Merge pull request #5 from Cadair/pfsspy

Merge in pfsspy repo

.github/workflows/ci.yml

@@ -27,6 +27,7 @@ jobs:
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
+      posargs: -n auto
       envs: |
         - linux: py312
     secrets:

.gitignore

@@ -74,6 +74,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/generated/
 # automodapi
 docs/api
 
@@ -259,3 +260,7 @@ package.json
 
 # Log files generated by 'vagrant up'
 *.log
+
+# repo specific
+examples/using_pfsspy/aia_map.fits
+docs/sg_execution_times.rst

.mailmap

@@ -0,0 +1,5 @@
+Samuel Badman <samuel.badman@cfa.harvard.edu> sam.badman <sam.badman@ssl.berkeley.edu>
+Samuel Badman <samuel.badman@cfa.harvard.edu> Samuel Badman <54911235+STBadman@users.noreply.github.com>
+Samuel Badman <samuel.badman@cfa.harvard.edu> STBadman <samuel_badman@berkeley.edu>
+Stuart Mumford <stuart@cadair.com> Cadair <1391051+Cadair@users.noreply.github.com>
+Matthieu Ancellin <31126826+mancellin@users.noreply.github.com>

.ruff.toml

@@ -18,6 +18,11 @@ extend-ignore = [
   "PT007", # Parametrize should be lists of tuples  # TODO! fix
   "PT011", # Too broad exception assert             # TODO! fix
   "PT023", # Always use () on pytest decorators
+
+  # pfsspy
+  # TODO: Fix these
+  "E741",
+  "F811",
 ]
 
 [lint.flake8-tidy-imports]

docs/conf.py

@@ -4,6 +4,7 @@
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/master/config
 
+import os
 
 # -- Project information -----------------------------------------------------
 
@@ -12,7 +13,7 @@
 release = __version__
 
 project = "sunkit-magex"
-copyright = "2022, The SunPy Community"
+copyright = "2024, The SunPy Community"
 author = "The SunPy Community"
 
 # -- General configuration ---------------------------------------------------
@@ -32,6 +33,7 @@
     "sphinx.ext.mathjax",
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",
+    'sphinx_gallery.gen_gallery',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -51,25 +53,39 @@
 
 # -- Options for intersphinx extension ---------------------------------------
 
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"python": ("https://docs.python.org/", None)}
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/", None),
+    "astropy": ("https://docs.astropy.org/en/stable", None),
+    "sunpy": ("https://docs.sunpy.org/en/stable", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "streamtracer": ("https://streamtracer.readthedocs.io/en/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "reproject": ("https://reproject.readthedocs.io/en/stable/", 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"]
-
-# By default, when rendering docstrings for classes, sphinx.ext.autodoc will
-# make docs with the class-level docstring and the class-method docstrings,
-# but not the __init__ docstring, which often contains the parameters to
-# class constructors across the scientific Python ecosystem. The option below
-# will append the __init__ docstring to the class-level docstring when rendering
-# the docs. For more options, see:
-# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autoclass_content
-autoclass_content = "both"
+html_theme = "sunpy"
+
+# -- Sphinx Gallery ----------------------------------------------------------
+
+from sphinx_gallery.sorting import ExplicitOrder  # noqa
+
+sphinx_gallery_conf = {
+    "ignore_pattern": ".*helpers.py",
+    "examples_dirs": "../examples",
+    "gallery_dirs": os.path.join("generated", "gallery"),
+    "subsection_order": ExplicitOrder(["../examples/using_pfsspy",
+                                       "../examples/finding_data",
+                                       "../examples/utils",
+                                       "../examples/pfsspy_info",
+                                       "../examples/testing"]),
+    "reference_url": {"sphinx_gallery": None}
+}
+
+# -- Other options ----------------------------------------------------------
+default_role = 'py:obj'
+
+os.environ["JSOC_EMAIL"] = 'jsoc@sunpy.org'
+
+nitpicky = True

docs/index.rst

@@ -7,9 +7,9 @@ This is the documentation for sunkit-magex.
    :maxdepth: 2
    :caption: Contents:
 
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   installing
+   generated/gallery/index
+   pfsspy
+   performance
+   numerical_method
+   synoptic_fits

docs/installing.rst

@@ -0,0 +1,15 @@
+Installing
+----------
+sunkit_magex can be installed from PyPI using
+
+.. code::
+
+    pip install sunkit-magex
+
+This will install sunkit_magex and all of its dependencies. In addition to the core
+dependencies, there are two optional dependencies (numba, streamtracer) that
+improve code performance. These can be installed with
+
+.. code::
+
+    pip install sunkit-magex[performance]