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

- Drop old content:
  - Commented GAMS_VERSION.
  - Workaround for pyam-iamc exclusion of Python 3.13.
- Narrow workaround for ts-graphviz/setup-graphviz#630.
- Adjust 'tutorials' jobs parallel to #909, #910.
- Simplify installation of reticulate.
  - Drop use of "remotes"; call install.packages() directly.

.github/workflows/pytest.yaml

@@ -14,14 +14,8 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  # Version used until 2024-11-20; disabled
-  # GAMS_VERSION: 29.1.0
-  # First version including a macOS arm64 distribution
-  GAMS_VERSION: 43.4.1
-
-  # See description in lint.yml
-  depth: 100
-
+  GAMS_VERSION: 43.4.1   # First version including a macOS arm64 distribution
+  depth: 100  # Must be large enough to include the most recent release
   label: "safe to test"
 
 jobs:
@@ -86,17 +80,17 @@ jobs:
     - name: Fetch tags (for setuptools-scm)
       run: git fetch --tags --depth=${{ env.depth }}
 
-    - 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'
 
-    - name: Cache GAMS installer and R packages
+    - name: Cache GAMS installer
       uses: actions/cache@v4
       with:
         path: |
@@ -110,17 +104,13 @@ jobs:
         version: ${{ env.GAMS_VERSION }}
         license: ${{ secrets.GAMS_LICENSE }}
 
-    - name: Install Python package and dependencies
+    - name: Install the package and dependencies
       # By default, the below installs ixmp from the main branch. To run against
       # other code, e.g. other branches for open PRs), temporarily edit as
       # appropriate. DO NOT merge such changes to `main`.
       run: |
-        pip install --upgrade "ixmp @ git+https://github.com/iiasa/ixmp.git@main"
-        pip install .[tests]
-
-        # TEMPORARY With Python 3.13 pyam-iamc resolves to 1.3.1, which in turn
-        # limits pint < 0.17. Override.
-        pip install --upgrade pint
+        uv pip install --upgrade "ixmp @ git+https://github.com/iiasa/ixmp.git@main"
+        uv pip install .[tests]
 
     - name: Run test suite using pytest
       env:
@@ -129,7 +119,7 @@ jobs:
       run: |
         pytest message_ix \
           -m "not nightly and not tutorial" \
-          -rA --verbose --color=yes --durations=20 \
+          --color=yes --durations=20 -rA --verbose \
           --cov-report=xml \
           --numprocesses=auto --dist=loadgroup
       shell: bash
@@ -140,9 +130,7 @@ jobs:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   tutorials:
-    if: >
-      github.event_name != 'workflow_run' ||
-      github.event.workflow_run.conclusion == 'success'
+    needs: [ check ]
 
     strategy:
       matrix:
@@ -158,33 +146,22 @@ jobs:
 
     steps:
     - name: Check out message_ix
-      if: github.event_name != 'workflow_run'
       uses: actions/checkout@v4
       with:
         fetch-depth: ${{ env.depth }}
+        ref: ${{ github.event.pull_request.head.sha }}
 
-    - name: Check out message_ix (workflow_run)
-      if: github.event_name == 'workflow_run'
-      uses: actions/checkout@v4
-      with:
-        repository: ${{ github.event.workflow_run.repository.fullname }}
-        ref: ${{ github.event.workflow_run.head_branch }}
-
-    - uses: actions/setup-python@v5
+    - name: Set up uv, Python
+      uses: astral-sh/setup-uv@v5
       with:
+        cache-dependency-glob: "**/pyproject.toml"
         python-version: "3.13"
-        cache: pip
-        cache-dependency-path: "**/pyproject.toml"
 
     - 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
 
-    - uses: ts-graphviz/setup-graphviz@v2
-      # TEMPORARY Work around ts-graphviz/setup-graphviz#630
-      if: ${{ ! startswith(matrix.os, 'macos-') }}
-
     - uses: r-lib/actions/setup-r@v2
       id: setup-r
       with:
@@ -206,34 +183,25 @@ jobs:
         version: ${{ env.GAMS_VERSION }}
         license: ${{ secrets.GAMS_LICENSE }}
 
-    - name: Install Python package and dependencies
+    - name: Install the package and dependencies
       # By default, the below installs ixmp from the main branch. To run against
       # other code, e.g. other branches for open PRs), temporarily edit as
       # appropriate. DO NOT merge such changes to `main`.
       run: |
-        pip install --upgrade "ixmp @ git+https://github.com/iiasa/ixmp.git@main"
-        pip install .[tests]
-
-        # TEMPORARY With Python 3.13 pyam-iamc resolves to 1.3.1, which in turn
-        # limits pint < 0.17. Override.
-        pip install --upgrade pint
+        uv pip install --upgrade "ixmp @ git+https://github.com/iiasa/ixmp.git@main"
+        uv pip install .[tests]
 
     - name: Install R dependencies and tutorial requirements
       run: |
-        install.packages("remotes")
-        remotes::install_cran(
-          c("dplyr", "IRkernel", "reticulate"),
-          dependencies = TRUE,
-          # force = TRUE,
-        )
+        install.packages(c("dplyr", "IRkernel", "reticulate"))
         IRkernel::installspec()
       shell: Rscript {0}
 
     - name: Run test suite using pytest
       run: |
         pytest message_ix \
           -m "tutorial" \
-          -rA --verbose --color=yes --durations=20 \
+          --color=yes --durations=20 -rA --verbose \
           --cov-report=xml \
           --numprocesses=auto --dist=loadgroup
       shell: bash
@@ -250,13 +218,11 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:  # Same as the "Latest version supported by message_ix", above
-        python-version: "3.13"
-
-    - name: Force recreation of pre-commit virtual environment for mypy
-      if: github.event_name == 'schedule'  # Comment this line to run on a PR
-      run: gh cache list -L 999 | cut -f2 | grep pre-commit | xargs -I{} gh cache delete "{}" || true
-      env: { GH_TOKEN: "${{ github.token }}" }
-
-    - uses: pre-commit/[email protected]
+    - uses: astral-sh/setup-uv@v5
+      with: { cache-dependency-glob: "**/pyproject.toml" }
+    - uses: actions/cache@v4
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ 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