pertpy 0.11.0__py3-none-any.whl → 0.11.2__py3-none-any.whl

pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.11.0"
+__version__ = "0.11.2"
 
 import warnings
 

pertpy/data/_dataloader.py

@@ -15,8 +15,8 @@ from rich.progress import Progress
 
 def _download(  # pragma: no cover
     url: str,
-    output_file_name: str = None,
-    output_path: str | Path = None,
+    output_file_name: str | None = None,
+    output_path: str | Path | None = None,
     block_size: int = 1024,
     overwrite: bool = False,
     is_zip: bool = False,

pertpy/metadata/_cell_line.py

@@ -215,7 +215,7 @@ class CellLine(MetaData):
         For each cell, we fetch cell line annotation from either the Dependency Map (DepMap) or The Genomics of Drug Sensitivity in Cancer Project (Cancerxgene).
 
         Args:
-            adata: The data object to annotate.
+            adata: The AnnData object to annotate.
             query_id: The column of ``.obs`` with cell line information.
             reference_id: The type of cell line identifier in the metadata, e.g. ModelID, CellLineName	or StrippedCellLineName.
                           If fetching cell line metadata from Cancerrxgene, it is recommended to choose "stripped_cell_line_name".
@@ -311,11 +311,9 @@ class CellLine(MetaData):
 
         else:
             raise ValueError(
-                f"The requested cell line type {reference_id} is currently unavailable in the database.\n"
-                "Refer to the available reference identifier in the chosen database.\n"
-                "DepMap_ID is compared by default.\n"
-                "Alternatively, create a `CellLineMetaData.lookup()` object to "
-                "obtain the available reference identifiers in the metadata."
+                f"The requested cell line type {reference_id} is unavailable."
+                "Refer to the available reference identifier in the chosen database."
+                "Alternatively, create a `CellLineMetaData.lookup()` object to obtain the available reference identifiers in the metadata."
             )
 
         return adata
@@ -362,11 +360,9 @@ class CellLine(MetaData):
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns and query_id is not None:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in the adata.obs for the annotation."
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling 'annotate_bulk_rna()'. "
-                "This ensures that the required query ID is included in your data, e.g. stripped_cell_line_name, DepMap ID."
+                f"Specified `query_id` {query_id} can't be found in `adata.obs`. \n"
+                "If the desired query ID is not available, fetch the cell line metadata "
+                "using the `annotate()` function before calling 'annotate_bulk_rna()'."
             )
         if query_id is None:
             query_id = "cell_line_name" if cell_line_source == "sanger" else "DepMap_ID"
@@ -376,9 +372,8 @@ class CellLine(MetaData):
         if cell_line_source == "sanger":
             if query_id not in adata.obs.columns:
                 raise ValueError(
-                    "To annotate bulk RNA data from Wellcome Sanger Institute, `cell_line_name` is used as default reference and query identifier if no `query_id` is given."
-                    "Ensure that you have column `cell_line_name` in `adata.obs` or specify column name in which cell line name is stored."
-                    "If cell line name isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
+                    f"Missing '{query_id}' in `adata.obs`. For Sanger, need `cell_line_name` column "
+                    f"or specify column with cell line names via `query_id` parameter."
                 )
             if self.bulk_rna_sanger is None:
                 self._download_bulk_rna(cell_line_source="sanger")
@@ -387,9 +382,8 @@ class CellLine(MetaData):
         else:
             if query_id not in adata.obs.columns:
                 raise ValueError(
-                    "To annotate bulk RNA data from Broad Institue, `DepMap_ID` is used as default reference and query identifier if no `query_id` is given."
-                    "Ensure that you have column `DepMap_ID` in `adata.obs` or specify column name in which DepMap ID is stored."
-                    "If DepMap ID isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
+                    f"Missing '{query_id}' in `adata.obs`. For Broad Institute data, need `DepMap_ID` column "
+                    f"or specify column with DepMap IDs via `query_id` parameter."
                 )
             reference_id = "DepMap_ID"
 
@@ -472,19 +466,16 @@ class CellLine(MetaData):
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in `adata.obs`. \n"
-                "If the desired query ID is not available, you can fetch the cell line metadata \n"
-                "using the `annotate()` function before calling annotate_protein_expression(). \n"
-                "This ensures that the required query ID is included in your data."
+                f"The specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Fetch cell line metadata with `annotate()` before calling `annotate_protein_expression()`."
             )
         # Lazily download the proteomics data
         if self.proteomics is None:
             self._download_proteomics()
         if reference_id not in self.proteomics.columns:
             raise ValueError(
-                f"The specified `reference_id`{reference_id} can't be found in the protein expression data. \n"
-                "To solve the issue, please use the reference identifier available in the metadata.  \n"
-                "Alternatively, create a `CellLineMetaData.lookup()` object to obtain the available reference identifiers in the metadata."
+                f"Specified `reference_id` `{reference_id}` not found in protein expression data. "
+                f"Use available reference identifiers in metadata or create `CellLineMetaData.lookup()` object."
             )
 
         identifier_num_all = len(adata.obs[query_id].unique())
@@ -551,11 +542,8 @@ class CellLine(MetaData):
             adata = adata.copy()
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in 'adata.obs' for the annotation.\n"
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling `annotate_from_gdsc()`. "
-                "This ensures that the required query ID is included in your data."
+                f"Specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Use an available ID or fetch cell line metadata with `annotate()` before calling `annotate_from_gdsc()`."
             )
         # Lazily download the GDSC data
         if gdsc_dataset == "gdsc_1":
@@ -626,11 +614,8 @@ class CellLine(MetaData):
             adata = adata.copy()
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in 'adata.obs' for the annotation.\n"
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling `annotate_from_prism()`. "
-                "This ensures that the required query ID is included in your data."
+                f"Specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Use an available ID or fetch cell line metadata with `annotate()` before calling `annotate_from_prism()`."
             )
         if self.drug_response_prism is None:
             self._download_prism()
@@ -700,7 +685,6 @@ class CellLine(MetaData):
         if self.drug_response_prism is None:
             self._download_prism()
 
-        # Transfer the data
         return LookUp(
             type="cell_line",
             transfer_metadata=[
@@ -775,7 +759,7 @@ class CellLine(MetaData):
             and sum(adata.obsm[metadata_key].columns != adata.var.index.values) > 0
         ):
             raise ValueError(
-                "Column name of metadata is not the same as the index of adata.var. Ensure that the genes are in the same order."
+                "Column name of metadata is not the same as the index of `adata.var`. Ensure that the genes are in the same order."
             )
 
         # Divide cell lines into those are present and not present in the metadata
@@ -832,7 +816,7 @@ class CellLine(MetaData):
         """
         if corr is None or pval is None:
             raise ValueError(
-                "Missing required input parameter: 'corr' or 'pval'. Please call the function `pt.md.CellLine.correlate()` to generate these outputs before proceeding."
+                "Missing required input parameter: 'corr' or 'pval'. Call `pt.md.CellLine.correlate()` before proceeding."
             )
 
         if category == "cell line":

pertpy/metadata/_compound.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 from typing import TYPE_CHECKING, Literal
 
 import pandas as pd
-import pubchempy as pcp
 
 from ._look_up import LookUp
 from ._metadata import MetaData
@@ -44,6 +43,8 @@ class Compound(MetaData):
         if query_id not in adata.obs.columns:
             raise ValueError(f"The requested query_id {query_id} is not in `adata.obs`.\n Please check again.")
 
+        import pubchempy as pcp
+
         query_dict = {}
         not_matched_identifiers = []
         for compound in adata.obs[query_id].dropna().astype(str).unique():

pertpy/metadata/_look_up.py

@@ -27,7 +27,7 @@ class LookUp:
         Args:
             type: Metadata type for annotation. One of 'cell_line', 'compound', 'moa' or 'drug.
             transfer_metadata: DataFrames used to generate Lookup object.
-                           This is currently set to None for CompoundMetaData which does not require any dataframes for transfer.
+                Currently set to None for CompoundMetaData which does not require any DataFrames for transfer.
         """
         self.type = type
         if type == "cell_line":

pertpy/metadata/_metadata.py

@@ -49,11 +49,8 @@ class MetaData:
             if metadata_type in ["protein expression", "bulk RNA", "drug response"]:
                 hint = "Additionally, call the `CellLineMetaData.annotate()` function to acquire more possible query IDs that can be used for cell line annotation purposes."
             raise ValueError(
-                f"Attempting to match the query id {query_id} in 'adata.obs' to the reference id {reference_id} in the metadata.\n"
-                "However, none of the query IDs could be found in the {metadata_type} annotation data.\n"
-                "To resolve this issue, call the `lookup()` function to create a LookUp object.\n"
-                "This enables obtaining the count of matched identifiers in the AnnData object for different types of reference and query IDs.\n"
-                f"{hint}"
+                f"No matches between `{query_id}` in adata.obs and `{reference_id}` in {metadata_type} data. "
+                f"Use `lookup()` to check compatible identifier types. {hint}"
             )
         if len(unmatched_identifiers) == 0:
             return
@@ -61,10 +58,8 @@ class MetaData:
             verbosity = min(verbosity, len(unmatched_identifiers))
             if verbosity > 0:
                 logger.info(
-                    f"There are {total_identifiers} identifiers in `adata.obs`."
-                    f"However, {len(unmatched_identifiers)} identifiers can't be found in the {metadata_type} annotation, "
-                    "leading to the presence of NA values for their respective metadata.\n"
-                    f"Please check again: *unmatched_identifiers[:verbosity]..."
+                    f"{total_identifiers} identifiers in `adata.obs`, {len(unmatched_identifiers)} not found in {metadata_type} data. "
+                    f"NA values present. Unmatched: {unmatched_identifiers[:verbosity]}"
                 )
         else:
             raise ValueError("Only 'all' or a non-negative value is accepted.")

pertpy/metadata/_moa.py

@@ -110,8 +110,6 @@ class Moa(MetaData):
         """Generate LookUp object for Moa metadata.
 
         The LookUp object provides an overview of the metadata to annotate.
-        annotate_moa function has a corresponding lookup function in the LookUp object,
-        where users can search the query_ids and targets in the metadata.
 
         Returns:
             Returns a LookUp object specific for MoA annotation.

pertpy/tools/__init__.py

@@ -1,7 +1,7 @@
 from importlib import import_module
 
 
-def lazy_import(module_path, class_name, extras):
+def lazy_import(module_path: str, class_name: str, extras: list[str]):
     try:
         for extra in extras:
             import_module(extra)
@@ -21,6 +21,7 @@ def lazy_import(module_path, class_name, extras):
 
 from pertpy.tools._augur import Augur
 from pertpy.tools._cinemaot import Cinemaot
+from pertpy.tools._coda._sccoda import Sccoda
 from pertpy.tools._dialogue import Dialogue
 from pertpy.tools._distances._distance_tests import DistanceTest
 from pertpy.tools._distances._distances import Distance
@@ -41,8 +42,7 @@ from pertpy.tools._perturbation_space._simple import (
 )
 from pertpy.tools._scgen import Scgen
 
-CODA_EXTRAS = ["toytree", "arviz", "ete4"]  # also pyqt6 technically
-Sccoda = lazy_import("pertpy.tools._coda._sccoda", "Sccoda", CODA_EXTRAS)
+CODA_EXTRAS = ["toytree", "ete4"]  # also "pyqt6" but it cannot be imported
 Tasccoda = lazy_import("pertpy.tools._coda._tasccoda", "Tasccoda", CODA_EXTRAS)
 
 DE_EXTRAS = ["formulaic", "pydeseq2"]
@@ -69,6 +69,7 @@ __all__ = [
     "Milo",
     "Mixscape",
     "ClusteringSpace",
+    "PerturbationComparison",
     "LRClassifierSpace",
     "MLPClassifierSpace",
     "CentroidSpace",

pertpy/tools/_augur.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 import random
 from collections import defaultdict
-from dataclasses import dataclass
 from math import floor, nan
 from typing import TYPE_CHECKING, Any, Literal
 

pertpy/tools/_coda/_base_coda.py

@@ -4,12 +4,10 @@ from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import TYPE_CHECKING, Literal
 
-import arviz as az
 import jax.numpy as jnp
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import patsy as pt
 import scanpy as sc
 import seaborn as sns
 from adjustText import adjust_text
@@ -126,7 +124,9 @@ class CompositionalModel2(ABC):
         sample_adata.X = sample_adata.X.astype(dtype)
 
         # Build covariate matrix from R-like formula, save in obsm
-        covariate_matrix = pt.dmatrix(formula, sample_adata.obs)
+        import patsy
+
+        covariate_matrix = patsy.dmatrix(formula, sample_adata.obs)
         covariate_names = covariate_matrix.design_info.column_names[1:]
         sample_adata.obsm["covariate_matrix"] = np.array(covariate_matrix[:, 1:]).astype(dtype)
 
@@ -461,6 +461,8 @@ class CompositionalModel2(ABC):
         else:
             raise ValueError("No valid model type!")
 
+        import arviz as az
+
         summ = az.summary(
             data=self.make_arviz(sample_adata, num_prior_samples=0, use_posterior_predictive=False),
             var_names=var_names,

pertpy/tools/_coda/_sccoda.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING, Literal
 
-import arviz as az
 import jax.numpy as jnp
 import numpy as np
 import numpyro as npy
@@ -17,6 +16,7 @@ from rich import print
 from pertpy.tools._coda._base_coda import CompositionalModel2, from_scanpy
 
 if TYPE_CHECKING:
+    import arviz as az
     import pandas as pd
 
 config.update("jax_enable_x64", True)
@@ -406,6 +406,8 @@ 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

pertpy/tools/_coda/_tasccoda.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING, Literal
 
-import arviz as az
 import jax.numpy as jnp
 import numpy as np
 import numpyro as npy
@@ -25,6 +24,7 @@ from pertpy.tools._coda._base_coda import (
 )
 
 if TYPE_CHECKING:
+    import arviz as az
     import pandas as pd
 
 config.update("jax_enable_x64", True)
@@ -572,6 +572,8 @@ class Tasccoda(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

pertpy/tools/_dialogue.py

@@ -20,7 +20,6 @@ from rich.live import Live
 from rich.progress import BarColumn, Progress, SpinnerColumn, TaskProgressColumn, TextColumn
 from scipy import stats
 from scipy.optimize import nnls
-from seaborn import PairGrid
 from sklearn.linear_model import LinearRegression
 from sparsecca import lp_pmd, multicca_permute, multicca_pmd
 from statsmodels.sandbox.stats.multicomp import multipletests

pertpy/tools/_distances/_distances.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import multiprocessing
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING, Literal, NamedTuple
 

pertpy/tools/_mixscape.py

@@ -26,11 +26,10 @@ if TYPE_CHECKING:
     from matplotlib.axes import Axes
     from matplotlib.colors import Colormap
     from matplotlib.pyplot import Figure
-    from scipy import sparse
 
 
 class Mixscape:
-    """Python implementation of Mixscape."""
+    """identify perturbation effects in CRISPR screens by separating cells into perturbation groups."""
 
     def __init__(self):
         pass
@@ -71,7 +70,7 @@ class Mixscape:
             use_rep: Use the indicated representation. `'X'` or any key for `.obsm` is valid.
                 If `None`, the representation is chosen automatically:
                 For `.n_vars` < 50, `.X` is used, otherwise 'X_pca' is used.
-                If 'X_pca' is not present, it’s computed with default parameters.
+                If 'X_pca' is not present, it's computed with default parameters.
             n_dims: Number of dimensions to use from the representation to calculate the perturbation signature.
                 If `None`, use all dimensions.
             n_pcs: If PCA representation is used, the number of principal components to compute.
@@ -1189,7 +1188,7 @@ class MixscapeGaussianMixture(GaussianMixture):
             n_components: Number of Gaussian components
             fixed_means: Means to fix (use None for those that should be estimated)
             fixed_covariances: Covariances to fix (use None for those that should be estimated)
-            kwargs: Additional arguments passed to scikit-learn's GaussianMixture
+            **kwargs: Additional arguments passed to scikit-learn's GaussianMixture
         """
         super().__init__(n_components=n_components, **kwargs)
         self.fixed_means = fixed_means

{pertpy-0.11.0.dist-info → pertpy-0.11.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.11.0
+Version: 0.11.2
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -67,7 +67,7 @@ Requires-Dist: sparsecca
 Provides-Extra: de
 Requires-Dist: formulaic; extra == 'de'
 Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'de'
-Requires-Dist: pydeseq2>=v0.5.0pre1; extra == 'de'
+Requires-Dist: pydeseq2>=v0.5.0; extra == 'de'
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc
@@ -88,7 +88,7 @@ Requires-Dist: sphinx-gallery; extra == 'doc'
 Requires-Dist: sphinx-issues; extra == 'doc'
 Requires-Dist: sphinx-last-updated-by-git; extra == 'doc'
 Requires-Dist: sphinx-remove-toctrees; extra == 'doc'
-Requires-Dist: sphinx>=6; extra == 'doc'
+Requires-Dist: sphinx>=8.1; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
 Provides-Extra: tcoda
@@ -101,7 +101,6 @@ Requires-Dist: leidenalg; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Description-Content-Type: text/markdown
 
-[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![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)
 [![License](https://img.shields.io/github/license/scverse/pertpy)](https://opensource.org/licenses/Apache2.0)
@@ -111,13 +110,16 @@ Description-Content-Type: text/markdown
 [![Test](https://github.com/scverse/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/test.yml)
 [![PyPI](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 
-# pertpy
+# pertpy - Perturbation Analysis in Python
+
+Pertpy is a scverse ecosystem framework for analyzing large-scale single-cell perturbation experiments.
+It provides tools for harmonizing perturbation datasets, automating metadata annotation, calculating perturbation distances, and efficiently analyzing how cells respond to various stimuli like genetic modifications, drug treatments, and environmental changes.
 
 ![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
 
 ## Documentation
 
-Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
+Please read the [documentation](https://pertpy.readthedocs.io/en/latest) for installation, tutorials, use cases, and more.
 
 ## Installation
 
@@ -149,7 +151,7 @@ bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/api.html
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

{pertpy-0.11.0.dist-info → pertpy-0.11.2.dist-info}/RECORD

@@ -1,34 +1,34 @@
-pertpy/__init__.py,sha256=2cNNXWvBztH3KQzxe5WEl_Krfh0tdax4pPg1iUYjhQE,716
+pertpy/__init__.py,sha256=wwZLpjFSDAZzGA0HGNuk8LoxXjWdrD9OKvpJ4fdsHZU,716
 pertpy/_doc.py,sha256=j5TMNC-DA9yIMqIIUNpjpcVgWfRqyBBfvbRjnCM_OLs,427
 pertpy/_types.py,sha256=IcHCojCUqx8CapibNkcYf2TUqjBFP2ujeELvn_IBSBQ,154
 pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/data/__init__.py,sha256=ah3yvoxkgbdMUNAWxS3SyqcUuVamBOSeuWkF2QRAEwM,2703
-pertpy/data/_dataloader.py,sha256=ZWDDvx8KmqkvMcjXEmGNeDyCceDur_osb-o2dDTHeQU,4397
+pertpy/data/_dataloader.py,sha256=Osml8irOaoL2n2MhKRKre70Poxiv6NfJBKaK8vRe07Q,4411
 pertpy/data/_datasets.py,sha256=4IceyYURpstZSFRrD6gBjoYg8uRbEPo1QLXTt-SwB5k,65507
 pertpy/metadata/__init__.py,sha256=wROPCXmJX2v5schJaBTPQtGW-FGCNWPfO_6bpnXwk-c,276
-pertpy/metadata/_cell_line.py,sha256=xzlJV_loGS5yA3QaB2xnp0mlEgCWdoG1VPCrfbJKtMw,44494
-pertpy/metadata/_compound.py,sha256=ywNNqtib0exHv0z8ctmTRf1Hk64tSGWSiUEffycxf6A,4755
+pertpy/metadata/_cell_line.py,sha256=hKmaZvjIsQ3wHo__0aKo3JlWvsf8-4OD-gIBNQnW8_E,42716
+pertpy/metadata/_compound.py,sha256=JsAv_KCcNkgVVrXTyhu-BeM8rBX8a93Wq5Z6avpxN7Y,4764
 pertpy/metadata/_drug.py,sha256=8QDSyxiFl25JdS80EQJC_krg6fEe5LIQEE6BsV1r8nY,9006
-pertpy/metadata/_look_up.py,sha256=4BuQlff_aAKFOKPojXDdxvH6uOkRlHzGeyxcjBc79OM,28682
-pertpy/metadata/_metadata.py,sha256=hV2LTFrExddLNU_RsDkZju6lQUSRoP4OIn_dumCyQao,3277
-pertpy/metadata/_moa.py,sha256=cSJimHZsPZ6tAXcl_aHOhyzUayf6fqtgAcJJ5KwRRsA,4698
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 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=ijL-bjQ-9qn4r3DlhBxzsqk-bD4RqPsFlok-Otj4hg8,15872
 pertpy/preprocessing/_guide_rna_mixture.py,sha256=pT_YkjmN4iEJ-THBROu_dpbr8E6u8GJw36YoGseikD0,6422
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 pertpy/tools/_cinemaot.py,sha256=54-rS0AEj31dMe7iU4kEmLoAunq3jNuhsBE3IEp9hrI,38071
-pertpy/tools/_dialogue.py,sha256=ngjDcJK0D6ukJwiyS9cLYjrDU82n1FJru8yx8TvKSt8,52384
+pertpy/tools/_dialogue.py,sha256=cCSwo9ge1pOLoA7QHTPb3b865juCFWUaKX5aD7UoSjo,52355
 pertpy/tools/_enrichment.py,sha256=55mwotLH9DXQOhl85MCkxXu-MX0RysLyrPheJysAnF0,21369
 pertpy/tools/_milo.py,sha256=r-kZcpAcoQuhi41AnVuzh-cMIcV3HB3-RGzynHyDc1A,43712
-pertpy/tools/_mixscape.py,sha256=ob22FI1hqUtaEZzCqrocy0-k8iUOChItc2tdCDeNDGY,57173
+pertpy/tools/_mixscape.py,sha256=qjXGyH-oeBFte0efuHJfhVEbivnzUVWREwC40ef6Se8,57203
 pertpy/tools/decoupler_LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 pertpy/tools/transferlearning_MMD_LICENSE,sha256=MUvDA-o_j9htRpI8fStVdCRuyLdPkQUuIH0a_EIc57w,1069
 pertpy/tools/_coda/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pertpy/tools/_coda/_base_coda.py,sha256=cITCEWyiPlxqS1Buhs8JzE3yHCdQksFitcXscEK7WX4,111504
-pertpy/tools/_coda/_sccoda.py,sha256=UjT9mha14YPk6jIqigAbyb1zqhrtBDV7b3NMWeoMFJ4,22575
-pertpy/tools/_coda/_tasccoda.py,sha256=hZBUhqpymFLu-l8CZ0FDLk04kUah9aSyHZwQhvHVm-U,30433
+pertpy/tools/_coda/_base_coda.py,sha256=-rpdipPLFd4cFXyLMN7uFgv-pFJseKaqDmyWRBrGfws,111519
+pertpy/tools/_coda/_sccoda.py,sha256=0Ret6O56kAfCNOdBvtxqiyuj2rUPp18SV1GVK1AvYGU,22607
+pertpy/tools/_coda/_tasccoda.py,sha256=BTaOAmL458zQ_og3x4ENlDnJHD6_F4YkdCoXWsF4i1U,30465
 pertpy/tools/_differential_gene_expression/__init__.py,sha256=SEydWg0iT3Y1pApjnCAOuHxFeI6xVUfgyBHv2s3LADU,487
 pertpy/tools/_differential_gene_expression/_base.py,sha256=PpfH_RZXsN79Bu0yBFPE9TXEqNsZ4bSzSbhM0wZou2I,38322
 pertpy/tools/_differential_gene_expression/_checks.py,sha256=hH_GP0lWGO-5zrCFX4YiIVCZBCuK0ZJ0jFmdlx2Qm4k,1639
@@ -39,7 +39,7 @@ pertpy/tools/_differential_gene_expression/_simple_tests.py,sha256=SfU8s_P2JzEA1
 pertpy/tools/_differential_gene_expression/_statsmodels.py,sha256=90h9EPuoCtNxAbJ1Xq4j_E4yYJJpk64zTP7GyTdmrxY,2220
 pertpy/tools/_distances/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/tools/_distances/_distance_tests.py,sha256=6_nqfHUfKxkI2Yhkzspq3ujMpq56zV_Ddn7bgPzgjyo,13513
-pertpy/tools/_distances/_distances.py,sha256=uzE8IcKPFYYXI0fKSgFHM_UIBZfA6uf9gBTSq8nZmZw,50496
+pertpy/tools/_distances/_distances.py,sha256=89d1zShW_9dhphup2oWx5hMOFC7RdogOY56doMuBFts,50473
 pertpy/tools/_perturbation_space/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pertpy/tools/_perturbation_space/_clustering.py,sha256=pNx_SpPkZfCbgF7vzHWqAaiiHdbxPaA-L-hTWTbzFhI,3528
 pertpy/tools/_perturbation_space/_comparison.py,sha256=-NzCPRT-IlhJ9hOz7NQLSk0riIzr2C0yZvX6zm3kon4,4291
@@ -52,7 +52,7 @@ pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_K
 pertpy/tools/_scgen/_scgen.py,sha256=31T8ez0FxABIbunJHCk8xvGulHFb8RHXSsyM_z1WsPY,30850
 pertpy/tools/_scgen/_scgenvae.py,sha256=bPk4v7EdJc7ROdLuDitHiX_Pvwa7Flw2qHRUwBvjLJY,3889
 pertpy/tools/_scgen/_utils.py,sha256=qz5QUn_Bvk2NGyYVzp3jgjWTFOMt1YyHwUo6HWtoThY,2871
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-pertpy-0.11.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-pertpy-0.11.0.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
-pertpy-0.11.0.dist-info/RECORD,,
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+pertpy-0.11.2.dist-info/RECORD,,