Fix the publish action

.github/workflows/publish.yml

@@ -1,7 +1,4 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: PyPI
+name: Publish to PyPI
 
 on:
   release:
@@ -10,21 +7,24 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
-
+    environment: pypi
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
+    - name: Checkout project
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine build
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        python-version-file: pyproject.toml
+
+    - name: Build
       run: |
-        python -m build --sdist --wheel .
-        twine upload dist/*
+        uv build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -1,6 +1,28 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.3.0 # Replace by any tag/version: https://github.com/psf/black/tags
-    hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.6+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: detect-private-key
+  - id: pretty-format-json
+    args: [--autofix]
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.15.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.12.7
+  hooks:
+    # Run the linter.
+  - id: ruff
+    types_or: [python, pyi, jupyter]
+    args: [--fix, --show-fixes]
+    # Run the formatter.
+  - id: ruff-format
+    types_or: [python, pyi, jupyter]

pyproject.toml

@@ -2,28 +2,71 @@
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "gopher-enrich"
+dynamic = ["version"]
+authors = [
+    {name = "William E Fondrie", email = "wfondrie@talus.bio"},
+]
+description = "Gene ontology enrichment analysis using protein expression."
+readme = "README.md"
+license = {text = "Apache 2.0"}
+requires-python = ">=3.12"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "numpy>=2.0",
+    "pandas",
+    "scipy>=1.7.1",
+    "statsmodels",
+    "requests",
+    "numba",
+    "seaborn",
+    "biopython",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/TalusBio/gopher"
+"Documentation" = "https://TalusBio.github.io/gopher"
+"Bug Tracker" = "https://github.com/TalusBio/gopher/issues"
+"Discussion Board" = "https://github.com/TalusBio/gopher/discussions"
+
+[project.optional-dependencies]
+docs = [
+    "numpydoc>=1.0.0",
+    "sphinx-argparse>=0.2.5",
+    "pydata-sphinx-theme>=0.4.3",
+    "nbsphinx>=0.7.1",
+    "ipykernel>=5.3.0",
+    "recommonmark>=0.5.0",
+]
+dev = [
+    "pre-commit>=2.7.1",
+    "ruff",
+    "pytest"
+]
+
+[project.scripts]
+gopher = "gopher.gopher:main"
+
 [tool.setuptools_scm]
 
-[tool.black]
+[tool.ruff]
 line-length = 79
-target-version = ['py37']
-include = '\.pyi?$'
-exclude = '''
-
-(
-  /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
-)
-'''
+target-version = "py312"
+
+[tool.ruff.lint]
+# D213 Multi-line docstring summary should start at the second lin
+# D203 1 blank line required before class docstring
+# D100 Missing docstring in public module
+# D401 First line of docstring should be in imperative mood
+ignore = ["D213", "D203", "D100", "D401"]
+select = ["E", "F", "W", "C", "I", "D", "UP", "N", "T20"]
+
+[tool.ruff.lint.per-file-ignores]
+"*tests/*.py" = ["ANN", "N806", "C408"]
+"__init__.py" = ["F401", "D104"]