Merge pull request legolason#68 from burke86/master

adding unit tests

.github/workflows/documentation.yml

@@ -0,0 +1,27 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx_rtd_theme myst_parser
+      - name: Sphinx build
+        run: |
+          sphinx-build doc _build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

.github/workflows/python-package.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f test-requirements.txt ]; then pip install -r requirements.txt -r test-requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        python -m pip install .
+        pytest tests/test_dr7sample.py

README.md

@@ -21,16 +21,3 @@ v1.1 (stable): https://github.com/legolason/PyQSOFit/releases/tag/v1.1
 
 ## Cite this code
 
-> The preferred citation for this code is Guo, Shen & Wang (2018), ascl:1809:008\
-> @misc{2018ascl.soft09008G,\
-> author = {{Guo}, H. and {Shen}, Y. and {Wang}, S.},\
-> title = "{PyQSOFit: Python code to fit the spectrum of quasars}",\
-> keywords = {Software },\
-> howpublished = {Astrophysics Source Code Library},\
-> year = 2018,\
-> month = sep,\
-> archivePrefix = "ascl",\
-> eprint = {1809.008},\
-> adsurl = {[http://adsabs.harvard.edu/abs/2018ascl.soft09008G}](http://adsabs.harvard.edu/abs/2018ascl.soft09008G%7D),\
-> adsnote = {Provided by the SAO/NASA Astrophysics Data System}\
-> }

doc/.placeholder

@@ -0,0 +1 @@
+

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     = .
+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/conf.py

@@ -0,0 +1,32 @@
+# 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
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+project = 'pyqsofit'
+copyright = '2024, Hengxiao Guo'
+author = 'Hengxiao Guo'
+release = '2.1.6'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

doc/index.rst

@@ -0,0 +1,20 @@
+.. pyqsofit documentation master file, created by
+   sphinx-quickstart on Fri Jun 28 18:21:35 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to pyqsofit's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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=.
+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/modules.rst

@@ -0,0 +1,7 @@
+pyqsofit
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   pyqsofit

doc/pyqsofit.rst

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+pyqsofit package
+================
+
+Submodules
+----------
+
+pyqsofit.HostDecomp module
+--------------------------
+
+.. automodule:: pyqsofit.HostDecomp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyqsofit.MESFit module
+----------------------
+
+.. automodule:: pyqsofit.MESFit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyqsofit.PyQSOFit module
+------------------------
+
+.. automodule:: pyqsofit.PyQSOFit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyqsofit.version module
+-----------------------
+
+.. automodule:: pyqsofit.version
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pyqsofit
+   :members:
+   :undoc-members:
+   :show-inheritance: