[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.pre-commit-config.yaml

@@ -49,4 +49,4 @@ repos:
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.2.5
 #   hooks:
-#   - id: codespell
+#   - id: codespell

README.md

@@ -97,7 +97,7 @@ print(sce)
 # alternative_experiments(2): ['repeat', 'ERCC']
 # row_pairs(0): []
 # column_pairs(0): []
-# metadata(0): 
+# metadata(0):
 ```
 
 For studies that generate multiple datasets, the dataset of interest must be explicitly requested via the `path` argument:
@@ -114,12 +114,12 @@ print(sce)
 # row_names(20125): ['A1BG', 'A1CF', 'A2M', ..., 'ZZEF1', 'ZZZ3', 'pk']
 # column_data columns(2): ['donor', 'label']
 # column_names(8569): ['human1_lib1.final_cell_0001', 'human1_lib1.final_cell_0002', 'human1_lib1.final_cell_0003', ..., 'human4_lib3.final_cell_0699', 'human4_lib3.final_cell_0700', 'human4_lib3.final_cell_0701']
-# main_experiment_name:  
+# main_experiment_name:
 # reduced_dims(0): []
 # alternative_experiments(0): []
 # row_pairs(0): []
 # column_pairs(0): []
-# metadata(0): 
+# metadata(0):
 ```
 
 By default, array data is loaded as a file-backed `DelayedArray` from the [HDF5Array](https://github.com/BiocPy/HDF5Array) package. Setting `realize_assays=True` and/or `realize_reduced_dims=True` will coerce file-backed arrays to numpy or scipy sparse (csr/csc) objects.
@@ -136,7 +136,7 @@ print(sce)
 # row_names(20125): ['A1BG', 'A1CF', 'A2M', ..., 'ZZEF1', 'ZZZ3', 'pk']
 # column_data columns(2): ['donor', 'label']
 # column_names(8569): ['human1_lib1.final_cell_0001', 'human1_lib1.final_cell_0002', 'human1_lib1.final_cell_0003', ..., 'human4_lib3.final_cell_0699', 'human4_lib3.final_cell_0700', 'human4_lib3.final_cell_0701']
-# main_experiment_name:  
+# main_experiment_name:
 # reduced_dims(0): []
 # alternative_experiments(0): []
 # row_pairs(0): []
@@ -215,12 +215,12 @@ Want to contribute your own dataset to this package? It's easy! Just follow thes
    - An Python file containing the code used to assemble the dataset. This should be added to the [`scripts/`](https://github.com/BiocPy/scRNAseq/tree/master/scripts) directory of this package, in order to provide some record of how the dataset was created.
 
 5. Wait for us to grant temporary upload permissions to your GitHub account.
-   
+
 6. Upload your staging directory to [**gypsum** backend](https://github.com/ArtifactDB/gypsum-worker) with `upload_dataset()`. On the first call to this function, it will automatically prompt you to log into GitHub so that the backend can authenticate you. If you are on a system without browser access (e.g., most computing clusters), a [token](https://github.com/settings/tokens) can be manually supplied via `set_access_token()`.
 
      ```python
      from scrnaseq import upload_dataset
-     
+
      upload_dataset(staging_dir, "my_dataset_name", "my_version")
      ```
 

docs/requirements.txt

@@ -1,8 +1,8 @@
+furo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-furo
-sphinx-autodoc-typehints
+sphinx-autodoc-typehints

pyproject.toml

@@ -21,4 +21,4 @@ convention = "google"
 "__init__.py" = ["E402", "F401"]
 
 [tool.black]
-force-exclude = "__init__.py"
+force-exclude = "__init__.py"

setup.py

@@ -1,11 +1,10 @@
-"""
-    Setup file for scrnaseq.
-    Use setup.cfg to configure your project.
+"""Setup file for scrnaseq. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.5.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.5.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
+
 from setuptools import setup
 
 if __name__ == "__main__":

src/scrnaseq/list_datasets.py

@@ -67,7 +67,7 @@ def list_datasets(
 
 
 def _format_query_results(results: list, key_names: list):
-    """Format the results from sqlite as a pandas dataframe
+    """Format the results from sqlite as a pandas dataframe.
 
     Key names must be in the exact same order as the query.
     """

src/scrnaseq/polish_dataset.py

@@ -1,8 +1,6 @@
 from typing import Type
-from warnings import warn
 
 import numpy as np
-from delayedarray import DelayedArray
 from scipy import sparse as sp
 from singlecellexperiment import SingleCellExperiment
 from summarizedexperiment import SummarizedExperiment

src/scrnaseq/save_dataset.py

@@ -29,7 +29,7 @@ def save_dataset(x: Any, path, metadata):
 
         metadata:
             Dictionary containing the metadata for this dataset.
-            see the schema returned by 
+            see the schema returned by
             :py:func:`~gypsum_client.fetch_metadata_schema.fetch_metadata_schema`.
 
             Note that the ``applications.takane`` property will be automatically

src/scrnaseq/search_datasets.py

@@ -6,8 +6,6 @@
 from gypsum_client import cache_directory, fetch_metadata_database
 from gypsum_client.search_metadata import (
     GypsumSearchClause,
-    define_text_query,
-    search_metadata_text,
     search_metadata_text_filter,
 )
 
@@ -25,8 +23,7 @@ def search_datasets(
     overwrite: bool = False,
     latest: bool = True,
 ) -> pd.DataFrame:
-    """Search for datasets of interest based on matching text in the
-    associated metadata.
+    """Search for datasets of interest based on matching text in the associated metadata.
 
     This is a wrapper around
     :py:func:`~gypsum_client.search_metadata.search_metadata_text`.

src/scrnaseq/utils.py

@@ -94,7 +94,7 @@ def format_object_metadata(x) -> dict:
     """Format object related metadata.
 
     Create object-related metadata to validate against the default
-    schema from 
+    schema from
     :py:func:`~gypsum_client.fetch_metadata_schema.fetch_metadata_schema`.
     This is intended for downstream package developers who are
     auto-generating metadata documents to be validated by

tests/conftest.py

@@ -1,10 +1,9 @@
-"""
-    Dummy conftest.py for scrnaseq.
+"""Dummy conftest.py for scrnaseq.
 
-    If you don't know what this is for, just leave it empty.
-    Read more about conftest.py under:
-    - https://docs.pytest.org/en/stable/fixture.html
-    - https://docs.pytest.org/en/stable/writing_plugins.html
+If you don't know what this is for, just leave it empty.
+Read more about conftest.py under:
+- https://docs.pytest.org/en/stable/fixture.html
+- https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
 # import pytest

tests/test_save_dataset.py

@@ -82,7 +82,8 @@ def test_save_dataset_anndata():
     assert isinstance(roundtrip.get_assays()["counts"], ReloadedArray)
     assert isinstance(adata.layers["counts"], np.ndarray)
     assert np.array_equal(
-        to_dense_array(roundtrip.get_assays()["counts"]).transpose(), adata.layers["counts"]
+        to_dense_array(roundtrip.get_assays()["counts"]).transpose(),
+        adata.layers["counts"],
     )
 
     # Load and check the metadata