Got sphinx almost working, building PDF outputs if I do some addition…

…al steps. Still lots of issues, but decent checkpoint.

docs/conf.py

@@ -1,4 +1,8 @@
 import os
+import sys
+sys.path.insert(0, os.path.abspath('../src'))
+sys.path.insert(0, os.path.abspath('../src/idmlaser_cholera/'))
+sys.path.insert(0, os.path.abspath('../src/idmlaser_cholera/mods'))
 
 extensions = [
     "sphinx.ext.autodoc",
@@ -39,6 +43,37 @@
 }
 html_short_title = f"{project}-{version}"
 
-napoleon_use_ivar = True
-napoleon_use_rtype = False
-napoleon_use_param = False
+# Napoleon settings (Napolean converts Google-style docstrings to reStructuredText)
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = True  # from Cookiecutter template, False is the default
+napoleon_use_param = False  # from Cookiecutter template, True is the default
+napoleon_use_rtype = False  # from Cookiecutter template, True is the default
+napoleon_preprocess_types = False
+napoleon_type_aliases = None
+napoleon_attr_annotations = True
+
+mathjax3_config = {"TeX": {"Macros": {"small": ["{\\scriptstyle #1}", 1]}}}
+
+# Prevent the following warning:
+# sphinx/builders/linkcheck.py:86: RemovedInSphinx80Warning: The default value for 'linkcheck_report_timeouts_as_broken' will change to False in Sphinx 8, meaning that request timeouts will be reported with a new 'timeout' status, instead of as 'broken'. This is intended to provide more detail as to the failure mode. See https://github.com/sphinx-doc/sphinx/issues/11868 for details.
+#   warnings.warn(deprecation_msg, RemovedInSphinx80Warning, stacklevel=1)
+linkcheck_report_timeouts_as_broken = False
+latex_documents = [
+    ('index', 'LASER_Cholera.tex', 'LASER_Cholera', 'IDM', 'manual'),
+]
+linkcheck_ignore = [
+    r"https://laser\.readthedocs\.io/",
+    r"https://pypi\.org/project/idmlaser"
+]
+
+exclude_patterns = [
+    'reference/idmlaser_cholera.tools.make_suitability_random_data.rst',  # Exclude this specific .rst file
+    'idmlaser_cholera/__main__.py',
+]

requirements.txt

@@ -4,7 +4,6 @@ h5py # caching
 pandas # sigh
 numba
 numpy
-pkg_resources
 requests
 taichi
 tqdm