pertpy 0.6.0__tar.gz → 0.7.0__tar.gz

{pertpy-0.6.0 → pertpy-0.7.0}/.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: "0.7.0 🌈"
+tag-template: 0.7.0
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.6.0 → pertpy-0.7.0}/.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-0.7.0}/.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-0.7.0}/.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-0.6.0 → pertpy-0.7.0}/.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
             matrix:
                 include:
                     - os: ubuntu-latest
-                      python: "3.9"
+                      python: "3.10"
                     - os: ubuntu-latest
                       python: "3.11"
                     - os: ubuntu-latest
@@ -34,25 +34,31 @@ jobs:
             PYTHON: ${{ matrix.python }}
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
 
             - name: Install test dependencies
-              run: python -m pip install --upgrade pip wheel
+              run: python -m pip install --upgrade uv wheel
             - name: Install dependencies
-              run: pip install ${{ matrix.pip-flags }} ".[dev,test,coda]"
+              run: uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda]"
 
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
-              run: pytest -v --cov --color=yes
+              run: coverage run -m pytest -v --color=yes
+
+            - name: Show coverage report
+              run: coverage report -m
 
             - name: Upload coverage
               uses: codecov/codecov-action@v3
+              with:
+                  fail_ci_if_error: true
+                  verbose: true

{pertpy-0.6.0 → pertpy-0.7.0}/.gitignore

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

{pertpy-0.6.0 → pertpy-0.7.0}/.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: v0.3.5
       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: v1.9.0
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-0.6.0 → pertpy-0.7.0}/PKG-INFO

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pertpy
-Version: 0.6.0
+Version: 0.7.0
 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
+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
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
 License: MIT License
         
@@ -29,18 +29,31 @@ 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: 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]
@@ -76,13 +89,13 @@ 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)
+[![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)
 [![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)
@@ -92,7 +105,7 @@ Description-Content-Type: text/markdown
 
 # pertpy
 
-![pertpy-wide1](https://user-images.githubusercontent.com/21954664/235677503-0c72f90d-3f6d-4a16-a1ff-ff8c11a540fb.png)
+![fig1](https://github.com/theislab/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -103,7 +116,13 @@ 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 please install it as:
+
+```console
+pip install pertpy[coda]
 ```
 
 [pip]: https://pip.pypa.io/

{pertpy-0.6.0 → pertpy-0.7.0}/README.md

@@ -1,6 +1,6 @@
 [![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)
+[![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)
 [![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)
@@ -10,7 +10,7 @@
 
 # pertpy
 
-![pertpy-wide1](https://user-images.githubusercontent.com/21954664/235677503-0c72f90d-3f6d-4a16-a1ff-ff8c11a540fb.png)
+![fig1](https://github.com/theislab/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -21,7 +21,13 @@ 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 please install it as:
+
+```console
+pip install pertpy[coda]
 ```
 
 [pip]: https://pip.pypa.io/

{pertpy-0.6.0 → pertpy-0.7.0}/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-0.7.0}/docs/_ext/edit_on_github.py

@@ -1,4 +1,5 @@
 """Based on gist.github.com/MantasVaitkunas/7c16de233812adcb7028."""
+
 import os
 from typing import Any
 

{pertpy-0.6.0 → pertpy-0.7.0}/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-0.7.0}/docs/conf.py

@@ -7,16 +7,15 @@ 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"
 github_repo = "pertpy"
 
-version = "0.6.0"
-release = "0.6.0"
+version = "0.7.0"
+release = "0.7.0"
 
 extensions = [
     "myst_parser",
@@ -181,9 +180,11 @@ 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/ontology_mapping": "_static/tutorials/ontology.png",
+    "tutorials/notebooks/perturbation_space": "_static/tutorials/perturbation_space.png",
 }

{pertpy-0.6.0 → pertpy-0.7.0}/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/
@@ -60,7 +51,6 @@ tutorials/index
 contributing
 code_of_conduct
 Discussions <https://github.com/theislab/pertpy/discussions>
-authors
 references
 ```
 

{pertpy-0.6.0 → pertpy-0.7.0}/docs/installation.md

@@ -14,8 +14,17 @@ $ 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.
+If you don't have [pip] installed, this [Python installation guide] can guide you through the process.
+
+## Google Colab and TascCODA support
+
+TascCODA requires an additional set of dependencies (ete3 and pyqt5) that can be installed using
+
+```console
+$ pip install pertpy[coda]
+```
+
+this also solves any "AttributeError: module 'pertpy.plot' has no attribute 'coda'" issues.
 
 ## From sources
 
@@ -34,12 +43,6 @@ Or download the [tarball]:
 $ curl -OJL https://github.com/theislab/pertpy/tarball/master
 ```
 
-Once you have a copy of the source, you can install it with:
-
-```console
-$ make install
-```
-
 ## Apple Silicon
 
 If you want to install and use pertpy on a machine with macOS and M-Chip, the installation is slightly more complex.
@@ -60,7 +63,7 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
 3. Create a new environment using mamba (here with python 3.10) and activate it
 
     ```console
-    $ mamba create -n pertpy-env python=3.10
+    $ mamba create -n pertpy-env python=3.11
     $ mamba activate pertpy-env
     ```
 

{pertpy-0.6.0 → pertpy-0.7.0}/docs/tutorials/index.md

@@ -5,10 +5,10 @@ orphan: true
 # Tutorials
 
 The easiest way to get familiar with pertpy is to follow along with our tutorials.
-Many are also designed to work seamlessly in Binder, a free cloud computing platform.
+Many are also designed to work seamlessly in Google colab.
 
 :::{note}
-For questions about the usage of pertpy use [Github Discussions].
+For questions about the usage of pertpy use the [scverse discourse](https://discourse.scverse.org/).
 :::
 
 ## Quick start
@@ -24,11 +24,13 @@ For questions about the usage of pertpy use [Github Discussions].
    notebooks/tasccoda
    notebooks/milo
    notebooks/dialogue
+   notebooks/enrichment
    notebooks/distances
    notebooks/distance_tests
+   notebooks/cinemaot
    notebooks/scgen_perturbation_prediction
-   notebooks/scgen_batch_removal
    notebooks/ontology_mapping
+   notebooks/perturbation_space
 ```
 
 ### Glossary
@@ -38,7 +40,7 @@ For questions about the usage of pertpy use [Github Discussions].
 
     .. tab-item:: AnnData
 
-        `AnnData <https://github.com/theislab/anndata>`_ is short for Annotated Data and is the primary datastructure that pertpy uses.
+        `AnnData <https://github.com/scverse/anndata>`_ is short for Annotated Data and is the primary datastructure that pertpy uses.
         It is based on the principle of a single Numpy matrix X embraced by two Pandas Dataframes.
         All rows are called observations (in our case cells or similar) and the columns
         are known as variables (any feature such as e.g. genes or similar).
@@ -49,5 +51,3 @@ For questions about the usage of pertpy use [Github Discussions].
 
         For a more in depth introduction please read the `Scanpy paper <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0>`_.
 ```
-
-[github discussions]: https://github.com/theislab/pertpy/discussions