punch-mission · jmbhughes · Dec 7, 2023 · Nov 10, 2023 · Nov 17, 2023 · Nov 19, 2023
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -12,24 +12,27 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+    - uses: docker://pandoc/core:2.9
 
     # Install dependencies
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: "3.10"
 
     - name: Install dependencies
       run: |
-        pip install . 
         pip install -r ./docs/requirements.txt
+        pip install -r requirements.txt
+
     # Build the book
-    - name: Build the book
+    - name: Sphinx build
       run: |
-        jupyter-book build docs/
+        cd ./docs; make html; cd ..
+
     # Push the book's HTML to github-pages
     - name: GitHub Pages action
       uses: peaceiris/[email protected]
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs/_build/html
+        publish_dir: ./docs/build/html
diff --git a/.gitignore b/.gitignore
@@ -128,3 +128,6 @@ dmypy.json
 # Pyre type checker
 .pyre/
 *.DS_Store
+
+*venv*
+.idea
diff --git a/README.md b/README.md
@@ -9,24 +9,34 @@
 `solpolpy` is a solar polarization resolver based on [Deforest et al. 2022](https://doi.org/10.3847/1538-4357/ac43b6).
 It converts between various polarization formats, e.g. from the native three triple version from observations
 (also known as the MZP convention) to polarization brightness (pB) and total polarization (B), Stokes I, Q and U, etc.
+As it is in early development, breaking changes may be frequent. 
+
 An example of transforming the polarization basis using the LASCO/C2 images is 
-shown in the image below.
-The images at polarizing angles of -60°, 0° and +60° is shown in the top panel as 
-Bm, Bz and Bp respectively.
-The bottom panel shows the output of the `solpolpy` to convert the initial basis 
+shown in the image below.  The images at polarizing angles of -60°, 0° and +60° is shown in the top panel as 
+Bm, Bz and Bp respectively. The bottom panel shows the output of the `solpolpy` to convert the initial basis 
 to the Stokes I, Q and U.
 ![Example result image](eg_image.png)
 
 ## Quickstart
 `pip install solpolpy`
 
-Note: We will be updating [the documentation](https://punch-mission.github.io/solpolpy/quickstart.html) soon! 
+We recommend following along the examples in [the documentation](https://punch-mission.github.io/solpolpy/quickstart.html)! 
 
 ## Getting Help
 Please open a discussion or issue for help. 
 
+## Features Coming Soon
+- [x] core transformation capability
+- [x] clearer examples in the documentation
+- [ ] quantification and propagation of error 
+- [ ] additional plotting utilities 
+- [ ] more comprehensive support for 4-polarizer systems
+- [ ] functions to deal with the IMAX effect in wide-field imagers
+
 ## Contributing
-We encourage all contributions. If you have a problem with the code or would like to see a new feature, please open an issue. Or you can submit a pull request. 
+We encourage all contributions. 
+If you have a problem with the code or would like to see a new feature, please open an issue. 
+Or you can submit a pull request. 
 
 ## Code of Conduct
 [Access here](CODE_OF_CONDUCT.md)

diff --git a/docs/Makefile b/docs/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)
diff --git a/docs/_config.yml b/docs/_config.yml
diff --git a/docs/_toc.yml b/docs/_toc.yml
diff --git a/docs/advanced_options.md b/docs/advanced_options.md
diff --git a/docs/api.rst b/docs/api.rst
diff --git a/docs/intro.md b/docs/intro.md
diff --git a/docs/logo.png b/docs/logo.png
diff --git a/docs/make.bat b/docs/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
diff --git a/docs/quickstart.md b/docs/quickstart.md
diff --git a/docs/references.bib b/docs/references.bib
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,5 @@
-jupyter-book
-matplotlib
-numpy
+sphinx
+pydata-sphinx-theme
+sphinx-autoapi
+nbsphinx
+ipython
diff --git a/docs/source/cite.rst b/docs/source/cite.rst
@@ -0,0 +1,18 @@
+Cite
+=======
+
+To cite the software::
+
+    @software{marcus_hughes_2023_10076327,
+        author       = {Marcus Hughes and
+                        Ritesh Patel and
+                        Dr Matthieu Wes and
+                        Bryce-Walbridge},
+        title        = {punch-mission/solpolpy: 0.0.1},
+        month        = nov,
+        year         = 2023,
+        publisher    = {Zenodo},
+        version      = {0.0.1},
+        doi          = {10.5281/zenodo.10076327},
+        url          = {https://doi.org/10.5281/zenodo.10076327}
+    }
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,80 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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 sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'solpolpy'
+copyright = '2023, PUNCH Science Operations Center'
+author = 'PUNCH Science Operations Center'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.0'
+
+
+# -- 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 = ['autoapi.extension',
+              'sphinx.ext.autodoc',
+              'sphinx.ext.napoleon',
+              'nbsphinx',
+              'IPython.sphinxext.ipython_console_highlighting']
+
+# 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 = []
+
+
+# -- 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 = "pydata_sphinx_theme"
+html_show_sourcelink = False
+html_static_path = ['_static']
+html_theme_options = {
+    "use_edit_page_button": True,
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/punch-mission/solpolpy",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        }
+    ],
+    "show_nav_level": 1,
+    "show_toc_level": 3
+}
+html_context = {
+    # "github_url": "https://github.com", # or your GitHub Enterprise site
+    "github_user": "punch-mission",
+    "github_repo": "solpolpy",
+    "github_version": "main",
+    "doc_path": "docs/source/",
+}
+
+
+autoapi_dirs = ['../../solpolpy']
+
diff --git a/docs/source/data/stereo_0.fts b/docs/source/data/stereo_0.fts
diff --git a/docs/source/data/stereo_120.fts b/docs/source/data/stereo_120.fts
diff --git a/docs/source/data/stereo_240.fts b/docs/source/data/stereo_240.fts