pertpy 0.11.2__tar.gz → 0.11.3__tar.gz

{pertpy-0.11.2 → pertpy-0.11.3}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.11.2 🌈"
-tag-template: 0.11.2
+name-template: "0.11.3 🌈"
+tag-template: 0.11.3
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.11.2 → pertpy-0.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.11.2
+Version: 0.11.3
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -132,22 +132,50 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
+### Differential gene expression
+
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install 'pertpy[de]'
+```
+
+### tascCODA
+
 if you want to use tascCODA, please install pertpy as follows:
 
 ```console
 pip install 'pertpy[tcoda]'
 ```
 
-If you want to use the differential gene expression interface, please install pertpy by running:
+### milo
+
+milo further requires edger, statmod, and rpy2 to be installed:
+
+```R
+BiocManager::install("edgeR")
+BiocManager::install("statmod")
+```
 
 ```console
-pip install 'pertpy[de]'
+pip install rpy2
 ```
 
 ## Citation
 
-[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
-bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/

{pertpy-0.11.2 → pertpy-0.11.3}/README.md

@@ -29,22 +29,50 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
+### Differential gene expression
+
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install 'pertpy[de]'
+```
+
+### tascCODA
+
 if you want to use tascCODA, please install pertpy as follows:
 
 ```console
 pip install 'pertpy[tcoda]'
 ```
 
-If you want to use the differential gene expression interface, please install pertpy by running:
+### milo
+
+milo further requires edger, statmod, and rpy2 to be installed:
+
+```R
+BiocManager::install("edgeR")
+BiocManager::install("statmod")
+```
 
 ```console
-pip install 'pertpy[de]'
+pip install rpy2
 ```
 
 ## Citation
 
-[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
-bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/

pertpy-0.11.3/docs/about/background.md

@@ -0,0 +1,49 @@
+# About Pertpy
+
+Pertpy is an end-to-end framework for the analysis of large-scale single-cell perturbation experiments.
+It provides access to harmonized perturbation datasets and metadata databases along with numerous fast and user-friendly implementations of both established and novel methods such as automatic metadata annotation or perturbation distances to efficiently analyze perturbation data.
+As part of the scverse ecosystem, pertpy interoperates with existing single-cell analysis libraries and is designed to be easily extended.
+If you find pertpy useful for your research, please check out {doc}`cite`.
+
+## Design principles
+
+Our framework is based on three key principles: `Modularity`, `Flexibility`, and `Scalability`.
+
+### Modularity
+
+Pertpy includes modules for analysis of single and combinatorial perturbations covering diverse types of perturbation data including genetic knockouts, drug screens, and disease states.
+The framework is designed for flexibility, offering more than 100 composable and interoperable analysis functions organized in modules which further ease downstream interpretation and visualization.
+These modules host fundamental building blocks for implementation and methods that share functionality and can be chained into custom pipelines.
+
+A typical Pertpy workflow consists of several steps:
+
+* Initial **data transformation** such as guide RNA assignment for CRISPR screens
+* **Quality control** to address confounding factors and technical variation
+* **Metadata annotation** against ontologies and enrichment from databases
+* **Perturbation space analysis** to learn biologically interpretable embeddings
+* **Downstream analysis** including differential expression, compositional analysis, and distance calculation
+
+This modular approach yields a powerful and flexible framework as many analysis steps can be independently applied or chained together.
+
+### Flexibility
+
+Pertpy is purpose-built to organize, analyze, and visualize complex perturbation datasets.
+It is flexible and can be applied to datasets of different assays, data types, sizes, and perturbations, thereby unifying previous data-type- or assay-specific single-problem approaches.
+Designed to integrate external metadata with measured data, it enables unprecedented contextualization of results through swiftly built, experiment-specific pipelines, leading to more robust outcomes.
+
+The inputs to a typical analysis with pertpy are unimodal scRNA-seq or multimodal perturbation readouts stored in AnnData or MuData objects.
+While pertpy is primarily designed to explore perturbations such as genetic modifications, drug treatments, exposure to pathogens, and other environmental conditions, its utility extends to various other perturbation settings, including diverse disease states where experimental perturbations have not been applied.
+
+### Scalability
+
+Pertpy addresses a wide array of use-cases and different types of growing datasets through its sparse and memory-efficient implementations, which leverage the parallelization and GPU acceleration library Jax, and numba, thereby making them substantially faster than original implementations.
+The framework can be applied to datasets ranging from thousands to millions of cells.
+
+For example, when analyzing CRISPR screens, Pertpy's implementation of Mixscape is optimized using PyNNDescent for nearest neighbor search during the calculation of perturbation signatures.
+Other methods such as scCODA and tascCODA are accelerated by replacing the Hamiltonian Monte Carlo algorithm in TensorFlow with the no-U-turn sampler from numpyro.
+CINEMA-OT is optimized with ott-jax to make the implementation portable across hardware, enabling GPU acceleration.
+
+## Why is it called "Pertpy"?
+
+Pertpy is named for its core purpose: The analysis of **pert**urbations in **Py**thon.
+The framework unifies perturbation analysis approaches across different data types and experimental designs, providing a comprehensive solution for understanding cellular responses to various stimuli.

pertpy-0.11.3/docs/about/cite.md

@@ -0,0 +1,20 @@
+# Citing pertpy
+
+If you find pertpy useful for your research, please consider citing our work as follows:
+
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
+
+If you are using any previously published tool, please also cite the original publication.
+All tool specific references can be found here: {doc}`../references`.

{pertpy-0.11.2 → pertpy-0.11.3}/docs/changelog.md

@@ -5,6 +5,14 @@ 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
+
+## 🚀 Features
+
+* add about page (#770) @Zethson
+* Simplify Metadata errors (#765) @Zethson
+* Standardize scCODA plot palette interface (#773) @mschilli87
+
 ## v0.11.2
 
 ### 🚀 Features

{pertpy-0.11.2 → pertpy-0.11.3}/docs/conf.py

@@ -128,6 +128,7 @@ nitpick_ignore = [
     ("py:class", "pertpy.tools._distances._distances.MeanVar"),
     ("py:class", "The requested data as a NumPy array."),
     ("py:class", "The full registry saved with the model"),
+    ("py:class", "The requested data."),
     ("py:class", "Model with loaded state dictionaries."),
     ("py:class", "pertpy.tools.lazy_import.<locals>.Placeholder"),
 ]

{pertpy-0.11.2 → pertpy-0.11.3}/docs/index.md

@@ -46,7 +46,7 @@ It provides tools for harmonizing perturbation datasets, automating metadata ann
 ```
 
 ```{toctree}
-:caption: 'General:'
+:caption: 'General'
 :hidden: true
 :maxdepth: 1
 
@@ -58,7 +58,7 @@ references
 ```
 
 ```{toctree}
-:caption: 'Gallery:'
+:caption: 'Gallery'
 :hidden: true
 :maxdepth: 1
 
@@ -66,10 +66,32 @@ tutorials
 usecases
 ```
 
+```{toctree}
+:caption: 'About'
+:hidden: true
+:maxdepth: 1
+
+about/background
+about/cite
+GitHub <https://github.com/scverse/pertpy>
+Discourse <https://discourse.scverse.org/c/ecosystem/pertpy/46>
+```
+
 ## Citation
 
-[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
-bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
 
 ## NumFOCUS
 

{pertpy-0.11.2 → pertpy-0.11.3}/docs/installation.md

@@ -16,17 +16,9 @@ This is the preferred method to install pertpy, as it will always install the mo
 
 If you don't have [pip] installed, this [Python installation guide] can guide you through the process.
 
-## Additional dependency groups
+### Additional dependency groups
 
-### scCODA and tascCODA
-
-TascCODA requires an additional set of dependencies (ete4, pyqt6, and toytree) that can be installed by running:
-
-```console
-pip install pertpy[tcoda]
-```
-
-## Differential gene expression interface
+#### Differential gene expression interface
 
 The DGE interface of pertpy requires additional dependencies that can be installed by running:
 
@@ -44,21 +36,25 @@ BiocManager::install("edgeR")
 pip install rpy2
 ```
 
-## From sources
+#### milo
 
-The sources for pertpy can be downloaded from the [Github repo].
-Please note that you require [poetry] to be installed.
+milo further requires edger, statmod, and rpy2 to be installed:
 
-You can either clone the public repository:
+```R
+BiocManager::install("edgeR")
+BiocManager::install("statmod")
+```
 
 ```console
-$ git clone git://github.com/scverse/pertpy
+pip install rpy2
 ```
 
-Or download the [tarball]:
+#### tascCODA
+
+TascCODA requires an additional set of dependencies (ete4, pyqt6, and toytree) that can be installed by running:
 
 ```console
-$ curl -OJL https://github.com/scverse/pertpy/tarball/master
+pip install pertpy[tcoda]
 ```
 
 ## Apple Silicon
@@ -100,6 +96,22 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
 
 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].
+
+You can either clone the public repository:
+
+```console
+$ git clone git://github.com/scverse/pertpy
+```
+
+Or download the [tarball]:
+
+```console
+$ 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/

{pertpy-0.11.2 → pertpy-0.11.3}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.11.2"
+__version__ = "0.11.3"
 
 import warnings
 

{pertpy-0.11.2 → pertpy-0.11.3}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "pertpy"
-version = "0.11.2"
+version = "0.11.3"
 description = "Perturbation Analysis in the scverse ecosystem."
 readme = "README.md"
 requires-python = ">=3.11,<3.14"