pertpy 1.0.0__tar.gz → 1.0.2__tar.gz

{pertpy-1.0.0 → pertpy-1.0.2}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "1.0.0 🌈"
-tag-template: 1.0.0
+name-template: "1.0.2 🌈"
+tag-template: 1.0.2
 exclude-labels:
     - "skip-changelog"
 

pertpy-1.0.2/.github/workflows/test_tutorials.yml

@@ -0,0 +1,94 @@
+name: Test tutorials
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ubuntu-latest
+        defaults:
+            run:
+              # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+              shell: bash -euo pipefail {0}
+
+        env:
+            NOTEBOOK_PATH: docs/tutorials/notebooks
+
+        strategy:
+            fail-fast: false
+            matrix:
+                notebook: [
+                        "augur.ipynb",
+                        "cinemaot.ipynb",
+                        "differential_gene_expression.ipynb",
+                        "distances.ipynb",
+                        "distance_tests.ipynb",
+                        "enrichment.ipynb",
+                        "guide_rna_assignment.ipynb",
+                        "milo.ipynb",
+                        "mixscape.ipynb",
+                        "perturbation_space.ipynb",
+                        "sccoda.ipynb",
+                        # "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
+                    ]
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                filter: blob:none
+                fetch-depth: 0
+                submodules: "true"
+
+            - name: Cache .pertpy_cache
+              uses: actions/cache@v4
+              with:
+                path: cache
+                key: ${{ runner.os }}-pertpy-cache-${{ hashFiles('pertpy/metadata/**') }}
+                restore-keys: |
+                  ${{ runner.os }}-pertpy-cache
+
+            - name: Set up Python
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.13"
+            - name: Install R
+              uses: r-lib/actions/setup-r@v2
+              with:
+                  r-version: "4.4.3"
+
+            - name: Cache R packages
+              id: r-cache
+              uses: actions/cache@v3
+              with:
+                path: ${{ env.R_LIBS_USER }}
+                key: ${{ runner.os }}-r-${{ hashFiles('**/pertpy/tools/_milo.py') }}
+                restore-keys: ${{ runner.os }}-r-
+
+            - name: Install R dependencies
+              if: steps.r-cache.outputs.cache-hit != 'true'
+              run: |
+                mkdir -p ${{ env.R_LIBS_USER }}
+                Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); BiocManager::install('edgeR', lib='${{ env.R_LIBS_USER }}')"
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v6
+              with:
+                enable-cache: true
+                cache-dependency-glob: pyproject.toml
+            - 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 nbconvert ipykernel
+
+            - name: Run ${{ matrix.notebook }} Notebook
+              run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }}

{pertpy-1.0.0 → pertpy-1.0.2}/.pre-commit-config.yaml

@@ -7,17 +7,17 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/biomejs/pre-commit
-      rev: v1.9.4
+      rev: v2.1.4
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.9
+      rev: v0.12.8
       hooks:
-          - id: ruff
+          - id: ruff-check
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v5.0.0
+      rev: v6.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -33,7 +33,7 @@ repos:
           - id: no-commit-to-branch
             args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.15.0
+      rev: v1.17.1
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-1.0.0 → pertpy-1.0.2}/PKG-INFO

@@ -1,41 +1,17 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 1.0.0
+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
-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
+Requires-Dist: openpyxl
+Requires-Dist: pubchempy
+Requires-Dist: pyarrow
+Requires-Dist: blitzgsea
+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
 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: tcoda
-Requires-Dist: ete4; extra == 'tcoda'
-Requires-Dist: pyqt6; extra == 'tcoda'
-Requires-Dist: toytree; 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)
@@ -205,3 +183,4 @@ If you like scverse® and want to support our mission, please consider making a
   >
 </a>
 </div>
+

pertpy-1.0.2/biome.jsonc

@@ -0,0 +1,34 @@
+{
+    "$schema": "https://biomejs.dev/schemas/2.0.5/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "includes": [".vscode/**/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+    "linter": {
+        "rules": {
+            "style": {
+                "noParameterAssign": "error",
+                "useAsConstAssertion": "error",
+                "useDefaultParameterLast": "error",
+                "useEnumInitializers": "error",
+                "useSelfClosingElements": "error",
+                "useSingleVarDeclarator": "error",
+                "noUnusedTemplateLiteral": "error",
+                "useNumberNamespace": "error",
+                "noInferrableTypes": "error",
+                "noUselessElse": "error",
+            },
+        },
+    },
+}

{pertpy-1.0.0 → pertpy-1.0.2}/docs/api/tools_index.md

@@ -423,8 +423,6 @@ ps_adata = ps.compute(
     target_col="gene_target",
     groups_col="gene_target",
     mode="mean",
-    min_cells=0,
-    min_counts=0,
 )
 ```
 

{pertpy-1.0.0 → pertpy-1.0.2}/docs/changelog.md

@@ -5,6 +5,26 @@ 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).
 
+## v1.0.2
+
+### 🐛 Bug Fixes
+
+* 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
+
+## v1.0.1
+
+### 🚀 Features
+
+* Add support for gamma parameter in MMD distance ([#825](https://github.com/scverse/pertpy/pull/825)) @Zethson
+* Run notebooks in CI ([#815](https://github.com/scverse/pertpy/pull/815)) @Zethson
+
+### 🐛 Bug Fixes
+
+* Fix milo output writing ([#821](https://github.com/scverse/pertpy/pull/821)) @Zethson
+
 ## v1.0.0
 
 ### 🚀 Features

pertpy-1.0.2/docs/tutorials/notebooks/.gitignore

@@ -0,0 +1,149 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+.pytype/
+
+# Pyre type checker
+.pyre/
+
+# Jetbrains IDE
+.idea/
+
+# Coala
+*.orig
+
+# Datasets
+*.h5ad
+*.h5md
+*.h5mu
+
+# pertpy cache
+cache
+data
+node_modules
+lightning_logs

pertpy-1.0.2/docs/tutorials/notebooks/.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.5.1
+    hooks:
+      - id: prettier
+        exclude: data
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.1
+    hooks:
+      - id: ruff-check
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.16.1
+    hooks:
+      - id: mypy
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies: ["types-requests", "types-attrs"]