From 4a5abaec9bad901869a831d0c845962bb179525a Mon Sep 17 00:00:00 2001 From: Vadym Moshynskyi Date: Wed, 26 Nov 2025 13:11:58 +0100 Subject: [PATCH 1/4] IEBH-353: Sync with the latest changes --- .github/workflows/hdc-pipeline.yml | 136 ++ .pre-commit-config.yaml | 18 +- README.md | 1 - app/resources/custom_help.py | 5 +- poetry.lock | 1873 ++++++++++++++++------------ pyproject.toml | 2 +- 6 files changed, 1241 insertions(+), 794 deletions(-) create mode 100644 .github/workflows/hdc-pipeline.yml diff --git a/.github/workflows/hdc-pipeline.yml b/.github/workflows/hdc-pipeline.yml new file mode 100644 index 0000000..9bc70f3 --- /dev/null +++ b/.github/workflows/hdc-pipeline.yml @@ -0,0 +1,136 @@ +name: HDC ci/cd pipeline + +permissions: + contents: write + issues: write + pull-requests: write + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + tests: + runs-on: ubuntu-20.04 + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: 3.10.14 + + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + version: 1.3.2 + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + + - name: Set up cache + id: cached-poetry-dependencies + uses: actions/cache@v3 + with: + path: .venv + key: venv-${{ hashFiles('**/poetry.lock') }} + + - name: Ensure cache is healthy + if: steps.cached-poetry-dependencies.outputs.cache-hit == 'true' + run: timeout 10s poetry run pip --version || rm -rf .venv + + - name: Install dependencies + run: poetry install --no-interaction --no-root + + - name: Run pre-commit hooks + uses: pre-commit/action@v3.0.0 + + - name: Run tests + run: poetry run pytest -vvv --exitfirst --cov=app --cov-report=term --cov-report=xml --cov-fail-under=23 + + - name: Coverage report comment + uses: mishakav/pytest-coverage-comment@v1.1.42 + with: + pytest-xml-coverage-path: ./coverage.xml + coverage-path-prefix: app/ + + extract-branch-name: + runs-on: ubuntu-20.04 + needs: [ tests ] + outputs: + branch: ${{steps.extract_branch.outputs.branch}} + steps: + - name: Extract Branch Name + id: extract_branch + shell: bash + run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT + push-binary: + needs: [ extract-branch-name ] + if: ${{ needs.extract-branch-name.outputs.branch == 'hdc' }} + runs-on: ubuntu-20.04 + steps: + - name: Checkout repository + uses: actions/checkout@v3 + with: + ref: ${{ needs.extract-branch-name.outputs.branch }} + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: 3.10.14 + + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + version: 1.3.2 + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + + - name: Set up cache + id: cached-poetry-dependencies + uses: actions/cache@v3 + with: + path: .venv + key: venv-${{ hashFiles('**/poetry.lock') }} + + - name: Ensure cache is healthy + if: steps.cached-poetry-dependencies.outputs.cache-hit == 'true' + run: timeout 10s poetry run pip --version || rm -rf .venv + + - name: Install dependencies + run: poetry install --no-interaction --no-root + + - name: Build binary + run: poetry run pyinstaller -F --distpath ./app/bundled_app/linux --specpath ./app/build/linux --workpath ./app/build/linux --paths=./.venv/lib/python3.9/site-packages ./app/pilotcli.py -n ${{ github.sha }} + + - name: Set version in env + run: poetry run echo "TAG_VERSION=`poetry version --short`" >> $GITHUB_ENV + + - name: Create Release + id: create_release + uses: actions/create-release@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token + with: + tag_name: ${{ env.TAG_VERSION }}-${{ needs.extract-branch-name.outputs.branch }} + release_name: Release ${{ needs.extract-branch-name.outputs.branch }} ${{ env.TAG_VERSION }} + body: ${{ github.event.head_commit.message }} + draft: false + prerelease: false + + - name: Upload Release Binary + id: upload-release-binary + uses: actions/upload-release-asset@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps + asset_path: ./app/bundled_app/linux/${{ github.sha }} + asset_name: pilotcli + asset_content_type: application/octet-stream diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9ffd5fa..96be327 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -67,15 +67,15 @@ repos: '--max-line-length=120', ] -# - repo: https://github.com/PyCQA/docformatter -# rev: v1.7.5 -# hooks: -# - id: docformatter -# args: [ -# '--wrap-summaries=120', -# '--wrap-descriptions=120', -# '--in-place', -# ] + - repo: https://github.com/PyCQA/docformatter + rev: v1.7.7 + hooks: + - id: docformatter + args: [ + '--wrap-summaries=120', + '--wrap-descriptions=120', + '--in-place', + ] - repo: https://github.com/Lucas-C/pre-commit-hooks rev: v1.5.5 diff --git a/README.md b/README.md index ce37e03..e4c07c9 100644 --- a/README.md +++ b/README.md @@ -44,4 +44,3 @@ The development of the HealthDataCloud open source software was supported by the This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement No 101058516. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or other granting authorities. Neither the European Union nor other granting authorities can be held responsible for them. ![EU HDC Acknowledgement](https://hdc.humanbrainproject.eu/img/HDC-EU-acknowledgement.png) - diff --git a/app/resources/custom_help.py b/app/resources/custom_help.py index f4fa2ff..ad85554 100644 --- a/app/resources/custom_help.py +++ b/app/resources/custom_help.py @@ -8,8 +8,9 @@ class HelpPage: page = { 'update': { - 'version': '2.2.6', - '1': 'CLI supports listing of all datasets a project administrator has access to.', + 'version': '2.2.7', + '1': 'Removed ability to upload to core zone and to download from greenroom zone' + ' for more secure file handling workflow.', }, 'dataset': { 'DATASET_DOWNLOAD': 'Download a dataset or a particular version of a dataset.', diff --git a/poetry.lock b/poetry.lock index 288421d..cb02042 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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--no-interaction --no-root - name: Build binary - run: poetry run pyinstaller -F --distpath ./app/bundled_app/linux --specpath ./app/build/linux --workpath ./app/build/linux --paths=./.venv/lib/python3.9/site-packages ./app/pilotcli.py -n ${{ github.sha }} + run: poetry run pyinstaller -F --distpath ./app/bundled_app/linux --specpath ./app/build/linux --workpath ./app/build/linux --paths=./.venv/lib/python3.10/site-packages ./app/pilotcli.py -n ${{ github.sha }} - name: Set version in env run: poetry run echo "TAG_VERSION=`poetry version --short`" >> $GITHUB_ENV From 9115900e410f5d8cf55400260838dd6843c99772 Mon Sep 17 00:00:00 2001 From: Vadym Moshynskyi Date: Wed, 26 Nov 2025 13:35:45 +0100 Subject: [PATCH 3/4] IEBH-353: Update release branch name --- .github/workflows/hdc-pipeline.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/hdc-pipeline.yml b/.github/workflows/hdc-pipeline.yml index 6d99e3e..9a92aa8 100644 --- 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name: Checkout repository uses: actions/checkout@v3 @@ -60,7 +60,7 @@ jobs: coverage-path-prefix: app/ extract-branch-name: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest needs: [ tests ] outputs: branch: ${{ steps.extract_branch.outputs.branch }} @@ -73,7 +73,7 @@ jobs: push-binary: needs: [ extract-branch-name ] if: ${{ needs.extract-branch-name.outputs.branch == 'main' }} - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout repository uses: actions/checkout@v3