Merge pull request #16 from ConorMacBride/refactor-to-base

Refactor common attributes and methods to ModelBase. Improve documentation and testing of mcalf.models.

.gitignore

@@ -14,6 +14,7 @@ __pycache__
 */cython_version.py
 htmlcov
 .coverage
+coverage.xml
 MANIFEST
 .ipynb_checkpoints
 

.readthedocs.yml

@@ -21,7 +21,7 @@ python:
     - requirements: docs/requirements.txt
     - method: pip
       path: .
-      extra_requirements:
-        - docs
-        - all
+# Build from requirements.txt to use https://github.com/astropy/sphinx-automodapi/pull/121
+#      extra_requirements:
+#        - docs
   system_packages: true

docs/conf.py

@@ -42,13 +42,20 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.coverage',
     'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
     'sphinx.ext.todo',
     'sphinx.ext.viewcode',
 ]
 numpydoc_show_class_members = False
 nbsphinx_execute = 'never'
+all_methods = [
+    'mcalf.models.base.ModelBase',
+    'mcalf.models.ModelBase',
+]
+automodsumm_private_methods_of = all_methods
+automodsumm_special_methods_of = all_methods
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -58,6 +65,14 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
+intersphinx_mapping = {
+    "python": ('https://docs.python.org/3', None),
+    "astropy": ("https://docs.astropy.org/en/stable/", None),
+    "matplotlib": ('https://matplotlib.org/', None),
+    "numpy": ('https://numpy.org/doc/stable', None),
+    "scipy": ('https://docs.scipy.org/doc/scipy/reference', None),
+    "sklearn": ('https://scikit-learn.org/stable', None),
+}
 
 # -- Options for HTML output -------------------------------------------------
 

docs/requirements.txt

@@ -1,5 +1,6 @@
 sphinx==3.1.2
-sphinx-automodapi==0.12
+#sphinx-automodapi==0.12
+-e git+https://github.com/astropy/sphinx-automodapi.git@refs/pull/121/head#egg=sphinx-automodapi
 ipykernel
 nbsphinx==0.7.1
 sphinx-rtd-theme==0.5.0

setup.cfg

@@ -54,6 +54,10 @@ docs =
 [options.packages.find]
 where = src
 
+[tool:pytest]
+filterwarnings =
+    ignore:Spectra should be fully processed before loading into MCALF.
+
 [coverage:run]
 omit =
   */mcalf/tests/*