pertpy 0.8.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.8.0"
+__version__ = "0.9.1"
 
 import warnings
 

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/tools/__init__.py

@@ -1,16 +1,25 @@
+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)
+
+    return _import
+
+
 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
@@ -30,6 +39,19 @@ from pertpy.tools._perturbation_space._simple import (
 )
 from pertpy.tools._scgen import Scgen
 
+# from pertpy.tools._differential_gene_expression import DGEEVAL
+
+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",
@@ -54,4 +76,5 @@ __all__ = [
     "KMeansSpace",
     "PseudobulkSpace",
     "Scgen",
+    "DGEEVAL",
 ]

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/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.dist-info → pertpy-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.8.0
+Version: 0.9.1
 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
@@ -134,6 +138,11 @@ If you want to use the differential gene expression interface, please install pe
 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.dist-info → pertpy-0.9.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-pertpy/__init__.py,sha256=GMFyfRErEysnlkYKMqQxtO7QbqjGki7SpvgtLxIuG6o,658
+pertpy/__init__.py,sha256=OaiANyTVOegBAYDyD4004b7LXIWFpN2HkvQpKLC8P3I,658
 pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/data/__init__.py,sha256=ah3yvoxkgbdMUNAWxS3SyqcUuVamBOSeuWkF2QRAEwM,2703
 pertpy/data/_dataloader.py,sha256=fl16n82nun01gGiP7qhr5sShfcDchp0szzZp7aXkfBI,2495
@@ -12,14 +12,14 @@ pertpy/metadata/_metadata.py,sha256=pvarnv3X5pblnvG8AQ8Omu5jQcC5ORzCxRk3FRhOLgs,
 pertpy/metadata/_moa.py,sha256=u_OcMonjOeeoW5P9xOltquVSoTH3Vs80ztHsXf-X1DY,4701
 pertpy/plot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/preprocessing/__init__.py,sha256=VAPFaeq2_qCvdFkQTCj_Hm460HC4Tersu8Rig_tnp_Y,71
-pertpy/preprocessing/_guide_rna.py,sha256=Xrv0cN16Ub1U1z-3LDNTkm98zs9JOjc2h1N7IAt_FaE,7612
-pertpy/tools/__init__.py,sha256=yhDyv5J-nd3SDqc3T08Nzca8dzj3SpoVG2m9VU1rFUk,1481
+pertpy/preprocessing/_guide_rna.py,sha256=IgKhXEyfRwEA7ccKJNLA_aIxKHm09QJINM09KaIwn68,7644
+pertpy/tools/__init__.py,sha256=laoRUOIjnjR4D41miOg6tISC_8pNJsu79785_CxMbSE,2603
 pertpy/tools/_augur.py,sha256=UWro1nIEZe_rWtjlQCBv4ucqeh3Vt1m8IRzKlux72Z8,55683
 pertpy/tools/_cinemaot.py,sha256=BD_oYC1TktbFMX7fpp0A57QAF6frLEgNQ_2wFUpxjyo,39509
 pertpy/tools/_dialogue.py,sha256=f2fbhKWdm4Co79ZzVgtVq9xYwjYWFLdGNDeGFOO_pfM,51990
 pertpy/tools/_enrichment.py,sha256=rjPHK9YBCJZfpa5Rvfxo3Ii7W5Mvm5dOdolAD7QazVg,21440
 pertpy/tools/_kernel_pca.py,sha256=_EJ9WlBLjHOafF34sZGdyBgZL6Fj0WiJ1elVT1XMmo4,1579
-pertpy/tools/_milo.py,sha256=kGnfx-CMOpYSl85fOW62J2X3utVjOsQFne7ixEptDmI,43691
+pertpy/tools/_milo.py,sha256=FDFGmGMkJiVrvATEnOeAMCe-Q2w7F0nbBMuACVbyIQI,43699
 pertpy/tools/_mixscape.py,sha256=FtH3PKvbLTe03LPgN4O9sS70oj_6AHz4Mz5otzEwRl8,52406
 pertpy/tools/decoupler_LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 pertpy/tools/transferlearning_MMD_LICENSE,sha256=MUvDA-o_j9htRpI8fStVdCRuyLdPkQUuIH0a_EIc57w,1069
@@ -42,7 +42,7 @@ pertpy/tools/_distances/_distances.py,sha256=iuHpBtWZbJhMZNSEjQkZUu6KPJXCjs_fX6Y
 pertpy/tools/_perturbation_space/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/tools/_perturbation_space/_clustering.py,sha256=m52-J8c8OnIXRCf3NoFabIO2yMHIuy1X0m0amtsK2vE,3556
 pertpy/tools/_perturbation_space/_comparison.py,sha256=rLO-EGU0I7t5MnLw4k1gYU-ypRu-JsDPLat1t4h2U2M,4329
-pertpy/tools/_perturbation_space/_discriminator_classifiers.py,sha256=BNMP-2g4X_9jhs3Vf2rwlIjSCAcADkxBAFYGlsQ5Irw,21609
+pertpy/tools/_perturbation_space/_discriminator_classifiers.py,sha256=OA2eZeG_4iuW1T5ilsRIkS0rU-azmwEch7IuB546KSY,21617
 pertpy/tools/_perturbation_space/_metrics.py,sha256=y8-baP8WRdB1iDgvP3uuQxSCDxA2lcxvEHHM2C_vWHY,3248
 pertpy/tools/_perturbation_space/_perturbation_space.py,sha256=cZPPzzK4_UZV7ktcD5BQVXEy6ITHrfkg1CLFov3TzsY,18497
 pertpy/tools/_perturbation_space/_simple.py,sha256=LH5EYvcAbzFMvgd9bH7AUPKFmdioPiy2xG8xGaXzmq0,12624
@@ -51,7 +51,7 @@ pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_K
 pertpy/tools/_scgen/_scgen.py,sha256=HPvFVjY9SS9bGqgTkCDuPYjmA4QHW7rKgHnI2yuI_Q4,30608
 pertpy/tools/_scgen/_scgenvae.py,sha256=v_6tZ4wY-JjdMH1QVd_wG4_N0PoaqB-FM8zC2JsDu1o,3935
 pertpy/tools/_scgen/_utils.py,sha256=1upgOt1FpadfvNG05YpMjYYG-IAlxrC3l_ZxczmIczo,2841
-pertpy-0.8.0.dist-info/METADATA,sha256=cLAhPubizJ7vgCThHv-kHsAAvepUyRTnTHTKRKX9kYQ,6054
-pertpy-0.8.0.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-pertpy-0.8.0.dist-info/licenses/LICENSE,sha256=OZ-ZkXM5CmExJiEMM90b_7dGNNvRpj7kdE-49AnrLuI,1070
-pertpy-0.8.0.dist-info/RECORD,,
+pertpy-0.9.1.dist-info/METADATA,sha256=JrAJR7n35TG8BZ30XmTdsrkaI6ADaz1PQE_DGLHT1TM,6848
+pertpy-0.9.1.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+pertpy-0.9.1.dist-info/licenses/LICENSE,sha256=OZ-ZkXM5CmExJiEMM90b_7dGNNvRpj7kdE-49AnrLuI,1070
+pertpy-0.9.1.dist-info/RECORD,,