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CU-869anj8ub: Add initial commit of WWC conversion #153
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Merged
mart-r
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feat/medcat-scripts/CU-869anj8ub-add-medcat-scripts
Oct 29, 2025
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bdc1009
CU-869anj8ub: Add initial commit of WWC conversion
mart-r e04eb76
CU-869anj8ub: Update dependency for medcat-den. Use PyPI version
mart-r 98458c8
Merge branch 'main' into feat/medcat-scripts/CU-869anj8ub-add-medcat-…
mart-r 321a8dc
CU-869anj8ub: Update permissions for workflow (minimal)
mart-r 86173e3
CU-869anj8ub: Update dependency to medcat 2.2
mart-r c41f8d3
CU-869anj8ub: Update workflow to drop 3.9 and add 3.13
mart-r c1fc061
CU-869anj8ub: Fix most typing issues
mart-r 5f24b6e
CU-869anj8ub: Add dunder init files for test folders
mart-r 375d032
CU-869anj8ub: Add CAT-included tests for MCT analysis
mart-r d6e8e52
CU-869anj8ub: Fix CAT-included tests for MCT analysis
mart-r 0ae7c44
CU-869anj8ub: Remove accidental line
mart-r de53689
CU-869anj8ub: Fix conditionals in mct export
mart-r 61e730d
CU-869anj8ub: Simplify meta-cat eval by using built in method (kind of)
mart-r c362bee
CU-869anj8ub: Small typos in comments
mart-r d697f5e
CU-869anj8ub: Force testing against current version of MedCAT on CI
mart-r 3f145a0
CU-869anj8ub: Install based on latest state without editable flag
mart-r f328310
Merge branch 'main' into feat/medcat-scripts/CU-869anj8ub-add-medcat-…
mart-r bf5b8f2
CU-869anj8ub: Add simple README
mart-r 9a5244b
CU-869anj8ub: Add example data for MetaCAT training
mart-r 3c5ed3e
CU-869anj8ub: Add meta-annotation training
mart-r d2c799f
CU-869anj8ub: Fix issue with category mapping
mart-r de82ef5
CU-869anj8ub: Simplfiy alternative category names somewhat
mart-r 86c6571
CU-869anj8ub: Fix trainer export passing to MetaCAT train method
mart-r 6239602
CU-869anj8ub: Remove 3rd class from example
mart-r 5b8172a
CU-869anj8ub: Fix category name issue
mart-r f61a0b3
CU-869anj8ub: Fix example for meta-cat on its own
mart-r 147b8b1
CU-869anj8ub: Fix save dir path for meta cat
mart-r 72ec0a8
CU-869anj8ub: Avoid running less supported MetaCAT-only workflow
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| name: medcat-scripts - Test | ||
|
|
||
| on: | ||
| push: | ||
| branches: [ main ] | ||
| pull_request: | ||
| paths: | ||
| - 'medcat-scripts/**' | ||
| - '.github/workflows/medcat-scripts**' | ||
|
|
||
| defaults: | ||
| run: | ||
| working-directory: ./medcat-scripts | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: [ '3.9', '3.10', '3.11', '3.12' ] | ||
| max-parallel: 4 | ||
| steps: | ||
| - uses: actions/checkout@v5 | ||
| - name: Install uv for Python ${{ matrix.python-version }} | ||
| uses: astral-sh/setup-uv@v6 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| enable-cache: true | ||
| - name: Install the project | ||
| run: | | ||
| uv venv .venv | ||
| source .venv/bin/activate | ||
| uv run python -m ensurepip | ||
| uv pip install -r requirements.txt | ||
| uv pip install -r requirements-dev.txt | ||
| - name: Check types | ||
| run: | | ||
| # NOTE: Only testing against .py files in this folder | ||
| uv run python -m mypy `git ls-tree --full-tree --name-only -r HEAD | grep ".py$" | grep "^medcat-scripts" | grep -v "tests/" | sed 's|^medcat-scripts/||'` --explicit-package-bases --follow-imports=normal | ||
|
|
||
| - name: Setup for notebook tests | ||
| run: | | ||
| # NOTE: this will make sure there's something in the den to work with below | ||
| uv run python tests/setup_for_tests.py | ||
|
|
||
| - name: Install IPython kernel | ||
| run: | | ||
| uv run python -m ipykernel install --name smoketests --user | ||
|
|
||
| - name: Run tests | ||
| run: | | ||
| uv run pytest tests | ||
|
|
||
| - name: Test notebooks | ||
| run: | | ||
| uv run pytest --collect-only --nbmake **/*.ipynb | ||
| uv run pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 **/*.ipynb | ||
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