pertpy 0.10.0__tar.gz → 0.11.1__tar.gz

{pertpy-0.10.0 → pertpy-0.11.1}/.editorconfig

@@ -15,7 +15,7 @@ indent_style = tab
 end_of_line = crlf
 
 [LICENSE]
-insert_final_newline = false
+insert_final_newline = true
 
 [Makefile]
 indent_style = tab

pertpy-0.11.1/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,69 @@
+name: Bug report
+description: pertpy doesn’t do what it should? Please help us fix it!
+#title: ...
+labels:
+  - Bug
+  - Triage
+#assignees: []
+body:
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Please make sure these conditions are met
+      # description: ...
+      options:
+        - label: I have checked that this issue has not already been reported.
+          required: true
+        - label: I have confirmed this bug exists on the latest version of pertpy.
+          required: true
+        - label: (optional) I have confirmed this bug exists on the main branch.
+          required: false
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide][] detailing how to provide the necessary information for us to reproduce your bug.
+
+        [this guide]: https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports
+  - type: textarea
+    id: Report
+    attributes:
+      label: Report
+      description: |
+        Describe the bug you encountered, and what you were trying to do. Please use [github markdown][] features for readability.
+
+        [github markdown]: https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax
+      value: |
+        Code:
+
+        ```python
+
+        ```
+
+        Traceback:
+
+        ```pytb
+
+        ```
+    validations:
+      required: true
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of pertpy and other related software you used.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button,
+        then paste the results into the text box below.
+
+        ```python
+        In[1]: import pertpy, session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python

{pertpy-0.10.0 → pertpy-0.11.1}/.github/pull_request_template.md

@@ -4,9 +4,9 @@
 
 <!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
 
-- [ ] Referenced issue is linked
-- [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] Documentation in `docs` is updated
+-   [ ] Referenced issue is linked
+-   [ ] If you've fixed a bug or added code that should be tested, add tests!
+-   [ ] Documentation in `docs` is updated
 
 **Description of changes**
 

{pertpy-0.10.0 → pertpy-0.11.1}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.10.0 🌈"
-tag-template: 0.10.0
+name-template: "0.11.1 🌈"
+tag-template: 0.11.1
 exclude-labels:
     - "skip-changelog"
 

pertpy-0.11.1/.github/workflows/build.yml

@@ -0,0 +1,36 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          cache-dependency-glob: pyproject.toml
+
+      - name: Build package
+        run: uv build
+
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

{pertpy-0.10.0 → pertpy-0.11.1}/.github/workflows/release.yml

@@ -13,16 +13,18 @@ jobs:
             - name: Checkout code
               uses: actions/checkout@v4
 
-            - name: Set up Python 3.12
+            - name: Set up Python
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.12"
+                  python-version: "3.x"
 
-            - name: Install hatch
-              run: pip install hatch
+            - name: Install uv
+              uses: astral-sh/setup-uv@v5
+              with:
+                cache-dependency-glob: pyproject.toml
 
-            - name: Build project for distribution
-              run: hatch build
+            - name: Build package
+              run: uv build
 
             - name: Publish a Python distribution to PyPI
               uses: pypa/gh-action-pypi-publish@release/v1

{pertpy-0.10.0 → pertpy-0.11.1}/.github/workflows/test.yml

@@ -15,22 +15,23 @@ jobs:
         runs-on: ${{ matrix.os }}
         defaults:
             run:
-                shell: bash -e {0} # -e to fail on error
+              # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+              shell: bash -euo pipefail {0}
 
         strategy:
             fail-fast: false
             matrix:
                 include:
-                    - os: ubuntu-22.04 # ubuntu-latest is currently broken for joblib
-                      python: "3.12"
+                    - os: ubuntu-latest
+                      python: "3.13"
                       run_mode: "slow"
-                    - os: ubuntu-22.04
-                      python: "3.12"
+                    - os: ubuntu-latest
+                      python: "3.13"
                       run_mode: "fast"
-                    # - os: ubuntu-latest
-                    #   python: "3.12"
-                    #   run_mode: slow
-                    #   pip-flags: "--pre"
+                    - os: ubuntu-latest
+                      python: "3.13"
+                      run_mode: slow
+                      pip-flags: "--pre"
 
         env:
             OS: ${{ matrix.os }}
@@ -38,26 +39,50 @@ jobs:
 
         steps:
             - uses: actions/checkout@v4
+              with:
+                filter: blob:none
+                fetch-depth: 0
+
+            - 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 ${{ matrix.python }}
               uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
-
-            - uses: actions/checkout@v4
             - name: Install R
               uses: r-lib/actions/setup-r@v2
               with:
-                  r-version: "4"
+                  r-version: "4.4.3"
 
-            - name: Install edgeR
-              run: Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')"
+            - 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 test dependencies
-              run: python -m pip install --upgrade uv wheel
+            - 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
-                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda,de]"
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
 
             - name: Test
               env:

{pertpy-0.10.0 → pertpy-0.11.1}/.gitignore

@@ -72,8 +72,11 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/usage/*
-!docs/usage/usage.md
+docs/api/data
+docs/api/metadata
+docs/api/tools
+docs/api/preprocessing
+!docs/api/api.md
 
 # PyBuilder
 target/

{pertpy-0.10.0 → pertpy-0.11.1}/.pre-commit-config.yaml

@@ -6,18 +6,18 @@ default_stages:
     - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
+    - repo: https://github.com/biomejs/pre-commit
+      rev: v1.9.4
       hooks:
-          - id: prettier
+          - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.8.6
+      rev: v0.11.5
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
+      rev: v5.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -26,6 +26,12 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
+          - id: check-added-large-files
+          - id: check-toml
+          - id: check-yaml
+          - id: check-merge-conflict
+          - id: no-commit-to-branch
+            args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v1.14.1
       hooks:

pertpy-0.11.1/.readthedocs.yml

@@ -0,0 +1,18 @@
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+      - uv venv
+      - uv pip install .[doc,tcoda,de]
+    build:
+      html:
+        - uv run sphinx-build -T -W -b html docs $READTHEDOCS_OUTPUT/html
+
+submodules:
+    include: all

{pertpy-0.10.0 → pertpy-0.11.1}/LICENSE

@@ -1,6 +1,7 @@
 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

{pertpy-0.10.0 → pertpy-0.11.1}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.10.0
+Version: 0.11.1
 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, Yuge Ji, Lilly May, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Tessa Green, Stefan Peidli, Antonia Schumacher, Gregor Sturm
+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
@@ -29,7 +30,7 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Framework :: Jupyter
 Classifier: Intended Audience :: Developers
@@ -39,66 +40,67 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 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: <3.13,>=3.10
+Requires-Python: <3.14,>=3.11
 Requires-Dist: adjusttext
+Requires-Dist: arviz
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
+Requires-Dist: fast-array-utils
 Requires-Dist: lamin-utils
-Requires-Dist: muon
+Requires-Dist: mudata
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
 Requires-Dist: pubchempy
 Requires-Dist: pyarrow
 Requires-Dist: requests
 Requires-Dist: rich
-Requires-Dist: scanpy[leiden]
+Requires-Dist: scanpy
 Requires-Dist: scikit-learn>=1.4
 Requires-Dist: scikit-misc
 Requires-Dist: scvi-tools
 Requires-Dist: sparsecca
-Provides-Extra: coda
-Requires-Dist: arviz; extra == 'coda'
-Requires-Dist: ete3; extra == 'coda'
-Requires-Dist: pyqt5; extra == 'coda'
-Requires-Dist: toytree; extra == 'coda'
 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
-Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
-Requires-Dist: furo; 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: myst-parser; extra == 'doc'
 Requires-Dist: nbsphinx; extra == 'doc'
 Requires-Dist: nbsphinx-link; extra == 'doc'
-Requires-Dist: pyenchant; 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>=4; 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
 
-[![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)
@@ -108,13 +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
 
@@ -127,10 +132,10 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA or tascCODA, please install pertpy as follows:
+if you want to use tascCODA, please install pertpy as follows:
 
 ```console
-pip install 'pertpy[coda]'
+pip install 'pertpy[tcoda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -146,4 +151,17 @@ 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/
-[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html
+[api]: https://pertpy.readthedocs.io/en/latest/api/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/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
+
+<div align="center">
+<a href="https://numfocus.org/project/scverse">
+  <img
+    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
+    width="200"
+  >
+</a>
+</div>

{pertpy-0.10.0 → pertpy-0.11.1}/README.md

@@ -1,4 +1,3 @@
-[![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)
@@ -8,13 +7,16 @@
 [![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
 
@@ -27,10 +29,10 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA or tascCODA, please install pertpy as follows:
+if you want to use tascCODA, please install pertpy as follows:
 
 ```console
-pip install 'pertpy[coda]'
+pip install 'pertpy[tcoda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -46,4 +48,17 @@ 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/
-[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html
+[api]: https://pertpy.readthedocs.io/en/latest/api/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/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
+
+<div align="center">
+<a href="https://numfocus.org/project/scverse">
+  <img
+    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
+    width="200"
+  >
+</a>
+</div>

pertpy-0.11.1/biome.jsonc

@@ -0,0 +1,18 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

{pertpy-0.10.0 → pertpy-0.11.1}/docs/_ext/edit_on_github.py

@@ -8,7 +8,7 @@ from sphinx.application import Sphinx
 __licence__ = "BSD (3 clause)"
 
 
-def get_github_repo(app: Sphinx, path: str) -> str:
+def get_github_repo(app: Sphinx, path: str) -> str:  # noqa: D103
     if path.endswith(".ipynb"):
         return str(app.config.github_nb_repo)
     if "auto_examples" in path:
@@ -43,7 +43,7 @@ def _html_page_context(
     context["conf_py_path"] = "/docs/source/"
 
 
-def setup(app: Sphinx) -> None:
+def setup(app: Sphinx) -> None:  # noqa: D103
     app.add_config_value("github_nb_repo", "", True)
     app.add_config_value("github_repo", "", True)
     app.connect("html-page-context", _html_page_context)

{pertpy-0.10.0 → pertpy-0.11.1}/docs/_ext/typed_returns.py

@@ -10,7 +10,7 @@ def _process_return(lines: Iterable[str]) -> Iterator[str]:
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'**{m["param"]}** : :class:`~{m["type"]}`'
+            yield f"**{m['param']}** : :class:`~{m['type']}`"
         else:
             yield line
 
@@ -23,5 +23,5 @@ def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
     return lines
 
 
-def setup(app: Sphinx) -> None:
+def setup(app: Sphinx) -> None:  # noqa: D103
     NumpyDocstring._parse_returns_section = _parse_returns_section

{pertpy-0.10.0 → pertpy-0.11.1}/docs/_static/css/overwrite.css

@@ -1,10 +1,3 @@
-/*
-  Furo CSS variables
-  https://github.com/pradyunsg/furo/blob/main/src/furo/assets/styles/variables/_index.scss
-  https://github.com/pradyunsg/furo/blob/main/src/furo/theme/partials/_head_css_variables.html
-https://github.com/streamlink/streamlink/blob/17a4088c38709123c0bcab4a150549bd16d19e07/docs/_static/styles/custom.css
-*/
-
 /* for the sphinx design cards */
 body {
     --sd-color-shadow: dimgrey;
@@ -72,3 +65,9 @@ li.toctree-l3 {
 li.toctree-l4 {
     font-size: 75% !important;
 }
+
+.bd-sidebar .caption-text {
+    color: #e63946;
+    font-weight: 600;
+    text-transform: uppercase;
+}

pertpy-0.11.1/docs/_static/pertpy_logo.svg

@@ -0,0 +1,5 @@
+<svg width="308" height="105" viewBox="0 0 308 105" fill="none" xmlns="http://www.w3.org/2000/svg">
+<rect width="308" height="105" fill="#1E1E1E"/>
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+</svg>