init commit

.github/workflows/ci_tests.yml

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+# GitHub Actions workflow for testing and continuous integration.
+#
+# This file performs testing using tox and tox.ini to define and configure the test environments.
+
+name: CI Tests
+
+on:
+  push:
+    branches:
+      - master  # GitHub now defaults to 'main' as the name of the primary branch. Change this as needed.
+  pull_request:
+     branches: # only build on PRs against 'main' if you need to further limit when CI is run.
+      - master
+
+jobs:
+  # Github Actions supports ubuntu, windows, and macos virtual environments:
+  # https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners
+  ci_tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - name: Code style checks
+            os: ubuntu-latest
+            python: 3.x
+            toxenv: codestyle
+
+          - name: Python 3.7 with minimal dependencies
+            os: ubuntu-latest
+            python: 3.7
+            toxenv: py37-test
+            toxposargs: --remote-data=any
+
+          - name: Python 3.9 with latest dev versions of key dependencies
+            os: ubuntu-latest
+            python: 3.9
+            toxenv: py39-test-devdeps
+            toxposargs: --remote-data=any
+
+          - name: Test building of Sphinx docs
+            os: ubuntu-latest
+            python: 3.x
+            toxenv: build_docs
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Set up python ${{ matrix.python }} on ${{ matrix.os }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda env update --file environment.yml --name base
+    - name: Install base dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install tox codecov
+    - name: Install graphviz dependency
+      if: ${{ contains(matrix.toxenv, 'build_docs') }}
+      run: sudo apt-get -y install graphviz
+    - name: Test with tox
+      run: |
+        tox -e ${{ matrix.toxenv }}

.gitignore

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+kelp/data/lightcurves.fits
+
+# Compiled files
+*.py[cod]
+*.a
+*.o
+*.so
+__pycache__
+
+# Ignore .c files by default to avoid including generated code. If you want to
+# add a non-generated .c extension, use `git add -f filename.c`.
+*.c
+
+# Other generated files
+*/version.py
+*/cython_version.py
+htmlcov
+.coverage
+MANIFEST
+.ipynb_checkpoints
+
+# Sphinx
+docs/api
+docs/_build
+
+# Eclipse editor project files
+.project
+.pydevproject
+.settings
+
+# Pycharm editor project files
+.idea
+
+# Floobits project files
+.floo
+.flooignore
+
+# Packages/installer info
+*.egg
+*.egg-info
+dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+
+# Other
+.cache
+.tox
+.*.sw[op]
+*~
+.project
+.pydevproject
+.settings
+pip-wheel-metadata/
+notebooks/
+
+# Mac OSX
+.DS_Store

.readthedocs.yml

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+version: 2
+
+build:
+  image: latest
+
+conda:
+  environment: environment.yml
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - all
+
+formats: []

MANIFEST.in

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+include README.rst
+include CHANGES.rst
+include setup.cfg
+include LICENSE.rst
+include pyproject.toml
+
+recursive-include jaxon *.pyx *.c *.pxd
+recursive-include docs *
+recursive-include licenses *
+recursive-include cextern *
+recursive-include scripts *
+
+prune build
+prune docs/_build
+prune docs/api
+
+global-exclude *.pyc *.o

README.rst

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+Phase curve models in JAX
+-------------------------
+
+License
+-------
+
+This project is Copyright (c) Brett M. Morris and licensed under
+the terms of the GNU GPL v3+ license. This package is based upon
+the `Openastronomy packaging guide <https://github.com/OpenAstronomy/packaging-guide>`_
+which is licensed under the BSD 3-clause licence. See the licenses folder for
+more information.
+
+
+Contributing
+------------
+
+We love contributions! jaxon is open source,
+built on open source, and we'd love to have you hang out in our community.
+
+**Imposter syndrome disclaimer**: We want your help. No, really.
+
+There may be a little voice inside your head that is telling you that you're not
+ready to be an open source contributor; that your skills aren't nearly good
+enough to contribute. What could you possibly offer a project like this one?
+
+We assure you - the little voice in your head is wrong. If you can write code at
+all, you can contribute code to open source. Contributing to open source
+projects is a fantastic way to advance one's coding skills. Writing perfect code
+isn't the measure of a good developer (that would disqualify all of us!); it's
+trying to create something, making mistakes, and learning from those
+mistakes. That's how we all improve, and we are happy to help others learn.
+
+Being an open source contributor doesn't just mean writing code, either. You can
+help out by writing documentation, tests, or even giving feedback about the
+project (and yes - that includes giving feedback about the contribution
+process). Some of these contributions may be the most valuable to the project as
+a whole, because you're coming to the project with fresh eyes, so you can see
+the errors and assumptions that seasoned contributors have glossed over.
+
+Note: This disclaimer was originally written by
+`Adrienne Lowe <https://github.com/adriennefriend>`_ for a
+`PyCon talk <https://www.youtube.com/watch?v=6Uj746j9Heo>`_, and was adapted by
+jaxon based on its use in the README file for the
+`MetPy project <https://github.com/Unidata/MetPy>`_.

docs/Makefile

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+# 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)

docs/conf.py

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+# -*- 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
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'jaxon'
+copyright = '2021, Brett M. Morris'
+author = 'Brett M. Morris'
+
+# The full version, including alpha/beta/rc tags
+from jaxon import __version__
+release = __version__
+
+# -- 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.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.doctest',
+    'sphinx.ext.mathjax',
+    'sphinx_automodapi.automodapi',
+    'sphinx_automodapi.smart_resolver',
+]
+
+# 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']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+# -- 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 = 'alabaster'
+
+# 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']

docs/index.rst

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+jaxon Documentation
+-------------------
+
+This is the documentation for jaxon.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

environment.yml

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+name: jaxon
+channels:
+  - conda-forge
+dependencies:
+  - astropy
+  - pip:
+    - pytest-astropy

jaxon/__init__.py

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+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+from .version import __version__  # noqa

jaxon/data/README.rst

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+Data directory
+==============
+
+This directory contains data files included with the package source
+code distribution. Note that this is intended only for relatively small files
+- large files should be externally hosted and downloaded as needed.

jaxon/tests/__init__.py

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+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+This module contains package tests.
+"""