Set up ruff
and fix trivial rules
#374
Workflow file for this run
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# Copyright (c) University College London Hospitals NHS Foundation Trust | |
# | |
# Licensed under the Apache License, Version 2.0 (the "License"); | |
# you may not use this file except in compliance with the License. | |
# You may obtain a copy of the License at | |
# | |
# http://www.apache.org/licenses/LICENSE-2.0 | |
# | |
# Unless required by applicable law or agreed to in writing, software | |
# distributed under the License is distributed on an "AS IS" BASIS, | |
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
# See the License for the specific language governing permissions and | |
# limitations under the License. | |
name: pixl-ci | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
workflow_dispatch: | |
jobs: | |
lint: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 5 | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v3 | |
- name: Ensure copyright and license header are present | |
run: ./.github/linters/check_headers_exist.sh | |
- name: Run pre-commit | |
uses: pre-commit/action@v3.0.0 | |
with: | |
extra_args: --all-files | |
- name: Validate Docker Compose config file | |
working-directory: . | |
run: | | |
cp .env.sample .env | |
docker compose config --quiet | |
hasher-tests: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 10 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Init Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.10' | |
cache: 'pip' | |
- name: Install package | |
run: | | |
pip install hasher/[test] | |
- name: Run tests | |
working-directory: hasher | |
run: pytest | |
env: | |
ENV: test | |
AZURE_KEY_VAULT_NAME: test | |
AZURE_KEY_VAULT_SECRET_NAME: test | |
core-tests: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 10 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Init Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.10' | |
cache: 'pip' | |
- name: Install Python dependencies | |
run: | | |
pip install pixl_core/[test] | |
- name: Run tests | |
working-directory: pixl_core/tests | |
run: | | |
docker compose up --build --exit-code-from test | |
docker compose down | |
env: | |
ENV: test | |
dicom-de-id-tests: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 10 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Init Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.9' | |
cache: 'pip' | |
- name: Install Python dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install -r pixl_dcmd/src/requirements.txt | |
- name: Run tests | |
working-directory: pixl_dcmd | |
run: | | |
bin/run-tests.sh | |
env: | |
ENV: test | |
cli-tests: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 10 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Init Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.10' | |
cache: 'pip' | |
- name: Install Python dependencies | |
run: | | |
pip install pixl_core/[test] cli/[test] | |
- name: Run tests | |
working-directory: cli/tests | |
run: | | |
./run-tests.sh | |
ehr-api-tests: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 15 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Init Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.10.6 | |
cache: 'pip' | |
- name: Install Python dependencies | |
run: | | |
pip install pixl_core/[test] pixl_ehr/[test] | |
python -m spacy download en_core_web_lg | |
- name: Run tests | |
working-directory: pixl_ehr/tests | |
env: | |
INFORMDB_PAT: ${{ secrets.INFORMDB_PAT }} | |
run: | | |
./run-tests.sh | |
pacs-api-tests: | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 10 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Init Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.10.6 | |
cache: 'pip' | |
- name: Install Python dependencies | |
run: | | |
pip install pixl_core/[test] pixl_pacs/[test] | |
- name: Run tests | |
working-directory: pixl_pacs/tests | |
run: | | |
./run-tests.sh |