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CHANGELOG.md

@@ -6,9 +6,9 @@
 
 ## [0.1.2] - 2024-11-11
 
--   No change in DRVI code
--   Fix github workflow, tests, docs, and pypi publishing pipelines
+- No change in DRVI code
+- Fix github workflow, tests, docs, and pypi publishing pipelines
 
 ## [0.1.0] - 2024-08-21
 
--   Moved all files from repo to scverse cookiecutter project template
+- Moved all files from repo to scverse cookiecutter project template

README.md

@@ -25,12 +25,12 @@ Unsupervised Deep Disentangled Representation of Single-Cell Omics
 
 Please refer to the [documentation][link-docs]. In particular, the
 
--   [Tutorials][link-tutorials], specially
-    -   [A demo](https://drvi.readthedocs.io/latest/notebooks/general_pipeline.html) of how to train DRVI and interpret the latent dimensions.
--   [API documentation][link-api], specially
-    -   [DRVI Model](https://drvi.readthedocs.io/latest/api/generated/drvi.model.DRVI.html)
-    -   [DRVI utility functions (tools)](https://drvi.readthedocs.io/latest/api/tools.html)
-    -   [DRVI plotting functions](https://drvi.readthedocs.io/latest/api/plotting.html)
+- [Tutorials][link-tutorials], specially
+    - [A demo](https://drvi.readthedocs.io/latest/notebooks/general_pipeline.html) of how to train DRVI and interpret the latent dimensions.
+- [API documentation][link-api], specially
+    - [DRVI Model](https://drvi.readthedocs.io/latest/api/generated/drvi.model.DRVI.html)
+    - [DRVI utility functions (tools)](https://drvi.readthedocs.io/latest/api/tools.html)
+    - [DRVI plotting functions](https://drvi.readthedocs.io/latest/api/plotting.html)
 
 ## System requirements
 

docs/contributing.md

@@ -100,11 +100,11 @@ Specify `vX.X.X` as a tag name and create a release. For more information, see [
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
 
--   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
--   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
--   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
@@ -121,10 +121,10 @@ repository.
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-    if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-    the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+  if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+  the `nitpick_ignore` list in `docs/conf.py`
 
 #### Building the docs locally
 

docs/extensions/typed_returns.py

@@ -12,7 +12,7 @@
 def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
     for line in lines:
         if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
-            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line
 

src/drvi/nn_modules/embedding.py

@@ -39,9 +39,7 @@ def __repr__(self):
         if self._freeze_hook is None:
             return f"Emb({self.num_embeddings}, {self.embedding_dim})"
         else:
-            return (
-                f"Emb({self.num_embeddings}, {self.embedding_dim} | " f"freeze: {self.n_freeze_x}, {self.n_freeze_y})"
-            )
+            return f"Emb({self.num_embeddings}, {self.embedding_dim} | freeze: {self.n_freeze_x}, {self.n_freeze_y})"
 
 
 class MultiEmbedding(nn.Module):
@@ -103,7 +101,7 @@ def from_pretrained(cls, feature_embedding_instance):
     def load_weights_from_trained_module(self, other, freeze_old=False):
         assert len(self.emb_list) >= len(other.emb_list)
         if len(self.emb_list) > len(other.emb_list):
-            logging.warning(f"Extending feature embedding {other} to {self} " f"with more feature categories.")
+            logging.warning(f"Extending feature embedding {other} to {self} with more feature categories.")
         else:
             logging.info(f"Extending feature embedding {other} to {self}")
         for self_emb, other_emb in zip(self.emb_list, other.emb_list, strict=False):

src/drvi/nn_modules/feature_interface.py

@@ -16,9 +16,7 @@ def __init__(self, feature_info_str_list: list[str], axis="var", total_dim=None,
         self.axis = axis
         if any(fi.dim is None for fi in self.feature_info_list):
             if total_dim is None and default_dim is None:
-                raise ValueError(
-                    f"missing dim in {feature_info_str_list}\n" f"Please provide `total_dim` or `default_dim`"
-                )
+                raise ValueError(f"missing dim in {feature_info_str_list}\nPlease provide `total_dim` or `default_dim`")
             if total_dim is not None:
                 self._fill_with_total_dim(total_dim)
             if default_dim is not None:

src/drvi/scvi_tools_based/model/base/_archesmixin.py

@@ -85,7 +85,7 @@ def load_query_data(
             raise ValueError("It appears you are loading a model from a different class.")
 
         if _SETUP_ARGS_KEY not in registry:
-            raise ValueError("Saved model does not contain original setup inputs. " "Cannot load the original setup.")
+            raise ValueError("Saved model does not contain original setup inputs. Cannot load the original setup.")
 
         cls.setup_anndata(
             adata,