pertpy 0.9.1__tar.gz → 0.9.4__tar.gz

{pertpy-0.9.1 → pertpy-0.9.4}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.9.1 🌈"
-tag-template: 0.9.1
+name-template: "0.9.4 🌈"
+tag-template: 0.9.4
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.9.1 → pertpy-0.9.4}/.github/workflows/test.yml

@@ -27,13 +27,13 @@ jobs:
                     - os: ubuntu-latest
                       python: "3.12"
                       run_mode: "slow"
-                    - os: ubuntu-latest
-                      python: "3.12"
-                      run_mode: "fast"
-                    - os: ubuntu-latest
-                      python: "3.12"
-                      run_mode: slow
-                      pip-flags: "--pre"
+#                    - os: ubuntu-latest
+#                      python: "3.12"
+#                      run_mode: "fast"
+#                    - os: ubuntu-latest
+#                      python: "3.12"
+#                      run_mode: slow
+#                      pip-flags: "--pre"
 
         env:
             OS: ${{ matrix.os }}

{pertpy-0.9.1 → pertpy-0.9.4}/PKG-INFO

@@ -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 → pertpy-0.9.4}/README.md

@@ -30,13 +30,13 @@ 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 → pertpy-0.9.4}/docs/installation.md

@@ -78,10 +78,10 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
     brew install --cask mambaforge
     ```
 
-3. Create a new environment using mamba (here with python 3.10) and activate it
+3. Create a new environment using mamba and activate it
 
     ```console
-    mamba create -n pertpy-env python=3.11
+    mamba create -n pertpy-env
     mamba activate pertpy-env
     ```
 

{pertpy-0.9.1 → pertpy-0.9.4}/docs/usage/usage.md

@@ -450,7 +450,7 @@ See [scGen predicts single-cell perturbation responses](https://www.nature.com/a
 .. autosummary::
     :toctree: tools
 
-    tools.SCGEN
+    tools.Scgen
 ```
 
 Example implementation:

{pertpy-0.9.1 → pertpy-0.9.4}/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-0.9.1 → pertpy-0.9.4}/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-0.9.1 → pertpy-0.9.4}/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-0.9.1 → pertpy-0.9.4}/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-0.9.1 → pertpy-0.9.4}/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 → pertpy-0.9.4}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "pertpy"
-version = "0.9.1"
+version = "0.9.4"
 description = "Perturbation Analysis in the scverse ecosystem."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -64,7 +64,8 @@ dependencies = [
     "pubchempy",
     "pyarrow",
     "blitzgsea",
-    "lamin_utils"
+    "lamin_utils",
+    "anndata <0.10.9"  # pydeseq2 bug
 ]
 
 [project.optional-dependencies]