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build: bump the pip group across 3 directories with 7 updates #558

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build: bump the pip group across 3 directories with 7 updates

build: bump the pip group across 3 directories with 7 updates #558

Workflow file for this run

.github/workflows/medcat-v2-tutorials_main.yml at e0e57e4
name: medcat-v2-tutorials - Test
on:
push:
branches: [ main ]
pull_request:
paths:
- 'medcat-v2/**'
- 'medcat-v2-tutorials/**'
- '.github/workflows/medcat-v2**'
- '.github/workflows/medcat-v2-tutorials**'
defaults:
run:
working-directory: ./medcat-v2-tutorials
jobs:
basic-and-meta:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v5
- name: Setup Python
uses: actions/setup-python@v6
with:
python-version: "3.11"
cache: 'pip'
- name: Update install targets in notebooks
run: |
python .ci/patch_notebook_installs.py .
- name: Install dependencies
run: |
pip install -U pip
pip install -r requirements.txt
pip install "../medcat-v2[spacy,deid,rel-cat,meta-cat]"
- name: Install IPython kernel
run: |
python -m ipykernel install --name smoketests --user
- name: Smoke test tutorial
# NOTE: these need to be run separately so that order is guaranteed
run: |
pytest --collect-only --nbmake ./notebooks/introductory/basic/1*.ipynb
pytest --collect-only --nbmake ./notebooks/introductory/basic/2*.ipynb
pytest --collect-only --nbmake ./notebooks/introductory/basic/3*.ipynb
pytest --collect-only --nbmake ./notebooks/introductory/meta/*.ipynb
pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ./notebooks/introductory/basic/1*.ipynb
pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ./notebooks/introductory/basic/2*.ipynb
pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ./notebooks/introductory/basic/3*.ipynb
pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ./notebooks/introductory/meta/*.ipynb
pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ./notebooks/introductory/custom/*.ipynb
migrate-and-advanved:
runs-on: ubuntu-latest
strategy:
matrix:
part: [
./notebooks/introductory/migration/*.ipynb,
./notebooks/introductory/relcat/*.ipynb,
./notebooks/advanced/*.ipynb,
]
steps:
- uses: actions/checkout@v5
- name: Setup Python
uses: actions/setup-python@v6
with:
python-version: "3.11"
- name: Update install targets in notebooks
run: |
python .ci/patch_notebook_installs.py .
- name: Install dependencies
run: |
pip install -U pip
pip install -r requirements.txt
pip install "../medcat-v2[spacy,deid,rel-cat,meta-cat]"
- name: Install IPython kernel
run: |
python -m ipykernel install --name smoketests --user
- name: Smoke test tutorial
run: |
pytest --capture=no --collect-only --nbmake ${{ matrix.part }}
pytest --capture=no --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 ${{ matrix.part }}