BLD Build with uv, hatchling, updated CI/pre-commit and SPEC 0 compliant package versions (#416)

* Move to uv and newer dependencies and Python versions

* Allow manually triggering the workflow

* Fix version

* Fix docs building

* Fix ruff version

* Fix mypy errors

* Fix mypy errors

* Fix mypy errors

* Make main dependencies SPEC0 compliant

* Fix numpy casting bug

* Fix docstrings error

* Update install instructions for contribution

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update requirements in docs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Remove uv.lock

* Fix mypy error by explicitly typing sum of booleans as int

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: maltekuehl

.binder/postBuild

@@ -14,4 +14,4 @@ mv docs/build/html/jupyter_notebooks .
 shopt -s extglob
 rm -rf .[!.]*
 rm -rf !(jupyter_notebooks|docs)
-(cd docs && rm -rf !(src))
+(cd docs && rm -rf !(src))

.binder/requirements.txt

@@ -1 +1 @@
--r ../requirements.txt
+-r ../requirements.txt

.binder/runtime.txt

@@ -1 +1 @@
-python-3.9
+python-3.9

.github/ISSUE_TEMPLATE/bug_report.md

@@ -12,7 +12,7 @@ A clear and concise description of what the bug is.
 *NB:* for questions about pydeseq2 that are not related to a bug, please open a topic on the [scverse ecosystem Discourse forum](https://discourse.scverse.org/c/ecosystem/38).
 
 **To Reproduce**
-Provide snippets of code and steps on how to reproduce the behavior. 
+Provide snippets of code and steps on how to reproduce the behavior.
 Please also specify the version you are using.
 
 **Expected behavior**

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,4 +14,3 @@ https://github.com/blog/1506-closing-issues-via-pull-requests
 
 
 #### What does your PR implement? Be specific.
-

.github/workflows/pr_validation.yml

@@ -2,6 +2,7 @@ name: pr-validation
 
 # Controls when the workflow will run
 on:
+  workflow_dispatch:
   push:
     branches:
       - '**'
@@ -18,31 +19,41 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python: "3.10"
+            python: "3.11"
           - os: ubuntu-latest
-            python: "3.10"
-            pip-flags: "--pre"
+            python: "3.12"
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.13"
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.13"
             pip-flags: "--pre"
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "latest"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -e ."[dev]"
-          pip install -r docs/requirements.txt
+          uv sync --extra doc --extra dev
+      - name: Lint with ruff
+        run: |
+          uv run ruff check --fix --exit-non-zero-on-fix pydeseq2
+      - name: Format with ruff
+        run: |
+          uv run ruff format --check pydeseq2
+      - name: Type check with mypy
+        run: |
+          uv run mypy -p pydeseq2
       - name: Test with pytest
         run: |
-          coverage run -m pytest
+          uv run coverage run -m pytest
       - name: Generate code coverage report
         run: |
-          coverage html
+          uv run coverage html
       - name: Upload coverage artifacts
         uses: actions/upload-artifact@v4
         with:
@@ -51,5 +62,9 @@ jobs:
           retention-days: 20
       - name: Compile docs
         run: |
+          uv pip freeze > requirements.txt
           cd docs
-          make clean html
+          uv run make clean html
+      - name: Build package
+        run: |
+          uv build

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -133,3 +134,12 @@ dmypy.json
 
 # IDEs
 .vscode
+
+# Docs files
+output_files/
+docs/source/auto_examples/
+docs/source/sg_execution_times.rst
+
+# Requirement files
+uv.lock
+requirements.txt

.pre-commit-config.yaml

@@ -1,18 +1,35 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
 repos:
--   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.9.0
-    hooks:
-    - id: black
-      additional_dependencies: ['click==8.0.4']
-      args: # arguments to configure black
-       - --line-length=89
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.0
-    hooks:
-    - id: ruff
-      args: [ --fix, --exit-non-zero-on-fix]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+    - id: detect-private-key
+    - id: check-ast
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+      args: [--fix=lf]
+    - id: check-added-large-files
+      stages: [pre-commit]
+      args: ["--maxkb=50000"]
+    - id: trailing-whitespace
+    - id: check-case-conflict
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.14.0
+  hooks:
+    - id: ruff-check
+      types_or: [python, pyi, jupyter]
+      args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
+      types_or: [python, pyi, jupyter]
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.18.2
     hooks:
     - id: mypy
-      exclude: ^(tests/|docs/source/conf.py)
+      pass_filenames: false
+      args: [-p, pydeseq2, --ignore-missing-imports]

CONTRIBUTING.md

@@ -11,4 +11,4 @@ Code of Conduct
 ---------------
 
 `PyDeseq2` follows the code of conduct defined by
-the Python Software Foundation: https://www.python.org/psf/codeofconduct/.
+the Python Software Foundation: https://www.python.org/psf/codeofconduct/.

README.md

@@ -6,14 +6,14 @@
 [![condaDownloads](https://img.shields.io/conda/dn/bioconda/pydeseq2?logo=Anaconda)](https://anaconda.org/bioconda/pydeseq2)
 [![license](https://img.shields.io/pypi/l/pydeseq2)](LICENSE)
 
-PyDESeq2 is a python implementation of the [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) 
+PyDESeq2 is a python implementation of the [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
 method [1] for differential expression analysis (DEA) with bulk RNA-seq data, originally in R.
 It aims to facilitate DEA experiments for python users.
 
-As PyDESeq2 is a re-implementation of [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) from 
+As PyDESeq2 is a re-implementation of [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) from
 scratch, you may experience some differences in terms of retrieved values or available features.
 
-Currently, available features broadly correspond to the default settings of DESeq2 (v1.34.0) for single-factor and 
+Currently, available features broadly correspond to the default settings of DESeq2 (v1.34.0) for single-factor and
 multi-factor analysis (with categorical or continuous factors) using Wald tests.
 We plan to implement more in the future.
 In case there is a feature you would particularly like to be implemented, feel free to open an issue.
@@ -40,17 +40,25 @@ In case there is a feature you would particularly like to be implemented, feel f
 
 `PyDESeq2` can be installed from PyPI using `pip`:
 
-`pip install pydeseq2`
+```bash
+pip install pydeseq2
+```
 
 We recommend installing within a conda environment:
 
-```
+```bash
 conda create -n pydeseq2
 conda activate pydeseq2
 conda install pip
 pip install pydeseq2
 ```
 
+You can also add it to your projects through `uv`:
+
+```bash
+uv add pydeseq2
+```
+
 ### Bioconda
 
 `PyDESeq2` can also be installed from Bioconda with `conda`:
@@ -61,16 +69,20 @@ If you're interested in contributing or want access to the development version,
 
 ### Requirements
 
-The list of package version requirements is available in `setup.py`.
+The list of package version requirements is available in `pyproject.toml`.
 
 For reference, the code is being tested in a github workflow (CI) with python
-3.10 to 3.11 and the following package versions:
+3.11 to 3.13 and the latest versions of the following packages:
+
 ```
-- anndata 0.8.0
-- numpy 1.23.0
-- pandas 1.4.3
-- scikit-learn 1.1.1
-- scipy 1.11.0
+- anndata
+- formulaic
+- numpy
+- pandas
+- scikit-learn
+- scipy
+- formulaic-contrasts
+- matplotlib
 ```
 
 Please don't hesitate to open an issue in case you encounter any issue due to possible deprecations.
@@ -84,7 +96,7 @@ contains downloadable examples on how to use PyDESeq2.
 
 ### Documentation
 
-The documentation is hosted [here on ReadTheDocs](https://pydeseq2.readthedocs.io/en/latest/). 
+The documentation is hosted [here on ReadTheDocs](https://pydeseq2.readthedocs.io/en/latest/).
 If you want to have the latest version of the documentation, you can build it from source.
 Please go to the dedicated [README.md](https://github.com/owkin/PyDESeq2/blob/main/docs/README.md) for information on how to do so.
 
@@ -105,12 +117,12 @@ documentation to see how you can contribute to PyDESeq2.
 
 `git clone https://github.com/owkin/PyDESeq2.git`
 
-### 2 - Create a conda environment
+### 2 - Create a uv environment
 
-Run `conda create -n pydeseq2 python=3.10` (or higher python version) to create the `pydeseq2` environment and then activate it:
-`conda activate pydeseq2`.
+Run `uv venv --python 3.13` (or higher python version) to create the `pydeseq2` environment and then activate it:
+`source .venv/bin/activate`.
 
-`cd` to the root of the repo and run `pip install -e ."[dev]"` to install in developer mode.
+`cd` to the root of the repo and run `uv sync --extra dev --extra doc` to install in developer mode.
 
 Then, run `pre-commit install`.
 
@@ -145,4 +157,3 @@ PyDESeq2 is a living project and any contributions are welcome! Feel free to ope
 ## License
 
 PyDESeq2 is released under an [MIT license](https://github.com/owkin/PyDESeq2/blob/main/LICENSE).
-