stlearn 1.2.2__tar.gz → 1.4.0__tar.gz

{stlearn-1.2.2 → stlearn-1.4.0}/CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/duypham2108/stlearn/issues.
+Report bugs at https://github.com/BiomedicalMachineLearning/stLearn/issues
 
 If you are reporting a bug, please include:
 
@@ -70,20 +70,17 @@ Ready to contribute? Here's how to set up `stlearn` for local development.
     $ conda create -n stlearn-dev python=3.12 --y
     $ conda activate stlearn-dev
     $ cd stlearn/
-    $ pip install -e .[dev,test]
-
-    If you get an error for louvain package on MacOS, make sure you have cmake installed first (if you have brew):
-    $ brew install cmake
+    $ pip install -e ".[dev,test]"
 
     You can also use conda to install these dependencies (after creating the environment):
-    $ conda install -c conda-forge louvain leidenalg python-igraph
+    $ conda install -c conda-forge leidenalg python-igraph
 
    Or if you prefer pip/virtualenv::
 
     $ python -m venv stlearn-env
     $ source stlearn-env/bin/activate  # On Windows: stlearn-env\Scripts\activate
     $ cd stlearn/
-    $ pip install -e .[dev,test]
+    $ pip install -e ".[dev,test]"
 
 4. Create a branch for local development::
 
@@ -119,9 +116,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
-   https://travis-ci.org/duypham2108/stlearn/pull_requests
-   and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.12 and above.
 
 Tips
 ----

{stlearn-1.2.2 → stlearn-1.4.0}/HISTORY.rst

@@ -2,6 +2,27 @@
 History
 =======
 
+1.4.0 (2026-05-01)
+------------------
+* Removed tensorflow and keras and replaced with torch and torchvision.
+* The CCI implementation removed string comparisons for LR pairs lists and replaced it with one set of two
+  packed 32 bit integers. Removed deduplication pass (m^2) with a hash lookup (O(n)).
+* Upgrade libraries: numpy >=2.4.0, scanpy >= 1.12.0, scipy >= 1.17.0, added spatialdata, shapely, geopandas.
+
+API and Bug Fixes:
+* Added row and polygon annotations.
+* Fixed exception handling to catch previous exceptions when rethrown.
+
+1.3.0 (2026-02-24)
+------------------
+* Removed interactive stLearn/embedded web application.
+* Removed louvain clustering - replaced with leiden.
+
+API and Bug Fixes:
+* Fix import on MutableVertexPartition to use leidenalg.VertexPartition.
+* Switch default flavour in leiden to use igraph (and its required parameters).
+* Renamed methods and classes to follow lowercase standard.
+
 1.2.2 (2025-10-20)
 ------------------
 * Added support for Python 3.11 and 3.12.
@@ -25,6 +46,7 @@ API and Bug Fixes:
 * datasets.xenium_sge - loads Xenium data (and caches it) similar to scanpy.visium_sge.
 
 API and Bug Fixes:
+
 * Xenium TIFF and cell positions are now aligned.
 * Consistent with type annotations - mainly missing None annotations.
 * pl.cluster_plot - Does not keep colours from previous runs when clustering.

{stlearn-1.2.2 → stlearn-1.4.0}/LICENSE

@@ -1,6 +1,6 @@
 BSD License
 
-Copyright (c) 2020-2025, Genomics and Machine Learning lab
+Copyright (c) 2020-2026, Genomics and Machine Learning lab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

{stlearn-1.2.2 → stlearn-1.4.0}/PKG-INFO

@@ -1,38 +1,51 @@
 Metadata-Version: 2.4
 Name: stlearn
-Version: 1.2.2
+Version: 1.4.0
 Summary: A downstream analysis toolkit for Spatial Transcriptomic data
-Author-email: Genomics and Machine Learning lab <andrew.newman@uq.edu.au>
+Author-email: Genomics and Machine Learning Lab <andrew.newman@uq.edu.au>
 License: BSD license
 Project-URL: Homepage, https://github.com/BiomedicalMachineLearning/stLearn
 Project-URL: Repository, https://github.com/BiomedicalMachineLearning/stLearn
 Keywords: stlearn
 Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Framework :: Jupyter
 Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Natural Language :: English
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: <3.13,>=3.10
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.rst
+Requires-Dist: anndata>=0.12.0
 Requires-Dist: bokeh<4.0,>=3.7.0
 Requires-Dist: click<9.0,>=8.2.0
-Requires-Dist: leidenalg<0.11,>=0.10.0
-Requires-Dist: louvain>=0.8.2
+Requires-Dist: igraph>=1.0.0
+Requires-Dist: leidenalg>=0.11.0
 Requires-Dist: numba>=0.58.1
-Requires-Dist: numpy<2.0,>=1.26.0
+Requires-Dist: numpy>=2.4.0
 Requires-Dist: pillow<12.0,>=11.0.0
-Requires-Dist: scanpy<2.0,>=1.11.0
-Requires-Dist: scikit-image<0.23,>=0.22.0
-Requires-Dist: tensorflow>=2.14.1
-Requires-Dist: keras>=2.14.0
+Requires-Dist: scanpy>=1.12.0
+Requires-Dist: scikit-image>=0.22.0
 Requires-Dist: pandas>=2.3.0
 Requires-Dist: imageio<3.0,>=2.37.0
-Requires-Dist: scipy<2.0,>=1.11.0
-Requires-Dist: scikit-learn<2.0,>=1.7.0
+Requires-Dist: scipy<2.0,>=1.17.0
+Requires-Dist: scikit-learn<2.0,>=1.8.0
+Requires-Dist: zarr>=3.1
+Requires-Dist: dask>=2024.11.2
+Requires-Dist: spatialdata>=0.7.0
+Requires-Dist: spatialdata-io>=0.6.0
+Requires-Dist: spatialdata-plot>=0.3.0
+Requires-Dist: torch>=2.0
+Requires-Dist: torchvision>=0.15
+Requires-Dist: geopandas<2.0,>=1.0.0
+Requires-Dist: shapely<3.0,>=2.0.0
 Provides-Extra: dev
 Requires-Dist: black>=23.0; extra == "dev"
 Requires-Dist: ruff>=0.1.0; extra == "dev"
@@ -50,17 +63,12 @@ Requires-Dist: sphinx-autosummary-accessors>=2023.4.0; extra == "dev"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
-Provides-Extra: webapp
-Requires-Dist: flask>=2.0.0; extra == "webapp"
-Requires-Dist: flask-wtf>=1.0.0; extra == "webapp"
-Requires-Dist: wtforms>=3.0.0; extra == "webapp"
-Requires-Dist: markupsafe>2.1.0; extra == "webapp"
 Provides-Extra: jupyter
 Requires-Dist: jupyter>=1.0.0; extra == "jupyter"
 Requires-Dist: jupyterlab>=3.0.0; extra == "jupyter"
-Requires-Dist: ipywidgets>=7.6.0; extra == "jupyter"
+Requires-Dist: ipywidgets>=8.0.0; extra == "jupyter"
 Requires-Dist: plotly>=5.0.0; extra == "jupyter"
-Requires-Dist: bokeh>=2.4.0; extra == "jupyter"
+Requires-Dist: bokeh<4.0,>=3.7.0; extra == "jupyter"
 Requires-Dist: rpy2>=3.4.0; extra == "jupyter"
 Dynamic: license-file
 

{stlearn-1.2.2 → stlearn-1.4.0}/docs/api.rst

@@ -18,13 +18,14 @@ Wrapper functions: `wrapper`
 .. autosummary::
    :toctree: api/
 
-   Read10X
-   ReadOldST
-   ReadSlideSeq
-   ReadMERFISH
-   ReadSeqFish
-   convert_scanpy
+   read_10x
+   read_old_st
+   read_slide_seq
+   read_merfish
+   read_seq_fish
+   read_xenium
    create_stlearn
+   convert_scanpy
 
 
 Add: `add`
@@ -115,15 +116,15 @@ Spatial: `spatial`
 
    spatial.morphology.adjust
 
-.. module:: stlearn.spatial.SME
+.. module:: stlearn.spatial.sme
 .. currentmodule:: stlearn
 
 .. autosummary::
    :toctree: api/
 
-   spatial.SME.SME_impute0
-   spatial.SME.pseudo_spot
-   spatial.SME.SME_normalize
+   spatial.sme.sme_impute0
+   spatial.sme.pseudo_spot
+   spatial.sme.sme_normalize
 
 Tools: `tl`
 -------------------
@@ -135,7 +136,6 @@ Tools: `tl`
 
    tl.clustering.kmeans
    tl.clustering.leiden
-   tl.clustering.louvain
    tl.cci.load_lrs
    tl.cci.grid
    tl.cci.run
@@ -151,7 +151,7 @@ Plot: `pl`
 .. autosummary::
    :toctree: api/
 
-   pl.QC_plot
+   pl.qc_plot
    pl.gene_plot
    pl.gene_plot_interactive
    pl.cluster_plot
@@ -183,7 +183,7 @@ Plot: `pl`
    pl.trajectory.local_plot
    pl.trajectory.tree_plot
    pl.trajectory.transition_markers_plot
-   pl.trajectory.DE_transition_plot
+   pl.trajectory.de_transition_plot
 
 Datasets: `datasets`
 ---------------------------

{stlearn-1.2.2 → stlearn-1.4.0}/docs/conf.py

@@ -34,7 +34,7 @@ def download_gdrive_file(file_id, filename):
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'stLearn'
-copyright = '2022-2025, Genomics and Machine Learning Lab'
+copyright = '2022-2026, Genomics and Machine Learning Lab'
 author = 'Genomics and Machine Learning Lab'
 html_logo = "images/logo.png"
 
@@ -56,7 +56,7 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 def setup(app):
     if not os.path.isdir("./tutorials"):
-        download_gdrive_file("1FNMzO4-KsHK8tPd8k5-sTiRS40S97Qs4", "tutorials.zip")
+        download_gdrive_file("1DZ57n1S9_LYTyG10F6VXmo5lQ58wxvOC", "tutorials.zip")
         os.system("unzip tutorials.zip")
     return
 

{stlearn-1.2.2 → stlearn-1.4.0}/docs/index.rst

@@ -38,6 +38,10 @@ undissociated tissue sample.
 Latest Additions
 ----------------
 
+.. include:: release_notes/1.4.0.rst
+
+.. include:: release_notes/1.3.0.rst
+
 .. include:: release_notes/1.2.2.rst
 
 .. include:: release_notes/1.1.5.rst

{stlearn-1.2.2 → stlearn-1.4.0}/docs/references.rst

@@ -24,7 +24,7 @@ References
    *UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction*,
    `arXiv <https://arxiv.org/abs/1802.03426>`__.
 
-.. [Weinreb16] Weinreb *et al.* (2016),
+.. [Weinreb17] Weinreb *et al.* (2017),
    *SPRING: a kinetic interface for visualizing high dimensional single-cell expression data*,
    `bioRxiv <https://doi.org/10.1101/090332>`__.
 
@@ -36,10 +36,6 @@ References
    *Massively parallel digital transcriptional profiling of single cells*,
    `Nature Communications <https://doi.org/10.1038/ncomms14049>`__.
 
-.. [Weinreb17] Weinreb *et al.* (2016),
-   *SPRING: a kinetic interface for visualizing high dimensional single-cell expression data*,
-   `bioRxiv <https://doi.org/10.1101/090332>`__.
-
 .. [Blondel08] Blondel *et al.* (2008),
    *Fast unfolding of communities in large networks*,
    `J. Stat. Mech. <https://doi.org/10.1088/1742-5468/2008/10/P10008>`__.

stlearn-1.4.0/docs/release_notes/1.3.0.rst

@@ -0,0 +1,10 @@
+1.3.0 `2026-02-24`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Features
+
+* Removed interactive stLearn/embedded web application.
+* Removed louvain clustering.
+* Renamed methods and classes to follow lowercase standard.
+
+

stlearn-1.4.0/docs/release_notes/1.4.0.rst

@@ -0,0 +1,14 @@
+1.4.0 `2026-05-01`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Features
+
+* Removed tensorflow and keras and replaced with torch and torchvision.
+* The CCI implementation removed string comparisons for LR pairs lists and replaced it with one set of two
+  packed 32 bit integers. Removed deduplication pass (m^2) with a hash lookup (O(n)).
+* Added row and polygon annotations.
+* Upgrade libraries: numpy >=2.4.0, scanpy >= 1.12.0, scipy >= 1.17.0, added spatialdata, shapely, geopandas.
+
+.. rubric:: Bugs
+
+* Fixed exception handling to catch previous exceptions when rethrown.

{stlearn-1.2.2 → stlearn-1.4.0}/docs/release_notes/index.rst

@@ -1,6 +1,10 @@
 Release Notes
 ===================================================
 
+.. include:: 1.4.0.rst
+
+.. include:: 1.3.0.rst
+
 .. include:: 1.2.2.rst
 
 .. include:: 1.1.5.rst

stlearn-1.4.0/pyproject.toml

@@ -0,0 +1,131 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "stlearn"
+version = "1.4.0"
+authors = [
+    { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
+]
+description = "A downstream analysis toolkit for Spatial Transcriptomic data"
+readme = { file = "README.md", content-type = "text/markdown" }
+license = { text = "BSD license" }
+requires-python = ">=3.12"
+dependencies = [
+    "anndata>=0.12.0",
+    "bokeh>=3.7.0,<4.0",
+    "click>=8.2.0,<9.0",
+    "igraph>=1.0.0",
+    "leidenalg>=0.11.0",
+    "numba>=0.58.1",
+    "numpy>=2.4.0",
+    "pillow>=11.0.0,<12.0",
+    "scanpy>=1.12.0",
+    "scikit-image>=0.22.0",
+    "pandas>=2.3.0",
+    "imageio>=2.37.0,<3.0",
+    "scipy>=1.17.0,<2.0",
+    "scikit-learn>=1.8.0,<2.0",
+    "zarr>=3.1",
+    "dask>=2024.11.2",
+    "spatialdata>=0.7.0",
+    "spatialdata-io>=0.6.0",
+    "spatialdata-plot>=0.3.0",
+    "torch>=2.0",
+    "torchvision>=0.15",
+    "geopandas>=1.0.0,<2.0",
+    "shapely>=2.0.0,<3.0",
+]
+keywords = ["stlearn"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Framework :: Jupyter",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+[project.optional-dependencies]
+dev = [
+    "black>=23.0",
+    "ruff>=0.1.0",
+    "mypy>=1.16",
+    "pytest>=7.0",
+    "tox>=4.0",
+    "ghp-import>=2.1.0",
+    "sphinx>=4.0",
+    "furo==2024.8.6",
+    "myst-parser>=0.18",
+    "nbsphinx>=0.9.0",
+    "types-tensorflow>=2.8.0",
+    "sphinx-autodoc-typehints>=1.24.0",
+    "sphinx-autosummary-accessors>=2023.4.0",
+]
+test = [
+    "pytest",
+    "pytest-cov",
+]
+jupyter = [
+    "jupyter>=1.0.0",
+    "jupyterlab>=3.0.0",
+    "ipywidgets>=8.0.0",
+    "plotly>=5.0.0",
+    "bokeh>=3.7.0,<4.0",
+    "rpy2>=3.4.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/BiomedicalMachineLearning/stLearn"
+Repository = "https://github.com/BiomedicalMachineLearning/stLearn"
+
+[project.scripts]
+stlearn = "stlearn.app.cli:main"
+
+[tool.setuptools.packages.find]
+include = ["stlearn", "stlearn.*"]
+
+[tool.setuptools.package-data]
+"*" = ["*"]
+
+[tool.ruff]
+target-version = "py312"
+line-length = 88
+exclude = [".git", "__pycache__", "build", "dist", "docs/_build"]
+
+[tool.ruff.lint]
+select = [
+    "E", "F", "W",      # pycodestyle + pyflakes
+    "I",                # isort
+    "N",                # pep8-naming
+    "UP",               # pyupgrade
+    "NPY",              # numpy-specific (NPY001, NPY002, NPY003, NPY201)
+    "PD",               # pandas-vet
+    "B",                # flake8-bugbear (catches real bugs)
+    "SIM",              # flake8-simplify
+    "RUF",              # ruff-specific rules
+]
+ignore = [
+    "E722",             # bare except — you've already accepted these
+    "F811",             # redefinition — accepted
+    "N803", "N806",     # naming: lowercase args/vars — too invasive to fix
+    "N818",             # exception naming
+    "PD011",            # .values vs .to_numpy() — too noisy, mostly false positives
+    "B008",             # function calls in default args — used by typer/click
+    "SIM108",           # ternary suggestions can hurt readability
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["B", "N"]                 # tests can be loose
+"docs/conf.py" = ["E", "F", "UP"]      # generated/config file
+"**/__init__.py" = ["F401"]            # re-exports
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"

{stlearn-1.2.2 → stlearn-1.4.0}/stlearn/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Genomics and Machine Learning Lab"""
 __email__ = "andrew.newman@uq.edu.au"
-__version__ = "1.1.1"
+__version__ = "1.4.0"
 
 from . import add, datasets, em, pl, pp, spatial, tl, types
 from ._settings import settings
@@ -11,33 +11,33 @@ from .wrapper.convert_scanpy import convert_scanpy
 
 # Wrapper
 from .wrapper.read import (
-    Read10X,
-    ReadMERFISH,
-    ReadOldST,
-    ReadSeqFish,
-    ReadSlideSeq,
-    ReadXenium,
     create_stlearn,
+    read_10x,
+    read_merfish,
+    read_old_st,
+    read_seq_fish,
+    read_slide_seq,
+    read_xenium,
 )
 
 # from . import cli
 __all__ = [
     "add",
-    "pp",
+    "concatenate_spatial_adata",
+    "convert_scanpy",
+    "create_stlearn",
+    "datasets",
     "em",
-    "tl",
     "pl",
-    "spatial",
-    "datasets",
-    "ReadSlideSeq",
-    "Read10X",
-    "ReadOldST",
-    "ReadMERFISH",
-    "ReadSeqFish",
-    "ReadXenium",
-    "create_stlearn",
+    "pp",
+    "read_10x",
+    "read_merfish",
+    "read_old_st",
+    "read_seq_fish",
+    "read_slide_seq",
+    "read_xenium",
     "settings",
+    "spatial",
+    "tl",
     "types",
-    "convert_scanpy",
-    "concatenate_spatial_adata",
 ]

stlearn-1.4.0/stlearn/_compat.py

@@ -0,0 +1,16 @@
+import spatialdata as sd
+from anndata import AnnData
+
+
+def get_adata(data, table_key="table"):
+    """Extract AnnData from either SpatialData or AnnData input."""
+    if isinstance(data, sd.SpatialData):
+        return data.tables[table_key]
+    elif isinstance(data, AnnData):
+        return data
+    else:
+        raise TypeError(f"Expected SpatialData or AnnData, got {type(data)}")
+
+
+def is_spatial_data(data):
+    return isinstance(data, sd.SpatialData)

{stlearn-1.2.2 → stlearn-1.4.0}/stlearn/_datasets/_datasets.py

@@ -12,7 +12,7 @@ def visium_sge(
     *,
     include_hires_tiff: bool = False,
 ) -> AnnData:
-    """Processed Visium Spatial Gene Expression data from 10x Genomics’ database.
+    """Processed Visium Spatial Gene Expression data from 10x Genomics' database.
 
     The database_ can be browsed online to find the ``sample_id`` you want.
 
@@ -21,7 +21,7 @@ def visium_sge(
     Parameters
     ----------
     sample_id
-        The ID of the data sample in 10x’s spatial database.
+        The ID of the data sample in 10x's spatial database.
     include_hires_tiff
         Download and include the high-resolution tissue image (tiff) in
         `adata.uns["spatial"][sample_id]["metadata"]["source_image_path"]`.
@@ -85,5 +85,5 @@ def xenium_sge(
                 for zip_filename in files_to_extract:
                     with open(library_dir / zip_filename, "wb") as file_name:
                         file_name.write(zip_ref.read(f"outs/{zip_filename}"))
-        except zf.BadZipFile:
-            raise ValueError(f"Invalid zip file: {library_dir / zip_filename}")
+        except zf.BadZipFile as b:
+            raise ValueError(f"Invalid zip file: {library_dir / zip_filename}") from b

{stlearn-1.2.2 → stlearn-1.4.0}/stlearn/_settings.py

@@ -1,3 +1,4 @@
+import builtins
 import inspect
 import sys
 from collections.abc import Iterable, Iterator
@@ -56,7 +57,8 @@ def _type_check(var: Any, varname: str, types: type | tuple[type, ...]):
     else:
         type_names = [t.__name__ for t in types]
         possible_types_str = "{} or {}".format(
-            ", ".join(type_names[:-1]), type_names[-1]
+            ", ".join(type_names[:-1]),
+            type_names[-1],
         )
     raise TypeError(f"{varname} must be of type {possible_types_str}")
 
@@ -155,7 +157,7 @@ class stLearnConfig:  # noqa N801
             if verbosity not in verbosity_str_options:
                 raise ValueError(
                     f"Cannot set verbosity to {verbosity}. "
-                    f"Accepted string values are: {verbosity_str_options}"
+                    f"Accepted string values are: {verbosity_str_options}",
                 )
             else:
                 new_verbosity = Verbosity(verbosity_str_options.index(verbosity))
@@ -188,7 +190,7 @@ class stLearnConfig:  # noqa N801
         if file_format not in file_format_options:
             raise ValueError(
                 f"Cannot set file_format_data to {file_format}. "
-                f"Must be one of {file_format_options}"
+                f"Must be one of {file_format_options}",
             )
         self._file_format_data = file_format
 
@@ -297,7 +299,7 @@ class stLearnConfig:  # noqa N801
         if cache_compression not in {"lzf", "gzip", None}:
             raise ValueError(
                 f"`cache_compression` ({cache_compression}) "
-                "must be in {'lzf', 'gzip', None}"
+                "must be in {'lzf', 'gzip', None}",
             )
         self._cache_compression = cache_compression
 
@@ -341,7 +343,7 @@ class stLearnConfig:  # noqa N801
         else:
             _type_check(logpath, "logpath", (str, Path))
             # set via “file object” branch of logfile.setter
-            self.logfile = Path(logpath).open("a")
+            self.logfile = Path(logpath).open("a")  # noqa: SIM115
             self._logpath = Path(logpath)
 
     @property
@@ -424,7 +426,7 @@ class stLearnConfig:  # noqa N801
         Parameters
         ----------
         dpi
-            Resolution of rendered figures – this influences the size of figures
+            Resolution of rendered figures - this influences the size of figures
             in notebooks.
         dpi_save
             Resolution of saved figures. This should typically be higher to achieve
@@ -472,17 +474,13 @@ class stLearnConfig:  # noqa N801
 
         Only affects progress bars.
         """
-        try:
-            __IPYTHON__
-            return True
-        except NameError:
-            return False
+        return getattr(builtins, "__IPYTHON__", False)
 
     def __str__(self) -> str:
         return "\n".join(
             f"{k} = {v!r}"
             for k, v in inspect.getmembers(self)
-            if not k.startswith("_") and not k == "getdoc"
+            if not k.startswith("_") and k != "getdoc"
         )