[pre-commit.ci] pre-commit autoupdate

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
   "context": {
     "cookiecutter": {
       "project_name": "infercnvpy",
@@ -12,7 +12,8 @@
       "project_repo": "https://github.com/icbi-lab/infercnvpy",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,
@@ -24,5 +25,5 @@
     }
   },
   "directory": null,
-  "checkout": "v0.3.0"
+  "checkout": "v0.4.0"
 }

.github/workflows/test.yaml

@@ -24,13 +24,13 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python: "3.9"
+            python: "3.10"
             r: release
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.12"
             r: release
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.12"
             r: release
             pip-flags: "--pre"
 

.gitignore

@@ -18,6 +18,7 @@ __pycache__/
 /.pytest_cache/
 /.cache/
 /data/
+/node_modules/
 
 # docs
 /docs/generated/

.pre-commit-config.yaml

@@ -13,15 +13,15 @@ repos:
         # doesn't work in combination with jupytext hook yet. See https://github.com/mwouts/jupytext/issues/580
         exclude: "docs/notebooks/.*\\.md"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.4.8
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: detect-private-key
       - id: check-ast

README.md

@@ -32,7 +32,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.9 or newer installed on your system. If you don't have
+You need to have Python 3.10 or newer installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 There are several alternative options to install infercnvpy:

docs/conf.py

@@ -1,5 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
-#
+
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html

docs/contributing.md

@@ -51,7 +51,7 @@ and [prettier][prettier-editors].
 ## Writing tests
 
 ```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
+Remember to first install the package with `pip install -e '.[dev,test]'`
 ```
 
 This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
@@ -93,7 +93,7 @@ Before making a release, you need to update the version number in the `pyproject
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
 
 ## Writing documentation
 
@@ -157,3 +157,4 @@ open _build/html/index.html
 [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
 [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 [pypi]: https://pypi.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository

pyproject.toml

@@ -8,7 +8,7 @@ name = "infercnvpy"
 dynamic = ["version"]
 description = "Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by InferCNV, but plays nicely with scanpy and is much more scalable."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 authors = [
     {name = "Gregor Sturm"},
@@ -47,7 +47,7 @@ doc = [
     "docutils>=0.8,!=0.18.*,!=0.19.*",
     "sphinx>=4.2",
     "sphinx-book-theme>=1.0.0",
-    "myst-nb",
+    "myst-nb>=1.1.0",
     "sphinxcontrib-bibtex>=1.0.0",
     "sphinx-autodoc-typehints",
     "sphinxext-opengraph",
@@ -83,12 +83,15 @@ filterwarnings = [
     # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
-[tool.black]
-line-length = 120
-
 [tool.ruff]
 src = ["src"]
 line-length = 120
+extend-include = ["*.ipynb"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
@@ -103,7 +106,7 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
     "E501",
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
@@ -117,7 +120,7 @@ ignore = [
     "D107",
     # Errors from function calls in argument defaults. These are fine when the result is immutable.
     "B008",
-    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    # __magic__ methods are often self-explanatory, allow missing docstrings
     "D105",
     # first line should end with a period [Bug: doesn't work with single-line docstrings]
     "D400",
@@ -130,10 +133,10 @@ ignore = [
     "D213",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]
@@ -147,5 +150,5 @@ skip = [
     "docs/changelog.md",
     "docs/references.bib",
     "docs/references.md",
-    "docs/notebooks/example.ipynb"
+    "docs/notebooks/example.ipynb",
 ]

src/infercnvpy/io/_genepos.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Literal, Union
+from typing import Literal
 
 import gtfparse
 import numpy as np
@@ -9,13 +9,13 @@
 
 
 def genomic_position_from_gtf(
-    gtf_file: Union[Path, str],
-    adata: Union[AnnData, None] = None,
+    gtf_file: Path | str,
+    adata: AnnData | None = None,
     *,
     gtf_gene_id: Literal["gene_id", "gene_name"] = "gene_name",
-    adata_gene_id: Union[str, None] = None,
+    adata_gene_id: str | None = None,
     inplace: bool = True,
-) -> Union[pd.DataFrame, None]:
+) -> pd.DataFrame | None:
     """Get genomic gene positions from a GTF file.
 
     The GTF file needs to match the genome annotation used for your single cell dataset.

src/infercnvpy/io/_scevan.py

@@ -1,7 +1,6 @@
 """Read in result files from scevan."""
 
 from pathlib import Path
-from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -26,14 +25,14 @@ def _get_chr_pos_from_array(chr_pos_array):
 
 def read_scevan(
     adata: AnnData,
-    scevan_res_dir: Union[str, Path],
-    scevan_res_table: Optional[Union[str, Path]] = None,
+    scevan_res_dir: str | Path,
+    scevan_res_table: str | Path | None = None,
     *,
     subclones: bool = True,
     inplace: bool = True,
     subset: bool = True,
     key_added: str = "scevan",
-) -> Optional[AnnData]:
+) -> AnnData | None:
     """Load results from SCEVAN :cite:`DeFalco2021` for downstream analysis with infercnvpy.
 
     Requires that the cell barcodes used for SCEVAN and `adata.obs_names` match,

src/infercnvpy/pl/_chromosome_heatmap.py

@@ -1,5 +1,3 @@
-from typing import Optional, Union
-
 import matplotlib.axes
 import numpy as np
 import pandas as pd
@@ -15,12 +13,12 @@ def chromosome_heatmap(
     *,
     groupby: str = "cnv_leiden",
     use_rep: str = "cnv",
-    cmap: Union[str, Colormap] = "bwr",
+    cmap: str | Colormap = "bwr",
     figsize: tuple[int, int] = (16, 10),
-    show: Optional[bool] = None,
-    save: Union[str, bool, None] = None,
+    show: bool | None = None,
+    save: str | bool | None = None,
     **kwargs,
-) -> Optional[dict[str, matplotlib.axes.Axes]]:
+) -> dict[str, matplotlib.axes.Axes] | None:
     """Plot a heatmap of smoothed gene expression by chromosome.
 
     Wrapper around :func:`scanpy.pl.heatmap`.
@@ -71,7 +69,7 @@ def chromosome_heatmap(
     kwargs["norm"] = TwoSlopeNorm(0, vmin=vmin, vmax=vmax)
 
     # add chromosome annotations
-    var_group_positions = list(zip(chr_pos, chr_pos[1:] + [tmp_adata.shape[1]]))
+    var_group_positions = list(zip(chr_pos, chr_pos[1:] + [tmp_adata.shape[1]], strict=False))
 
     return_ax_dic = sc.pl.heatmap(
         tmp_adata,
@@ -99,12 +97,12 @@ def chromosome_heatmap_summary(
     *,
     groupby: str = "cnv_leiden",
     use_rep: str = "cnv",
-    cmap: Union[str, Colormap] = "bwr",
+    cmap: str | Colormap = "bwr",
     figsize: tuple[int, int] = (16, 10),
-    show: Optional[bool] = None,
-    save: Union[str, bool, None] = None,
+    show: bool | None = None,
+    save: str | bool | None = None,
     **kwargs,
-) -> Optional[dict[str, matplotlib.axes.Axes]]:
+) -> dict[str, matplotlib.axes.Axes] | None:
     """Plot a heatmap of average of the smoothed gene expression by chromosome per category in groupby.
 
     Wrapper around :func:`scanpy.pl.heatmap`.
@@ -172,7 +170,7 @@ def _get_group_mean(group):
     kwargs["norm"] = TwoSlopeNorm(0, vmin=vmin, vmax=vmax)
 
     # add chromosome annotations
-    var_group_positions = list(zip(chr_pos, chr_pos[1:] + [tmp_adata.shape[1]]))
+    var_group_positions = list(zip(chr_pos, chr_pos[1:] + [tmp_adata.shape[1]], strict=False))
 
     return_ax_dic = sc.pl.heatmap(
         tmp_adata,

src/infercnvpy/tl/__init__.py

@@ -38,27 +38,27 @@ def pca(
     use_rep: str = "cnv",
     key_added: str = "cnv_pca",
     **kwargs,
-) -> Union[np.ndarray, None]:
+) -> np.ndarray | None:
     """Compute the PCA on the result of :func:`infercnvpy.tl.infercnv`.
 
-    Thin wrapper around :func:`scanpy.tl.pca`.
+    Thin wrapper around :func:`scanpy.pp.pca`.
 
     Parameters
     ----------
     adata
         annotated data matrix
     svd_solver
-        See :func:`scanpy.tl.pca`.
+        See :func:`scanpy.pp.pca`.
     zero_center
-        See :func:`scanpy.tl.pca`.
+        See :func:`scanpy.pp.pca`.
     inplace
         If True, store the result in adata.obsm. Otherwise return the PCA matrix.
     use_rep
         Key under which the result of infercnv is stored in adata
     key_added
         Key under which the result will be stored in adata.obsm if `inplace=True`.
     **kwargs
-        Additional arguments passed to :func:`scanpy.tl.pca`.
+        Additional arguments passed to :func:`scanpy.pp.pca`.
     """
     if f"X_{use_rep}" not in adata.obsm:
         raise KeyError(f"X_{use_rep} is not in adata.obsm. Did you run `tl.infercnv`?")

src/infercnvpy/tl/_copykat.py

@@ -1,6 +1,5 @@
 import os
 from multiprocessing import cpu_count
-from typing import Optional
 
 import pandas as pd
 from anndata import AnnData
@@ -18,8 +17,8 @@ def copykat(
     min_genes_chr: int = 5,
     key_added: str = "cnv",
     inplace: bool = True,
-    layer: Optional[str] = None,
-    n_jobs: Optional[int] = None,
+    layer: str | None = None,
+    n_jobs: int | None = None,
     norm_cell_names: str = "",
     cell_line="no",
     window_size=25,
@@ -172,7 +171,7 @@ def copykat(
 
     if inplace:
         adata.uns[key_added] = chrom_pos
-        adata.obsm["X_%s" % key_added] = new_cpkat_trans
+        adata.obsm[f"X_{key_added}"] = new_cpkat_trans
         adata.obs[key_added] = copyKAT_pred
     else:
         return new_cpkat_trans, copyKAT_pred