pertpy 0.11.4__tar.gz → 1.0.0__tar.gz

{pertpy-0.11.4 → pertpy-1.0.0}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.11.4 🌈"
-tag-template: 0.11.4
+name-template: "1.0.0 🌈"
+tag-template: 1.0.0
 exclude-labels:
     - "skip-changelog"
 

pertpy-1.0.0/.github/workflows/release.yml

@@ -0,0 +1,34 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    shell: bash -euo pipefail {0}
+
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pertpy
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

{pertpy-0.11.4 → pertpy-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.11.4
+Version: 1.0.0
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -131,6 +131,12 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
+or [conda-forge]:
+
+```console
+conda install -c conda-forge pertpy
+```
+
 ### Differential gene expression
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -149,7 +155,13 @@ pip install 'pertpy[tcoda]'
 
 ### milo
 
-milo further requires edger, statmod, and rpy2 to be installed:
+milo requires either the "de" extra for the "pydeseq2" solver:
+
+```console
+pip install 'pertpy[de]'
+```
+
+or, edger, statmod, and rpy2 for the "edger" solver:
 
 ```R
 BiocManager::install("edgeR")
@@ -179,6 +191,7 @@ pip install rpy2
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [api]: https://pertpy.readthedocs.io/en/latest/api.html
+[conda-forge]: https://anaconda.org/conda-forge/pertpy
 [//]: # "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-0.11.4 → pertpy-1.0.0}/README.md

@@ -29,6 +29,12 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
+or [conda-forge]:
+
+```console
+conda install -c conda-forge pertpy
+```
+
 ### Differential gene expression
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -47,7 +53,13 @@ pip install 'pertpy[tcoda]'
 
 ### milo
 
-milo further requires edger, statmod, and rpy2 to be installed:
+milo requires either the "de" extra for the "pydeseq2" solver:
+
+```console
+pip install 'pertpy[de]'
+```
+
+or, edger, statmod, and rpy2 for the "edger" solver:
 
 ```R
 BiocManager::install("edgeR")
@@ -77,6 +89,7 @@ pip install rpy2
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [api]: https://pertpy.readthedocs.io/en/latest/api.html
+[conda-forge]: https://anaconda.org/conda-forge/pertpy
 [//]: # "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-0.11.4 → pertpy-1.0.0}/docs/changelog.md

@@ -5,19 +5,40 @@ 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).
 
-## v0.11.3
+## v1.0.0
+
+### 🚀 Features
+
+* Simplify guide assignment tutorial ([#796](https://github.com/scverse/pertpy/pull/796)) @Zethson
+* Add milo pydeseq2 solver ([#795](https://github.com/scverse/pertpy/pull/795)) @Zethson
+
+## v0.11.5
+
+### 🚀 Features
+
+* Move to trusted publishing ([#790](https://github.com/scverse/pertpy/pull/790)) @Zethson
+* Add conda-forge to installation instructions ([#789](https://github.com/scverse/pertpy/pull/789)) @Zethson
+* Fix seaborn 0.14 compat & testing dependencies & speed up tests ([#787](https://github.com/scverse/pertpy/pull/787)) @Zethson
+* Support > 2 colors in `pt.tl.Sccoda.plot_boxplots` ([#784](https://github.com/scverse/pertpy/pull/784)) @mschilli87
+
+### 🐛 Bug Fixes
+
+* Fix LIL support for AnnData 0.12 ([#792](https://github.com/scverse/pertpy/pull/792)) @Zethson
+* Fix compatibility with rpy 3.6.0 in milo ([#791](https://github.com/scverse/pertpy/pull/791)) @seohyonkim
+
+## v0.11.4
 
 ### 🧰 Maintenance
 
-* Remove decoupler [#783]((https://github.com/scverse/pertpy/pull/783)) @Zethson
+* Remove decoupler ([#783](https://github.com/scverse/pertpy/pull/783)) @Zethson
 
 ## v0.11.3
 
-## 🚀 Features
+### 🚀 Features
 
-* add about page [#770]((https://github.com/scverse/pertpy/pull/770)) @Zethson
-* Simplify Metadata errors [#765]((https://github.com/scverse/pertpy/pull/765)) @Zethson
-* Standardize scCODA plot palette interface [#773]((https://github.com/scverse/pertpy/pull/773)) @mschilli87
+* add about page ([#770](https://github.com/scverse/pertpy/pull/770)) @Zethson
+* Simplify Metadata errors ([#765](https://github.com/scverse/pertpy/pull/765)) @Zethson
+* Standardize scCODA plot palette interface ([#773](https://github.com/scverse/pertpy/pull/773)) @mschilli87
 
 ## v0.11.2
 

{pertpy-0.11.4 → pertpy-1.0.0}/docs/conf.py

@@ -62,32 +62,40 @@ pygments_style = "sphinx"
 templates_path = ["_templates"]
 bibtex_bibfiles = ["references.bib"]
 nitpicky = True  # Warn about broken links
-# source_suffix = ".md"
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
 
 suppress_warnings = ["toc.not_included"]
 
 autosummary_generate = True
 autosummary_imported_members = True
-autodoc_member_order = "bysource"
+autodoc_member_order = "groupwise"
 napoleon_google_docstring = True
 napoleon_include_init_with_doc = False
 napoleon_use_rtype = True
 napoleon_use_param = True
+myst_heading_anchors = 6
 napoleon_custom_sections = [("Params", "Parameters")]
 todo_include_todos = False
-numpydoc_show_class_members = False
 annotate_defaults = True
 myst_enable_extensions = [
+    "amsmath",
     "colon_fence",
+    "deflist",
     "dollarmath",
-    "amsmath",
+    "html_image",
+    "html_admonition",
 ]
+myst_url_schemes = ("http", "https", "mailto")
 nb_execution_mode = "off"
+nb_merge_streams = True
 warn_as_error = True
 
 typehints_defaults = "comma"
 
-# html_show_sourcelink = True
 html_theme = "scanpydoc"
 html_title = "pertpy"
 html_logo = "_static/pertpy_logo.svg"

{pertpy-0.11.4 → pertpy-1.0.0}/docs/index.md

@@ -48,7 +48,7 @@ It provides tools for harmonizing perturbation datasets, automating metadata ann
 ```{toctree}
 :caption: 'General'
 :hidden: true
-:maxdepth: 1
+:maxdepth: 2
 
 installation
 api
@@ -60,7 +60,7 @@ references
 ```{toctree}
 :caption: 'Gallery'
 :hidden: true
-:maxdepth: 1
+:maxdepth: 3
 
 tutorials
 usecases
@@ -69,7 +69,7 @@ usecases
 ```{toctree}
 :caption: 'About'
 :hidden: true
-:maxdepth: 1
+:maxdepth: 2
 
 about/background
 about/cite

{pertpy-0.11.4 → pertpy-1.0.0}/docs/installation.md

@@ -6,6 +6,8 @@
 
 ## Stable release
 
+### PyPI
+
 To install pertpy, run this command in your terminal:
 
 ```console
@@ -13,9 +15,16 @@ pip install pertpy
 ```
 
 This is the preferred method to install pertpy, as it will always install the most recent stable release.
-
 If you don't have [pip] installed, this [Python installation guide] can guide you through the process.
 
+### conda-forge
+
+Alternatively, you can install pertpy from [conda-forge]:
+
+```console
+conda install -c conda-forge pertpy
+```
+
 ### Additional dependency groups
 
 #### Differential gene expression interface
@@ -38,7 +47,13 @@ pip install rpy2
 
 #### milo
 
-milo further requires edger, statmod, and rpy2 to be installed:
+milo requires either the "de" extra for the "pydeseq2" solver:
+
+```console
+pip install 'pertpy[de]'
+```
+
+or, edger, statmod, and rpy2 for the "edger" solver:
 
 ```R
 BiocManager::install("edgeR")
@@ -57,45 +72,6 @@ TascCODA requires an additional set of dependencies (ete4, pyqt6, and toytree) t
 pip install pertpy[tcoda]
 ```
 
-## Apple Silicon
-
-If you want to install and use pertpy on a machine with macOS and M-Chip, the installation is slightly more complex.
-This is because pertpy depends on [scvi-tools], which can currently only run on Apple Silicon machines when installed
-using a native python version (due to a dependency on jax, which cannot be run via Rosetta).
-
-Follow these steps to install pertpy on an Apple Silicon machine (tested on a MacBook Pro with M1 chip and macOS 14.0):
-
-1. Install [Homebrew]
-
-2. Install Apple Silicon version of Mambaforge (If you already have Anaconda/Miniconda installed, make sure
-   having both mamba and conda won't cause conflicts)
-
-    ```console
-    brew install --cask mambaforge
-    ```
-
-3. Create a new environment using mamba and activate it
-
-    ```console
-    mamba create -n pertpy-env
-    mamba activate pertpy-env
-    ```
-
-4. Clone the GitHub Repository
-
-    ```console
-    git clone https://github.com/scverse/pertpy.git
-    ```
-
-5. Go inside the pertpy folder and install pertpy
-
-    ```console
-    cd pertpy
-    pip install .
-    ```
-
-Now you're ready to use pertpy as usual within the environment (`import pertpy`).
-
 ## From sources
 
 The sources for pertpy can be downloaded from the [Github repo].
@@ -114,8 +90,7 @@ $ curl -OJL https://github.com/scverse/pertpy/tarball/master
 
 [github repo]: https://github.com/scverse/pertpy
 [pip]: https://pip.pypa.io
-[poetry]: https://python-poetry.org/
+[conda-forge]: https://anaconda.org/conda-forge/pertpy
 [python installation guide]: http://docs.python-guide.org/en/latest/starting/installation/
 [tarball]: https://github.com/scverse/pertpy/tarball/master
-[scvi-tools]: https://docs.scvi-tools.org/en/latest/installation.html
 [Homebrew]: https://brew.sh/

{pertpy-0.11.4 → pertpy-1.0.0}/pertpy/__init__.py

@@ -2,10 +2,11 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.11.4"
+__version__ = "1.0.0"
 
 import warnings
 
+from anndata._core.aligned_df import ImplicitModificationWarning
 from matplotlib import MatplotlibDeprecationWarning
 from numba import NumbaDeprecationWarning
 
@@ -13,6 +14,8 @@ warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
 warnings.filterwarnings("ignore", category=MatplotlibDeprecationWarning)
 warnings.filterwarnings("ignore", category=SyntaxWarning)
 warnings.filterwarnings("ignore", category=UserWarning, module="scvi._settings")
+warnings.filterwarnings("ignore", message="Environment variable.*redefined by R")
+warnings.filterwarnings("ignore", message="Transforming to str index.", category=ImplicitModificationWarning)
 
 import mudata
 

{pertpy-0.11.4 → pertpy-1.0.0}/pertpy/tools/_coda/_base_coda.py

@@ -1538,7 +1538,7 @@ class CompositionalModel2(ABC):
         if isinstance(data, MuData):
             data = data[modality_key]
         if isinstance(palette, Colormap):
-            palette = palette(range(2))
+            palette = list(palette(range(len(data.obs[feature_name].unique()))))
 
         # y scale transformations
         if y_scale == "relative":

{pertpy-0.11.4 → pertpy-1.0.0}/pertpy/tools/_distances/_distances.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING, Literal, NamedTuple
 
+import jax
 import numpy as np
 import pandas as pd
 from numba import jit
@@ -685,6 +686,7 @@ class WassersteinDistance(AbstractDistance):
     def __init__(self) -> None:
         super().__init__()
         self.accepts_precomputed = False
+        self.solver = jax.jit(Sinkhorn())
 
     def __call__(self, X: np.ndarray, Y: np.ndarray, **kwargs) -> float:
         X = np.asarray(X, dtype=np.float64)
@@ -699,8 +701,7 @@ class WassersteinDistance(AbstractDistance):
 
     def solve_ot_problem(self, geom: Geometry, **kwargs):
         ot_prob = LinearProblem(geom)
-        solver = Sinkhorn()
-        ot = solver(ot_prob, **kwargs)
+        ot = self.solver(ot_prob, **kwargs)
         cost = float(ot.reg_ot_cost)
 
         # Check for NaN or invalid cost