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put in the outline for the joss publication #2190

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put in the outline for the joss publication

put in the outline for the joss publication #2190

Workflow file for this run

.github/workflows/main.yml at 8d93e28
# 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
- "renovate/**"
pull_request:
workflow_dispatch:
# Only run actions on the most recent push to a branch
concurrency:
group: "${{ github.workflow }}-${{ github.head_ref }}"
cancel-in-progress: true
jobs:
lint:
runs-on: ubuntu-22.04
timeout-minutes: 5
steps:
- name: Checkout
uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
- name: Run pre-commit
uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
with:
extra_args: --all-files
- name: Validate Docker Compose config file
working-directory: .
run: |
cp .env.sample .env
docker compose config --quiet
test:
runs-on: ubuntu-22.04
timeout-minutes: 30
strategy:
fail-fast: false # run all tests if even if one fails
matrix:
package_dir: [pixl_core, hasher, pixl_dcmd, cli, pixl_export, pixl_imaging, pytest-pixl]
steps:
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
- name: Init Python
uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
pip install -e pytest-pixl/
pip install -e pixl_core/[test]
pip install -e ${{ matrix.package_dir }}/[test]
- name: Run tests and generate coverage report
working-directory: ${{ matrix.package_dir }}
run: COV_CORE_SOURCE=src COV_CORE_CONFIG=.coveragerc COV_CORE_DATAFILE=.coverage.eager pytest --cov=src --cov-append --cov-report=xml --cov-report=term-missing
env:
ENV: test
AZURE_KEY_VAULT_NAME: test
AZURE_KEY_VAULT_SECRET_NAME: test
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@e28ff129e5465c2c0dcc6f003fc735cb6ae0c673 # v4.5.0
with:
directory: ${{ matrix.package_dir }}
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
system-test:
if: ${{ ! github.event.pull_request.draft || contains(github.event.pull_request.title, '[force-system-test]') }}
runs-on: ubuntu-22.04
timeout-minutes: 30
steps:
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
- uses: docker/setup-buildx-action@988b5a0280414f521da01fcc63a27aeeb4b104db # v3
- name: Init Python
uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
# The -e option is required here due to the way the
# code determines the export directory. See issue #318.
run: |
pip install -e pytest-pixl/
pip install -e pixl_core/[test]
pip install -e cli/[test]
- name: Create .secrets.env
run: touch test/.secrets.env
- name: Build test services
working-directory: test
run: |
docker compose build
- name: Build services
run: |
docker compose build
- name: Run tests
working-directory: test
env:
EXPORT_AZ_CLIENT_ID: ${{ secrets.EXPORT_AZ_CLIENT_ID }}
EXPORT_AZ_CLIENT_PASSWORD: ${{ secrets.EXPORT_AZ_CLIENT_PASSWORD }}
EXPORT_AZ_TENANT_ID: ${{ secrets.EXPORT_AZ_TENANT_ID }}
EXPORT_AZ_KEY_VAULT_NAME: ${{ secrets.EXPORT_AZ_KEY_VAULT_NAME }}
HASHER_API_AZ_CLIENT_ID: ${{ secrets.EXPORT_AZ_CLIENT_ID }}
HASHER_API_AZ_CLIENT_PASSWORD: ${{ secrets.EXPORT_AZ_CLIENT_PASSWORD }}
HASHER_API_AZ_TENANT_ID: ${{ secrets.EXPORT_AZ_TENANT_ID }}
HASHER_API_AZ_KEY_VAULT_NAME: ${{ secrets.EXPORT_AZ_KEY_VAULT_NAME }}
run: |
./run-system-test.sh coverage
echo FINISHED SYSTEM TEST SCRIPT
- name: Dump queue docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-queue-1 2>&1
- name: Dump postgres docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-postgres-1 2>&1
- name: Dump imaging-api docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-imaging-api-1 2>&1
- name: Dump orthanc-raw docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-orthanc-raw-1 2>&1
- name: Dump orthanc-anon docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-orthanc-anon-1 2>&1
- name: Dump hasher-api docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-hasher-api-1 2>&1
- name: Dump export-api docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-export-api-1 2>&1
- name: Dump VNA docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-vna-qr-1 2>&1
- name: Dump DICOMWeb docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-dicomweb-server-1 2>&1
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@e28ff129e5465c2c0dcc6f003fc735cb6ae0c673 # v4.5.0
with:
directory: test
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}