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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| # 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: Bug Report | ||
| description: Have you got a bug? Please report it here! | ||
| projects: [ "SAFEHR-data/13" ] | ||
| body: | ||
| - type: markdown | ||
| attributes: | ||
| value: | | ||
| A clear and concise description of what the bug is. Please use a short, concise title for the bug and elaborate here | ||
| - type: textarea | ||
| id: actual_behaviour | ||
| attributes: | ||
| label: What happened? | ||
| description: A clear and concise description of what actually happens. | ||
| placeholder: "If you have a code sample, error messages, stack traces, please provide it here as well" | ||
| validations: | ||
| required: false | ||
| - type: textarea | ||
| id: logs | ||
| attributes: | ||
| label: Relevant log output (optional) | ||
| description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks. | ||
| validations: | ||
| required: false | ||
| - type: textarea | ||
| id: expected_behaviour | ||
| attributes: | ||
| label: What did you expect? (optional) | ||
| description: A clear and concise description of what you expected to happen. | ||
| validations: | ||
| required: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| # 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: Feature Request | ||
| description: Submit a proposal/request for a new feature | ||
| projects: [ "SAFEHR-data/13" ] | ||
| body: | ||
| - type: markdown | ||
| attributes: | ||
| value: | | ||
| A clear and concise description of the feature proposal | ||
| - type: textarea | ||
| id: motivation | ||
| attributes: | ||
| label: Motivation | ||
| description: Please outline the motivation for the proposal. | ||
| placeholder: "Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too" | ||
| validations: | ||
| required: true | ||
| - type: textarea | ||
| id: pitch | ||
| attributes: | ||
| label: Pitch | ||
| description: A clear and concise description of what you want to happen. | ||
| validations: | ||
| required: false | ||
| - type: textarea | ||
| id: alternatives | ||
| attributes: | ||
| label: Alternatives | ||
| description: A clear and concise description of any alternative solutions or features you've considered, if any. | ||
| placeholder: | ||
| validations: | ||
| required: false | ||
| - type: textarea | ||
| id: additional_context | ||
| attributes: | ||
| label: Additional context | ||
| description: Add any other context or screenshots about the feature request here. | ||
| validations: | ||
| required: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| <!-- Replace {issue_number} with the issue that will be closed after merging this PR --> | ||
| ## Description | ||
| Fixes #{issue_number}: A few words or sentences describing the changes proposed in this pull request (PR). | ||
|
|
||
| ## Type of change | ||
| Please delete options accordingly to the description. | ||
|
|
||
| <!-- Write an `x` in all the boxes that apply --> | ||
| - [ ] Bug fix (non-breaking change which fixes an issue) | ||
| - [ ] New feature (non-breaking change which adds functionality) | ||
| - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected) | ||
| - [ ] This change requires a documentation update | ||
|
|
||
|
|
||
| ### Suggested Checklist | ||
| <!-- You do not need to complete all the items by the time you submit the pull request, but most likely the changes will only be merged if all the tasks are done. --> | ||
|
|
||
| <!-- Write an `x` in all the boxes that apply --> | ||
| - [ ] I have performed a self-review of my own code. | ||
| - [ ] I have made corresponding changes to the documentation. | ||
| - [ ] My changes generate no new warnings. | ||
| - [ ] I have commented my code, particularly in hard-to-understand areas. | ||
| - [ ] I have passed on my local host device. (see further details at the [CONTRIBUTING](https://github.com/SAFEHR-data/PIXL/blob/main/CONTRIBUTING.md#local-testing) document) | ||
| - [ ] Make sure your branch is up-to-date with main branch. See [CONTRIBUTING](https://github.com/SAFEHR-data/PIXL/blob/main/CONTRIBUTING.md) for a general example to syncronise your branch with the `main` branch. | ||
| - [ ] I have requested review to this PR. | ||
| - [ ] I have addressed and marked as resolved all the review comments in my PR. | ||
| - [ ] Finally, I have selected `squash and merge` | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -17,6 +17,7 @@ on: | |
| push: | ||
| branches: | ||
| - main | ||
| - "renovate/**" | ||
| pull_request: | ||
| workflow_dispatch: | ||
|
|
||
|
|
@@ -27,14 +28,14 @@ concurrency: | |
|
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||
| jobs: | ||
| lint: | ||
| runs-on: ubuntu-22.04 | ||
| runs-on: ubuntu-24.04 | ||
| timeout-minutes: 5 | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
|
|
||
| - name: Run pre-commit | ||
| uses: pre-commit/[email protected] | ||
| uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | ||
| with: | ||
| extra_args: --all-files | ||
|
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|
|
@@ -45,18 +46,18 @@ jobs: | |
| docker compose config --quiet | ||
| test: | ||
| runs-on: ubuntu-22.04 | ||
| runs-on: ubuntu-24.04 | ||
| 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] | ||
| package_dir: [pixl_core, hasher, pixl_dcmd, cli, pixl_export, pixl_imaging, pytest-pixl] | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
|
|
||
| - name: Init Python | ||
| uses: actions/setup-python@v5 | ||
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
| with: | ||
| python-version: "3.11" | ||
| cache: "pip" | ||
|
|
@@ -70,28 +71,28 @@ jobs: | |
| - name: Run tests and generate coverage report | ||
| working-directory: ${{ matrix.package_dir }} | ||
| run: pytest --cov --cov-report=xml | ||
| 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@v4.2.0 | ||
| uses: codecov/codecov-action@7f8b4b4bde536c465e797be725718b88c5d95e0e # v5.1.1 | ||
| 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 | ||
| runs-on: ubuntu-24.04 | ||
| timeout-minutes: 30 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: docker/setup-buildx-action@v3 | ||
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
| - uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3 | ||
| - name: Init Python | ||
| uses: actions/setup-python@v5 | ||
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
| with: | ||
| python-version: "3.11" | ||
| cache: "pip" | ||
|
|
@@ -131,23 +132,54 @@ jobs: | |
| ./run-system-test.sh coverage | ||
| echo FINISHED SYSTEM TEST SCRIPT | ||
| - name: Dump export-api docker logs for debugging | ||
| - name: Dump queue docker logs for debugging | ||
| if: ${{ failure() }} | ||
| run: | | ||
| docker logs -t system-test-export-api-1 2>&1 | ||
| docker logs -t system-test-queue-1 2>&1 | ||
| - name: Dump orthanc-anon docker logs for debugging | ||
| - name: Dump postgres docker logs for debugging | ||
| if: ${{ failure() }} | ||
| run: | | ||
| docker logs -t system-test-orthanc-anon-1 2>&1 | ||
| 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@v4.2.0 | ||
| uses: codecov/codecov-action@7f8b4b4bde536c465e797be725718b88c5d95e0e # v5.1.1 | ||
| with: | ||
| directory: test | ||
| env: | ||
|
|
||
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