Clean up CI & miscellaneous updates for 3.10

.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:
@@ -30,8 +24,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - if: >
-        github.repository != github.event.pull_request.head.repo.full_name &&
-        ! contains(github.event.pull_request.labels.*.name, env.label)
+        !(
+          github.event_name == "schedule"
+          || github.repository == github.event.pull_request.head.repo.full_name
+          || contains(github.event.pull_request.labels.*.name, env.label)
+        )
       run: |
         echo "Pytest workflow will not run for branch in fork without label \`${{ env.label }}\`." >>$GITHUB_STEP_SUMMARY
         exit 1
@@ -86,17 +83,17 @@ 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 +107,13 @@ 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 +122,7 @@ 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 +133,7 @@ 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 +149,22 @@ 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 +186,25 @@ 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 +221,11 @@ 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

.pre-commit-config.yaml

@@ -1,16 +1,10 @@
 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 >= 1.12.0
     - asyncssh
     - git+https://github.com/iiasa/ixmp.git@main
     - importlib_resources
@@ -20,9 +14,8 @@ repos:
     - Sphinx
     - types-PyYAML
     - types-requests
-    args: ["."]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.4
+  rev: v0.9.1
   hooks:
   - id: ruff
   - id: ruff-format

README.md

@@ -6,7 +6,7 @@
 [![Documentation build](https://readthedocs.com/projects/iiasa-energy-program-message-ix/badge/?version=stable)](https://docs.messageix.org/en/stable/)
 [![Build status](https://github.com/iiasa/message_ix/actions/workflows/pytest.yaml/badge.svg)](https://github.com/iiasa/message_ix/actions/workflows/pytest.yaml)
 [![Test coverage](https://codecov.io/gh/iiasa/message_ix/branch/main/graph/badge.svg)](https://codecov.io/gh/iiasa/message_ix)
-[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md) 
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 
 
 MESSAGEix is a versatile, dynamic, model framework for energy-engineering-economy-environment (E4) systems research.
@@ -20,11 +20,11 @@ The `message_ix` Python package—also fully usable from R—includes:
 - Application programming interfaces (APIs) and tools for model building and scientific programming,
 - Extensive documentation and a complete test suite.
 
-The framework is built on IIASA's [*ix* modeling platform (`ixmp`)](https://github.com/iiasa/ixmp), which provides data warehouse features for high-powered numerical scenario analysis.
+The framework is built on IIASA's [*ix* modeling platform (`ixmp`)](https://github.com/iiasa/ixmp), which provides data warehouse features for numerical scenario analysis.
 
 ## Documentation
 
-Complete documentation of the framework is avaiable at **https://docs.messageix.org/**.
+Complete documentation of the framework is available at **https://docs.messageix.org**.
 This includes:
 
 - **Installation** and recommended pre-requisite learning.
@@ -39,23 +39,31 @@ This includes:
 Other forms of documentation:
 
 - The online documentation is built automatically from the contents of the
-[`message_ix` GitHub repository](https://github.com/iiasa/messag_ix).
+[`message_ix` GitHub repository](https://github.com/iiasa/message_ix).
 - Documentation for the ‘latest’ or ‘stable’ release is shown by default.
 - Use the chooser to access the [‘latest’ version](https://docs.messageix.org/en/latest/), corresponding to the ``main`` branch and including the latest development code; or to access docs for a specific release, e.g. `v3.2.0`.
 - For offline use, the documentation can be built from the source code.
   See the file [`doc/README.rst`](doc/README.rst)
 
 ## Commitment to our Community
 
-- We aim to create a community that is welcoming to everyone. Please respect our [Code of Conduct](CODE_OF_CONDUCT.md) at all times when interacting with `message_ix` and the community.
+- We aim to create a community that is welcoming to everyone.
+  Please respect our [Code of Conduct](CODE_OF_CONDUCT.md) at all times when interacting with `message_ix` and the community.
 - We warmly welcome all contributions to our community. Please take a look at our [guidelines for contributing to development](https://docs.messageix.org/en/latest/contributing.html).
 - If you are looking to understand how the `message_ix` team operates and how we decide what to do with your contributions, please read our [governance guidelines](GOVERNANCE.md).
-- We highly value code security. To learn more about our security practice and advice, please visit our [security policy](.github/SECURITY.md).
-- We strive to entertain a welcoming and inclusive community. If you struggle to use `message_ix`, please check our [guidelines for getting support](SUPPORT.md).
+- We highly value code security.
+  To learn more about our security practice and advice, please visit our [security policy](.github/SECURITY.md).
+- We strive to entertain a welcoming and inclusive community.
+  If you struggle to use `message_ix`, please check our [guidelines for getting support](SUPPORT.md).
+- We also:
+  - Host an annual [MESSAGEix Community Meeting](https://iiasa.ac.at/search?search_api_fulltext=MESSAGEix+Community+Meeting).
+  - Publish, at least once per year, a community newsletter.
+    You are cordially invited to subscribe by filling [this form](https://iiasa.ac.at/signup) and ticking the box for “MESSAGEix Community”.
+
 
 ## License
 
-Copyright © 2018–2024 IIASA Energy, Climate, and Environment (ECE) Program
+Copyright © 2018–2025 IIASA Energy, Climate, and Environment (ECE) Program
 
 The MESSAGEix framework 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. You may obtain a copy of the License in [`LICENSE`](LICENSE) or at <http://www.apache.org/licenses/LICENSE-2.0>.
 

RELEASE_NOTES.rst

@@ -4,7 +4,7 @@ Next release
 GitHub community guidelines
 ---------------------------
 
-Add community guidelines for interaction on GitHub (:pull:`871`).
+Add community guidelines for interaction on GitHub (:pull:`871`, :pull:`911`).
 Please familiarize yourself with these to foster an open and welcoming community!
 
 All changes

doc/conf.py

@@ -12,7 +12,7 @@
 # -- Project information ---------------------------------------------------------------
 
 project = "MESSAGEix"
-copyright = "2018–2024, IIASA Energy, Climate, and Environment (ECE) Program"
+copyright = "2018–%Y, IIASA Energy, Climate, and Environment (ECE) Program"
 author = "MESSAGEix Developers"
 
 # The major project version, used as the replacement for |version|.