pertpy 0.11.1__tar.gz → 0.11.2__tar.gz

{pertpy-0.11.1 → pertpy-0.11.2}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.11.1 🌈"
-tag-template: 0.11.1
+name-template: "0.11.2 🌈"
+tag-template: 0.11.2
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.11.1 → pertpy-0.11.2}/.github/workflows/test.yml

@@ -24,13 +24,8 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.13"
-                      run_mode: "slow"
                     - os: ubuntu-latest
                       python: "3.13"
-                      run_mode: "fast"
-                    - os: ubuntu-latest
-                      python: "3.13"
-                      run_mode: slow
                       pip-flags: "--pre"
 
         env:
@@ -91,9 +86,6 @@ jobs:
                   DISPLAY: :42
               run: |
                   pytest_args="-m pytest -v --color=yes"
-                  if [ "${{ matrix.run_mode }}" = "slow" ]; then
-                    pytest_args="$pytest_args --runslow"
-                  fi
                   coverage run $pytest_args
 
             - name: Show coverage report

{pertpy-0.11.1 → pertpy-0.11.2}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.5
+      rev: v0.11.9
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -33,7 +33,7 @@ repos:
           - id: no-commit-to-branch
             args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.14.1
+      rev: v1.15.0
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-0.11.1 → pertpy-0.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.11.1
+Version: 0.11.2
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -151,7 +151,7 @@ bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/api.html
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

{pertpy-0.11.1 → pertpy-0.11.2}/README.md

@@ -48,7 +48,7 @@ bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/api.html
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

{pertpy-0.11.1 → pertpy-0.11.2}/docs/_static/pertpy_logo.svg

@@ -1,5 +1,4 @@
 <svg width="308" height="105" viewBox="0 0 308 105" fill="none" xmlns="http://www.w3.org/2000/svg">
-<rect width="308" height="105" fill="#1E1E1E"/>
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 </svg>

{pertpy-0.11.1 → pertpy-0.11.2}/docs/changelog.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.11.2
+
+### 🚀 Features
+
+* Simplify Metadata errors ([#765](https://github.com/scverse/pertpy/pull/765)) @Zethson
+
 ## v0.11.1
 
 ### 🐛 Bug Fixes

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.11.1"
+__version__ = "0.11.2"
 
 import warnings
 

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/data/_dataloader.py

@@ -15,8 +15,8 @@ from rich.progress import Progress
 
 def _download(  # pragma: no cover
     url: str,
-    output_file_name: str = None,
-    output_path: str | Path = None,
+    output_file_name: str | None = None,
+    output_path: str | Path | None = None,
     block_size: int = 1024,
     overwrite: bool = False,
     is_zip: bool = False,

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/metadata/_cell_line.py

@@ -215,7 +215,7 @@ class CellLine(MetaData):
         For each cell, we fetch cell line annotation from either the Dependency Map (DepMap) or The Genomics of Drug Sensitivity in Cancer Project (Cancerxgene).
 
         Args:
-            adata: The data object to annotate.
+            adata: The AnnData object to annotate.
             query_id: The column of ``.obs`` with cell line information.
             reference_id: The type of cell line identifier in the metadata, e.g. ModelID, CellLineName	or StrippedCellLineName.
                           If fetching cell line metadata from Cancerrxgene, it is recommended to choose "stripped_cell_line_name".
@@ -311,11 +311,9 @@ class CellLine(MetaData):
 
         else:
             raise ValueError(
-                f"The requested cell line type {reference_id} is currently unavailable in the database.\n"
-                "Refer to the available reference identifier in the chosen database.\n"
-                "DepMap_ID is compared by default.\n"
-                "Alternatively, create a `CellLineMetaData.lookup()` object to "
-                "obtain the available reference identifiers in the metadata."
+                f"The requested cell line type {reference_id} is unavailable."
+                "Refer to the available reference identifier in the chosen database."
+                "Alternatively, create a `CellLineMetaData.lookup()` object to obtain the available reference identifiers in the metadata."
             )
 
         return adata
@@ -362,11 +360,9 @@ class CellLine(MetaData):
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns and query_id is not None:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in the adata.obs for the annotation."
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling 'annotate_bulk_rna()'. "
-                "This ensures that the required query ID is included in your data, e.g. stripped_cell_line_name, DepMap ID."
+                f"Specified `query_id` {query_id} can't be found in `adata.obs`. \n"
+                "If the desired query ID is not available, fetch the cell line metadata "
+                "using the `annotate()` function before calling 'annotate_bulk_rna()'."
             )
         if query_id is None:
             query_id = "cell_line_name" if cell_line_source == "sanger" else "DepMap_ID"
@@ -376,9 +372,8 @@ class CellLine(MetaData):
         if cell_line_source == "sanger":
             if query_id not in adata.obs.columns:
                 raise ValueError(
-                    "To annotate bulk RNA data from Wellcome Sanger Institute, `cell_line_name` is used as default reference and query identifier if no `query_id` is given."
-                    "Ensure that you have column `cell_line_name` in `adata.obs` or specify column name in which cell line name is stored."
-                    "If cell line name isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
+                    f"Missing '{query_id}' in `adata.obs`. For Sanger, need `cell_line_name` column "
+                    f"or specify column with cell line names via `query_id` parameter."
                 )
             if self.bulk_rna_sanger is None:
                 self._download_bulk_rna(cell_line_source="sanger")
@@ -387,9 +382,8 @@ class CellLine(MetaData):
         else:
             if query_id not in adata.obs.columns:
                 raise ValueError(
-                    "To annotate bulk RNA data from Broad Institue, `DepMap_ID` is used as default reference and query identifier if no `query_id` is given."
-                    "Ensure that you have column `DepMap_ID` in `adata.obs` or specify column name in which DepMap ID is stored."
-                    "If DepMap ID isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
+                    f"Missing '{query_id}' in `adata.obs`. For Broad Institute data, need `DepMap_ID` column "
+                    f"or specify column with DepMap IDs via `query_id` parameter."
                 )
             reference_id = "DepMap_ID"
 
@@ -472,19 +466,16 @@ class CellLine(MetaData):
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in `adata.obs`. \n"
-                "If the desired query ID is not available, you can fetch the cell line metadata \n"
-                "using the `annotate()` function before calling annotate_protein_expression(). \n"
-                "This ensures that the required query ID is included in your data."
+                f"The specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Fetch cell line metadata with `annotate()` before calling `annotate_protein_expression()`."
             )
         # Lazily download the proteomics data
         if self.proteomics is None:
             self._download_proteomics()
         if reference_id not in self.proteomics.columns:
             raise ValueError(
-                f"The specified `reference_id`{reference_id} can't be found in the protein expression data. \n"
-                "To solve the issue, please use the reference identifier available in the metadata.  \n"
-                "Alternatively, create a `CellLineMetaData.lookup()` object to obtain the available reference identifiers in the metadata."
+                f"Specified `reference_id` `{reference_id}` not found in protein expression data. "
+                f"Use available reference identifiers in metadata or create `CellLineMetaData.lookup()` object."
             )
 
         identifier_num_all = len(adata.obs[query_id].unique())
@@ -551,11 +542,8 @@ class CellLine(MetaData):
             adata = adata.copy()
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in 'adata.obs' for the annotation.\n"
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling `annotate_from_gdsc()`. "
-                "This ensures that the required query ID is included in your data."
+                f"Specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Use an available ID or fetch cell line metadata with `annotate()` before calling `annotate_from_gdsc()`."
             )
         # Lazily download the GDSC data
         if gdsc_dataset == "gdsc_1":
@@ -626,11 +614,8 @@ class CellLine(MetaData):
             adata = adata.copy()
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in 'adata.obs' for the annotation.\n"
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling `annotate_from_prism()`. "
-                "This ensures that the required query ID is included in your data."
+                f"Specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Use an available ID or fetch cell line metadata with `annotate()` before calling `annotate_from_prism()`."
             )
         if self.drug_response_prism is None:
             self._download_prism()
@@ -700,7 +685,6 @@ class CellLine(MetaData):
         if self.drug_response_prism is None:
             self._download_prism()
 
-        # Transfer the data
         return LookUp(
             type="cell_line",
             transfer_metadata=[
@@ -775,7 +759,7 @@ class CellLine(MetaData):
             and sum(adata.obsm[metadata_key].columns != adata.var.index.values) > 0
         ):
             raise ValueError(
-                "Column name of metadata is not the same as the index of adata.var. Ensure that the genes are in the same order."
+                "Column name of metadata is not the same as the index of `adata.var`. Ensure that the genes are in the same order."
             )
 
         # Divide cell lines into those are present and not present in the metadata
@@ -832,7 +816,7 @@ class CellLine(MetaData):
         """
         if corr is None or pval is None:
             raise ValueError(
-                "Missing required input parameter: 'corr' or 'pval'. Please call the function `pt.md.CellLine.correlate()` to generate these outputs before proceeding."
+                "Missing required input parameter: 'corr' or 'pval'. Call `pt.md.CellLine.correlate()` before proceeding."
             )
 
         if category == "cell line":

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/metadata/_compound.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 from typing import TYPE_CHECKING, Literal
 
 import pandas as pd
-import pubchempy as pcp
 
 from ._look_up import LookUp
 from ._metadata import MetaData
@@ -44,6 +43,8 @@ class Compound(MetaData):
         if query_id not in adata.obs.columns:
             raise ValueError(f"The requested query_id {query_id} is not in `adata.obs`.\n Please check again.")
 
+        import pubchempy as pcp
+
         query_dict = {}
         not_matched_identifiers = []
         for compound in adata.obs[query_id].dropna().astype(str).unique():

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/metadata/_look_up.py

@@ -27,7 +27,7 @@ class LookUp:
         Args:
             type: Metadata type for annotation. One of 'cell_line', 'compound', 'moa' or 'drug.
             transfer_metadata: DataFrames used to generate Lookup object.
-                           This is currently set to None for CompoundMetaData which does not require any dataframes for transfer.
+                Currently set to None for CompoundMetaData which does not require any DataFrames for transfer.
         """
         self.type = type
         if type == "cell_line":

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/metadata/_metadata.py

@@ -49,11 +49,8 @@ class MetaData:
             if metadata_type in ["protein expression", "bulk RNA", "drug response"]:
                 hint = "Additionally, call the `CellLineMetaData.annotate()` function to acquire more possible query IDs that can be used for cell line annotation purposes."
             raise ValueError(
-                f"Attempting to match the query id {query_id} in 'adata.obs' to the reference id {reference_id} in the metadata.\n"
-                "However, none of the query IDs could be found in the {metadata_type} annotation data.\n"
-                "To resolve this issue, call the `lookup()` function to create a LookUp object.\n"
-                "This enables obtaining the count of matched identifiers in the AnnData object for different types of reference and query IDs.\n"
-                f"{hint}"
+                f"No matches between `{query_id}` in adata.obs and `{reference_id}` in {metadata_type} data. "
+                f"Use `lookup()` to check compatible identifier types. {hint}"
             )
         if len(unmatched_identifiers) == 0:
             return
@@ -61,10 +58,8 @@ class MetaData:
             verbosity = min(verbosity, len(unmatched_identifiers))
             if verbosity > 0:
                 logger.info(
-                    f"There are {total_identifiers} identifiers in `adata.obs`."
-                    f"However, {len(unmatched_identifiers)} identifiers can't be found in the {metadata_type} annotation, "
-                    "leading to the presence of NA values for their respective metadata.\n"
-                    f"Please check again: *unmatched_identifiers[:verbosity]..."
+                    f"{total_identifiers} identifiers in `adata.obs`, {len(unmatched_identifiers)} not found in {metadata_type} data. "
+                    f"NA values present. Unmatched: {unmatched_identifiers[:verbosity]}"
                 )
         else:
             raise ValueError("Only 'all' or a non-negative value is accepted.")

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/metadata/_moa.py

@@ -110,8 +110,6 @@ class Moa(MetaData):
         """Generate LookUp object for Moa metadata.
 
         The LookUp object provides an overview of the metadata to annotate.
-        annotate_moa function has a corresponding lookup function in the LookUp object,
-        where users can search the query_ids and targets in the metadata.
 
         Returns:
             Returns a LookUp object specific for MoA annotation.

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/tools/_augur.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 import random
 from collections import defaultdict
-from dataclasses import dataclass
 from math import floor, nan
 from typing import TYPE_CHECKING, Any, Literal
 

{pertpy-0.11.1 → pertpy-0.11.2}/pertpy/tools/_mixscape.py

@@ -26,11 +26,10 @@ if TYPE_CHECKING:
     from matplotlib.axes import Axes
     from matplotlib.colors import Colormap
     from matplotlib.pyplot import Figure
-    from scipy import sparse
 
 
 class Mixscape:
-    """Python implementation of Mixscape."""
+    """identify perturbation effects in CRISPR screens by separating cells into perturbation groups."""
 
     def __init__(self):
         pass
@@ -71,7 +70,7 @@ class Mixscape:
             use_rep: Use the indicated representation. `'X'` or any key for `.obsm` is valid.
                 If `None`, the representation is chosen automatically:
                 For `.n_vars` < 50, `.X` is used, otherwise 'X_pca' is used.
-                If 'X_pca' is not present, it’s computed with default parameters.
+                If 'X_pca' is not present, it's computed with default parameters.
             n_dims: Number of dimensions to use from the representation to calculate the perturbation signature.
                 If `None`, use all dimensions.
             n_pcs: If PCA representation is used, the number of principal components to compute.
@@ -1189,7 +1188,7 @@ class MixscapeGaussianMixture(GaussianMixture):
             n_components: Number of Gaussian components
             fixed_means: Means to fix (use None for those that should be estimated)
             fixed_covariances: Covariances to fix (use None for those that should be estimated)
-            kwargs: Additional arguments passed to scikit-learn's GaussianMixture
+            **kwargs: Additional arguments passed to scikit-learn's GaussianMixture
         """
         super().__init__(n_components=n_components, **kwargs)
         self.fixed_means = fixed_means

{pertpy-0.11.1 → pertpy-0.11.2}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "pertpy"
-version = "0.11.1"
+version = "0.11.2"
 description = "Perturbation Analysis in the scverse ecosystem."
 readme = "README.md"
 requires-python = ">=3.11,<3.14"
@@ -131,7 +131,6 @@ addopts = [
 markers = [
     "conda: marks a subset of tests to be ran on the Bioconda CI.",
     "extra: marks tests that require extra dependencies.",
-    "slow: mark test as slow to run"
 ]
 minversion = 6.0
 norecursedirs = [ '.*', 'build', 'dist', '*.egg', 'data', '__pycache__']

pertpy-0.11.2/tests/conftest.py

@@ -0,0 +1,7 @@
+import numpy as np
+import pytest
+
+
+@pytest.fixture
+def rng():
+    return np.random.default_rng()

{pertpy-0.11.1 → pertpy-0.11.2}/tests/metadata/test_cell_line.py

@@ -76,7 +76,6 @@ def test_protein_expression_annotation(adata):
     )
 
 
-@pytest.mark.slow
 def test_bulk_rna_expression_annotation(adata):
     pt_metadata.annotate(adata)
     pt_metadata.annotate_bulk_rna(adata, query_id="DepMap_ID", cell_line_source="broad")

{pertpy-0.11.1 → pertpy-0.11.2}/tests/tools/_coda/test_sccoda.py

@@ -90,7 +90,6 @@ def test_credible_effects(adata):
     assert sccoda.credible_effects(mdata)["condition[T.Salmonella]"]["Enterocyte"]
 
 
-@pytest.mark.slow
 def test_make_arviz(adata):
     adata_salm = adata[adata.obs["condition"].isin(["Control", "Salmonella"])]
     mdata = sccoda.load(

{pertpy-0.11.1 → pertpy-0.11.2}/tests/tools/_distances/test_distance_tests.py

@@ -39,9 +39,6 @@ def adata():
 
 @pytest.mark.parametrize("distance", distances)
 def test_distancetest(adata, distance):
-    if distance == "wasserstein":
-        pytest.mark.apply(pytest.mark.slow)
-
     etest = pt.tl.DistanceTest(distance, n_perms=10, obsm_key="X_pca", alpha=0.05, correction="holm-sidak")
     tab = etest(adata, groupby="perturbation", contrast="control")
 

{pertpy-0.11.1 → pertpy-0.11.2}/tests/tools/test_augur.py

@@ -149,7 +149,6 @@ def test_select_variance(adata):
     assert len(ad.var.index[ad.var["highly_variable"]]) == 3672
 
 
-@pytest.mark.slow
 def test_differential_prioritization():
     """Test differential prioritization run."""
     # Requires the full dataset or it fails because of a lack of statistical power

{pertpy-0.11.1 → pertpy-0.11.2}/tests/tools/test_dialogue.py

@@ -1,6 +1,5 @@
 import pandas as pd
 import pertpy as pt
-import pytest
 import scanpy as sc
 
 # This is not a proper test!
@@ -8,7 +7,6 @@ import scanpy as sc
 # The pipeline is obtained from https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/dialogue.html
 
 
-@pytest.mark.slow
 def test_dialogue_pipeline():
     adata = pt.dt.dialogue_example()
 

pertpy-0.11.1/tests/conftest.py

@@ -1,20 +0,0 @@
-import numpy as np
-import pytest
-
-
-def pytest_addoption(parser):
-    parser.addoption("--runslow", action="store_true", default=False, help="run slow tests")
-
-
-def pytest_collection_modifyitems(config, items):
-    """Conditionally skip slow tests unless '--runslow' is specified"""
-    if not config.getoption("--runslow"):
-        skip_slow = pytest.mark.skip(reason="need --runslow option to run")
-        for item in items:
-            if "slow" in item.keywords:
-                item.add_marker(skip_slow)
-
-
-@pytest.fixture
-def rng():
-    return np.random.default_rng()