Adding llm as an extra, adding llm implementation for annotation #1683
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# Built from: | |
# https://docs.github.com/en/actions/guides/building-and-testing-python | |
# https://github.com/snok/install-poetry#workflows-and-tips | |
name: Build and test | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
jobs: | |
lint: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: [ '3.9', '3.10' ] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/[email protected] | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
pip install tox | |
- name: Check code quality with flake8 | |
run: tox -e flake8 | |
test: | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-latest, windows-latest ] | |
python-version: [ "3.9", "3.10" ] | |
exclude: | |
- os: windows-latest | |
python-version: "3.9" | |
runs-on: ${{ matrix.os }} | |
steps: | |
#---------------------------------------------- | |
# check-out repo and set-up python | |
#---------------------------------------------- | |
- name: Check out repository | |
uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
#---------------------------------------------- | |
# install & configure poetry | |
#---------------------------------------------- | |
- name: Install Poetry | |
run: | | |
pip install --upgrade pip | |
pip install poetry | |
# uses: snok/[email protected] | |
# with: | |
# virtualenvs-create: true | |
# virtualenvs-in-project: true | |
#---------------------------------------------- | |
# load cached venv if cache exists | |
#---------------------------------------------- | |
# - name: Load cached venv | |
# id: cached-poetry-dependencies | |
# uses: actions/cache@v3 | |
# with: | |
# path: .venv | |
# key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} | |
#---------------------------------------------- | |
# install dependencies if cache does not exist | |
#---------------------------------------------- | |
- name: Install dependencies | |
# if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' | |
run: poetry install --no-interaction --no-root | |
#---------------------------------------------- | |
# install your root project, if required | |
#---------------------------------------------- | |
- name: Install library | |
run: poetry install --no-interaction --extras "gilda" | |
- name: Get Gilda resources | |
run: | | |
poetry run python -c "import nltk; nltk.download('punkt'); nltk.download('stopwords')" | |
poetry run python -m adeft.download | |
#---------------------------------------------- | |
# run test suite + coverage report | |
#---------------------------------------------- | |
- name: Generate coverage results | |
run: | | |
poetry run pip install -U pytest | |
poetry run coverage run -p -m pytest tests/ | |
poetry run coverage combine | |
poetry run coverage xml | |
poetry run coverage report -m | |
shell: bash | |
env: | |
BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }} | |
#---------------------------------------------- | |
# upload coverage results | |
#---------------------------------------------- | |
- name: Upload coverage report | |
uses: codecov/[email protected] | |
with: | |
name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }} | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
fail_ci_if_error: false |