IEBH-353: Sync with the latest changes

.github/workflows/hdc-pipeline.yml

@@ -0,0 +1,137 @@
+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-latest
+    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-latest
+    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 == 'main' }}
+    runs-on: ubuntu-latest
+    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/python3.10/site-packages ./app/pilotcli.py -n ${{ github.sha }}
+
+      - name: Set version in env
+        run: poetry run echo "TAG_VERSION=`poetry version --short`" >> $GITHUB_ENV
+
+      - 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

.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

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)
-

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.',