Add type annotations to code base #1244
padix-keytest_and_deploy.yml
on: pull_request
Build CCD and wheel for reusing it in several CI jobs
3m 57s
Check code style
26s
Generate wheels matrix
13s
Build source distribution
27s
Test interfaces to databases and applications
1m 3s
Test interface to Muscle 5
5m 22s
Build documentation
4m 37s
Run benchmarks
16m 20s
Upload CCD to GitHub Releases
8s
Matrix: Build & Test
Upload documentation to GitHub Releases and documentation website
0s
Upload package to GitHub Releases & PyPI
0s
Annotations
29 errors, 21 warnings, and 3 notices
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Check code style
Process completed with exit code 1.
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Test interfaces to databases and applications
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Build & Test (cp313-macosx_arm64, macos-latest)
Process completed with exit code 1.
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Build & Test (cp313-macosx_arm64, macos-latest)
cibuildwheel: Command ['/bin/sh', '-c', 'pytest /Users/runner/work/biotite/biotite --durations=50 --ignore=/Users/runner/work/biotite/biotite//tests//sequence//align//test_statistics.py --ignore=/Users/runner/work/biotite/biotite//tests//application --ignore=/Users/runner/work/biotite/biotite//tests//interface --ignore=/Users/runner/work/biotite/biotite//tests//database --ignore=/Users/runner/work/biotite/biotite//tests//test_doctest.py --ignore=/Users/runner/work/biotite/biotite//tests//test_modname.py\n'] failed with code 2.
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Build & Test (cp314-win_amd64, windows-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp314-win_amd64, windows-latest)
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Build & Test (cp312-win_amd64, windows-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp312-win_amd64, windows-latest)
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Build & Test (cp313-win_amd64, windows-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp313-win_amd64, windows-latest)
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Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
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Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
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Build & Test (cp312-manylinux_aarch64, ubuntu-24.04-arm)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp312-manylinux_aarch64, ubuntu-24.04-arm)
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Build & Test (cp314-manylinux_aarch64, ubuntu-24.04-arm)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp314-manylinux_aarch64, ubuntu-24.04-arm)
The operation was canceled.
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Build & Test (cp314-manylinux_x86_64, ubuntu-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp314-manylinux_x86_64, ubuntu-latest)
The operation was canceled.
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Build & Test (cp313-manylinux_aarch64, ubuntu-24.04-arm)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp313-manylinux_aarch64, ubuntu-24.04-arm)
The operation was canceled.
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Build & Test (cp312-macosx_arm64, macos-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp312-macosx_arm64, macos-latest)
The operation was canceled.
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Build & Test (cp314-macosx_arm64, macos-latest)
The strategy configuration was canceled because "test-and-build.cp313-macosx_arm64_macos-" failed
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Build & Test (cp314-macosx_arm64, macos-latest)
The operation was canceled.
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Test interface to Muscle 5
Process completed with exit code 2.
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Run benchmarks
Process completed with exit code 1.
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Run benchmarks
Error: failed to execute the benchmark process, exit code: 1
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Generate wheels matrix
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Check code style
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build CCD and wheel for reusing it in several CI jobs
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/setup-python@v5, actions/upload-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Upload CCD to GitHub Releases
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build source distribution
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Test interfaces to databases and applications
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp313-macosx_arm64, macos-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp314-win_amd64, windows-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp312-win_amd64, windows-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp313-win_amd64, windows-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp312-manylinux_aarch64, ubuntu-24.04-arm)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp314-manylinux_aarch64, ubuntu-24.04-arm)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp314-manylinux_x86_64, ubuntu-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp313-manylinux_aarch64, ubuntu-24.04-arm)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, docker/setup-qemu-action@v3. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp312-macosx_arm64, macos-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp314-macosx_arm64, macos-latest)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build documentation
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache/restore@v4, actions/checkout@v4, actions/download-artifact@v4, actions/upload-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Test interface to Muscle 5
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Run benchmarks
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, actions/download-artifact@v4, actions/setup-python@v5. Actions will be forced to run with Node.js 24 by default starting June 16th, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Build & Test (cp314-win_amd64, windows-latest)
NOTICE: windows-latest requests are being redirected to windows-2025-vs2026 by June 15, 2026
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Build & Test (cp312-win_amd64, windows-latest)
NOTICE: windows-latest requests are being redirected to windows-2025-vs2026 by June 15, 2026
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Build & Test (cp313-win_amd64, windows-latest)
NOTICE: windows-latest requests are being redirected to windows-2025-vs2026 by June 15, 2026
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37.9 MB |
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