Merge pull request #36 from samaloney/docs-example-gallery

Add doc gallery and paper figure example

.isort.cfg

@@ -0,0 +1,16 @@
+[settings]
+balanced_wrapping = true
+skip =
+    docs/conf.py
+    chimerapy/__init__.py
+default_section = THIRDPARTY
+include_trailing_comma = true
+known_astropy = astropy, asdf
+known_chimerapy = chimerapy
+known_first_party = chimerapy
+length_sort = false
+length_sort_sections = stdlib
+line_length = 110
+multi_line_output = 3
+no_lines_before = LOCALFOLDER
+sections = STDLIB, THIRDPARTY, ASTROPY, CHIMERAPY, FIRSTPARTY, LOCALFOLDER

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.8"
+    rev: "v0.6.1"
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -27,3 +27,7 @@ repos:
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|.json)$|^CITATION.rst$"
       - id: mixed-line-ending
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
+
+ci:
+  autofix_prs: false
+  autoupdate_schedule: "quarterly"

chimerapy/chimera.py

@@ -1,19 +1,20 @@
 """ """
 
-import glob
 import sys
+import glob
 
-import astropy.units as u
 import cv2
 import mahotas
 import matplotlib.pyplot as plt
 import numpy as np
-import scipy.interpolate
 import sunpy.map
+from scipy.interpolate import RectBivariateSpline
+from skimage.util import img_as_ubyte
+
+import astropy.units as u
 from astropy import wcs
 from astropy.io import fits
 from astropy.modeling.models import Gaussian2D
-from skimage.util import img_as_ubyte
 
 
 def chimera_legacy():
@@ -46,15 +47,15 @@ def chimera(im171, im193, im211, imhmi):
     hdu_number = 0
     heda = fits.getheader(im171[0], hdu_number)
     data = fits.getdata(im171[0], ext=0) / (heda["EXPTIME"])
-    dn = scipy.interpolate.interp2d(x, x, data)
+    dn = RectBivariateSpline(x, x, data, kx=1, ky=1)
     data = dn(np.arange(0, 4096), np.arange(0, 4096))
     hedb = fits.getheader(im193[0], hdu_number)
     datb = fits.getdata(im193[0], ext=0) / (hedb["EXPTIME"])
-    dn = scipy.interpolate.interp2d(x, x, datb)
+    dn = RectBivariateSpline(x, x, datb, kx=1, ky=1)
     datb = dn(np.arange(0, 4096), np.arange(0, 4096))
     hedc = fits.getheader(im211[0], hdu_number)
     datc = fits.getdata(im211[0], ext=0) / (hedc["EXPTIME"])
-    dn = scipy.interpolate.interp2d(x, x, datc)
+    dn = RectBivariateSpline(x, x, datc, kx=1, ky=1)
     datc = dn(np.arange(0, 4096), np.arange(0, 4096))
     hedm = fits.getheader(imhmi[0], hdu_number)
     datm = fits.getdata(imhmi[0], ext=0)

docs/conf.py

@@ -4,7 +4,7 @@
 # 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
-
+import pathlib
 
 # -- Project information -----------------------------------------------------
 
@@ -24,16 +24,17 @@
 # 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.inheritance_diagram",
+    "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",
+    "sphinx_gallery.gen_gallery",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -75,3 +76,17 @@
 # the docs. For more options, see:
 # https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autoclass_content
 autoclass_content = "both"
+
+# -- Options for the Sphinx gallery -------------------------------------------
+path = pathlib.Path.cwd()
+example_dir = path.parent.joinpath("examples")
+sphinx_gallery_conf = {
+    "backreferences_dir": str(path.joinpath("generated", "modules")),
+    "filename_pattern": "^((?!skip_).)*$",
+    "examples_dirs": example_dir,
+    "gallery_dirs": path.joinpath("generated", "gallery"),
+    "abort_on_example_error": False,
+    "plot_gallery": "True",
+    "remove_config_comments": True,
+    "only_warn_on_example_error": True,
+}

docs/index.rst

@@ -4,8 +4,8 @@ CHIMERApy Documentation
 This is the documentation for CHIMERApy.
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+
+    ../generated/gallery/index
 
 Indices and tables
 ==================

examples/README.rst

@@ -0,0 +1,2 @@
+Gallery
+=======