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Update test workflows to use uv for package management #34

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Dialpuri wants to merge 5 commits into from
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Update test workflows to use uv for package management #34

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e126b47
Update test workflows to use `uv` for package management
Dialpuri Mar 24, 2026
3852bf6
Update test workflows to replace `setup-python` with `uv` for Python …
Dialpuri Mar 24, 2026
d408849
Clean up workflow: fix formatting and adjust step spacing in `test-py…
Dialpuri Mar 24, 2026
69b0cb5
Set `UV_SYSTEM_PYTHON` environment variable for all test workflows
Dialpuri Mar 24, 2026
f3b6677
Update `test-python.yml` to add `--break-system-packages` flag for pi…
Dialpuri Mar 24, 2026
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62 changes: 39 additions & 23 deletions .github/workflows/test-python.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ on:

jobs:
run_unix_tests:
env:
UV_SYSTEM_PYTHON: 1

name: Run Python tests on Ubuntu
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.9'

- name: Install Clang
run: |
Expand All @@ -41,30 +41,38 @@ jobs:
./get_sources
working-directory: ./package

- name: Install uv
uses: astral-sh/setup-uv@v7
with:
python-version: '3.9'

- name: Set up Python
run: uv python install

- name: Install NucleoFind
run: pip install .
run: uv pip install . --break-system-packages
working-directory: ./package

- name: Install pytest
run: pip install pytest
run: uv pip install pytest --break-system-packages

- name: Install NucleoFind models
run: |
nucleofind-install -m core
nucleofind-install -m nano

- name: Run tests
run : pytest tests
run: uv run pytest tests
working-directory: ./package

run_windows_tests:
name: Run Python tests on Windows
runs-on: windows-latest
env:
UV_SYSTEM_PYTHON: 1

steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: '3.9'

- uses: TheMrMilchmann/setup-msvc-dev@v3
with:
Expand All @@ -76,31 +84,39 @@ jobs:
sh get_sources
working-directory: ./package

- name: Install uv
uses: astral-sh/setup-uv@v7
with:
python-version: '3.9'

- name: Set up Python
run: uv python install

- name: Install NucleoFind
run: pip install .
run: uv pip install . --break-system-packages
working-directory: ./package

- name: Install pytest
run: pip install pytest
run: uv pip install pytest

- name: Install NucleoFind models
run: |
run: |
nucleofind-install -m nano
nucleofind-install -m core

- name: Run tests
run : pytest tests
run: uv run pytest tests --break-system-packages
working-directory: ./package


debug:
needs: [run_unix_tests, run_windows_tests]
runs-on: ubuntu-latest
if: ${{ failure() }}
steps:
- uses: actions/checkout@v3
- name: Notify chat
uses: teknatha136/actions-google-chat-text-message@main
with:
google-chat-webhook: ${{ secrets.WEBHOOK_URL }}
text-message: ${{ github.actor }} attempted to merge a change into NucleoFind, but this PR failed testing. Link ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} \n
needs: [ run_unix_tests, run_windows_tests ]
runs-on: ubuntu-latest
if: ${{ failure() }}
steps:
- uses: actions/checkout@v3
- name: Notify chat
uses: teknatha136/actions-google-chat-text-message@main
with:
google-chat-webhook: ${{ secrets.WEBHOOK_URL }}
text-message: ${{ github.actor }} attempted to merge a change into NucleoFind, but this PR failed testing. Link ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} \n
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