Merge pull request #555 from iiasa/enh/code-quality

Update code quality configuration

.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 +46,29 @@ 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: TEMPORARY Work around actions/checkout#2041
+      run: git fetch --tags
+
+    - 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
@@ -95,45 +86,21 @@ 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
-      if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
-      run: |
-        install.packages(c("remotes", "Rcpp"))
-        remotes::install_cran(
-          c("IRkernel", "reticulate"),
-          dependencies = TRUE,
-          # force = TRUE,
-        )
-
-        reticulate::py_config()
-      shell: Rscript {0}
+    - name: "Install libpng-dev"  # for R 'png', required by reticulate
+      if: startsWith(matrix.os, 'ubuntu-')
+      run: sudo apt install libpng-dev
 
     - name: Install R dependencies and tutorial requirements
-      if: ${{ ! (matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12') }}
       run: |
-        install.packages(c("remotes", "Rcpp"))
-        remotes::install_cran(
-          c("IRkernel", "reticulate"),
-          dependencies = TRUE,
-          # force = TRUE,
-        )
+        install.packages(c("IRkernel", "reticulate"))
 
         # commented: for debugging
         # print(reticulate::py_config())
@@ -142,23 +109,20 @@ 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 +131,11 @@ 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: "${{ github.token }}" }
-
-    - uses: pre-commit/[email protected]
+    - uses: astral-sh/setup-uv@v5
+      with: { cache-dependency-glob: "**/pyproject.toml" }
+    - uses: actions/cache@v4
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ 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

.pre-commit-config.yaml

@@ -1,27 +1,20 @@
 repos:
-- repo: local
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.14.1
   hooks:
   - id: mypy
-    name: mypy
-    always_run: true
-    require_serial: true
     pass_filenames: false
-
-    language: python
-    entry: bash -c ". ${PRE_COMMIT_MYPY_VENV:-/dev/null}/bin/activate 2>/dev/null; mypy $0 $@"
     additional_dependencies:
-    - mypy >= 1.9.0
     - genno
     - GitPython
     - nbclient
     - pandas-stubs
     - pytest
-    - sphinx
+    - Sphinx
     - werkzeug
     - xarray
-    args: ["."]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.3.4
+  rev: v0.9.1
   hooks:
   - id: ruff
   - id: ruff-format

README.md

@@ -45,7 +45,7 @@ See [`doc/README.rst`](doc/README.rst) for further details.
 
 ## License
 
-Copyright © 2017–2024 IIASA Energy, Climate, and Environment (ECE) program
+Copyright © 2017–2025 IIASA Energy, Climate, and Environment (ECE) program
 
 `ixmp` is licensed under the Apache License, Version 2.0 (the "License"); you
 may not use the files in this repository except in compliance with the License.

doc/conf.py

@@ -10,7 +10,7 @@
 # -- Project information ---------------------------------------------------------------
 
 project = "ixmp"
-copyright = "2017–2024, IIASA Energy, Climate, and Environment (ECE) program"
+copyright = "2017–%Y, IIASA Energy, Climate, and Environment (ECE) program"
 author = "ixmp Developers"
 
 

ixmp/backend/jdbc.py

@@ -170,7 +170,7 @@ def _domain_enum(domain):
         return domain_enum.valueOf(domain.upper())
     except java.IllegalArgumentException:
         domains = ", ".join([d.name().lower() for d in domain_enum.values()])
-        raise ValueError(f"No such domain: {domain}, " f"existing domains: {domains}")
+        raise ValueError(f"No such domain: {domain}, existing domains: {domains}")
 
 
 def _unwrap(v):
@@ -886,8 +886,7 @@ def clone(
         # Raise exceptions for limitations of JDBCBackend
         if not isinstance(platform_dest._backend, self.__class__):
             raise NotImplementedError(  # pragma: no cover
-                f"Clone between {self.__class__} and"
-                f"{platform_dest._backend.__class__}"
+                f"Clone between {self.__class__} and{platform_dest._backend.__class__}"
             )
         elif platform_dest._backend is not self:
             package = s.__class__.__module__.split(".")[0]

ixmp/cli.py

@@ -91,7 +91,7 @@ def report(context, config, key):
 
     if not context:
         raise click.UsageError(
-            "give either --url, --platform or --dbprops " "before command report"
+            "give either --url, --platform or --dbprops before command report"
         )
 
     # Instantiate the Reporter with the Scenario loaded by main()
@@ -227,8 +227,7 @@ def import_group(context):
     """
     if not context or "scen" not in context:
         raise click.UsageError(
-            "give --url, or --platform, --model, and "
-            "--scenario, before command import"
+            "give --url, or --platform, --model, and --scenario, before command import"
         )
 
 
@@ -407,7 +406,7 @@ def list_scenarios(context, **kwargs):
 
     if not context:
         raise click.UsageError(
-            "give either --url, --platform or --dbprops " "before command list"
+            "give either --url, --platform or --dbprops before command list"
         )
 
     print(

ixmp/tests/backend/test_jdbc.py

@@ -373,8 +373,7 @@ def test_verbose_exception(test_mp, exception_verbose_true):
 
     exc_msg = exc_info.value.args[0]
     assert (
-        "There exists no Scenario 'foo|bar' "
-        "(version: -1)  in the database!" in exc_msg
+        "There exists no Scenario 'foo|bar' (version: -1)  in the database!" in exc_msg
     )
     assert "at.ac.iiasa.ixmp.database.DbDAO.getRunId" in exc_msg
     assert "at.ac.iiasa.ixmp.Platform.getScenario" in exc_msg
@@ -595,7 +594,7 @@ def test_reload_cycle(
         mp = ixmp.Platform(**platform_args)
 
         # Load existing Scenario
-        s0 = ixmp.Scenario(mp, model="foo", scenario=f"bar {i-1}", version=1)
+        s0 = ixmp.Scenario(mp, model="foo", scenario=f"bar {i - 1}", version=1)
 
         memory_usage(f"pass {i} -- platform instantiated")
 

ixmp/tests/core/test_scenario.py

@@ -137,7 +137,7 @@ def test_init_set(self, scen):
         # Add set on a locked scenario
         with pytest.raises(
             RuntimeError,
-            match="This Scenario cannot be edited" ", do a checkout first!",
+            match="This Scenario cannot be edited, do a checkout first!",
         ):
             scen.init_set("foo")
 
@@ -399,7 +399,7 @@ def test_excel_io(self, scen, scen_empty, tmp_path, caplog):
 
         # With init_items=False, can't be read into an empty Scenario.
         # Exception raised is the first index set, alphabetically
-        with pytest.raises(ValueError, match="no set 'i'; " "try init_items=True"):
+        with pytest.raises(ValueError, match="no set 'i'; try init_items=True"):
             scen_empty.read_excel(tmp_path)
 
         # File can be read with init_items=True
@@ -441,7 +441,7 @@ def test_excel_io(self, scen, scen_empty, tmp_path, caplog):
 
         # Fails with add_units=False
         with pytest.raises(
-            ValueError, match="The unit 'pounds' does not exist" " in the database!"
+            ValueError, match="The unit 'pounds' does not exist in the database!"
         ):
             s.read_excel(tmp_path, init_items=True)
 
@@ -623,7 +623,7 @@ def test_set(scen_empty) -> None:
         scen.add_set("i", ["i9", "extra"], ["i9 comment"])
     # Missing element in the index set
     with pytest.raises(
-        ValueError, match="The index set 'i' does not have an " "element 'bar'!"
+        ValueError, match="The index set 'i' does not have an element 'bar'!"
     ):
         scen.add_set("foo", "bar")
 

pyproject.toml

@@ -82,8 +82,9 @@ exclude_also = [
 omit = ["ixmp/util/sphinx_linkcode_github.py"]
 
 [tool.mypy]
-exclude = [
-  "build/",
+files = [
+  "doc",
+  "ixmp",
 ]
 
 [[tool.mypy.overrides]]