pertpy 1.0.0__py3-none-any.whl → 1.0.2__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.
@@ -1,41 +1,17 @@
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  Metadata-Version: 2.4
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  Name: pertpy
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- Version: 1.0.0
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+ Version: 1.0.2
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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
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- Project-URL: Home-page, https://github.com/scverse/pertpy
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  Author: Lukas Heumos, Lilly May, Stefan Peidli, Johannes Ostner, Gregor Sturm, Emma Dann, Yuge Ji, Xinyue Zhang, Xichen Wu, Tessa Green, Antonia Schumacher
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  Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
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- License: MIT License
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-
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- Copyright (c) 2021, Lukas Heumos
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- Copyright (c) 2025, scverse®
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-
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- Permission is hereby granted, free of charge, to any person obtaining a copy
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- of this software and associated documentation files (the "Software"), to deal
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- in the Software without restriction, including without limitation the rights
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- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- copies of the Software, and to permit persons to whom the Software is
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- furnished to do so, subject to the following conditions:
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-
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- The above copyright notice and this permission notice shall be included in all
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- copies or substantial portions of the Software.
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-
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- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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- SOFTWARE.
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- License-File: LICENSE
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+ Requires-Python: >=3.11,<3.14
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+ Description-Content-Type: text/markdown
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+ Classifier: License :: OSI Approved :: Apache Software License
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  Classifier: Development Status :: 5 - Production/Stable
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  Classifier: Environment :: Console
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  Classifier: Framework :: Jupyter
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  Classifier: Intended Audience :: Developers
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  Classifier: Intended Audience :: Science/Research
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- Classifier: License :: OSI Approved :: Apache Software License
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  Classifier: Natural Language :: English
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  Classifier: Operating System :: MacOS :: MacOS X
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  Classifier: Operating System :: POSIX :: Linux
@@ -45,60 +21,62 @@ Classifier: Programming Language :: Python :: 3.12
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  Classifier: Programming Language :: Python :: 3.13
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Classifier: Topic :: Scientific/Engineering :: Visualization
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- Requires-Python: <3.14,>=3.11
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- Requires-Dist: adjusttext
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- Requires-Dist: arviz
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- Requires-Dist: blitzgsea
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- Requires-Dist: fast-array-utils
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- Requires-Dist: lamin-utils
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- Requires-Dist: mudata
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- Requires-Dist: openpyxl
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- Requires-Dist: ott-jax
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- Requires-Dist: pubchempy
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- Requires-Dist: pyarrow
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- Requires-Dist: requests
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+ License-File: LICENSE
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  Requires-Dist: rich
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  Requires-Dist: scanpy
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- Requires-Dist: scikit-learn>=1.4
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+ Requires-Dist: mudata
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+ Requires-Dist: requests
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  Requires-Dist: scikit-misc
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  Requires-Dist: scvi-tools
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+ Requires-Dist: adjusttext
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+ Requires-Dist: ott-jax
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  Requires-Dist: sparsecca
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+ Requires-Dist: openpyxl
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+ Requires-Dist: pubchempy
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+ Requires-Dist: pyarrow
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+ Requires-Dist: blitzgsea
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+ Requires-Dist: scikit-learn>=1.4
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+ Requires-Dist: fast-array-utils[accel, sparse]
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+ Requires-Dist: lamin_utils
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+ Requires-Dist: arviz
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+ Requires-Dist: formulaic-contrasts>=0.2.0 ; extra == "de"
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+ Requires-Dist: formulaic ; extra == "de"
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+ Requires-Dist: pydeseq2>=v0.5.0 ; extra == "de"
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+ Requires-Dist: pre-commit ; extra == "dev"
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+ Requires-Dist: docutils>=0.8 ; extra == "doc"
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+ Requires-Dist: sphinx>=8.1 ; extra == "doc"
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+ Requires-Dist: scanpydoc ; extra == "doc"
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+ Requires-Dist: sphinx-book-theme ; extra == "doc"
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+ Requires-Dist: myst-nb ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-bibtex>=1.0.0 ; extra == "doc"
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+ Requires-Dist: sphinx-issues ; extra == "doc"
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+ Requires-Dist: sphinx-gallery ; extra == "doc"
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+ Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
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+ Requires-Dist: sphinx-copybutton ; extra == "doc"
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+ Requires-Dist: sphinx-remove-toctrees ; extra == "doc"
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+ Requires-Dist: sphinx-design ; extra == "doc"
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+ Requires-Dist: sphinx-last-updated-by-git ; extra == "doc"
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+ Requires-Dist: sphinx-automodapi ; extra == "doc"
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+ Requires-Dist: sphinxext-opengraph ; extra == "doc"
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+ Requires-Dist: pygments ; extra == "doc"
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+ Requires-Dist: nbsphinx ; extra == "doc"
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+ Requires-Dist: nbsphinx-link ; extra == "doc"
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+ Requires-Dist: ipykernel ; extra == "doc"
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+ Requires-Dist: ipython ; extra == "doc"
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+ Requires-Dist: toytree>=3.0 ; extra == "tcoda"
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+ Requires-Dist: ete4 ; extra == "tcoda"
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+ Requires-Dist: pyqt6 ; extra == "tcoda"
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+ Requires-Dist: pytest ; extra == "test"
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+ Requires-Dist: coverage ; extra == "test"
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+ Requires-Dist: leidenalg ; extra == "test"
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+ Project-URL: Documentation, https://pertpy.readthedocs.io
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+ Project-URL: Home-page, https://github.com/scverse/pertpy
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+ Project-URL: Source, https://github.com/scverse/pertpy
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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>=v0.5.0; 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
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- Requires-Dist: docutils>=0.8; extra == 'doc'
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- Requires-Dist: ipykernel; extra == 'doc'
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- Requires-Dist: ipython; extra == 'doc'
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- Requires-Dist: myst-nb; extra == 'doc'
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- Requires-Dist: nbsphinx; extra == 'doc'
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- Requires-Dist: nbsphinx-link; extra == 'doc'
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- Requires-Dist: pygments; extra == 'doc'
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- Requires-Dist: scanpydoc; extra == 'doc'
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- Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
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- Requires-Dist: sphinx-automodapi; extra == 'doc'
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- Requires-Dist: sphinx-book-theme; extra == 'doc'
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- Requires-Dist: sphinx-copybutton; extra == 'doc'
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- Requires-Dist: sphinx-design; extra == 'doc'
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- 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>=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
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- Requires-Dist: ete4; extra == 'tcoda'
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- Requires-Dist: pyqt6; extra == 'tcoda'
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- Requires-Dist: toytree; extra == 'tcoda'
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  Provides-Extra: test
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- Requires-Dist: coverage; extra == 'test'
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- 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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  [![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)
@@ -205,3 +183,4 @@ If you like scverse® and want to support our mission, please consider making a
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  >
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  </a>
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  </div>
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+
@@ -1,12 +1,12 @@
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- pertpy/__init__.py,sha256=cZHJ7PIOhtLkxJMlHbJ2rzei5xhLB4vg0c8AaIShfzc,972
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+ pertpy/__init__.py,sha256=BTYM-9jQll7SwO4GNHDYKoD5duQXVPwifZYGOvtDD-E,972
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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
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  pertpy/data/__init__.py,sha256=ah3yvoxkgbdMUNAWxS3SyqcUuVamBOSeuWkF2QRAEwM,2703
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- pertpy/data/_dataloader.py,sha256=Osml8irOaoL2n2MhKRKre70Poxiv6NfJBKaK8vRe07Q,4411
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+ pertpy/data/_dataloader.py,sha256=Cb08iJj7vH-VishU4NJ5nzPPgviFLY1f5p3K4eVvTeg,4679
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  pertpy/data/_datasets.py,sha256=4IceyYURpstZSFRrD6gBjoYg8uRbEPo1QLXTt-SwB5k,65507
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  pertpy/metadata/__init__.py,sha256=wROPCXmJX2v5schJaBTPQtGW-FGCNWPfO_6bpnXwk-c,276
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- pertpy/metadata/_cell_line.py,sha256=hKmaZvjIsQ3wHo__0aKo3JlWvsf8-4OD-gIBNQnW8_E,42716
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+ pertpy/metadata/_cell_line.py,sha256=dtHjyFPtVzA31fib3IdURCBbsHDjbKyGDrJo9veSEU8,42854
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  pertpy/metadata/_compound.py,sha256=JsAv_KCcNkgVVrXTyhu-BeM8rBX8a93Wq5Z6avpxN7Y,4764
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  pertpy/metadata/_drug.py,sha256=8QDSyxiFl25JdS80EQJC_krg6fEe5LIQEE6BsV1r8nY,9006
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  pertpy/metadata/_look_up.py,sha256=0nrI_xy-qBZ3tyt4dwhEBwm0A9WP95ZaDiUQFf_88FU,28663
@@ -16,43 +16,43 @@ 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=xjfw3Dd_KGytjjCID0uEs6Fz7DalH46fCjVL2Zf2kOo,2629
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+ pertpy/tools/__init__.py,sha256=oOhB99SZBx1XUohaqXV7T_hZoN6xf-WMOpqgvw5gn1I,2073
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  pertpy/tools/_augur.py,sha256=tc1YKyc0BwzrEGgctsfyy7DsTNKxyvy7ZvWraTWCc1A,55262
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  pertpy/tools/_cinemaot.py,sha256=54-rS0AEj31dMe7iU4kEmLoAunq3jNuhsBE3IEp9hrI,38071
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- pertpy/tools/_dialogue.py,sha256=mygIZm5i_bnEE37TTQtr1efl_KJq-ejzeL3V1Bmr7Pg,52354
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+ pertpy/tools/_dialogue.py,sha256=xWW5XiQUEHTvB7WURzndmm-EF4EhLeEnOV_-7NP6heU,52360
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  pertpy/tools/_enrichment.py,sha256=55mwotLH9DXQOhl85MCkxXu-MX0RysLyrPheJysAnF0,21369
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- pertpy/tools/_milo.py,sha256=9yoB9gkBNujqYDTKOlH2v3wiWhs5PdCuB8RgZ3xVI0Y,48049
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+ pertpy/tools/_milo.py,sha256=PfLgEsYa5i35j25BNgGEkXk9UPM-ZhFxQbEWDA1e_fc,48192
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  pertpy/tools/_mixscape.py,sha256=HfrpBeRlxHXaOpZkF2FmX7dg35kUB1rL0_-n2aSi2_0,57905
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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
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- pertpy/tools/_coda/_base_coda.py,sha256=NjKIQBtTIUENnRmeIC2O8cMdU_9DKaJ5_AHPvFnc8XQ,111744
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- pertpy/tools/_coda/_sccoda.py,sha256=0Ret6O56kAfCNOdBvtxqiyuj2rUPp18SV1GVK1AvYGU,22607
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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=SEydWg0iT3Y1pApjnCAOuHxFeI6xVUfgyBHv2s3LADU,487
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- pertpy/tools/_differential_gene_expression/_base.py,sha256=ELx0e9DChJGO3yRpCLUOykt3oNOyDAPOQZZGSwzBSR0,38265
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+ pertpy/tools/_coda/_base_coda.py,sha256=2YIB7rVf9CxwYyQCpC8e3VYCxfurvyAqUs-4qJ5pubg,111817
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+ pertpy/tools/_coda/_sccoda.py,sha256=BzxR6x8DvyHAYGM9SEeJGh3opm3MfSqals6yOw77tqI,24136
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+ pertpy/tools/_coda/_tasccoda.py,sha256=oNMFKdKfY_TUtaaDQpGbzctApQVtDeQUEDovBaXFjD0,32153
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+ pertpy/tools/_differential_gene_expression/__init__.py,sha256=8_u7nsHY5GfFITT0Rs3v1p1vXpsGIWcBzwipuhXM3Ww,1653
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+ pertpy/tools/_differential_gene_expression/_base.py,sha256=GbBi8o7rTA3wH5DZJ9C1QzfqB5yak4r3xMvKQrizsTY,38274
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  pertpy/tools/_differential_gene_expression/_dge_comparison.py,sha256=LXhp5djKKCAk9VI7OqxOuja849G5lnd8Ehcs9Epk8rg,4159
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- pertpy/tools/_differential_gene_expression/_edger.py,sha256=nSHMDA4drGq_sJwUXs5I2EbMHwqjiS08GqOU_1_dXPc,4798
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- pertpy/tools/_differential_gene_expression/_pydeseq2.py,sha256=OowFb67jHT-UwibvRolR6Vw_yHEAxQ_ybJ7a65HJg8M,2943
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+ pertpy/tools/_differential_gene_expression/_edger.py,sha256=P7smGNOIsEF5-zHDP1IPU0vhR5yF9Y54akrZYjjg9H0,4658
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+ pertpy/tools/_differential_gene_expression/_pydeseq2.py,sha256=dtRgVkfqLlLw-N0-Y8cEJ06KVjr6LIUWJAeDQx4ZA1I,2917
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  pertpy/tools/_differential_gene_expression/_simple_tests.py,sha256=SfU8s_P2JzEA1RkmS0_xsARs4-BdnIYAwMmQv9-fxRg,6610
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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=_XbVU8dlYt_Jl2thYPUWg7HT6OXVe-Ki6qthF566sqQ,50503
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+ pertpy/tools/_distances/_distance_tests.py,sha256=wDDRkM-WmcfT5m5Zat-3ianGU1aC6HfRy51tuWA_sJg,13524
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+ pertpy/tools/_distances/_distances.py,sha256=iJNqMc9CxgZfEMHcxIocKGc4X4S2dJsRy3YerxVnFKo,51003
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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/_discriminator_classifiers.py,sha256=a53-YmUwDHQBCT7ZWe_RH7PZsGXvoSHmJaQyL0CBJng,23383
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+ pertpy/tools/_perturbation_space/_discriminator_classifiers.py,sha256=ARdNatcmsz370CF-PexDHPwUrih7KW4A5URzHVDNrcw,23126
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  pertpy/tools/_perturbation_space/_metrics.py,sha256=y8-baP8WRdB1iDgvP3uuQxSCDxA2lcxvEHHM2C_vWHY,3248
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- pertpy/tools/_perturbation_space/_simple.py,sha256=AJlHRaEP-vViBeMDvvMtUnXMuIKqZVc7wggnjsHMfMw,12721
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+ pertpy/tools/_perturbation_space/_simple.py,sha256=xS7Lrq3RzJC8IgVKKs2Utqbs7iJ5L1DANquCRcS3Fhg,13109
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  pertpy/tools/_scgen/__init__.py,sha256=uERFlFyF88TH0uLiwmsUGEfHfLVCiZMFuk8gO5f7164,45
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  pertpy/tools/_scgen/_scgen.py,sha256=AQNGsDe-9HEqli3oq7UBDg68ofLCoXm-R_jnLFQ-rlc,30856
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  pertpy/tools/_scgen/_scgenvae.py,sha256=bPk4v7EdJc7ROdLuDitHiX_Pvwa7Flw2qHRUwBvjLJY,3889
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- pertpy-1.0.0.dist-info/METADATA,sha256=PnK9O-MyIPzSy5DNOqMN7G6zcxZ2ZTJnMFB5cEr5XJQ,8920
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- pertpy-1.0.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- pertpy-1.0.0.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
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- pertpy-1.0.0.dist-info/RECORD,,
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+ pertpy-1.0.2.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
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+ pertpy-1.0.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
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+ pertpy-1.0.2.dist-info/METADATA,sha256=yWRzoCvdQNhn5sy0rtuPjRHH8H9UKmgKbrogxNWiJmM,7694
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+ pertpy-1.0.2.dist-info/RECORD,,
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  Wheel-Version: 1.0
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- Generator: hatchling 1.27.0
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  Root-Is-Purelib: true
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  Tag: py3-none-any