Use astral-sh/setup-uv in "pytest" GHA workflow

- Discard commented workflow contents for pandas 2.0.0 pre-release.
- Reduce scope of exclusion for ts-graphviz/setup-graphviz#630
  workaround.
- Use Python location from setup-uv instead of $pythonLocation.
- Drop workaround for pyam-iamc exclusion of Python 3.13.
- Add --durations=20 to pytest invocation.
- Drop workaround for codecov/codecov-action#1316.

.github/workflows/pytest.yaml

@@ -30,16 +30,7 @@ jobs:
         - "3.12"
         - "3.13"  # Latest supported by ixmp
         gams-version:
-        # Version used until 2024-07; disabled
-        # - 25.1.1
-        # First version including a macOS arm64 distribution
-        - 43.4.1
-
-        # commented: force a specific version of pandas, for e.g. pre-release
-        # testing
-        # pandas-version:
-        # - ""
-        # - "==2.0.0rc0"
+        - "43.4.1"  # First version including a macOS arm64 distribution
 
         exclude:
         # Specific version combinations that are invalid / not to be used
@@ -55,29 +46,26 @@ jobs:
 
     runs-on: ${{ matrix.os }}
     name: ${{ matrix.os }}-py${{ matrix.python-version }}
-    # commented: use with "pandas-version" in the matrix, above
-    # name: ${{ matrix.os }}-py${{ matrix.python-version }}-pandas${{ matrix.pandas-version }}
 
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: ${{ env.depth }}
         fetch-tags: true
 
-    - uses: actions/setup-python@v5
+    - name: Set up uv, Python
+      uses: astral-sh/setup-uv@v5
       with:
+        cache-dependency-glob: "**/pyproject.toml"
         python-version: ${{ matrix.python-version }}
-        cache: pip
-        cache-dependency-path: "**/pyproject.toml"
 
     - uses: ts-graphviz/setup-graphviz@v2
-      # TEMPORARY Work around ts-graphviz/setup-graphviz#630
-      if: ${{ ! startswith(matrix.os, 'macos-') }}
+      # Work around ts-graphviz/setup-graphviz#630
+      if: matrix.os != 'macos-13'
 
     - uses: r-lib/actions/setup-r@v2
       id: setup-r
-      with:
-        r-version: "4.4.1"
+      with: { r-version: "4.4.1" }
 
     - name: Cache GAMS installer and R packages
       uses: actions/cache@v4
@@ -95,21 +83,13 @@ jobs:
         license: ${{ secrets.GAMS_LICENSE }}
 
     - name: Set RETICULATE_PYTHON
-      # Use the environment variable set by the setup-python action, above.
-      run: echo "RETICULATE_PYTHON=$pythonLocation" >> $GITHUB_ENV
+      # Retrieve the Python executable set up above
+      run: echo "RETICULATE_PYTHON=$(uv python find)" >> $GITHUB_ENV
       shell: bash
 
-    - name: Install Python package and dependencies
-      # [docs] contains [tests], which contains [report,tutorial]
-      run: |
-        pip install .[docs]
-
-        # commented: use with "pandas-version" in the matrix, above
-        # pip install --upgrade pandas${{ matrix.pandas-version }}
-
-        # TEMPORARY With Python 3.13 pyam-iamc resolves to 1.3.1, which in turn
-        # limits pint < 0.17. Override. cf. iiasa/ixmp#544
-        pip install --upgrade pint
+    - name: Install the package and dependencies
+      # [docs] requires [tests] which requires [report,tutorial]
+      run: uv pip install .[docs]
 
     - name: Install R dependencies and tutorial requirements
       # Workaround for https://github.com/actions/runner-images/issues/11137
@@ -142,23 +122,20 @@ jobs:
         IRkernel::installspec()
       shell: Rscript {0}
 
-    - name: Run test suite using pytest
+    - name: Run tests
       run: |
-        pytest ixmp \
+        uv run --no-sync \
+          pytest ixmp \
           -m "not performance" \
-          --color=yes -rA --verbose \
+          --color=yes --durations=20 -rA --verbose \
           --cov-report=xml \
           --numprocesses=auto --dist=loadgroup
       shell: bash
 
     - name: Upload test coverage to Codecov.io
       uses: codecov/codecov-action@v5
-      # FIXME Limit runtime until
-      # https://github.com/codecov/codecov-action/issues/1316 is resolved
-      timeout-minutes: 1
-      continue-on-error: true
       with:
-        token: ${{ secrets.CODECOV_TOKEN }} # required
+        token: ${{ secrets.CODECOV_TOKEN}}
 
   pre-commit:
     name: Code quality
@@ -167,12 +144,11 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with: { python-version: "3.12" }
-
-    - name: Force recreation of pre-commit virtual environment for mypy
-      if: github.event_name == 'schedule'
-      run: gh cache list -L 999 | cut -f2 | grep pre-commit | xargs -I{} gh cache delete "{}" || true
-      env: { GH_TOKEN: "${{ github.token }}" }
-
-    - uses: pre-commit/action@v3.0.1
+    - uses: astral-sh/setup-uv@v5
+      with: { cache-dependency-glob: "**/pyproject.toml" }
+    - uses: actions/cache@v4
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ env.UV_PYTHON }}|${{ hashFiles('.pre-commit-config.yaml') }}
+        lookup-only: ${{ github.event_name == 'schedule' }}  # Set 'true' to recreate cache
+    - run: uvx pre-commit run --all-files --color=always --show-diff-on-failure