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CU-86964zm4d fix preprocessing #1317

CU-86964zm4d fix preprocessing

CU-86964zm4d fix preprocessing #1317

Workflow file for this run

name: build
on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
jobs:
build:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [ '3.8', '3.9', '3.10', '3.11' ]
max-parallel: 4
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements-dev.txt
- name: Check types
run: |
python -m mypy --follow-imports=normal medcat
- name: Lint
run: |
flake8 medcat
- name: Test
run: |
all_files=$(git ls-files | grep '^tests/.*\.py$' | grep -v '/__init__\.py$' | sed 's/\.py$//' | sed 's/\//./g')
num_files=$(echo "$all_files" | wc -l)
midpoint=$((num_files / 2))
first_half_nl=$(echo "$all_files" | head -n $midpoint)
second_half_nl=$(echo "$all_files" | tail -n +$(($midpoint + 1)))
timeout 25m python -m unittest ${first_half_nl[@]}
timeout 25m python -m unittest ${second_half_nl[@]}
- name: Regression
run: source tests/resources/regression/run_regression.sh
- name: Get the latest release version
id: get_latest_release
uses: actions/github-script@v6
with:
script: |
const latestRelease = await github.rest.repos.getLatestRelease({
owner: context.repo.owner,
repo: context.repo.repo
});
core.setOutput('latest_version', latestRelease.data.tag_name);
- name: Make sure there's no deprecated methods that should be removed.
# only run this for master -> production PR. I.e just before doing a release.
if: github.event.pull_request.base.ref == 'main' && github.event.pull_request.head.ref == 'production'
env:
VERSION: ${{ steps.get_latest_release.outputs.latest_version }}
run: |
python tests/check_deprecations.py "$VERSION" --next-version --remove-prefix
publish-to-test-pypi:
if: |
github.repository == 'CogStack/MedCAT' &&
github.ref == 'refs/heads/master' &&
github.event_name == 'push' &&
startsWith(github.ref, 'refs/tags') != true
runs-on: ubuntu-20.04
timeout-minutes: 45
concurrency: publish-to-test-pypi
needs: [build]
steps:
- name: Checkout master
uses: actions/checkout@v4
with:
ref: 'master'
fetch-depth: 0
- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.9
- name: Install pypa/build
run: >-
python -m
pip install
build
--user
- name: Configure the version
run: >-
sed --in-place
"s/node-and-date/no-local-version/g"
setup.py
- name: Build a binary wheel and a source tarball
run: >-
python -m
build
--sdist
--wheel
--outdir dist/
.
- name: Publish dev distribution to Test PyPI
uses: pypa/[email protected]
with:
password: ${{ secrets.TEST_PYPI_API_TOKEN }}
repository_url: https://test.pypi.org/legacy/
continue-on-error: true