pertpy 0.11.0__tar.gz → 0.11.2__tar.gz

{pertpy-0.11.0 → pertpy-0.11.2}/.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-0.11.0 → pertpy-0.11.2}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.11.0 🌈"
-tag-template: 0.11.0
+name-template: "0.11.2 🌈"
+tag-template: 0.11.2
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.11.0 → pertpy-0.11.2}/.github/workflows/release.yml

@@ -18,11 +18,13 @@ jobs:
               with:
                   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-0.11.0 → pertpy-0.11.2}/.github/workflows/test.yml

@@ -24,13 +24,8 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.13"
-                      run_mode: "slow"
                     - os: ubuntu-latest
                       python: "3.13"
-                      run_mode: "fast"
-                    - os: ubuntu-latest
-                      python: "3.13"
-                      run_mode: slow
                       pip-flags: "--pre"
 
         env:
@@ -91,9 +86,6 @@ jobs:
                   DISPLAY: :42
               run: |
                   pytest_args="-m pytest -v --color=yes"
-                  if [ "${{ matrix.run_mode }}" = "slow" ]; then
-                    pytest_args="$pytest_args --runslow"
-                  fi
                   coverage run $pytest_args
 
             - name: Show coverage report

{pertpy-0.11.0 → pertpy-0.11.2}/.gitignore

@@ -72,7 +72,10 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/api/*
+docs/api/data
+docs/api/metadata
+docs/api/tools
+docs/api/preprocessing
 !docs/api/api.md
 
 # PyBuilder

{pertpy-0.11.0 → pertpy-0.11.2}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.5
+      rev: v0.11.9
       hooks:
           - id: ruff
             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: v1.14.1
+      rev: v1.15.0
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

pertpy-0.11.2/.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-0.11.0 → pertpy-0.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.11.0
+Version: 0.11.2
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -67,7 +67,7 @@ Requires-Dist: sparsecca
 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
@@ -88,7 +88,7 @@ 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>=6; 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
@@ -101,7 +101,6 @@ 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)
@@ -111,13 +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
 
@@ -149,7 +151,7 @@ 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/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/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/).

{pertpy-0.11.0 → pertpy-0.11.2}/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
 
@@ -46,7 +48,7 @@ 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/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/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/).

{pertpy-0.11.0 → pertpy-0.11.2}/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-0.11.0 → pertpy-0.11.2}/docs/_static/pertpy_logo.svg

@@ -1,5 +1,4 @@
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pertpy-0.11.2/docs/api/datasets_index.md

@@ -0,0 +1,70 @@
+```{eval-rst}
+.. currentmodule:: pertpy
+```
+
+# Datasets
+
+pertpy provides access to several curated single-cell datasets spanning several types of perturbations.
+Many of the datasets originate from [scperturb](http://projects.sanderlab.org/scperturb/) {cite}`Peidli2024`.
+
+```{eval-rst}
+.. autosummary::
+    :toctree: data
+
+    data.adamson_2016_pilot
+    data.adamson_2016_upr_epistasis
+    data.adamson_2016_upr_perturb_seq
+    data.aissa_2021
+    data.bhattacherjee
+    data.burczynski_crohn
+    data.chang_2021
+    data.combosciplex
+    data.cinemaot_example
+    data.datlinger_2017
+    data.datlinger_2021
+    data.dialogue_example
+    data.distance_example
+    data.dixit_2016
+    data.dixit_2016_raw
+    data.dong_2023
+    data.frangieh_2021
+    data.frangieh_2021_protein
+    data.frangieh_2021_raw
+    data.frangieh_2021_rna
+    data.gasperini_2019_atscale
+    data.gasperini_2019_highmoi
+    data.gasperini_2019_lowmoi
+    data.gehring_2019
+    data.haber_2017_regions
+    data.hagai_2018
+    data.kang_2018
+    data.mcfarland_2020
+    data.norman_2019
+    data.norman_2019_raw
+    data.papalexi_2021
+    data.replogle_2022_k562_essential
+    data.replogle_2022_k562_gwps
+    data.replogle_2022_rpe1
+    data.sc_sim_augur
+    data.schiebinger_2019_16day
+    data.schiebinger_2019_18day
+    data.schraivogel_2020_tap_screen_chr8
+    data.schraivogel_2020_tap_screen_chr11
+    data.sciplex_gxe1
+    data.sciplex3_raw
+    data.shifrut_2018
+    data.smillie_2019
+    data.srivatsan_2020_sciplex2
+    data.srivatsan_2020_sciplex3
+    data.srivatsan_2020_sciplex4
+    data.stephenson_2021_subsampled
+    data.tasccoda_example
+    data.tian_2019_day7neuron
+    data.tian_2019_ipsc
+    data.tian_2021_crispra
+    data.tian_2021_crispri
+    data.weinreb_2020
+    data.xie_2017
+    data.zhao_2021
+    data.zhang_2021
+```

pertpy-0.11.2/docs/api/metadata_index.md

@@ -0,0 +1,55 @@
+```{eval-rst}
+.. currentmodule:: pertpy
+```
+
+# Metadata
+
+The metadata module provides tooling to annotate perturbations by querying databases.
+Such metadata can aid with the development of biologically informed models and can be used for enrichment tests.
+
+## Cell line
+
+This module allows for the retrieval of various types of information related to cell lines,
+including cell line annotation, bulk RNA and protein expression data.
+
+Available databases for cell line metadata:
+
+-   [The Cancer Dependency Map Project at Broad](https://depmap.org/portal/)
+-   [The Cancer Dependency Map Project at Sanger](https://depmap.sanger.ac.uk/)
+-   [Genomics of Drug Sensitivity in Cancer (GDSC)](https://www.cancerrxgene.org/)
+
+## Compound
+
+The Compound module enables the retrieval of various types of information related to compounds of interest, including the most common synonym, pubchemID and canonical SMILES.
+
+Available databases for compound metadata:
+
+-   [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
+
+## Mechanism of Action
+
+This module aims to retrieve metadata of mechanism of action studies related to perturbagens of interest, depending on the molecular targets.
+
+Available databases for mechanism of action metadata:
+
+-   [CLUE](https://clue.io/)
+
+## Drug
+
+This module allows for the retrieval of Drug target information.
+
+Available databases for drug metadata:
+
+-   [chembl](https://www.ebi.ac.uk/chembl/)
+
+```{eval-rst}
+.. autosummary::
+    :toctree: metadata
+    :recursive:
+
+    metadata.CellLine
+    metadata.Compound
+    metadata.Moa
+    metadata.Drug
+    metadata.LookUp
+```

pertpy-0.11.2/docs/api/preprocessing_index.md

@@ -0,0 +1,37 @@
+```{eval-rst}
+.. currentmodule:: pertpy
+```
+
+# Preprocessing
+
+## Guide Assignment
+
+Guide assignment is essential for quality control in single-cell Perturb-seq data, ensuring accurate mapping of guide RNAs to cells for reliable interpretation of gene perturbation effects.
+pertpy provides a simple function to assign guides based on thresholds and a Gaussian mixture model {cite}`Replogle2022`.
+
+```{eval-rst}
+.. autosummary::
+    :toctree: preprocessing
+    :nosignatures:
+
+    preprocessing.GuideAssignment
+```
+
+Example implementation:
+
+```python
+import pertpy as pt
+import scanpy as sc
+
+mdata = pt.dt.papalexi_2021()
+gdo = mdata.mod["gdo"]
+gdo.layers["counts"] = gdo.X.copy()
+sc.pp.log1p(gdo)
+
+ga = pt.pp.GuideAssignment()
+ga.assign_by_threshold(gdo, 5, layer="counts", output_layer="assigned_guides")
+
+ga.plot_heatmap(gdo, layer="assigned_guides")
+```
+
+See [guide assignment tutorial](https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/guide_rna_assignment.html).