 +1,76 @@
+Code of Conduct
+=====================================
+
+The community of participants in open-source relativstic astrophysics
+projects is made up of members from around the globe with a diverse set
+of skills, personalities, and experiences. It is through these
+differences that our community experiences success and continued growth.
+We expect everyone in our community to follow these guidelines when
+interacting with others both inside and outside of our community. Our
+goal is to keep ours a positive, inclusive, successful, and growing
+community.
+
+As members of the community,
+
+-  We pledge to treat all people with respect and provide a harassment-
+   and bullying-free environment, regardless of sex, sexual orientation
+   and/or gender identity, disability, physical appearance, body size,
+   race, nationality, ethnicity, and religion. In particular, sexual
+   language and imagery, sexist, racist, or otherwise exclusionary jokes
+   are not appropriate.
+
+-  We pledge to respect the work of others by recognizing
+   acknowledgment/citation requests of original authors. As authors, we
+   pledge to be explicit about how we want our own work to be cited or
+   acknowledged.
+
+-  We pledge to welcome those interested in joining the community, and
+   realize that including people with a variety of opinions and
+   backgrounds will only serve to enrich our community. In particular,
+   discussions relating to pros/cons of various technologies,
+   programming languages, and so on are welcome, but these should be
+   done with respect, taking proactive measure to ensure that all
+   participants are heard and feel confident that they can freely
+   express their opinions.
+
+-  We pledge to welcome questions and answer them respectfully, paying
+   particular attention to those new to the community. We pledge to
+   provide respectful criticisms and feedback in forums, especially in
+   discussion threads resulting from code contributions.
+
+-  We pledge to be conscientious of the perceptions of the wider
+   community and to respond to criticism respectfully. We will strive to
+   model behaviors that encourage productive debate and disagreement,
+   both within our community and where we are criticized. We will treat
+   those outside our community with the same respect as people within
+   our community.
+
+-  We pledge to help the entire community follow the code of conduct,
+   and to not remain silent when we see violations of the code of
+   conduct. We will take action when members of our community violate
+   this code such as contacting a Maintainer (a list of emails of
+   current Maintainers is made publicly available) or talking privately
+   with the person.
+
+This code of conduct applies to all community situations online (to
+include Github Issues, Pull Requests and any communication therein as
+well as Slack, Mattermost, and similar online communication platforms)
+and offline, including mailing lists, forums, social media, conferences,
+meetings, associated social events, and one-to-one interactions.
+
+Any related activity or project organized by members of the ``Phoebus``
+community, including affiliated packages, are welcome to have their own
+codes of conduct, but agree to also abide by the present code of
+conduct.
+
+--------------
+
+This Community Code of Conduct was adapted from the `Astropy Community
+Code of
+Conduct <https://www.astropy.org/code_of_conduct.html#:~:text=We%20pledge%20to%20treat%20all,nationality%2C%20ethnicity%2C%20and%20religion.>`__
+available under a `Creative Commons Attribution 4.0 International
+License <https://creativecommons.org/licenses/by/4.0/>`__. The above
+Code of Conduct was modified for use as part of ``Phoebus``.
+
+Parts of this code of conduct have been adapted from the PSF code of
+conduct.
diff --git a/doc/sphinx/src/contributing.rst b/doc/sphinx/src/contributing.rst
@@ -0,0 +1,88 @@
+Contributing
+=============================
+
+For the purpose of our development model, we label *Contributors* or
+*Maintainers* of ``Phoebus``. Below we describe these labels and the
+process for contributing to ``Phoebus``.
+
+Becoming a Contributor
+----------------------
+
+We welcome contributions from scientists from a large variety of
+relativistic astrophysics. New users are welcome to contributions to
+``Phoebus`` via the *Contributors* process. Contributors with 6 merged
+pull requests into the ``main`` branch (over a minimum of 6 months) will
+be eligible to join as a *Maintainer* of ``Phoebus`` with additional
+repository access and roles. However, final approval of *Maintainer*
+status will require a unanimous approval by vote by existing
+*Maintainers*, a necessary step to ensure the safety and integrity of
+the code base for all users of ``Phoebus``.
+
+The *Maintainers* of ``Phoebus`` consist of the original developers of
+the code and those that have a demonstrated history in the development
+of ``Phoebus`` prior to the implementation of the *Development Model*
+described here. Maintainers hold admin access, serve consistently as
+reviewers for pull requests, and are in charge of the maintaining,
+deployment, and improvement of efforts towards: regression testing,
+documentation, science test cases (gold standards), and continuous
+integration.
+
+To maintain their active status as Maintainer, all members will agree to
+adhere to our Community Code of Conduct and sign a Memorandum of
+Understanding described `here <GOVERNANCE.md>`__.
+
+Contributing to ``Phoebus``
+-----------------------------
+
+**Contributors**: (process for most users of ``Phoebus``)
+
+1. Create a new fork of ``main`` where your changes can be made.
+2. After completing, create a pull request, describe the final approach
+   and ensure the branch has no conflicts with current Regression Tests
+   and Formatting Checks.
+3. Assign external reviewers (a minimum of 1, one of which should be a
+   Maintainer, and which cannot be the contributor). Provide concise
+   description of changes.
+4. Once comments/feedback is addressed, the PR will be merged into the
+   main branch and changes will be added to list of changes in the next
+   release.
+5. At present, Releases (with a git version tag) for the ``main`` branch
+   of ``Phoebus`` will occur at a 6 to 12 month cadence or following
+   implementation of a major enhancement or capability to the code base.
+
+*Maintainers* of ``Phoebus`` will follow the same process for
+contributions as above except for the following differences: they may
+create branches directly within ``Phoebus``, they will hold repository
+admin privileges, and actively participate in the technical review of
+contributions to ``Phoebus``.
+
+List of Current Maintainers of ``Phoebus``
+------------------------------------------
+
++-------------------+--------------------------------+-----------------------+
+| Name              | Handle                         | Team                  |
++===================+================================+=======================+
+| Brandon Barker    |                                | Los Alamos National   |
+|                   | `@AstroBarker <https://www.g   | Lab                   |
+|                   | ithub.com/AstroBarker>`__      |                       |
++-------------------+--------------------------------+-----------------------+
+| Josh Dolence      | `@jdolence <https://ww         | Los Alamos National   |
+|                   | w.github.com/jdolence>`__      | Lab                   |
++-------------------+--------------------------------+-----------------------+
+| Carl Fields       |                                | University of Arizona |
+|                   | `@carlnotsagan <https://www.gi |                       |
+|                   | thub.com/carlnotsagan>`__      |                       |
++-------------------+--------------------------------+-----------------------+
+| Mariam            | `@mari2895 <https://ww         | Niels Bohr Institute  |
+| Gogilashvili      | w.github.com/mari2895>`__      |                       |
++-------------------+--------------------------------+-----------------------+
+| Jonah Miller      | `@Yurlungur <https://www       | Los Alamos National   |
+|                   | .github.com/Yurlungur>`__      | Lab                   |
++-------------------+--------------------------------+-----------------------+
+| Jeremiah Murphy   |                                | Florida State         |
+|                   | `@curiousmiah <https://www.g   | University            |
+|                   | ithub.com/curiousmiah>`__      |                       |
++-------------------+--------------------------------+-----------------------+
+| Ben Ryan          | `@brryan <https://             | Los Alamos National   |
+|                   | www.github.com/brryan>`__      | Lab                   |
++-------------------+--------------------------------+-----------------------+