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Align minimum supported dependencies with SPEC 0 #454

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2 changes: 0 additions & 2 deletions .github/workflows/pr_validation.yml
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Expand Up @@ -18,8 +18,6 @@ jobs:
strategy:
matrix:
include:
- os: ubuntu-latest
python: "3.11"
- os: ubuntu-latest
python: "3.12"
- os: ubuntu-latest
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -72,7 +72,7 @@ If you're interested in contributing or want access to the development version,
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
3.11 to 3.13 and the latest versions of the following packages:
3.12 to 3.13 and the latest versions of the following packages:

```
- anndata
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17 changes: 9 additions & 8 deletions docs/source/usage/requirements.rst
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@@ -1,17 +1,18 @@
Requirements
------------

The list of package version requirements is available in ``setup.py``, and will be automatically installed along PyDESeq2 when using PyPI.
For reference, the code was tested with python 3.11 and the following package versions::
The list of package version requirements is available in ``pyproject.toml``, and will be automatically installed along PyDESeq2 when using PyPI.
For reference, the code was tested with python 3.12 and the following package versions::

- anndata>=0.11.0
- formulaic>=1.0.2
- numpy>=2.0.0
- pandas>=2.2.0
- scikit-learn>=1.4.0
- scipy>=1.12.0
- numpy>=2.2.0
- pandas>=2.3.0
- scikit-learn>=1.6.0
- scipy>=1.15.0
- formulaic-contrasts>=0.2.0
- matplotlib>=3.9.0
- matplotlib>=3.10.0

Note that starting from pydeseq2 0.5.3, python 3.10 is no longer supported.
Minimum supported versions of Python and the core scientific Python packages follow `SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_.
Python versions are dropped 3 years after their initial release, and core package versions 2 years after theirs.
Please don't hesitate to open an issue in case you encounter any problems due to possible deprecations.
13 changes: 6 additions & 7 deletions pyproject.toml
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Expand Up @@ -17,22 +17,21 @@ authors = [
{ name = "Vincent Cabelli" },
{ name = "Mathieu Andreux" },
]
requires-python = ">=3.11"
requires-python = ">=3.12"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
]
dependencies = [
"anndata>=0.11.0",
"formulaic>=1.0.2",
"numpy>=2.0.0",
"pandas>=2.2.0",
"scikit-learn>=1.4.0",
"scipy>=1.12.0",
"numpy>=2.2.0",
"pandas>=2.3.0",
"scikit-learn>=1.6.0",
"scipy>=1.15.0",
"formulaic-contrasts>=0.2.0",
"matplotlib>=3.9.0",
"matplotlib>=3.10.0",
]
optional-dependencies.dev = [
"pytest>=8.4.0",
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