pertpy 0.6.0__tar.gz → 0.8.0__tar.gz

{pertpy-0.6.0 → pertpy-0.8.0}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.6.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.6.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.8.0 🌈"
+tag-template: 0.8.0
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.6.0 → pertpy-0.8.0}/.github/workflows/build.yml

@@ -14,10 +14,10 @@ jobs:
     package:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
 
             - name: Set up Python 3.11
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.11"
                   cache: "pip"

{pertpy-0.6.0 → pertpy-0.8.0}/.github/workflows/labeler.yml

@@ -11,7 +11,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Run Labeler
               uses: crazy-max/ghaction-github-labeler@v4.1.0

{pertpy-0.6.0 → pertpy-0.8.0}/.github/workflows/release.yml

@@ -11,10 +11,10 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Checkout code
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Set up Python 3.11
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.11"
 

pertpy-0.8.0/.github/workflows/test.yml

@@ -0,0 +1,85 @@
+name: Test
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                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:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v5
+              with:
+                  python-version: ${{ matrix.python }}
+
+            - 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 rpy2
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda,de]"
+
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: |
+                  pytest_args="-m pytest -v --color=yes"
+                  if [ "${{ matrix.run_mode }}" = "slow" ]; then
+                    pytest_args="$pytest_args --runslow"
+                  fi
+                  coverage run $pytest_args
+
+            - name: Show coverage report
+              run: coverage report -m
+
+            - name: Upload coverage
+              uses: codecov/codecov-action@v4
+              with:
+                  token: ${{ secrets.CODECOV_TOKEN }}
+                  fail_ci_if_error: true
+                  verbose: true

{pertpy-0.6.0 → pertpy-0.8.0}/.gitignore

@@ -153,3 +153,5 @@ cache
 
 lightning_logs/*
 */lightning_logs/*
+
+node_modules

{pertpy-0.6.0 → 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-0.6.0 → pertpy-0.8.0}/.pre-commit-config.yaml

@@ -7,23 +7,17 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.3
+      rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
-            # Newer versions of node don't work on systems that have an older version of GLIBC
-            # (in particular Ubuntu 18.04 and Centos 7)
-            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
-            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
-            # https://github.com/jupyterlab/jupyterlab/issues/12675
-            language_version: "17.9.1"
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.3
+      rev: v0.4.7
       hooks:
           - id: ruff
-            args: [--fix, --exit-non-zero-on-fix]
+            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.5.0
+      rev: v4.6.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -33,7 +27,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.6.1
+      rev: v1.10.0
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-0.6.0 → pertpy-0.8.0}/.readthedocs.yml

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

{pertpy-0.6.0 → pertpy-0.8.0}/PKG-INFO

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pertpy
-Version: 0.6.0
+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
+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
         
@@ -29,18 +29,30 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Requires-Python: >=3.9
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Framework :: Jupyter
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.10
 Requires-Dist: adjusttext
-Requires-Dist: anndata
-Requires-Dist: arviz
+Requires-Dist: blitzgsea
 Requires-Dist: decoupler
-Requires-Dist: ipywidgets
+Requires-Dist: lamin-utils
 Requires-Dist: muon
-Requires-Dist: numba
-Requires-Dist: numpyro
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
-Requires-Dist: plotnine
+Requires-Dist: pubchempy
+Requires-Dist: pyarrow
 Requires-Dist: requests
 Requires-Dist: rich
 Requires-Dist: scanpy[leiden]
@@ -48,10 +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
@@ -76,23 +92,23 @@ Requires-Dist: sphinx>=4; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
 Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; 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/branch/master/graph/badge.svg)](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
 
-![pertpy-wide1](https://user-images.githubusercontent.com/21954664/235677503-0c72f90d-3f6d-4a16-a1ff-ff8c11a540fb.png)
+![fig1](https://github.com/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -103,7 +119,19 @@ Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
 You can install _pertpy_ via [pip] from [PyPI]:
 
 ```console
-$ pip install pertpy
+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]
 ```
 
 [pip]: https://pip.pypa.io/

pertpy-0.8.0/README.md

@@ -0,0 +1,41 @@
+[![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/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
+
+## Documentation
+
+Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
+
+## Installation
+
+You can install _pertpy_ 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]
+```
+
+[pip]: https://pip.pypa.io/
+[pypi]: https://pypi.org/
+[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

{pertpy-0.6.0 → pertpy-0.8.0}/codecov.yml

@@ -5,7 +5,7 @@ coverage:
     status:
         project:
             default:
-                # Require 1% coverage, i.e., always succeed
+                # Require 1% coverage, i.e., succeed as long as coverage collection works
                 target: 1
         patch: false
         changes: false

{pertpy-0.6.0 → pertpy-0.8.0}/docs/_ext/edit_on_github.py

@@ -1,4 +1,5 @@
 """Based on gist.github.com/MantasVaitkunas/7c16de233812adcb7028."""
+
 import os
 from typing import Any
 
@@ -36,7 +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-0.6.0 → pertpy-0.8.0}/docs/_templates/autosummary/class.rst

@@ -24,11 +24,25 @@ Methods table
 ~~~~~~~~~~~~~
 
 .. autosummary::
+
+{% set plotting_methods = [] %}
+{% set other_methods = [] %}
+
 {% for item in methods %}
-    {%- if item != '__init__' %}
+    {%- if item.startswith('plot_') %}
+        {%- set _ = plotting_methods.append(item) %}
+    {% elif item != '__init__' %}
+        {%- set _ = other_methods.append(item) %}
+    {%- endif %}
+{% endfor %}
+
+{% for item in other_methods %}
     ~{{ fullname }}.{{ item }}
-    {%- endif -%}
-{%- endfor %}
+{% endfor %}
+
+{% for item in plotting_methods %}
+    ~{{ fullname }}.{{ item }}
+{% endfor %}
 {% endif %}
 {% endblock %}
 

{pertpy-0.6.0 → pertpy-0.8.0}/docs/conf.py

@@ -2,21 +2,25 @@
 # mypy: ignore-errors
 
 import sys
+from datetime import datetime
+from importlib.metadata import metadata
 from pathlib import Path
 
 HERE = Path(__file__).parent
 sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
 
-needs_sphinx = "4.3"  # Nicer param docs
+needs_sphinx = "4.3"
 
-# General information about the project.
-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 = "0.6.0"
-release = "0.6.0"
 
 extensions = [
     "myst_parser",
@@ -98,7 +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"
 
@@ -167,7 +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>
@@ -181,9 +186,13 @@ nbsphinx_thumbnails = {
     "tutorials/notebooks/tasccoda": "_static/tutorials/tasccoda.png",
     "tutorials/notebooks/milo": "_static/tutorials/milo.png",
     "tutorials/notebooks/dialogue": "_static/tutorials/dialogue.png",
+    "tutorials/notebooks/enrichment": "_static/tutorials/enrichment.png",
     "tutorials/notebooks/distances": "_static/tutorials/distances.png",
     "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/scgen_batch_removal": "_static/tutorials/scgen_batch_removal.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-0.6.0 → 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-0.6.0 → pertpy-0.8.0}/docs/index.md

@@ -24,15 +24,6 @@
     The tutorials walk you through real-world applications of pertpy.
 ```
 
-```{eval-rst}
-.. card:: Use cases :octicon:`info;1em;`
-    :link: user_guide/index
-    :link-type: doc
-
-    pertpy has been applied to many use-cases. We highlight some of them here.
-    Interested in adding your use-case? Please talk to us.
-```
-
 ```{eval-rst}
 .. card:: Discussion :octicon:`megaphone;1em;`
     :link: https://discourse.scverse.org/
@@ -43,7 +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.
 
@@ -59,8 +50,7 @@ usage/usage
 tutorials/index
 contributing
 code_of_conduct
-Discussions <https://github.com/theislab/pertpy/discussions>
-authors
+Discussions <https://github.com/scverse/pertpy/discussions>
 references
 ```