try to move to uv+hatch

Author: selmanozleyen

.github/workflows/test.yml

@@ -34,19 +34,27 @@ jobs:
       UV_PRERELEASE: ${{ matrix.pre-release || 'disallow' }}
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
       - name: Set up Python ${{ matrix.python }}
-        uses: astral-sh/setup-uv@v6
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
           enable-cache: true
 
+      - name: Install hatch
+        run: uv tool install hatch
+
       - name: Install dependencies
         run: |
           ./.scripts/ci/install_dependencies.sh
 
-      - name: Install pip dependencies
-        run: uv tool install tox --with=tox-uv --with=tox-gh-actions
 
       - name: Restore data cache
         id: data-cache
@@ -59,15 +67,7 @@ jobs:
       - name: Download datasets
         if: steps.data-cache.outputs.cache-hit != 'true'
         run: |
-          tox -e download-data
-
-      # caching .tox is not encouraged, but since we're private and this shaves off ~1min from the step
-      # if any problems occur and/or once the package is public, this can be removed
-      - name: Restore tox cache
-        uses: actions/cache@v4
-        with:
-          path: .tox
-          key: tox-${{ runner.os }}-${{ matrix.python }}-${{ hashFiles('**/requirements.txt', '**/tox.ini') }}
+          hatch run data:download
 
       - name: Test
         timeout-minutes: 60
@@ -77,10 +77,7 @@ jobs:
           DISPLAY: :42
           PYTEST_ADDOPTS: "-n auto"
         run: |
-          tox -vv
-      # check if this can be deprecated
-      #- name: List figures for potential debugging
-      #      ls -alh /home/runner/work/squidpy/squidpy/tests/figures
+          hatch test --python ${{ matrix.python }} --randomize --parallel --cover --all
 
       - name: Archive figures generated during testing
         if: always()

tox.ini _tox.initox.ini renamed to _tox.ini

@@ -0,0 +1,51 @@
+# Default environment - what gets installed when you do "hatch shell"
+[envs.default]
+installer = "uv"
+features = ["dev"]
+
+# Test environment - for running tests
+[envs.test]
+features = ["test"]
+extra-dependencies = [
+    "pytest",
+    "pytest-xdist", 
+    "pytest-cov",
+    "pytest-mock",
+    "pytest-timeout",
+]
+
+# What you can run in the test environment
+[envs.test.scripts]
+test = "python -m pytest --color=yes --cov --cov-append --cov-report=xml --cov-config=pyproject.toml --ignore docs/ {args:-vv}"
+
+# Coverage environment - for coverage reports
+[envs.coverage]
+extra-dependencies = [
+    "coverage[toml]",
+    "diff_cover",
+]
+
+# What you can run in the coverage environment
+[envs.coverage.scripts]
+clean = "coverage erase"
+report = "coverage report --omit='tox/*'"
+xml = "coverage xml --omit='tox/*' -o coverage.xml"
+diff = "diff-cover --compare-branch origin/main coverage.xml"
+
+# Docs environment - for building documentation
+[envs.docs]
+features = ["docs"]
+extra-dependencies = [
+    "setuptools",
+]
+
+# What you can run in the docs environment
+[envs.docs.scripts]
+build = "make -C docs html {args}"
+clean = "make -C docs clean"
+check = "make -C docs linkcheck {args}"
+
+# Data environment - for downloading data
+[envs.data]
+[envs.data.scripts]
+download = "python ./.scripts/ci/download_data.py {args}"

hatch.toml

@@ -77,7 +77,7 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "pre-commit>=3.0.0",
-    "tox>=4.0.0",
+    "hatch>=1.9.0",
 ]
 test = [
     "scanpy[leiden]",
@@ -101,7 +101,6 @@ docs = [
     "myst-nb>=0.17.1",
     "sphinx_copybutton>=0.5.0",
 ]
-
 [project.urls]
 Homepage = "https://github.com/scverse/squidpy"
 "Bug Tracker" = "https://github.com/scverse/squidpy/issues"
@@ -120,6 +119,9 @@ source = "vcs"
 [tool.hatch.metadata]
 allow-direct-references = true
 
+[tool.hatch.build.targets.wheel]
+packages = ["src/squidpy"]
+
 [tool.hatch.metadata.hooks.fancy-pypi-readme]
 content-type = "text/x-rst"
 [[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
@@ -237,5 +239,44 @@ ban-relative-imports = "all"
 
 [tool.pytest.ini_options]
 filterwarnings = [
-    "error::numba.NumbaPerformanceWarning"
+    "error::numba.NumbaPerformanceWarning",
+    "ignore::UserWarning",
+    "ignore::anndata.OldFormatWarning",
+    "ignore:.*pkg_resources:DeprecationWarning",
+]
+python_files = "test_*.py"
+testpaths = ["tests/"]
+xfail_strict = true
+addopts = [
+    "--ignore=tests/plotting/test_interactive.py",
+]
+
+
+[tool.coverage.run]
+branch = true
+parallel = true
+source = ["squidpy"]
+omit = [
+    "*/__init__.py",
+    "*/_version.py",
+    "squidpy/pl/_interactive/*",
+]
+
+[tool.coverage.paths]
+source = [
+    "squidpy",
+    "*/site-packages/squidpy",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "\\#.*pragma:\\s*no.?cover",
+    "^if __name__ == .__main__.:$",
+    "^\\s*raise AssertionError\\b",
+    "^\\s*raise NotImplementedError\\b",
+    "^\\s*return NotImplemented\\b",
 ]
+show_missing = true
+precision = 2
+skip_empty = true
+sort = "Miss"