pertpy 0.7.0__tar.gz → 0.8.0__tar.gz

{pertpy-0.7.0 → pertpy-0.8.0}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.7.0 🌈"
-tag-template: 0.7.0
+name-template: "0.8.0 🌈"
+tag-template: 0.8.0
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.7.0 → pertpy-0.8.0}/.github/workflows/test.yml

@@ -23,10 +23,16 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.10"
+                      run_mode: "slow"
                     - os: ubuntu-latest
                       python: "3.11"
+                      run_mode: "slow"
                     - os: ubuntu-latest
                       python: "3.11"
+                      run_mode: "fast"
+                    - os: ubuntu-latest
+                      python: "3.11"
+                      run_mode: slow
                       pip-flags: "--pre"
 
         env:
@@ -39,26 +45,41 @@ jobs:
               uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
+
+            - uses: actions/checkout@v4
+            - name: Install R
+              uses: r-lib/actions/setup-r@v2
+              with:
+                  r-version: "4"
+
+            - name: Install edgeR
+              run: Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')"
 
             - name: Install test dependencies
               run: python -m pip install --upgrade uv wheel
             - name: Install dependencies
-              run: uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda]"
+              run: |
+                  uv pip install --system rpy2
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda,de]"
 
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
-              run: coverage run -m pytest -v --color=yes
+              run: |
+                  pytest_args="-m pytest -v --color=yes"
+                  if [ "${{ matrix.run_mode }}" = "slow" ]; then
+                    pytest_args="$pytest_args --runslow"
+                  fi
+                  coverage run $pytest_args
 
             - name: Show coverage report
               run: coverage report -m
 
             - name: Upload coverage
-              uses: codecov/codecov-action@v3
+              uses: codecov/codecov-action@v4
               with:
+                  token: ${{ secrets.CODECOV_TOKEN }}
                   fail_ci_if_error: true
                   verbose: true

{pertpy-0.7.0 → pertpy-0.8.0}/.gitmodules

@@ -1,3 +1,3 @@
 [submodule "docs/notebooks"]
 	path = docs/tutorials/notebooks
-	url = https://github.com/theislab/pertpy-tutorials/
+	url = https://github.com/scverse/pertpy-tutorials/

{pertpy-0.7.0 → pertpy-0.8.0}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.3.5
+      rev: v0.4.7
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -27,7 +27,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.9.0
+      rev: v1.10.0
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-0.7.0 → pertpy-0.8.0}/.readthedocs.yml

@@ -17,6 +17,7 @@ python:
           extra_requirements:
               - doc
               - coda
+              - de
 
 submodules:
     include: all

{pertpy-0.7.0 → pertpy-0.8.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.7.0
+Version: 0.8.0
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
-Project-URL: Source, https://github.com/theislab/pertpy
-Project-URL: Home-page, https://github.com/theislab/pertpy
-Author: Lukas Heumos, Yuge Ji, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Amir Moinfar, Sergei Rybakov, Tessa Green, Stefan Peidli, Antonia Schumacher, Lilly May
+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
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
 License: MIT License
         
@@ -45,11 +45,10 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
 Requires-Dist: adjusttext
-Requires-Dist: arviz
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
+Requires-Dist: lamin-utils
 Requires-Dist: muon
-Requires-Dist: numpyro
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
 Requires-Dist: pubchempy
@@ -61,10 +60,14 @@ Requires-Dist: scikit-misc
 Requires-Dist: scipy
 Requires-Dist: scvi-tools
 Requires-Dist: sparsecca
-Requires-Dist: toytree
 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: pydeseq2; extra == 'de'
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc
@@ -94,18 +97,18 @@ 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/theislab/pertpy/actions/workflows/build.yml/badge.svg)](https://github.com/theislab/pertpy/actions/workflows/build.yml)
-[![codecov](https://codecov.io/gh/theislab/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/theislab/pertpy)
-[![License](https://img.shields.io/github/license/theislab/pertpy)](https://opensource.org/licenses/Apache2.0)
+[![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)
 [![PyPI](https://img.shields.io/pypi/v/pertpy.svg)](https://pypi.org/project/pertpy/)
 [![Python Version](https://img.shields.io/pypi/pyversions/pertpy)](https://pypi.org/project/pertpy)
 [![Read the Docs](https://img.shields.io/readthedocs/pertpy/latest.svg?label=Read%20the%20Docs)](https://pertpy.readthedocs.io/)
-[![Test](https://github.com/theislab/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/theislab/pertpy/actions/workflows/test.yml)
+[![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
 
-![fig1](https://github.com/theislab/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
+![fig1](https://github.com/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -119,12 +122,18 @@ You can install _pertpy_ via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA please install it as:
+if you want to use scCODA or tascCODA, please install pertpy as follows:
 
 ```console
 pip install pertpy[coda]
 ```
 
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install pertpy[de]
+```
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

{pertpy-0.7.0 → pertpy-0.8.0}/README.md

@@ -1,16 +1,16 @@
 [![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![Build](https://github.com/theislab/pertpy/actions/workflows/build.yml/badge.svg)](https://github.com/theislab/pertpy/actions/workflows/build.yml)
-[![codecov](https://codecov.io/gh/theislab/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/theislab/pertpy)
-[![License](https://img.shields.io/github/license/theislab/pertpy)](https://opensource.org/licenses/Apache2.0)
+[![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)
 [![PyPI](https://img.shields.io/pypi/v/pertpy.svg)](https://pypi.org/project/pertpy/)
 [![Python Version](https://img.shields.io/pypi/pyversions/pertpy)](https://pypi.org/project/pertpy)
 [![Read the Docs](https://img.shields.io/readthedocs/pertpy/latest.svg?label=Read%20the%20Docs)](https://pertpy.readthedocs.io/)
-[![Test](https://github.com/theislab/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/theislab/pertpy/actions/workflows/test.yml)
+[![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
 
-![fig1](https://github.com/theislab/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
+![fig1](https://github.com/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -24,12 +24,18 @@ You can install _pertpy_ via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA please install it as:
+if you want to use scCODA or tascCODA, please install pertpy as follows:
 
 ```console
 pip install pertpy[coda]
 ```
 
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install pertpy[de]
+```
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

{pertpy-0.7.0 → pertpy-0.8.0}/docs/_ext/edit_on_github.py

@@ -37,7 +37,7 @@ def _html_page_context(
 
     # For sphinx_rtd_theme.
     context["display_github"] = True
-    context["github_user"] = "theislab"
+    context["github_user"] = "scverse"
     context["github_version"] = "master"
     context["github_repo"] = repo
     context["conf_py_path"] = "/docs/source/"

{pertpy-0.7.0 → pertpy-0.8.0}/docs/conf.py

@@ -2,6 +2,8 @@
 # mypy: ignore-errors
 
 import sys
+from datetime import datetime
+from importlib.metadata import metadata
 from pathlib import Path
 
 HERE = Path(__file__).parent
@@ -9,13 +11,16 @@ sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
 
 needs_sphinx = "4.3"
 
-project = "pertpy"
-copyright = "2021, Lukas Heumos, Theislab"
-author = "Lukas Heumos"
+info = metadata("pertpy")
+project_name = info["Name"]
+author = info["Author"]
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
+release = info["Version"]
 github_repo = "pertpy"
 
-version = "0.7.0"
-release = "0.7.0"
 
 extensions = [
     "myst_parser",
@@ -97,7 +102,8 @@ intersphinx_mapping = {
 
 language = "en"
 
-# The name of the Pygments (syntax highlighting) style to use.
+typehints_defaults = "comma"
+
 pygments_style = "default"
 pygments_dark_style = "native"
 
@@ -166,7 +172,7 @@ nbsphinx_prolog = r"""
         <p class="admonition-title">Note</p>
         <p>
         This page was generated from
-        <a class="reference external" href="https://github.com/theislab/pertpy/tree/{version}/">{docname}</a>.
+        <a class="reference external" href="https://github.com/scverse/pertpy/tree/{version}/">{docname}</a>.
         Some tutorial content may look better in light mode.
         </p>
     </div>
@@ -185,6 +191,8 @@ nbsphinx_thumbnails = {
     "tutorials/notebooks/distance_tests": "_static/tutorials/distances_tests.png",
     "tutorials/notebooks/cinemaot": "_static/tutorials/cinemaot.png",
     "tutorials/notebooks/scgen_perturbation_prediction": "_static/tutorials/scgen_perturbation_prediction.png",
-    "tutorials/notebooks/ontology_mapping": "_static/tutorials/ontology.png",
     "tutorials/notebooks/perturbation_space": "_static/tutorials/perturbation_space.png",
+    "tutorials/notebooks/differential_gene_expression": "_static/tutorials/dge.png",
+    "tutorials/notebooks/metadata_annotation": "_static/tutorials/metadata.png",
+    "tutorials/notebooks/ontology_mapping": "_static/tutorials/ontology.png",
 }

{pertpy-0.7.0 → pertpy-0.8.0}/docs/contributing.md

@@ -13,7 +13,7 @@ In addition to the packages needed to _use_ this package, you need additional py
 the documentation_. It's easy to install them using `pip`:
 
 ```bash
-git clone https://github.com/theislab/pertpy.git
+git clone https://github.com/scverse/pertpy.git
 cd pertpy
 pip install -e ".[dev,test,doc]"
 ```
@@ -146,7 +146,7 @@ on how to write documentation.
 The documentation is set-up to render jupyter notebooks stored in the `docs/tutorials` directory using [myst-nb][].
 Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
 
-These notebooks come from [pert-tutorials](https://github.com/theislab/pertpy-tutorials) which is a git submodule of pertpy.
+These notebooks come from [pert-tutorials](https://github.com/scverse/pertpy-tutorials) which is a git submodule of pertpy.
 
 #### Hints
 

{pertpy-0.7.0 → pertpy-0.8.0}/docs/index.md

@@ -34,7 +34,7 @@
 
 ```{eval-rst}
 .. card:: GitHub :octicon:`mark-github;1em;`
-    :link: https://github.com/theislab/pertpy
+    :link: https://github.com/scverse/pertpy
 
     Find a bug? Interested in improving pertpy? Checkout our GitHub for the latest developments.
 
@@ -50,7 +50,7 @@ usage/usage
 tutorials/index
 contributing
 code_of_conduct
-Discussions <https://github.com/theislab/pertpy/discussions>
+Discussions <https://github.com/scverse/pertpy/discussions>
 references
 ```
 

{pertpy-0.7.0 → pertpy-0.8.0}/docs/installation.md

@@ -9,7 +9,7 @@
 To install pertpy, run this command in your terminal:
 
 ```console
-$ pip install pertpy
+pip install pertpy
 ```
 
 This is the preferred method to install pertpy, as it will always install the most recent stable release.
@@ -18,14 +18,32 @@ If you don't have [pip] installed, this [Python installation guide] can guide yo
 
 ## Google Colab and TascCODA support
 
-TascCODA requires an additional set of dependencies (ete3 and pyqt5) that can be installed using
+TascCODA requires an additional set of dependencies (ete3 and pyqt5) that can be installed by running:
 
 ```console
-$ pip install pertpy[coda]
+pip install pertpy[coda]
 ```
 
 this also solves any "AttributeError: module 'pertpy.plot' has no attribute 'coda'" issues.
 
+## Differential gene expression interface
+
+The DGE interface of pertpy requires additional dependencies that can be installed by running:
+
+```console
+pip install pertpy[de]
+```
+
+Note that edger in pertpy requires edger and rpy2 to be installed:
+
+```R
+BiocManager::install("edgeR")
+```
+
+```console
+pip install rpy2
+```
+
 ## From sources
 
 The sources for pertpy can be downloaded from the [Github repo].
@@ -34,13 +52,13 @@ Please note that you require [poetry] to be installed.
 You can either clone the public repository:
 
 ```console
-$ git clone git://github.com/theislab/pertpy
+$ git clone git://github.com/scverse/pertpy
 ```
 
 Or download the [tarball]:
 
 ```console
-$ curl -OJL https://github.com/theislab/pertpy/tarball/master
+$ curl -OJL https://github.com/scverse/pertpy/tarball/master
 ```
 
 ## Apple Silicon
@@ -57,35 +75,35 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
    having both mamba and conda won't cause conflicts)
 
     ```console
-    $ brew install --cask mambaforge
+    brew install --cask mambaforge
     ```
 
 3. Create a new environment using mamba (here with python 3.10) and activate it
 
     ```console
-    $ mamba create -n pertpy-env python=3.11
-    $ mamba activate pertpy-env
+    mamba create -n pertpy-env python=3.11
+    mamba activate pertpy-env
     ```
 
 4. Clone the GitHub Repository
 
     ```console
-    $ git clone https://github.com/theislab/pertpy.git
+    git clone https://github.com/scverse/pertpy.git
     ```
 
 5. Go inside the pertpy folder and install pertpy
 
     ```console
-    $ cd pertpy
-    $ pip install .
+    cd pertpy
+    pip install .
     ```
 
 Now you're ready to use pertpy as usual within the environment (`import pertpy`).
 
-[github repo]: https://github.com/theislab/pertpy
+[github repo]: https://github.com/scverse/pertpy
 [pip]: https://pip.pypa.io
 [poetry]: https://python-poetry.org/
 [python installation guide]: http://docs.python-guide.org/en/latest/starting/installation/
-[tarball]: https://github.com/theislab/pertpy/tarball/master
+[tarball]: https://github.com/scverse/pertpy/tarball/master
 [scvi-tools]: https://docs.scvi-tools.org/en/latest/installation.html
 [Homebrew]: https://brew.sh/

{pertpy-0.7.0 → pertpy-0.8.0}/docs/tutorials/index.md

@@ -29,8 +29,10 @@ For questions about the usage of pertpy use the [scverse discourse](https://disc
    notebooks/distance_tests
    notebooks/cinemaot
    notebooks/scgen_perturbation_prediction
-   notebooks/ontology_mapping
    notebooks/perturbation_space
+   notebooks/differential_gene_expression
+   notebooks/metadata_annotation
+   notebooks/ontology_mapping
 ```
 
 ### Glossary

{pertpy-0.7.0 → pertpy-0.8.0}/docs/usage/usage.md

@@ -38,8 +38,10 @@ harmonized names and be loadable as MuData objects.
     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
@@ -49,6 +51,7 @@ harmonized names and be loadable as MuData objects.
     data.gasperini_2019_lowmoi
     data.gehring_2019
     data.haber_2017_regions
+    data.hagai_2018
     data.kang_2018
     data.mcfarland_2020
     data.norman_2019
@@ -62,6 +65,7 @@ harmonized names and be loadable as MuData objects.
     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
@@ -69,6 +73,7 @@ harmonized names and be loadable as MuData objects.
     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
@@ -76,6 +81,7 @@ harmonized names and be loadable as MuData objects.
     data.weinreb_2020
     data.xie_2017
     data.zhao_2021
+    data.zhang_2021
 ```
 
 ## Preprocessing
@@ -126,7 +132,11 @@ Pertpy provides utilities to conduct differential gene expression tests through
     :toctree: preprocessing
     :nosignatures:
 
-    tools.DifferentialGeneExpression
+    tools.PyDESeq2
+    tools.EdgeR
+    tools.WilcoxonTest
+    tools.TTest
+    tools.Statsmodels
 ```
 
 ### Pooled CRISPR screens
@@ -455,8 +465,8 @@ train_new = train[
 ]
 train_new = train_new.copy()
 
-pt.tl.SCGEN.setup_anndata(train_new, batch_key="condition", labels_key="cell_type")
-scgen = pt.tl.SCGEN(train_new)
+pt.tl.Scgen.setup_anndata(train_new, batch_key="condition", labels_key="cell_type")
+scgen = pt.tl.Scgen(train_new)
 scgen.train(max_epochs=100, batch_size=32)
 
 pred, delta = scgen.predict(

{pertpy-0.7.0 → pertpy-0.8.0}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.7.0"
+__version__ = "0.8.0"
 
 import warnings
 
@@ -11,6 +11,7 @@ from numba import NumbaDeprecationWarning
 
 warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
 warnings.filterwarnings("ignore", category=MatplotlibDeprecationWarning)
+warnings.filterwarnings("ignore", category=SyntaxWarning)
 warnings.filterwarnings("ignore", category=UserWarning, module="scvi._settings")
 
 from . import data as dt

pertpy-0.8.0/pertpy/data/__init__.py

@@ -0,0 +1,117 @@
+from pertpy.data._datasets import (
+    adamson_2016_pilot,
+    adamson_2016_upr_epistasis,
+    adamson_2016_upr_perturb_seq,
+    aissa_2021,
+    bhattacherjee,
+    burczynski_crohn,
+    chang_2021,
+    cinemaot_example,
+    combosciplex,
+    datlinger_2017,
+    datlinger_2021,
+    dialogue_example,
+    distance_example,
+    dixit_2016,
+    dixit_2016_raw,
+    dong_2023,
+    frangieh_2021,
+    frangieh_2021_protein,
+    frangieh_2021_raw,
+    frangieh_2021_rna,
+    gasperini_2019_atscale,
+    gasperini_2019_highmoi,
+    gasperini_2019_lowmoi,
+    gehring_2019,
+    haber_2017_regions,
+    hagai_2018,
+    kang_2018,
+    mcfarland_2020,
+    norman_2019,
+    norman_2019_raw,
+    papalexi_2021,
+    replogle_2022_k562_essential,
+    replogle_2022_k562_gwps,
+    replogle_2022_rpe1,
+    sc_sim_augur,
+    schiebinger_2019_16day,
+    schiebinger_2019_18day,
+    schraivogel_2020_tap_screen_chr8,
+    schraivogel_2020_tap_screen_chr11,
+    sciplex3_raw,
+    sciplex_gxe1,
+    shifrut_2018,
+    smillie_2019,
+    srivatsan_2020_sciplex2,
+    srivatsan_2020_sciplex3,
+    srivatsan_2020_sciplex4,
+    stephenson_2021_subsampled,
+    tasccoda_example,
+    tian_2019_day7neuron,
+    tian_2019_ipsc,
+    tian_2021_crispra,
+    tian_2021_crispri,
+    weinreb_2020,
+    xie_2017,
+    zhang_2021,
+    zhao_2021,
+)
+
+__all__ = [
+    "adamson_2016_pilot",
+    "adamson_2016_upr_epistasis",
+    "adamson_2016_upr_perturb_seq",
+    "aissa_2021",
+    "bhattacherjee",
+    "burczynski_crohn",
+    "chang_2021",
+    "cinemaot_example",
+    "combosciplex",
+    "datlinger_2017",
+    "datlinger_2021",
+    "dialogue_example",
+    "distance_example",
+    "dixit_2016",
+    "dixit_2016_raw",
+    "dong_2023",
+    "frangieh_2021",
+    "frangieh_2021_protein",
+    "frangieh_2021_raw",
+    "frangieh_2021_rna",
+    "gasperini_2019_atscale",
+    "gasperini_2019_highmoi",
+    "gasperini_2019_lowmoi",
+    "gehring_2019",
+    "haber_2017_regions",
+    "hagai_2018",
+    "kang_2018",
+    "mcfarland_2020",
+    "norman_2019",
+    "norman_2019_raw",
+    "papalexi_2021",
+    "replogle_2022_k562_essential",
+    "replogle_2022_k562_gwps",
+    "replogle_2022_rpe1",
+    "sc_sim_augur",
+    "schiebinger_2019_16day",
+    "schiebinger_2019_18day",
+    "schraivogel_2020_tap_screen_chr8",
+    "schraivogel_2020_tap_screen_chr11",
+    "sciplex3_raw",
+    "sciplex_gxe1",
+    "shifrut_2018",
+    "smillie_2019",
+    "srivatsan_2020_sciplex2",
+    "srivatsan_2020_sciplex3",
+    "srivatsan_2020_sciplex4",
+    "stephenson_2021_subsampled",
+    "tasccoda_example",
+    "tian_2019_day7neuron",
+    "tian_2019_ipsc",
+    "tian_2021_crispra",
+    "tian_2021_crispri",
+    "weinreb_2020",
+    "xie_2017",
+    "zhao_2021",
+    "zhang_2021",
+]