Build with uv, hatchling, updated CI/pre-commit and SPEC 0 compliant package versions

.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).
-

datasets/README.md

@@ -3,9 +3,9 @@
 This directory stores example data which can be retrieved using the `load_example_data` function from
 `pydeseq2.utils`. Only synthetic data is provided for now, but new datasets might be available in the future.
 
-The `tests_clinical.csv` and `test_counts.csv` files were generated using a custom modification of the 
-`makeExampleDESeqDataSet` method of [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html), 
-to handle several factors. 
+The `tests_clinical.csv` and `test_counts.csv` files were generated using a custom modification of the
+`makeExampleDESeqDataSet` method of [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html),
+to handle several factors.
 
 
 ## Folder organisation
@@ -15,7 +15,7 @@ PyDESeq2
 │
 └───datasets
         │
-        └───synthetic   
+        └───synthetic
             │       test_clinical.csv
             │       test_counts.csv
 ```

docs/Makefile

@@ -23,4 +23,3 @@ help:
 
 livehtml:
 	sphinx-autobuild -b html $(SOURCEDIR) $(BUILDDIR)/html
-

docs/README.md

@@ -1,29 +1,25 @@
 # Documentation
 
-The documentation of PyDESeq2 is generated using Sphinx and hosted on ReadTheDoc. 
+The documentation of PyDESeq2 is generated using Sphinx and hosted on ReadTheDocs.
 If you want to build the documentation from source, start by cloning the repository, if you have not done it yet.
 
 ```bash
 git clone https://github.com/owkin/PyDESeq2.git
 cd PyDESeq2
 ```
 
-We recommend installing within a conda environment, using the `environment.yaml` provided with the sources.:
+We recommend installing with `uv`:
 
 ```bash
-conda env create -f environment.yml
-conda activate pydeseq2
+uv venv
+source .venv/bin/activate
+uv sync --extra dev --extra doc
+uv pip freeze > requirements.txt # Required for Binder to work
 ```
 
-Now go to the doc folder, and install the extraneeded dependencies.
+You can now go to the doc folder and trigger the build using `make` command line.
 
 ```bash
 cd docs
-pip install -r requirements.txt
-```
-
-You can now trigger the build using `make` command line.
-
-```bash
 make clean html
-```
+```