pertpy 0.7.0__tar.gz → 0.9.1__tar.gz

{pertpy-0.7.0 → pertpy-0.9.1}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.7.0 🌈"
-tag-template: 0.7.0
+name-template: "0.9.1 🌈"
+tag-template: 0.9.1
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.7.0 → pertpy-0.9.1}/.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"
+                      python: "3.12"
+                      run_mode: "slow"
                     - os: ubuntu-latest
-                      python: "3.11"
+                      python: "3.12"
+                      run_mode: "fast"
+                    - os: ubuntu-latest
+                      python: "3.12"
+                      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-0.9.1}/.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-0.9.1}/.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-0.9.1}/.readthedocs.yml

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

{pertpy-0.7.0 → pertpy-0.9.1}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.7.0
+Version: 0.9.1
 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
         
@@ -41,15 +41,15 @@ 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: 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 +61,14 @@ 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 +98,18 @@ 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/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
 
 ## Documentation
 
@@ -113,18 +117,32 @@ Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
 
 ## Installation
 
-You can install _pertpy_ via [pip] from [PyPI]:
+We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS).
+No particular hardware beyond a standard laptop is required.
+
+You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 
 ```console
 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]
+```
+
+## 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)
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

pertpy-0.9.1/README.md

@@ -0,0 +1,49 @@
+[![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)
+[![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/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/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
+
+## Documentation
+
+Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
+
+## Installation
+
+We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS).
+No particular hardware beyond a standard laptop is required.
+
+You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
+
+```console
+pip install pertpy
+```
+
+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]
+```
+
+## 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)
+
+[pip]: https://pip.pypa.io/
+[pypi]: https://pypi.org/
+[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

{pertpy-0.7.0 → pertpy-0.9.1}/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-0.9.1}/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-0.9.1}/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-0.9.1}/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-0.9.1}/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-0.9.1}/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-0.9.1}/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-0.9.1}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.7.0"
+__version__ = "0.9.1"
 
 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