pertpy 1.0.2__tar.gz → 1.0.3__tar.gz

{pertpy-1.0.2 → pertpy-1.0.3}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "1.0.2 🌈"
-tag-template: 1.0.2
+name-template: "1.0.3 🌈"
+tag-template: 1.0.3
 exclude-labels:
     - "skip-changelog"
 

{pertpy-1.0.2 → pertpy-1.0.3}/.github/workflows/test.yml

@@ -77,7 +77,7 @@ jobs:
             - name: Install dependencies
               run: |
                   uv pip install --system rpy2
-                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,all]"
 
             - name: Test
               env:

{pertpy-1.0.2 → pertpy-1.0.3}/.github/workflows/test_tutorials.yml

@@ -34,8 +34,8 @@ jobs:
                         "guide_rna_assignment.ipynb",
                         "milo.ipynb",
                         "mixscape.ipynb",
-                        "perturbation_space.ipynb",
                         "sccoda.ipynb",
+                        # "perturbation_space.ipynb",  seems to run OOM as of Jax implementation
                         # "dialogue.ipynb", takes too long
                         # "tasccoda.ipynb", a pain to get running because of the required QT dependency. The QT action leads to a dead kernel
                         # also no use cases yet
@@ -48,7 +48,7 @@ jobs:
                 fetch-depth: 0
                 submodules: "true"
 
-            - name: Cache .pertpy_cache
+            - name: Cache pertpy's cache folder
               uses: actions/cache@v4
               with:
                 path: cache
@@ -87,7 +87,7 @@ jobs:
             - name: Install dependencies
               run: |
                   uv pip install --system rpy2 decoupler muon
-                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
+                  uv pip install --system ".[dev,test,all]"
                   uv pip install --system nbconvert ipykernel
 
             - name: Run ${{ matrix.notebook }} Notebook

{pertpy-1.0.2 → pertpy-1.0.3}/.gitignore

@@ -148,7 +148,6 @@ dmypy.json
 
 # Datasets
 *.h5ad
-*.h5md
 *.h5mu
 
 # Test cache
@@ -157,8 +156,7 @@ cache
 # Apple stuff
 .DS_Store
 
-lightning_logs/*
-*/lightning_logs/*
+lightning_logs/
 
 node_modules
 
@@ -169,3 +167,6 @@ test-bug
 
 # uv
 uv.lock
+
+# Ruff
+.ruff_cache

{pertpy-1.0.2 → pertpy-1.0.3}/.pre-commit-config.yaml

@@ -7,11 +7,11 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/biomejs/pre-commit
-      rev: v2.1.4
+      rev: v2.2.4
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.12.8
+      rev: v0.13.1
       hooks:
           - id: ruff-check
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -33,7 +33,7 @@ repos:
           - id: no-commit-to-branch
             args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.17.1
+      rev: v1.18.2
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-1.0.2 → pertpy-1.0.3}/.readthedocs.yml

@@ -9,7 +9,7 @@ build:
       - asdf install uv latest
       - asdf global uv latest
       - uv venv
-      - uv pip install .[doc,tcoda,de]
+      - uv pip install .[doc,all]
     build:
       html:
         - uv run sphinx-build -T -W -b html docs $READTHEDOCS_OUTPUT/html

{pertpy-1.0.2 → pertpy-1.0.3}/PKG-INFO

@@ -1,17 +1,41 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 1.0.2
+Version: 1.0.3
 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>
-Requires-Python: >=3.11,<3.14
-Description-Content-Type: text/markdown
-Classifier: License :: OSI Approved :: Apache Software License
+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
 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
@@ -21,62 +45,72 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
-License-File: LICENSE
-Requires-Dist: rich
-Requires-Dist: scanpy
-Requires-Dist: mudata
-Requires-Dist: requests
-Requires-Dist: scikit-misc
-Requires-Dist: scvi-tools
+Requires-Python: <3.14,>=3.11
 Requires-Dist: adjusttext
-Requires-Dist: ott-jax
-Requires-Dist: sparsecca
+Requires-Dist: arviz
+Requires-Dist: blitzgsea
+Requires-Dist: fast-array-utils[accel,sparse]
+Requires-Dist: flax
+Requires-Dist: funsor
+Requires-Dist: lamin-utils
+Requires-Dist: mudata
+Requires-Dist: numpyro
 Requires-Dist: openpyxl
+Requires-Dist: ott-jax
 Requires-Dist: pubchempy
 Requires-Dist: pyarrow
-Requires-Dist: blitzgsea
+Requires-Dist: requests
+Requires-Dist: rich
+Requires-Dist: scanpy
 Requires-Dist: scikit-learn>=1.4
-Requires-Dist: fast-array-utils[accel, sparse]
-Requires-Dist: lamin_utils
-Requires-Dist: arviz
-Requires-Dist: formulaic-contrasts>=0.2.0 ; extra == "de"
-Requires-Dist: formulaic ; extra == "de"
-Requires-Dist: pydeseq2>=v0.5.0 ; extra == "de"
-Requires-Dist: pre-commit ; extra == "dev"
-Requires-Dist: docutils>=0.8 ; extra == "doc"
-Requires-Dist: sphinx>=8.1 ; extra == "doc"
-Requires-Dist: scanpydoc ; extra == "doc"
-Requires-Dist: sphinx-book-theme ; extra == "doc"
-Requires-Dist: myst-nb ; extra == "doc"
-Requires-Dist: sphinxcontrib-bibtex>=1.0.0 ; extra == "doc"
-Requires-Dist: sphinx-issues ; extra == "doc"
-Requires-Dist: sphinx-gallery ; extra == "doc"
-Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
-Requires-Dist: sphinx-copybutton ; extra == "doc"
-Requires-Dist: sphinx-remove-toctrees ; extra == "doc"
-Requires-Dist: sphinx-design ; extra == "doc"
-Requires-Dist: sphinx-last-updated-by-git ; extra == "doc"
-Requires-Dist: sphinx-automodapi ; extra == "doc"
-Requires-Dist: sphinxext-opengraph ; extra == "doc"
-Requires-Dist: pygments ; extra == "doc"
-Requires-Dist: nbsphinx ; extra == "doc"
-Requires-Dist: nbsphinx-link ; extra == "doc"
-Requires-Dist: ipykernel ; extra == "doc"
-Requires-Dist: ipython ; extra == "doc"
-Requires-Dist: toytree>=3.0 ; extra == "tcoda"
-Requires-Dist: ete4 ; extra == "tcoda"
-Requires-Dist: pyqt6 ; extra == "tcoda"
-Requires-Dist: pytest ; extra == "test"
-Requires-Dist: coverage ; extra == "test"
-Requires-Dist: leidenalg ; extra == "test"
-Project-URL: Documentation, https://pertpy.readthedocs.io
-Project-URL: Home-page, https://github.com/scverse/pertpy
-Project-URL: Source, https://github.com/scverse/pertpy
+Requires-Dist: scikit-misc
+Requires-Dist: sparsecca
+Provides-Extra: all
+Requires-Dist: ete4; extra == 'all'
+Requires-Dist: formulaic; extra == 'all'
+Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'all'
+Requires-Dist: pydeseq2>=v0.5.0; extra == 'all'
+Requires-Dist: pyqt6; extra == 'all'
+Requires-Dist: scvi-tools[jax]; extra == 'all'
+Requires-Dist: toytree>=3.0; extra == 'all'
 Provides-Extra: de
+Requires-Dist: formulaic; extra == 'de'
+Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'de'
+Requires-Dist: pydeseq2>=v0.5.0; extra == 'de'
 Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc
+Requires-Dist: docutils>=0.8; extra == 'doc'
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb; extra == 'doc'
+Requires-Dist: nbsphinx; extra == 'doc'
+Requires-Dist: nbsphinx-link; extra == 'doc'
+Requires-Dist: pygments; extra == 'doc'
+Requires-Dist: scanpydoc; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
+Requires-Dist: sphinx-automodapi; extra == 'doc'
+Requires-Dist: sphinx-book-theme; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx-design; extra == 'doc'
+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>=8.1; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: scgen
+Requires-Dist: scvi-tools[jax]; extra == 'scgen'
 Provides-Extra: tcoda
+Requires-Dist: ete4; extra == 'tcoda'
+Requires-Dist: pyqt6; extra == 'tcoda'
+Requires-Dist: toytree>=3.0; extra == 'tcoda'
 Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: leidenalg; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
 
 [![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)
@@ -183,4 +217,3 @@ If you like scverse® and want to support our mission, please consider making a
   >
 </a>
 </div>
-

{pertpy-1.0.2 → pertpy-1.0.3}/docs/changelog.md

@@ -5,14 +5,22 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.3
+
+### 🚀 Features
+
+* Move from figshare to scverse AWS S3 ([#848](https://github.com/scverse/pertpy/pull/848)) @Zethson
+* Rename `label_transfer` `column` parameter to `target_column` ([#848](https://github.com/scverse/pertpy/pull/848)) @Zethson
+* Rename `mixscape` `labels` parameter to `pert_key` ([#848](https://github.com/scverse/pertpy/pull/848)) @Zethson
+
 ## v1.0.2
 
 ### 🐛 Bug Fixes
 
-* Fix: Validate 'type' parameter in Tasccoda.load ([#839](https://github.com/scverse/pertpy/pull/839)) @JuanTejedor
+* Fix Validate 'type' parameter in Tasccoda.load ([#839](https://github.com/scverse/pertpy/pull/839)) @JuanTejedor
 * Partial fixes for make_arviz ([#834](https://github.com/scverse/pertpy/pull/834)) @jpintar
 * Fix setting of `rng_key` in `make_arviz` ([#831](https://github.com/scverse/pertpy/pull/831)) @jpintar
-* Fixed GDSC and PRISM annotation warnings ([#835](https://github.com/scverse/pertpy/pull/835)) @Lilly-May
+* Fix GDSC and PRISM annotation warnings ([#835](https://github.com/scverse/pertpy/pull/835)) @Lilly-May
 
 ## v1.0.1
 

{pertpy-1.0.2 → pertpy-1.0.3}/docs/conf.py

@@ -14,7 +14,7 @@ needs_sphinx = "4.3"
 info = metadata("pertpy")
 project_name = info["Name"]
 author = info["Author"]
-copyright = f"{datetime.now():%Y}, {author}."
+copyright = f"{datetime.now():%Y}, {author}"
 version = info["Version"]
 urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
 repository_url = urls["Source"]

{pertpy-1.0.2 → pertpy-1.0.3}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "1.0.2"
+__version__ = "1.0.3"
 
 import warnings
 

{pertpy-1.0.2 → pertpy-1.0.3}/pertpy/data/_dataloader.py

@@ -17,7 +17,7 @@ def _download(  # pragma: no cover
     url: str,
     output_file_name: str | None = None,
     output_path: str | Path | None = None,
-    block_size: int = 1024,
+    block_size: int = 8192,
     overwrite: bool = False,
     is_zip: bool = False,
     timeout: int = 30,
@@ -74,7 +74,7 @@ def _download(  # pragma: no cover
                     response.raise_for_status()
                     total = int(response.headers.get("content-length", 0))
 
-                    with Progress(refresh_per_second=5) as progress:
+                    with Progress(refresh_per_second=3) as progress:
                         task = progress.add_task("[red]Downloading...", total=total)
                         with Path(temp_file_name).open("wb") as file:
                             for data in response.iter_content(block_size):