migrate to hatch + uv

.coveragerc

@@ -1,28 +1,13 @@
-# .coveragerc to control coverage.py
 [run]
-branch = True
-source = biocframe
-# omit = bad_file.py
-
-[paths]
-source =
-    src/
-    */site-packages/
+source = src
+omit = tests/*
 
 [report]
-# Regexes for lines to exclude from consideration
 exclude_lines =
-    # Have to re-enable the standard pragma
     pragma: no cover
-
-    # Don't complain about missing debug-only code:
     def __repr__
-    if self\.debug
-
-    # Don't complain if tests don't hit defensive assertion code:
+    if self.debug:
     raise AssertionError
     raise NotImplementedError
-
-    # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"

.github/workflows/pre-commit.yml

@@ -0,0 +1,16 @@
+# name: pre-commit
+
+# on:
+#   pull_request:
+#   push:
+#     branches: [main]
+
+# jobs:
+#   pre-commit:
+#     runs-on: ubuntu-latest
+#     steps:
+#     - uses: actions/checkout@v4
+#     - uses: actions/setup-python@v5
+#       with:
+#         python-version: '3.12'
+#     - uses: pre-commit/action@v3.0.1

.github/workflows/publish-pypi.yml

@@ -24,15 +24,16 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tox
+          pip install uv tox
+          uv sync
 
-      - name: Test with tox
+      - name: Test
         run: |
-          tox
+          tox -e default
 
-      - name: Build Project and Publish
+      - name: Build Project
         run: |
-          python -m tox -e clean,build
+          tox -e clean,build
 
       # This uses the trusted publisher workflow so no token is required.
       - name: Publish to PyPI

.github/workflows/run-tests.yml

@@ -46,13 +46,12 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tox coverage
+          pip install uv tox
+          uv sync --python ${{ matrix.python }}
 
       - name: Run tests
-        run: >-
-          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
-          tox
-          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
+        run: |
+          tox -e default -- --cov --cov-branch --cov-report=xml
 
       - name: Check for codecov token availability
         id: codecov-check

.gitignore

@@ -52,3 +52,59 @@ MANIFEST
 .venv*/
 .conda*/
 .python-version
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*$py.class
+# C extensions
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+# PyInstaller
+*.manifest
+*.spec
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.cache
+nosetests.xml
+*.cover
+*.py,cover
+.hypothesis/
+cover/
+# Sphinx documentation
+docs/_build/
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+# mypy, ruff, etc
+.mypy_cache/
+.ruff_cache/
+.pyre/
+# Editors
+.vscode/
+.idea/
+*.swp
+*.swo

.pre-commit-config.yaml

@@ -33,10 +33,12 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.6
+  rev: v0.16.2
   hooks:
-    - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
+    # Run the linter.
+    - id: ruff-check
+      args: [--fix, --exit-zero]
+    # Run the formatter.
     - id: ruff-format
 
 ## If like to embrace black styles even in the docs: