pertpy 0.9.1__py3-none-any.whl → 0.9.4__py3-none-any.whl

pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.9.1"
+__version__ = "0.9.4"
 
 import warnings
 

pertpy/data/_dataloader.py

@@ -23,10 +23,10 @@ def _download(  # pragma: no cover
     Args:
         url: URL to download
         output_file_name: Name of the downloaded file
-        output_path: Path to download/extract the files to (default: OS tmpdir)
-        block_size: Block size for downloads in bytes (default: 1024)
-        overwrite: Whether to overwrite existing files (default: False)
-        is_zip: Whether the downloaded file needs to be unzipped (default: False)
+        output_path: Path to download/extract the files to.
+        block_size: Block size for downloads in bytes.
+        overwrite: Whether to overwrite existing files.
+        is_zip: Whether the downloaded file needs to be unzipped.
     """
     if output_file_name is None:
         letters = ascii_lowercase

pertpy/data/_datasets.py

@@ -1100,7 +1100,7 @@ def shifrut_2018() -> AnnData:  # pragma: no cover
     output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/10044268/files/ShifrutMarson2018.h5ad?download=1",
+            url="https://zenodo.org/record/13350497/files/ShifrutMarson2018.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1160,7 +1160,7 @@ def srivatsan_2020_sciplex3() -> AnnData:  # pragma: no cover
     output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/records/10044268/files/SrivatsanTrapnell2020_sciplex3.h5ad?download=1",
+            url="https://zenodo.org/records/13350497/files/SrivatsanTrapnell2020_sciplex3.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,

pertpy/tools/__init__.py

@@ -2,19 +2,21 @@ 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
+    try:
+        for extra in extras:
+            import_module(extra)
         module = import_module(module_path)
         return getattr(module, class_name)
+    except ImportError:
 
-    return _import
+        class Placeholder:
+            def __init__(self, *args, **kwargs):
+                raise ImportError(
+                    f"Extra dependencies required: {', '.join(extras)}. "
+                    f"Please install with: pip install {' '.join(extras)}"
+                )
+
+        return Placeholder
 
 
 from pertpy.tools._augur import Augur
@@ -39,14 +41,12 @@ 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"])
+EdgeR = lazy_import("pertpy.tools._differential_gene_expression", "EdgeR", DE_EXTRAS) # edgeR will be imported via rpy2
 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)
@@ -76,5 +76,4 @@ __all__ = [
     "KMeansSpace",
     "PseudobulkSpace",
     "Scgen",
-    "DGEEVAL",
 ]

pertpy/tools/_cinemaot.py

@@ -190,7 +190,7 @@ class Cinemaot:
         TE.obsm["X_embedding"] = embedding
 
         if return_matching:
-            TE.obsm["ot"] = ot_sink.matrix.T
+            TE.obsm["ot"] = np.asarray(ot_sink.matrix.T)
             return TE
         else:
             return TE

{pertpy-0.9.1.dist-info → pertpy-0.9.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.9.1
+Version: 0.9.4
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -46,6 +46,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
 Requires-Dist: adjusttext
+Requires-Dist: anndata<0.10.9
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
 Requires-Dist: lamin-utils
@@ -129,13 +130,13 @@ 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

{pertpy-0.9.1.dist-info → pertpy-0.9.4.dist-info}/RECORD

@@ -1,8 +1,8 @@
-pertpy/__init__.py,sha256=OaiANyTVOegBAYDyD4004b7LXIWFpN2HkvQpKLC8P3I,658
+pertpy/__init__.py,sha256=k0tPuH0DdvQraT7I-zYrI1TwJHK3GnBx-Nvi-cMobvM,658
 pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/data/__init__.py,sha256=ah3yvoxkgbdMUNAWxS3SyqcUuVamBOSeuWkF2QRAEwM,2703
-pertpy/data/_dataloader.py,sha256=fl16n82nun01gGiP7qhr5sShfcDchp0szzZp7aXkfBI,2495
-pertpy/data/_datasets.py,sha256=I-keaJSTsRBySCPjiVonKmC9rRIM0AEgo0_0UlEX804,65616
+pertpy/data/_dataloader.py,sha256=ENbk1T3w3N6tVI11V4FVUxuWFEwOHP8_kIB-ehiMlVQ,2428
+pertpy/data/_datasets.py,sha256=OwI0HSSXnUPnUw_lAG9w5jNMILjLnPZS2Wj_LfrXSoI,65616
 pertpy/metadata/__init__.py,sha256=zoE_VXNyuKa4nlXlUk2nTgsHRW3jSQSpDEulcCnzOT0,222
 pertpy/metadata/_cell_line.py,sha256=-8KSqmP5XjmLEmNX3TavxSM_MtIHwLWS_x3MVkk6JEw,38595
 pertpy/metadata/_compound.py,sha256=JEFwP_TOTyMzfd2qFMb2VkJJvPhCVIvu6gs9Bq_stgs,4756
@@ -13,9 +13,9 @@ 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=IgKhXEyfRwEA7ccKJNLA_aIxKHm09QJINM09KaIwn68,7644
-pertpy/tools/__init__.py,sha256=laoRUOIjnjR4D41miOg6tISC_8pNJsu79785_CxMbSE,2603
+pertpy/tools/__init__.py,sha256=guh4QL8ac_CKP8S2nFHmxWJ6epCFB_Jfga4eK9HYGnE,2598
 pertpy/tools/_augur.py,sha256=UWro1nIEZe_rWtjlQCBv4ucqeh3Vt1m8IRzKlux72Z8,55683
-pertpy/tools/_cinemaot.py,sha256=BD_oYC1TktbFMX7fpp0A57QAF6frLEgNQ_2wFUpxjyo,39509
+pertpy/tools/_cinemaot.py,sha256=vMm9oTNW6pb8HBe993-BvkVKjSHbfbqlZY1SSCvj12Y,39521
 pertpy/tools/_dialogue.py,sha256=f2fbhKWdm4Co79ZzVgtVq9xYwjYWFLdGNDeGFOO_pfM,51990
 pertpy/tools/_enrichment.py,sha256=rjPHK9YBCJZfpa5Rvfxo3Ii7W5Mvm5dOdolAD7QazVg,21440
 pertpy/tools/_kernel_pca.py,sha256=_EJ9WlBLjHOafF34sZGdyBgZL6Fj0WiJ1elVT1XMmo4,1579
@@ -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-0.9.1.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,,
+pertpy-0.9.4.dist-info/METADATA,sha256=0gKL9NKX-_hyYAGZvXqTNZySfUSG-VuJdOL_zNCBDrs,6882
+pertpy-0.9.4.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+pertpy-0.9.4.dist-info/licenses/LICENSE,sha256=OZ-ZkXM5CmExJiEMM90b_7dGNNvRpj7kdE-49AnrLuI,1070
+pertpy-0.9.4.dist-info/RECORD,,