improve config and env file

related to #41
ArcInstitute · Apr 6, 2024 · 0891b07 · 0891b07
1 parent ef37050
commit 0891b07
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Showing 3 changed files with 26 additions and 23 deletions.
diff --git a/docs/environment.yaml b/docs/environment.yaml
@@ -3,29 +3,11 @@ channels:
   - anaconda
   - conda-forge
 dependencies:
-  - python=3.9
-  - scanpy
-  - python-igraph
-  - leidenalg
-  - pandas<2.0
-  - anndata
-  - numpy
-  - scipy
-  - matplotlib<3.7
-  - seaborn
-  - pyarrow
-  - ipykernel
-  - mscorefonts
-  - rust>=1.72
+  - python
   - myst-parser=0.18.1
   - sphinx=5.3.0
   - sphinx_rtd_theme=1.1.1
   - sphinxcontrib-bibtex
   - pip
   - pip:
-      - click
-      - polars
-      - biobear
-      - numba
-      - pydeseq2
       - watermark
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,10 +1,7 @@
 sphinx
-pandas
-anndata
-scanpy
 myst-parser
 sphinx_bootstrap_theme
 pip
 nbsphinx
 sphinx-rtd-theme
-pydeseq2
+sphinxcontrib-bibtex
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -21,6 +21,30 @@
 
 language = 'en'
 
+# improve class docs
+# By default, Sphinx ignores docstrings for __init__.py and shows only top-level docstrings for the class itself. 
+
+autoclass_content = 'both'
+
+autodoc_mock_imports = [
+    "numpy",
+    "pandas",
+    "scipy",
+    "matplotlib",
+    "seaborn",
+    "scanpy",
+    "anndata",
+    "screenpro",
+    "pyarrow",
+    "biobear",
+    "click",
+    "polars",
+    "biobear",
+    "numba",
+    "pydeseq2",
+    "watermark"
+]
+
 # Bibliography settings
 bibtex_bibfiles = ["references.bib"]
 bibtex_reference_style = "author_year"