v0.2.0

.github/workflows/build.yml

@@ -25,4 +25,4 @@ jobs:
         run: uv sync --extra dev
 
       - name: Run ruff
-        run: uv run ruff check src/
+        run: uvx ruff check src/

.gitignore

@@ -1,3 +1,5 @@
+docs/generated/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CHANGELOG.md

@@ -8,6 +8,18 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## Version 0.2.0
+
+> [!WARNING]  
+> **Breaking changes**
+> New changes to the API, please see the documentation
+
+### Changed
+
+- new api documentation
+- new api changes
+- use uvx for running tools
+
 ## Version 0.1.0
 
 **NOTE**: Use this version with initial release of the AI models `v1.0`.

docs/api.md

@@ -1,5 +1,35 @@
 # API
 
+## scanvi_explainer
+
+### Utilities: `utils`
+
+```{eval-rst}
+.. currentmodule:: scanvi_explainer
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+
+    utils.train_test_group_split
+```
+
+### Plots: `plots`
+
+```{eval-rst}
+.. currentmodule:: scanvi_explainer
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+
+    plots.feature_plot
+```
+
 ## SCANVIDeep
 
 ```{eval-rst}
@@ -12,4 +42,4 @@
     :nosignatures:
 
     scanvi_deep
-```
+```

docs/conf.py

@@ -84,10 +84,14 @@
 }
 
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
-    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "huggingface_hub": ("https://huggingface.co/docs/huggingface_hub/main/en", None),
+    "matplotlib": ("https://matplotlib.org/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "python": ("https://docs.python.org/3", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "torch": ("https://pytorch.org/docs/master/", None),
 }
 
 # List of patterns, relative to source directory, that match files and
@@ -119,5 +123,5 @@
 nitpick_ignore = [
     # If building the documentation fails because of a missing link that is outside your control,
     # you can add an exception to this list.
-    #     ("py:class", "igraph.Graph"),
-]
+    ("optional"),
+]