pertpy 0.11.0__py3-none-any.whl → 0.11.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. pertpy/__init__.py +1 -1
  2. pertpy/tools/__init__.py +4 -3
  3. pertpy/tools/_coda/_base_coda.py +5 -3
  4. pertpy/tools/_coda/_sccoda.py +3 -1
  5. pertpy/tools/_coda/_tasccoda.py +3 -1
  6. pertpy/tools/_dialogue.py +0 -1
  7. pertpy/tools/_distances/_distances.py +0 -1
  8. {pertpy-0.11.0.dist-info → pertpy-0.11.1.dist-info}/METADATA +8 -6
  9. {pertpy-0.11.0.dist-info → pertpy-0.11.1.dist-info}/RECORD +11 -11
  10. {pertpy-0.11.0.dist-info → pertpy-0.11.1.dist-info}/WHEEL +0 -0
  11. {pertpy-0.11.0.dist-info → pertpy-0.11.1.dist-info}/licenses/LICENSE +0 -0
pertpy/__init__.py CHANGED
@@ -2,7 +2,7 @@
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  __author__ = "Lukas Heumos"
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  __email__ = "lukas.heumos@posteo.net"
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- __version__ = "0.11.0"
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+ __version__ = "0.11.1"
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  import warnings
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pertpy/tools/__init__.py CHANGED
@@ -1,7 +1,7 @@
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  from importlib import import_module
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- def lazy_import(module_path, class_name, extras):
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+ def lazy_import(module_path: str, class_name: str, extras: list[str]):
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  try:
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  for extra in extras:
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  import_module(extra)
@@ -21,6 +21,7 @@ def lazy_import(module_path, class_name, extras):
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  from pertpy.tools._augur import Augur
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  from pertpy.tools._cinemaot import Cinemaot
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+ from pertpy.tools._coda._sccoda import Sccoda
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  from pertpy.tools._dialogue import Dialogue
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  from pertpy.tools._distances._distance_tests import DistanceTest
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  from pertpy.tools._distances._distances import Distance
@@ -41,8 +42,7 @@ from pertpy.tools._perturbation_space._simple import (
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  )
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  from pertpy.tools._scgen import Scgen
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- CODA_EXTRAS = ["toytree", "arviz", "ete4"] # also pyqt6 technically
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- Sccoda = lazy_import("pertpy.tools._coda._sccoda", "Sccoda", CODA_EXTRAS)
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+ CODA_EXTRAS = ["toytree", "ete4"] # also "pyqt6" but it cannot be imported
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  Tasccoda = lazy_import("pertpy.tools._coda._tasccoda", "Tasccoda", CODA_EXTRAS)
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  DE_EXTRAS = ["formulaic", "pydeseq2"]
@@ -69,6 +69,7 @@ __all__ = [
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  "Milo",
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  "Mixscape",
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  "ClusteringSpace",
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+ "PerturbationComparison",
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  "LRClassifierSpace",
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  "MLPClassifierSpace",
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  "CentroidSpace",
pertpy/tools/_coda/_base_coda.py CHANGED
@@ -4,12 +4,10 @@ from abc import ABC, abstractmethod
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  from pathlib import Path
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  from typing import TYPE_CHECKING, Literal
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- import arviz as az
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  import jax.numpy as jnp
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  import matplotlib.pyplot as plt
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  import numpy as np
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  import pandas as pd
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- import patsy as pt
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  import scanpy as sc
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  import seaborn as sns
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  from adjustText import adjust_text
@@ -126,7 +124,9 @@ class CompositionalModel2(ABC):
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  sample_adata.X = sample_adata.X.astype(dtype)
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  # Build covariate matrix from R-like formula, save in obsm
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- covariate_matrix = pt.dmatrix(formula, sample_adata.obs)
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+ import patsy
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+
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+ covariate_matrix = patsy.dmatrix(formula, sample_adata.obs)
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  covariate_names = covariate_matrix.design_info.column_names[1:]
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  sample_adata.obsm["covariate_matrix"] = np.array(covariate_matrix[:, 1:]).astype(dtype)
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@@ -461,6 +461,8 @@ class CompositionalModel2(ABC):
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  else:
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  raise ValueError("No valid model type!")
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+ import arviz as az
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+
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  summ = az.summary(
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  data=self.make_arviz(sample_adata, num_prior_samples=0, use_posterior_predictive=False),
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  var_names=var_names,
pertpy/tools/_coda/_sccoda.py CHANGED
@@ -2,7 +2,6 @@ from __future__ import annotations
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  from typing import TYPE_CHECKING, Literal
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- import arviz as az
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  import jax.numpy as jnp
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  import numpy as np
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  import numpyro as npy
@@ -17,6 +16,7 @@ from rich import print
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  from pertpy.tools._coda._base_coda import CompositionalModel2, from_scanpy
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  if TYPE_CHECKING:
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+ import arviz as az
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  import pandas as pd
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  config.update("jax_enable_x64", True)
@@ -406,6 +406,8 @@ class Sccoda(CompositionalModel2):
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  else:
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  prior = None
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+ import arviz as az
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+
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  # Create arviz object
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  arviz_data = az.from_numpyro(
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  self.mcmc, prior=prior, posterior_predictive=posterior_predictive, dims=dims, coords=coords
pertpy/tools/_coda/_tasccoda.py CHANGED
@@ -2,7 +2,6 @@ from __future__ import annotations
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  from typing import TYPE_CHECKING, Literal
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- import arviz as az
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  import jax.numpy as jnp
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  import numpy as np
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  import numpyro as npy
@@ -25,6 +24,7 @@ from pertpy.tools._coda._base_coda import (
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  )
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  if TYPE_CHECKING:
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+ import arviz as az
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  import pandas as pd
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  config.update("jax_enable_x64", True)
@@ -572,6 +572,8 @@ class Tasccoda(CompositionalModel2):
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  else:
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  prior = None
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+ import arviz as az
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+
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  # Create arviz object
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  arviz_data = az.from_numpyro(
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  self.mcmc, prior=prior, posterior_predictive=posterior_predictive, dims=dims, coords=coords
pertpy/tools/_dialogue.py CHANGED
@@ -20,7 +20,6 @@ from rich.live import Live
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  from rich.progress import BarColumn, Progress, SpinnerColumn, TaskProgressColumn, TextColumn
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  from scipy import stats
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  from scipy.optimize import nnls
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- from seaborn import PairGrid
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  from sklearn.linear_model import LinearRegression
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  from sparsecca import lp_pmd, multicca_permute, multicca_pmd
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  from statsmodels.sandbox.stats.multicomp import multipletests
pertpy/tools/_distances/_distances.py CHANGED
@@ -1,6 +1,5 @@
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  from __future__ import annotations
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- import multiprocessing
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  from abc import ABC, abstractmethod
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  from typing import TYPE_CHECKING, Literal, NamedTuple
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{pertpy-0.11.0.dist-info → pertpy-0.11.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pertpy
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- Version: 0.11.0
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+ Version: 0.11.1
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  Summary: Perturbation Analysis in the scverse ecosystem.
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  Project-URL: Documentation, https://pertpy.readthedocs.io
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  Project-URL: Source, https://github.com/scverse/pertpy
@@ -67,7 +67,7 @@ Requires-Dist: sparsecca
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  Provides-Extra: de
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  Requires-Dist: formulaic; extra == 'de'
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  Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'de'
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- Requires-Dist: pydeseq2>=v0.5.0pre1; extra == 'de'
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+ Requires-Dist: pydeseq2>=v0.5.0; extra == 'de'
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  Provides-Extra: dev
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  Requires-Dist: pre-commit; extra == 'dev'
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  Provides-Extra: doc
@@ -88,7 +88,7 @@ Requires-Dist: sphinx-gallery; extra == 'doc'
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  Requires-Dist: sphinx-issues; extra == 'doc'
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  Requires-Dist: sphinx-last-updated-by-git; extra == 'doc'
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  Requires-Dist: sphinx-remove-toctrees; extra == 'doc'
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- Requires-Dist: sphinx>=6; extra == 'doc'
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+ Requires-Dist: sphinx>=8.1; extra == 'doc'
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  Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
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  Requires-Dist: sphinxext-opengraph; extra == 'doc'
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  Provides-Extra: tcoda
@@ -101,7 +101,6 @@ Requires-Dist: leidenalg; extra == 'test'
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  Requires-Dist: pytest; extra == 'test'
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  Description-Content-Type: text/markdown
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- [![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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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)
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  [![codecov](https://codecov.io/gh/scverse/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/scverse/pertpy)
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  [![License](https://img.shields.io/github/license/scverse/pertpy)](https://opensource.org/licenses/Apache2.0)
@@ -111,13 +110,16 @@ Description-Content-Type: text/markdown
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  [![Test](https://github.com/scverse/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/test.yml)
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  [![PyPI](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
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- # pertpy
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+ # pertpy - Perturbation Analysis in Python
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+
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+ Pertpy is a scverse ecosystem framework for analyzing large-scale single-cell perturbation experiments.
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+ 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.
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  ![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
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  ## Documentation
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- Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
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+ Please read the [documentation](https://pertpy.readthedocs.io/en/latest) for installation, tutorials, use cases, and more.
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  ## Installation
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{pertpy-0.11.0.dist-info → pertpy-0.11.1.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
1
- pertpy/__init__.py,sha256=2cNNXWvBztH3KQzxe5WEl_Krfh0tdax4pPg1iUYjhQE,716
1
+ pertpy/__init__.py,sha256=4KCpjhbsKaAAYJjZIPbAi12NCBtGGThexdh3QaausRg,716
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  pertpy/_doc.py,sha256=j5TMNC-DA9yIMqIIUNpjpcVgWfRqyBBfvbRjnCM_OLs,427
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  pertpy/_types.py,sha256=IcHCojCUqx8CapibNkcYf2TUqjBFP2ujeELvn_IBSBQ,154
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  pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -16,19 +16,19 @@ pertpy/plot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pertpy/preprocessing/__init__.py,sha256=VAPFaeq2_qCvdFkQTCj_Hm460HC4Tersu8Rig_tnp_Y,71
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  pertpy/preprocessing/_guide_rna.py,sha256=ijL-bjQ-9qn4r3DlhBxzsqk-bD4RqPsFlok-Otj4hg8,15872
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  pertpy/preprocessing/_guide_rna_mixture.py,sha256=pT_YkjmN4iEJ-THBROu_dpbr8E6u8GJw36YoGseikD0,6422
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- pertpy/tools/__init__.py,sha256=DhjK2mfjbtvg9vG1ox6dF7A7UgiPZ_qmVH5o0QaTQyk,2599
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+ pertpy/tools/__init__.py,sha256=xjfw3Dd_KGytjjCID0uEs6Fz7DalH46fCjVL2Zf2kOo,2629
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  pertpy/tools/_augur.py,sha256=7iB2_xq8knyxtmN0G_a0u37o8WPlMlJXZCwDqxGvoKQ,55296
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  pertpy/tools/_cinemaot.py,sha256=54-rS0AEj31dMe7iU4kEmLoAunq3jNuhsBE3IEp9hrI,38071
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- pertpy/tools/_dialogue.py,sha256=ngjDcJK0D6ukJwiyS9cLYjrDU82n1FJru8yx8TvKSt8,52384
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+ pertpy/tools/_dialogue.py,sha256=cCSwo9ge1pOLoA7QHTPb3b865juCFWUaKX5aD7UoSjo,52355
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  pertpy/tools/_enrichment.py,sha256=55mwotLH9DXQOhl85MCkxXu-MX0RysLyrPheJysAnF0,21369
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  pertpy/tools/_milo.py,sha256=r-kZcpAcoQuhi41AnVuzh-cMIcV3HB3-RGzynHyDc1A,43712
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  pertpy/tools/_mixscape.py,sha256=ob22FI1hqUtaEZzCqrocy0-k8iUOChItc2tdCDeNDGY,57173
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  pertpy/tools/decoupler_LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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  pertpy/tools/transferlearning_MMD_LICENSE,sha256=MUvDA-o_j9htRpI8fStVdCRuyLdPkQUuIH0a_EIc57w,1069
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  pertpy/tools/_coda/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
29
- pertpy/tools/_coda/_base_coda.py,sha256=cITCEWyiPlxqS1Buhs8JzE3yHCdQksFitcXscEK7WX4,111504
30
- pertpy/tools/_coda/_sccoda.py,sha256=UjT9mha14YPk6jIqigAbyb1zqhrtBDV7b3NMWeoMFJ4,22575
31
- pertpy/tools/_coda/_tasccoda.py,sha256=hZBUhqpymFLu-l8CZ0FDLk04kUah9aSyHZwQhvHVm-U,30433
29
+ pertpy/tools/_coda/_base_coda.py,sha256=-rpdipPLFd4cFXyLMN7uFgv-pFJseKaqDmyWRBrGfws,111519
30
+ pertpy/tools/_coda/_sccoda.py,sha256=0Ret6O56kAfCNOdBvtxqiyuj2rUPp18SV1GVK1AvYGU,22607
31
+ pertpy/tools/_coda/_tasccoda.py,sha256=BTaOAmL458zQ_og3x4ENlDnJHD6_F4YkdCoXWsF4i1U,30465
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  pertpy/tools/_differential_gene_expression/__init__.py,sha256=SEydWg0iT3Y1pApjnCAOuHxFeI6xVUfgyBHv2s3LADU,487
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  pertpy/tools/_differential_gene_expression/_base.py,sha256=PpfH_RZXsN79Bu0yBFPE9TXEqNsZ4bSzSbhM0wZou2I,38322
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  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
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  pertpy/tools/_differential_gene_expression/_statsmodels.py,sha256=90h9EPuoCtNxAbJ1Xq4j_E4yYJJpk64zTP7GyTdmrxY,2220
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  pertpy/tools/_distances/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pertpy/tools/_distances/_distance_tests.py,sha256=6_nqfHUfKxkI2Yhkzspq3ujMpq56zV_Ddn7bgPzgjyo,13513
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- pertpy/tools/_distances/_distances.py,sha256=uzE8IcKPFYYXI0fKSgFHM_UIBZfA6uf9gBTSq8nZmZw,50496
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+ pertpy/tools/_distances/_distances.py,sha256=89d1zShW_9dhphup2oWx5hMOFC7RdogOY56doMuBFts,50473
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  pertpy/tools/_perturbation_space/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  pertpy/tools/_perturbation_space/_clustering.py,sha256=pNx_SpPkZfCbgF7vzHWqAaiiHdbxPaA-L-hTWTbzFhI,3528
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  pertpy/tools/_perturbation_space/_comparison.py,sha256=-NzCPRT-IlhJ9hOz7NQLSk0riIzr2C0yZvX6zm3kon4,4291
@@ -52,7 +52,7 @@ pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_K
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  pertpy/tools/_scgen/_scgen.py,sha256=31T8ez0FxABIbunJHCk8xvGulHFb8RHXSsyM_z1WsPY,30850
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  pertpy/tools/_scgen/_scgenvae.py,sha256=bPk4v7EdJc7ROdLuDitHiX_Pvwa7Flw2qHRUwBvjLJY,3889
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  pertpy/tools/_scgen/_utils.py,sha256=qz5QUn_Bvk2NGyYVzp3jgjWTFOMt1YyHwUo6HWtoThY,2871
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- pertpy-0.11.0.dist-info/METADATA,sha256=k17pDMEOKlDxSvRvG7D8iAA3jGidVvkOGrwuGef1uGc,7706
56
- pertpy-0.11.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
57
- pertpy-0.11.0.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
58
- pertpy-0.11.0.dist-info/RECORD,,
55
+ pertpy-0.11.1.dist-info/METADATA,sha256=uLFTtFW3JuRShmdYTUR-byUMcRB3Zntu84xe_2BI3ZI,8051
56
+ pertpy-0.11.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
57
+ pertpy-0.11.1.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
58
+ pertpy-0.11.1.dist-info/RECORD,,