pertpy 0.8.0__tar.gz → 0.9.3__tar.gz

{pertpy-0.8.0 → pertpy-0.9.3}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.8.0 🌈"
-tag-template: 0.8.0
+name-template: "0.9.3 🌈"
+tag-template: 0.9.3
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.8.0 → pertpy-0.9.3}/.github/workflows/test.yml

@@ -25,13 +25,13 @@ jobs:
                       python: "3.10"
                       run_mode: "slow"
                     - os: ubuntu-latest
-                      python: "3.11"
+                      python: "3.12"
                       run_mode: "slow"
                     - os: ubuntu-latest
-                      python: "3.11"
+                      python: "3.12"
                       run_mode: "fast"
                     - os: ubuntu-latest
-                      python: "3.11"
+                      python: "3.12"
                       run_mode: slow
                       pip-flags: "--pre"
 

{pertpy-0.8.0 → pertpy-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.8.0
+Version: 0.9.3
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -41,6 +41,7 @@ Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
@@ -108,7 +109,7 @@ Description-Content-Type: text/markdown
 
 # pertpy
 
-![fig1](https://github.com/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
+![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
 
 ## Documentation
 
@@ -116,7 +117,10 @@ Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
 
 ## Installation
 
-You can install _pertpy_ via [pip] from [PyPI]:
+We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS).
+No particular hardware beyond a standard laptop is required.
+
+You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 
 ```console
 pip install pertpy
@@ -125,15 +129,20 @@ pip install pertpy
 if you want to use scCODA or tascCODA, please install pertpy as follows:
 
 ```console
-pip install pertpy[coda]
+pip install 'pertpy[coda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
 
 ```console
-pip install pertpy[de]
+pip install 'pertpy[de]'
 ```
 
+## Citation
+
+[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
+bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

{pertpy-0.8.0 → pertpy-0.9.3}/README.md

@@ -10,7 +10,7 @@
 
 # pertpy
 
-![fig1](https://github.com/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
+![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
 
 ## Documentation
 
@@ -18,7 +18,10 @@ Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
 
 ## Installation
 
-You can install _pertpy_ via [pip] from [PyPI]:
+We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS).
+No particular hardware beyond a standard laptop is required.
+
+You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 
 ```console
 pip install pertpy
@@ -27,15 +30,20 @@ pip install pertpy
 if you want to use scCODA or tascCODA, please install pertpy as follows:
 
 ```console
-pip install pertpy[coda]
+pip install 'pertpy[coda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
 
 ```console
-pip install pertpy[de]
+pip install 'pertpy[de]'
 ```
 
+## Citation
+
+[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
+bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

{pertpy-0.8.0 → pertpy-0.9.3}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.8.0"
+__version__ = "0.9.3"
 
 import warnings
 

{pertpy-0.8.0 → pertpy-0.9.3}/pertpy/preprocessing/_guide_rna.py

@@ -48,7 +48,7 @@ class GuideAssignment:
         """
         counts = adata.X if layer is None else adata.layers[layer]
         if scipy.sparse.issparse(counts):
-            counts = counts.A
+            counts = counts.toarray()
 
         assigned_grnas = np.where(counts >= assignment_threshold, 1, 0)
         assigned_grnas = scipy.sparse.csr_matrix(assigned_grnas)
@@ -92,7 +92,7 @@ class GuideAssignment:
         """
         counts = adata.X if layer is None else adata.layers[layer]
         if scipy.sparse.issparse(counts):
-            counts = counts.A
+            counts = counts.toarray()
 
         assigned_grna = np.where(
             counts.max(axis=1).squeeze() >= assignment_threshold,
@@ -152,9 +152,9 @@ class GuideAssignment:
 
         if order_by is None:
             if scipy.sparse.issparse(data):
-                max_values = data.max(axis=1).A.squeeze()
+                max_values = data.max(axis=1).toarray().squeeze()
                 data_argmax = data.argmax(axis=1).A.squeeze()
-                max_guide_index = np.where(max_values != data.min(axis=1).A.squeeze(), data_argmax, -1)
+                max_guide_index = np.where(max_values != data.min(axis=1).toarray().squeeze(), data_argmax, -1)
             else:
                 max_guide_index = np.where(
                     data.max(axis=1).squeeze() != data.min(axis=1).squeeze(), data.argmax(axis=1).squeeze(), -1

pertpy-0.9.3/pertpy/tools/__init__.py

@@ -0,0 +1,82 @@
+from functools import wraps
+from importlib import import_module
+
+
+def lazy_import(module_path, class_name, extras):
+    def _import():
+        try:
+            for extra in extras:
+                import_module(extra)
+        except ImportError as e:
+            raise ImportError(
+                f"Extra dependencies required: {', '.join(extras)}. "
+                f"Please install with: pip install {' '.join(extras)}"
+            ) from e
+        module = import_module(module_path)
+        return getattr(module, class_name)
+
+    @wraps(_import)
+    def wrapper(*args, **kwargs):
+        return _import()(*args, **kwargs)
+
+    return wrapper
+
+
+from pertpy.tools._augur import Augur
+from pertpy.tools._cinemaot import Cinemaot
+from pertpy.tools._dialogue import Dialogue
+from pertpy.tools._distances._distance_tests import DistanceTest
+from pertpy.tools._distances._distances import Distance
+from pertpy.tools._enrichment import Enrichment
+from pertpy.tools._milo import Milo
+from pertpy.tools._mixscape import Mixscape
+from pertpy.tools._perturbation_space._clustering import ClusteringSpace
+from pertpy.tools._perturbation_space._comparison import PerturbationComparison
+from pertpy.tools._perturbation_space._discriminator_classifiers import (
+    LRClassifierSpace,
+    MLPClassifierSpace,
+)
+from pertpy.tools._perturbation_space._simple import (
+    CentroidSpace,
+    DBSCANSpace,
+    KMeansSpace,
+    PseudobulkSpace,
+)
+from pertpy.tools._scgen import Scgen
+
+CODA_EXTRAS = ["toytree", "arviz", "ete3"]  # also pyqt5 technically
+Sccoda = lazy_import("pertpy.tools._coda._sccoda", "Sccoda", CODA_EXTRAS)
+Tasccoda = lazy_import("pertpy.tools._coda._tasccoda", "Tasccoda", CODA_EXTRAS)
+
+DE_EXTRAS = ["formulaic", "pydeseq2"]
+EdgeR = lazy_import("pertpy.tools._differential_gene_expression", "EdgeR", DE_EXTRAS + ["edger"])
+PyDESeq2 = lazy_import("pertpy.tools._differential_gene_expression", "PyDESeq2", DE_EXTRAS)
+Statsmodels = lazy_import("pertpy.tools._differential_gene_expression", "Statsmodels", DE_EXTRAS + ["statsmodels"])
+TTest = lazy_import("pertpy.tools._differential_gene_expression", "TTest", DE_EXTRAS)
+WilcoxonTest = lazy_import("pertpy.tools._differential_gene_expression", "WilcoxonTest", DE_EXTRAS)
+
+__all__ = [
+    "Augur",
+    "Cinemaot",
+    "Sccoda",
+    "Tasccoda",
+    "Dialogue",
+    "EdgeR",
+    "PyDESeq2",
+    "WilcoxonTest",
+    "TTest",
+    "Statsmodels",
+    "DistanceTest",
+    "Distance",
+    "Enrichment",
+    "Milo",
+    "Mixscape",
+    "ClusteringSpace",
+    "LRClassifierSpace",
+    "MLPClassifierSpace",
+    "CentroidSpace",
+    "DBSCANSpace",
+    "KMeansSpace",
+    "PseudobulkSpace",
+    "Scgen",
+]

{pertpy-0.8.0 → pertpy-0.9.3}/pertpy/tools/_milo.py

@@ -1014,7 +1014,7 @@ class Milo:
         if subset_nhoods is None:
             subset_nhoods = nhood_adata.obs_names
 
-        pl_df = pd.DataFrame(nhood_adata[subset_nhoods].X.A, columns=nhood_adata.var_names).melt(
+        pl_df = pd.DataFrame(nhood_adata[subset_nhoods].X.toarray(), columns=nhood_adata.var_names).melt(
             var_name=nhood_adata.uns["sample_col"], value_name="n_cells"
         )
         pl_df = pd.merge(pl_df, nhood_adata.var)

{pertpy-0.8.0 → pertpy-0.9.3}/pertpy/tools/_perturbation_space/_discriminator_classifiers.py

@@ -408,7 +408,7 @@ class PLDataset(Dataset):
 
     def __getitem__(self, idx):
         """Returns a sample and corresponding perturbations applied (labels)"""
-        sample = self.data[idx].A.squeeze() if scipy.sparse.issparse(self.data) else self.data[idx]
+        sample = self.data[idx].toarray().squeeze() if scipy.sparse.issparse(self.data) else self.data[idx]
         num_label = self.labels.iloc[idx]
         str_label = self.pert_labels.iloc[idx]
 

{pertpy-0.8.0 → pertpy-0.9.3}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "pertpy"
-version = "0.8.0"
+version = "0.9.3"
 description = "Perturbation Analysis in the scverse ecosystem."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -43,6 +43,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Visualization",
 ]

{pertpy-0.8.0 → pertpy-0.9.3}/tests/tools/_differential_gene_expression/test_dge.py

@@ -4,6 +4,8 @@ import pertpy as pt
 import pytest
 from anndata import AnnData
 
+pytest.skip("Disabled", allow_module_level=True)
+
 
 @pytest.fixture
 def adata(rng):

{pertpy-0.8.0 → pertpy-0.9.3}/tests/tools/_distances/test_distances.py

@@ -103,7 +103,11 @@ def test_distance_axioms(pairwise_distance, distance):
 def test_triangle_inequality(pairwise_distance, distance, rng):
     # Test if distances are well-defined in accordance with metric axioms
     # (M4) Triangle inequality (we just probe this for a few random triplets)
-    for _i in range(10):
+    # Some tests are not well defined for the triangle inequality. We skip those.
+    if distance in {"mahalanobis"}:
+        return
+
+    for _ in range(5):
         triplet = rng.choice(pairwise_distance.index, size=3, replace=False)
         assert (
             pairwise_distance.loc[triplet[0], triplet[1]] + pairwise_distance.loc[triplet[1], triplet[2]]

pertpy-0.8.0/pertpy/tools/__init__.py

@@ -1,57 +0,0 @@
-from pertpy.tools._augur import Augur
-from pertpy.tools._cinemaot import Cinemaot
-from pertpy.tools._coda._sccoda import Sccoda
-from pertpy.tools._coda._tasccoda import Tasccoda
-from pertpy.tools._dialogue import Dialogue
-from pertpy.tools._differential_gene_expression import (
-    DGEEVAL,
-    EdgeR,
-    PyDESeq2,
-    Statsmodels,
-    TTest,
-    WilcoxonTest,
-)
-from pertpy.tools._distances._distance_tests import DistanceTest
-from pertpy.tools._distances._distances import Distance
-from pertpy.tools._enrichment import Enrichment
-from pertpy.tools._milo import Milo
-from pertpy.tools._mixscape import Mixscape
-from pertpy.tools._perturbation_space._clustering import ClusteringSpace
-from pertpy.tools._perturbation_space._comparison import PerturbationComparison
-from pertpy.tools._perturbation_space._discriminator_classifiers import (
-    LRClassifierSpace,
-    MLPClassifierSpace,
-)
-from pertpy.tools._perturbation_space._simple import (
-    CentroidSpace,
-    DBSCANSpace,
-    KMeansSpace,
-    PseudobulkSpace,
-)
-from pertpy.tools._scgen import Scgen
-
-__all__ = [
-    "Augur",
-    "Cinemaot",
-    "Sccoda",
-    "Tasccoda",
-    "Dialogue",
-    "EdgeR",
-    "PyDESeq2",
-    "WilcoxonTest",
-    "TTest",
-    "Statsmodels",
-    "DistanceTest",
-    "Distance",
-    "Enrichment",
-    "Milo",
-    "Mixscape",
-    "ClusteringSpace",
-    "LRClassifierSpace",
-    "MLPClassifierSpace",
-    "CentroidSpace",
-    "DBSCANSpace",
-    "KMeansSpace",
-    "PseudobulkSpace",
-    "Scgen",
-]