pertpy 1.0.1__py3-none-any.whl → 1.0.2__py3-none-any.whl

pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "1.0.1"
+__version__ = "1.0.2"
 
 import warnings
 

pertpy/metadata/_cell_line.py

@@ -195,7 +195,9 @@ class CellLine(MetaData):
                 block_size=4096,
                 is_zip=False,
             )
-        df = pd.read_csv(drug_response_prism_file_path, index_col=0)[["depmap_id", "name", "ic50", "ec50", "auc"]]
+        df = pd.read_csv(
+            drug_response_prism_file_path, index_col=0, usecols=["broad_id", "depmap_id", "name", "ic50", "ec50", "auc"]
+        )
         df = df.dropna(subset=["depmap_id", "name"])
         df = df.groupby(["depmap_id", "name"]).mean().reset_index()
         self.drug_response_prism = df
@@ -568,7 +570,9 @@ class CellLine(MetaData):
             verbosity=verbosity,
         )
 
-        old_index_name = "index" if adata.obs.index.name is None else adata.obs.index.name
+        if adata.obs.index.name is None:
+            adata.obs.index.name = "original_index"
+        old_index_name = adata.obs.index.name
         adata.obs = (
             adata.obs.reset_index()
             .set_index([query_id, query_perturbation])
@@ -635,7 +639,9 @@ class CellLine(MetaData):
             verbosity=verbosity,
         )
 
-        old_index_name = "index" if adata.obs.index.name is None else adata.obs.index.name
+        if adata.obs.index.name is None:
+            adata.obs.index.name = "original_index"
+        old_index_name = adata.obs.index.name
         adata.obs = (
             adata.obs.reset_index()
             .set_index([query_id, "perturbation_lower"])

pertpy/tools/_coda/_sccoda.py

@@ -303,7 +303,7 @@ class Sccoda(CompositionalModel2):
         self,
         data: AnnData | MuData,
         modality_key: str = "coda",
-        rng_key=None,
+        rng_key: int | None = None,
         num_prior_samples: int = 500,
         use_posterior_predictive: bool = True,
     ) -> az.InferenceData:
@@ -381,34 +381,9 @@ class Sccoda(CompositionalModel2):
         if rng_key is None:
             rng = np.random.default_rng()
             rng_key = random.key(rng.integers(0, 10000))
-
-        if use_posterior_predictive:
-            posterior_predictive = Predictive(self.model, self.mcmc.get_samples())(
-                rng_key,
-                counts=None,
-                covariates=numpyro_covariates,
-                n_total=numpyro_n_total,
-                ref_index=ref_index,
-                sample_adata=sample_adata,
-            )
-        else:
-            posterior_predictive = None
-
-        if num_prior_samples > 0:
-            prior = Predictive(self.model, num_samples=num_prior_samples)(
-                rng_key,
-                counts=None,
-                covariates=numpyro_covariates,
-                n_total=numpyro_n_total,
-                ref_index=ref_index,
-                sample_adata=sample_adata,
-            )
         else:
-            prior = None
-
-        import arviz as az
+            rng_key = random.key(rng_key)
 
-        # Create arviz object
         if use_posterior_predictive:
             posterior_predictive = Predictive(self.model, self.mcmc.get_samples())(
                 rng_key,
@@ -451,6 +426,9 @@ class Sccoda(CompositionalModel2):
         else:
             prior = None
 
+        import arviz as az
+
+        # Create arviz object
         arviz_data = az.from_numpyro(
             self.mcmc, prior=prior, posterior_predictive=posterior_predictive, dims=dims, coords=coords
         )
@@ -468,76 +446,84 @@ class Sccoda(CompositionalModel2):
         *args,
         **kwargs,
     ):
-        """Examples:
-        >>> import pertpy as pt
-        >>> haber_cells = pt.dt.haber_2017_regions()
-        >>> sccoda = pt.tl.Sccoda()
-        >>> mdata = sccoda.load(haber_cells,
-        >>>                     type="cell_level",
-        >>>                     generate_sample_level=True,
-        >>>                     cell_type_identifier="cell_label",
-        >>>                     sample_identifier="batch",
-        >>>                     covariate_obs=["condition"])
-        >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
-        >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells,
+            >>>                     type="cell_level",
+            >>>                     generate_sample_level=True,
+            >>>                     cell_type_identifier="cell_label",
+            >>>                     sample_identifier="batch",
+            >>>                     covariate_obs=["condition"])
+            >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
+            >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42).
+        """  # noqa: D205, D212
         return super().run_nuts(data, modality_key, num_samples, num_warmup, rng_key, copy, *args, **kwargs)
 
     run_nuts.__doc__ = CompositionalModel2.run_nuts.__doc__ + run_nuts.__doc__
 
     def credible_effects(self, data: AnnData | MuData, modality_key: str = "coda", est_fdr: float = None) -> pd.Series:
-        """Examples:
-        >>> import pertpy as pt
-        >>> haber_cells = pt.dt.haber_2017_regions()
-        >>> sccoda = pt.tl.Sccoda()
-        >>> mdata = sccoda.load(haber_cells,
-        >>>                     type="cell_level",
-        >>>                     generate_sample_level=True,
-        >>>                     cell_type_identifier="cell_label",
-        >>>                     sample_identifier="batch",
-        >>>                     covariate_obs=["condition"])
-        >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
-        >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
-        >>> credible_effects = sccoda.credible_effects(mdata).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells,
+            >>>                     type="cell_level",
+            >>>                     generate_sample_level=True,
+            >>>                     cell_type_identifier="cell_label",
+            >>>                     sample_identifier="batch",
+            >>>                     covariate_obs=["condition"])
+            >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
+            >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
+            >>> credible_effects = sccoda.credible_effects(mdata).
+        """  # noqa: D205, D212
         return super().credible_effects(data, modality_key, est_fdr)
 
     credible_effects.__doc__ = CompositionalModel2.credible_effects.__doc__ + credible_effects.__doc__
 
     def summary(self, data: AnnData | MuData, extended: bool = False, modality_key: str = "coda", *args, **kwargs):
-        """Examples:
-        >>> import pertpy as pt
-        >>> haber_cells = pt.dt.haber_2017_regions()
-        >>> sccoda = pt.tl.Sccoda()
-        >>> mdata = sccoda.load(haber_cells,
-        >>>                     type="cell_level",
-        >>>                     generate_sample_level=True,
-        >>>                     cell_type_identifier="cell_label",
-        >>>                     sample_identifier="batch",
-        >>>                     covariate_obs=["condition"])
-        >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
-        >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
-        >>> sccoda.summary(mdata).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells,
+            >>>                     type="cell_level",
+            >>>                     generate_sample_level=True,
+            >>>                     cell_type_identifier="cell_label",
+            >>>                     sample_identifier="batch",
+            >>>                     covariate_obs=["condition"])
+            >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
+            >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
+            >>> sccoda.summary(mdata).
+        """  # noqa: D205, D212
         return super().summary(data, extended, modality_key, *args, **kwargs)
 
     summary.__doc__ = CompositionalModel2.summary.__doc__ + summary.__doc__
 
     def set_fdr(self, data: AnnData | MuData, est_fdr: float, modality_key: str = "coda", *args, **kwargs):
-        """Examples:
-        >>> import pertpy as pt
-        >>> haber_cells = pt.dt.haber_2017_regions()
-        >>> sccoda = pt.tl.Sccoda()
-        >>> mdata = sccoda.load(haber_cells,
-        >>>                     type="cell_level",
-        >>>                     generate_sample_level=True,
-        >>>                     cell_type_identifier="cell_label",
-        >>>                     sample_identifier="batch",
-        >>>                     covariate_obs=["condition"])
-        >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
-        >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
-        >>> sccoda.set_fdr(mdata, est_fdr=0.4).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells,
+            >>>                     type="cell_level",
+            >>>                     generate_sample_level=True,
+            >>>                     cell_type_identifier="cell_label",
+            >>>                     sample_identifier="batch",
+            >>>                     covariate_obs=["condition"])
+            >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
+            >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
+            >>> sccoda.set_fdr(mdata, est_fdr=0.4).
+        """  # noqa: D205, D212
         return super().set_fdr(data, est_fdr, modality_key, *args, **kwargs)
 
     set_fdr.__doc__ = CompositionalModel2.set_fdr.__doc__ + set_fdr.__doc__

pertpy/tools/_coda/_tasccoda.py

@@ -120,8 +120,10 @@ class Tasccoda(CompositionalModel2):
                 covariate_df=covariate_df,
             )
             mdata = MuData({modality_key_1: adata, modality_key_2: adata_coda})
-        else:
+        elif type == "sample_level":
             mdata = MuData({modality_key_1: AnnData(), modality_key_2: adata})
+        else:
+            raise ValueError(f'{type} is not a supported type, expected "cell_level" or "sample_level".')
         import_tree(
             data=mdata,
             modality_1=modality_key_1,
@@ -464,7 +466,7 @@ class Tasccoda(CompositionalModel2):
         self,
         data: AnnData | MuData,
         modality_key: str = "coda",
-        rng_key=None,
+        rng_key: int | None = None,
         num_prior_samples: int = 500,
         use_posterior_predictive: bool = True,
     ) -> az.InferenceData:
@@ -547,6 +549,8 @@ class Tasccoda(CompositionalModel2):
         if rng_key is None:
             rng = np.random.default_rng()
             rng_key = random.key(rng.integers(0, 10000))
+        else:
+            rng_key = random.key(rng_key)
 
         if use_posterior_predictive:
             posterior_predictive = Predictive(self.model, self.mcmc.get_samples())(
@@ -557,6 +561,15 @@ class Tasccoda(CompositionalModel2):
                 ref_index=ref_index,
                 sample_adata=sample_adata,
             )
+            # Remove problematic posterior predictive arrays with wrong dimensions
+            if posterior_predictive and "counts" in posterior_predictive:
+                counts_shape = posterior_predictive["counts"].shape
+                expected_dims = 2  # ['sample', 'cell_type']
+                if len(counts_shape) != expected_dims:
+                    posterior_predictive = {k: v for k, v in posterior_predictive.items() if k != "counts"}
+                    logger.warning(
+                        f"Removed 'counts' from posterior_predictive due to dimension mismatch: got {len(counts_shape)}D, expected {expected_dims}D"
+                    )
         else:
             posterior_predictive = None
 
@@ -569,6 +582,15 @@ class Tasccoda(CompositionalModel2):
                 ref_index=ref_index,
                 sample_adata=sample_adata,
             )
+            # Remove problematic prior arrays with wrong dimensions
+            if prior and "counts" in prior:
+                counts_shape = prior["counts"].shape
+                expected_dims = 2  # ['sample', 'cell_type']
+                if len(counts_shape) != expected_dims:
+                    prior = {k: v for k, v in prior.items() if k != "counts"}
+                    logger.warning(
+                        f"Removed 'counts' from prior due to dimension mismatch: got {len(counts_shape)}D, expected {expected_dims}D"
+                    )
         else:
             prior = None
 
@@ -592,80 +614,88 @@ class Tasccoda(CompositionalModel2):
         *args,
         **kwargs,
     ):
-        """Examples:
-        >>> import pertpy as pt
-        >>> adata = pt.dt.tasccoda_example()
-        >>> tasccoda = pt.tl.Tasccoda()
-        >>> mdata = tasccoda.load(
-        >>>     adata, type="sample_level",
-        >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
-        >>>     key_added="lineage", add_level_name=True
-        >>> )
-        >>> mdata = tasccoda.prepare(
-        >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
-        >>> )
-        >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.tasccoda_example()
+            >>> tasccoda = pt.tl.Tasccoda()
+            >>> mdata = tasccoda.load(
+            >>>     adata, type="sample_level",
+            >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
+            >>>     key_added="lineage", add_level_name=True
+            >>> )
+            >>> mdata = tasccoda.prepare(
+            >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+            >>> )
+            >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42).
+        """  # noqa: D205, D212
         return super().run_nuts(data, modality_key, num_samples, num_warmup, rng_key, copy, *args, **kwargs)
 
     run_nuts.__doc__ = CompositionalModel2.run_nuts.__doc__ + run_nuts.__doc__
 
     def summary(self, data: AnnData | MuData, extended: bool = False, modality_key: str = "coda", *args, **kwargs):
-        """Examples:
-        >>> import pertpy as pt
-        >>> adata = pt.dt.tasccoda_example()
-        >>> tasccoda = pt.tl.Tasccoda()
-        >>> mdata = tasccoda.load(
-        >>>     adata, type="sample_level",
-        >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
-        >>>     key_added="lineage", add_level_name=True
-        >>> )
-        >>> mdata = tasccoda.prepare(
-        >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
-        >>> )
-        >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
-        >>> tasccoda.summary(mdata).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.tasccoda_example()
+            >>> tasccoda = pt.tl.Tasccoda()
+            >>> mdata = tasccoda.load(
+            >>>     adata, type="sample_level",
+            >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
+            >>>     key_added="lineage", add_level_name=True
+            >>> )
+            >>> mdata = tasccoda.prepare(
+            >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+            >>> )
+            >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
+            >>> tasccoda.summary(mdata).
+        """  # noqa: D205, D212
         return super().summary(data, extended, modality_key, *args, **kwargs)
 
     summary.__doc__ = CompositionalModel2.summary.__doc__ + summary.__doc__
 
     def credible_effects(self, data: AnnData | MuData, modality_key: str = "coda", est_fdr: float = None) -> pd.Series:
-        """Examples:
-        >>> import pertpy as pt
-        >>> adata = pt.dt.tasccoda_example()
-        >>> tasccoda = pt.tl.Tasccoda()
-        >>> mdata = tasccoda.load(
-        >>>     adata, type="sample_level",
-        >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
-        >>>     key_added="lineage", add_level_name=True
-        >>> )
-        >>> mdata = tasccoda.prepare(
-        >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
-        >>> )
-        >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
-        >>> tasccoda.credible_effects(mdata).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.tasccoda_example()
+            >>> tasccoda = pt.tl.Tasccoda()
+            >>> mdata = tasccoda.load(
+            >>>     adata, type="sample_level",
+            >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
+            >>>     key_added="lineage", add_level_name=True
+            >>> )
+            >>> mdata = tasccoda.prepare(
+            >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+            >>> )
+            >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
+            >>> tasccoda.credible_effects(mdata).
+        """  # noqa: D205, D212
         return super().credible_effects(data, modality_key, est_fdr)
 
     credible_effects.__doc__ = CompositionalModel2.credible_effects.__doc__ + credible_effects.__doc__
 
     def set_fdr(self, data: AnnData | MuData, est_fdr: float, modality_key: str = "coda", *args, **kwargs):
-        """Examples:
-        >>> import pertpy as pt
-        >>> adata = pt.dt.tasccoda_example()
-        >>> tasccoda = pt.tl.Tasccoda()
-        >>> mdata = tasccoda.load(
-        >>>     adata, type="sample_level",
-        >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
-        >>>     key_added="lineage", add_level_name=True
-        >>> )
-        >>> mdata = tasccoda.prepare(
-        >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
-        >>> )
-        >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
-        >>> tasccoda.set_fdr(mdata, est_fdr=0.4).
-        """  # noqa: D205
+        """
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.tasccoda_example()
+            >>> tasccoda = pt.tl.Tasccoda()
+            >>> mdata = tasccoda.load(
+            >>>     adata, type="sample_level",
+            >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
+            >>>     key_added="lineage", add_level_name=True
+            >>> )
+            >>> mdata = tasccoda.prepare(
+            >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+            >>> )
+            >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
+            >>> tasccoda.set_fdr(mdata, est_fdr=0.4).
+        """  # noqa: D205, D212
         return super().set_fdr(data, est_fdr, modality_key, *args, **kwargs)
 
     set_fdr.__doc__ = CompositionalModel2.set_fdr.__doc__ + set_fdr.__doc__

{pertpy-1.0.1.dist-info → pertpy-1.0.2.dist-info}/METADATA

@@ -1,41 +1,17 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 1.0.1
+Version: 1.0.2
 Summary: Perturbation Analysis in the scverse ecosystem.
-Project-URL: Documentation, https://pertpy.readthedocs.io
-Project-URL: Source, https://github.com/scverse/pertpy
-Project-URL: Home-page, https://github.com/scverse/pertpy
 Author: Lukas Heumos, Lilly May, Stefan Peidli, Johannes Ostner, Gregor Sturm, Emma Dann, Yuge Ji, Xinyue Zhang, Xichen Wu, Tessa Green, Antonia Schumacher
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
-License: MIT License
-        
-        Copyright (c) 2021, Lukas Heumos
-        Copyright (c) 2025, scverse®
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-License-File: LICENSE
+Requires-Python: >=3.11,<3.14
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Framework :: Jupyter
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX :: Linux
@@ -45,60 +21,62 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: <3.14,>=3.11
-Requires-Dist: adjusttext
-Requires-Dist: arviz
-Requires-Dist: blitzgsea
-Requires-Dist: fast-array-utils[accel,sparse]
-Requires-Dist: lamin-utils
-Requires-Dist: mudata
-Requires-Dist: openpyxl
-Requires-Dist: ott-jax
-Requires-Dist: pubchempy
-Requires-Dist: pyarrow
-Requires-Dist: requests
+License-File: LICENSE
 Requires-Dist: rich
 Requires-Dist: scanpy
-Requires-Dist: scikit-learn>=1.4
+Requires-Dist: mudata
+Requires-Dist: requests
 Requires-Dist: scikit-misc
 Requires-Dist: scvi-tools
+Requires-Dist: adjusttext
+Requires-Dist: ott-jax
 Requires-Dist: sparsecca
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 [![Build](https://github.com/scverse/pertpy/actions/workflows/build.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/scverse/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/scverse/pertpy)
@@ -205,3 +183,4 @@ If you like scverse® and want to support our mission, please consider making a
   >
 </a>
 </div>
+

{pertpy-1.0.1.dist-info → pertpy-1.0.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
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+pertpy/__init__.py,sha256=BTYM-9jQll7SwO4GNHDYKoD5duQXVPwifZYGOvtDD-E,972
 pertpy/_doc.py,sha256=j5TMNC-DA9yIMqIIUNpjpcVgWfRqyBBfvbRjnCM_OLs,427
 pertpy/_types.py,sha256=IcHCojCUqx8CapibNkcYf2TUqjBFP2ujeELvn_IBSBQ,154
 pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -6,7 +6,7 @@ pertpy/data/__init__.py,sha256=ah3yvoxkgbdMUNAWxS3SyqcUuVamBOSeuWkF2QRAEwM,2703
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 pertpy/metadata/_compound.py,sha256=JsAv_KCcNkgVVrXTyhu-BeM8rBX8a93Wq5Z6avpxN7Y,4764
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 pertpy/metadata/_look_up.py,sha256=0nrI_xy-qBZ3tyt4dwhEBwm0A9WP95ZaDiUQFf_88FU,28663
@@ -27,8 +27,8 @@ pertpy/tools/decoupler_LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaY
 pertpy/tools/transferlearning_MMD_LICENSE,sha256=MUvDA-o_j9htRpI8fStVdCRuyLdPkQUuIH0a_EIc57w,1069
 pertpy/tools/_coda/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-pertpy/tools/_coda/_tasccoda.py,sha256=BTaOAmL458zQ_og3x4ENlDnJHD6_F4YkdCoXWsF4i1U,30465
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 pertpy/tools/_differential_gene_expression/__init__.py,sha256=8_u7nsHY5GfFITT0Rs3v1p1vXpsGIWcBzwipuhXM3Ww,1653
 pertpy/tools/_differential_gene_expression/_base.py,sha256=GbBi8o7rTA3wH5DZJ9C1QzfqB5yak4r3xMvKQrizsTY,38274
 pertpy/tools/_differential_gene_expression/_checks.py,sha256=hH_GP0lWGO-5zrCFX4YiIVCZBCuK0ZJ0jFmdlx2Qm4k,1639
@@ -52,7 +52,7 @@ pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_K
 pertpy/tools/_scgen/_scgen.py,sha256=AQNGsDe-9HEqli3oq7UBDg68ofLCoXm-R_jnLFQ-rlc,30856
 pertpy/tools/_scgen/_scgenvae.py,sha256=bPk4v7EdJc7ROdLuDitHiX_Pvwa7Flw2qHRUwBvjLJY,3889
 pertpy/tools/_scgen/_utils.py,sha256=qz5QUn_Bvk2NGyYVzp3jgjWTFOMt1YyHwUo6HWtoThY,2871
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-pertpy-1.0.1.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
-pertpy-1.0.1.dist-info/RECORD,,
+pertpy-1.0.2.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
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+pertpy-1.0.2.dist-info/RECORD,,

{pertpy-1.0.1.dist-info → pertpy-1.0.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
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 Root-Is-Purelib: true
 Tag: py3-none-any