scout-browser 4.93.1__tar.gz → 4.94__tar.gz

scout_browser-4.94/.coveragerc

@@ -0,0 +1,3 @@
+[run]
+source=scout
+omit=tests/*, setup.py

scout_browser-4.94/.dockerignore

@@ -0,0 +1,22 @@
+# configs
+.configs
+.coveragerc
+.editorconfig
+
+# git
+.git
+.github
+.gitignore
+.pre-commit-config.yaml
+
+# python
+mkdocs.yml
+docs
+site
+tests
+scripts
+
+# Docker
+Dockerfile*
+docker-compose.*yml
+volumes

scout_browser-4.94/.editorconfig

@@ -0,0 +1,16 @@
+# http://editorconfig.org
+root = true
+
+[*]
+indent_style = tab
+trim_trailing_whitespace = true
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+insert_final_newline = true
+
+[*.{py,html}]
+indent_style = space
+
+[*.{html,vue,js}]
+indent_size = 2

scout_browser-4.94/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Thank you for taking the time to contribute an issue!
+
+**⚠️ Important:** Please avoid sharing any sensitive or personal information, including text or images, in this issue.
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

scout_browser-4.94/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,22 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**⚠️ Important:** Please avoid sharing any sensitive or personal information, including text or images, in this issue.
+
+**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
+A clear and concise description of what the problem is or what the advance you would like us to incorporate is. Ex. when triaging structural variantS, I would like to [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

scout_browser-4.94/.github/ISSUE_TEMPLATE/other-issue.md

@@ -0,0 +1,13 @@
+---
+name: Other issue
+about: Describe your issue, request or question here
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Try to be as clear and precise as possible, adding sufficient detail and context.
+
+**⚠️ Important:** Please avoid sharing any sensitive or personal information, including text or images, in this issue.
+

scout_browser-4.94/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,43 @@
+This PR adds a functionality or fixes a bug.
+OR
+This PR marks a new Scout release. We apply semantic versioning. This is a major/minor/patch release for reasons.
+
+<details>
+<summary>Testing on cg-vm1 server (Clinical Genomics Stockholm)</summary>
+
+**Prepare for testing**
+1. Make sure the PR is pushed and available on [Docker Hub](https://hub.docker.com/repository/docker/clinicalgenomics/scout-server-stage)
+1. Fist book your testing time using the Pax software available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). The resource you are going to call dibs on is `scout-stage` and the server is `cg-vm1`.
+1. `ssh <USER.NAME>@cg-vm1.scilifelab.se`
+1. `sudo -iu hiseq.clinical`
+1. `ssh localhost`
+1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps`
+1. Stop the service with current deployed branch: `systemctl --user stop scout.target`
+1. Start the scout service with the branch to test: `systemctl --user start scout@<this_branch>`
+1. Make sure the branch is deployed: `systemctl --user status scout.target`
+1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](https://pax.scilifelab.se), which will release the allocated resource (`scout-stage`) to be used for testing by other users.
+</details>
+
+<details>
+<summary>Testing on hasta server (Clinical Genomics Stockholm)</summary>
+
+**Prepare for testing**
+1. `ssh <USER.NAME>@hasta.scilifelab.se`
+1. Book your testing time using the Pax software. `us; paxa -u <user> -s hasta -r scout-stage`. You can also use the WSGI Pax app available at [https://pax.scilifelab.se/](https://pax.scilifelab.se).
+1. (optional) Find out which scout branch is currently deployed on cg-vm1: `conda activate S_scout; pip freeze | grep scout-browser`
+1. Deploy the branch to test: `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>`
+1. Make sure the branch is deployed: `us; scout --version`
+1. After testing is done, repeat the `paxa` procedure, which will release the allocated resource (`scout-stage`) to be used for testing by other users.
+</details>
+
+
+**How to test**:
+1. how to test it, possibly with real cases/data
+
+**Expected outcome**:
+The functionality should be working
+Take a screenshot and attach or copy/paste the output.
+
+**Review:**
+- [ ] code approved by
+- [ ] tests executed by

scout_browser-4.94/.github/workflows/build_and_publish.yml

@@ -0,0 +1,71 @@
+name: Publish to PyPI, Docker Hub and GitHub IO
+
+on:
+ release:
+  types:
+   - created
+
+jobs:
+ build-n-publish:
+  name: Build and publish Python distribution to PyPI
+  runs-on: ubuntu-latest
+  permissions:
+    id-token: write
+  steps:
+     - uses: actions/checkout@v4
+     - uses: astral-sh/setup-uv@v3
+     - run: uv build
+     - run: uv publish --trusted-publishing always
+
+ docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Set up Docker Buildx
+      id: buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Publish server image (Dockerfile-server) to Registry
+      uses: docker/build-push-action@v6
+      with:
+        context: ./
+        file: ./Dockerfile-server
+        push: true
+        provenance: mode=max
+        sbom: true
+        tags: "clinicalgenomics/scout-server:latest, clinicalgenomics/scout-server:${{ github.event.release.tag_name }}"
+
+    - name: Publish server image (Dockerfile) to Registry
+      uses: docker/build-push-action@v6
+      with:
+        context: ./
+        file: ./Dockerfile
+        push: true
+        provenance: mode=max
+        sbom: true
+        tags: "clinicalgenomics/scout:latest, clinicalgenomics/scout:${{ github.event.release.tag_name }}"
+
+ deploy-docs:
+    name: Deploy Docs to GitHubIO
+    runs-on: ubuntu-latest
+    steps:
+     - name: Checkout repo
+       uses: actions/checkout@v4
+     - name: Setup environment for docs deployment
+       uses: actions/setup-python@v5
+       with:
+         python-version: 3.x
+     - name: Install mkdocs
+       run: pip install mkdocs mkdocs-material markdown-include
+     - name: Deploy documentation
+       run: mkdocs gh-deploy --force

scout_browser-4.94/.github/workflows/keep_a_changelog.yml

@@ -0,0 +1,15 @@
+name: "Changelog Reminder"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: dangoslen/changelog-enforcer@v3
+      with:
+        changeLogPath: 'CHANGELOG.md'
+        skipLabels: 'Skip-Changelog'

scout_browser-4.94/.github/workflows/linting_and_fixing.yml

@@ -0,0 +1,42 @@
+name: Lint files and fix lint errors
+
+# This will only correct linting in local PRs
+on: ["push"]
+
+jobs:
+  build:
+
+    name: Lint-and-fix
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+
+    steps:
+
+    # Check out Scout code
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    # Set up python
+    - name: Set up Python ${{ matrix.python-version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version}}
+
+    - name: Install Python Dependencies
+      run: |
+        pip install black flake8
+
+    - name: Run linters
+      uses: wearerequired/lint-action@v2
+      # Let linters fix problems if they can
+      with:
+        github_token: ${{ secrets.github_token }}
+        auto_fix: true
+        # Enable linters
+        black: true
+        black_args: "-l 100"
+        # stop the build if there are Python syntax errors or undefined names
+        flake8: true
+        flake8_args: "scout/ --count --select=E9,F63,F7,F82 --max-line-length 100 --show-source --statistics"

scout_browser-4.94/.github/workflows/linting_only.yml

@@ -0,0 +1,47 @@
+name: Lint files - no fixing
+
+# This will check linting in local PRs
+on: ["push", "pull_request"]
+
+jobs:
+  build:
+
+    name: Lint-only
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+
+    steps:
+
+    # Check out Scout code
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    # Set up python
+    - name: Set up Python ${{ matrix.python-version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version}}
+
+    - name: Install Python Dependencies
+      run: |
+        pip install black flake8 isort
+
+    - name: Run linters
+      uses: wearerequired/lint-action@v2
+      # Let linters fix problems if they can
+      with:
+        github_token: ${{ secrets.github_token }}
+        auto_fix: false
+        # Enable linters
+        black: true
+        black_args: "--check -l 100"
+        # stop the build if there are Python syntax errors or undefined names
+        flake8: true
+        flake8_args: "scout/ --count --select=E9,F63,F7,F82 --max-line-length 100 --show-source --statistics"
+
+    - name: Run isort
+      uses: jamescurtin/isort-action@master
+      with:
+          configuration: "--check-only --diff -m 3 --tc --fgw 0 --up -n -l 100"

scout_browser-4.94/.github/workflows/server_stage_docker_push.yml

@@ -0,0 +1,39 @@
+name: Publish to Docker stage
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  docker-stage-push:
+    name: Create staging docker image
+    runs-on: ubuntu-latest
+    steps:
+     - name: Check out git repository
+       uses: actions/checkout@v4
+
+     - name: Get branch name
+       id: branch-name
+       uses: tj-actions/branch-names@v7
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v3
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/setup-buildx-action@v3
+
+     - name: Build and push
+       if: steps.branch-name.outputs.is_default == 'false'
+       uses: docker/build-push-action@v6
+       with:
+         context: ./
+         file: ./Dockerfile-server
+         push: true
+         provenance: mode=max
+         sbom: true
+         tags: "clinicalgenomics/scout-server-stage:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/scout-server-stage:latest"

scout_browser-4.94/.github/workflows/tests_and_cov.yml

@@ -0,0 +1,93 @@
+name: Run tests and push coverage to Codecov
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+  test:
+    needs: setup
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        group: [1, 2, 3, 4, 5, 6, 7, 8]
+        mongodb-version: ['7']
+    steps:
+      - name: Start MongoDB
+        uses: supercharge/mongodb-github-action@1.10.0
+        with:
+         mongodb-version: ${{ matrix.mongodb-version }}
+
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the HTML 2 PDF renderer
+        run: sudo apt-get update || true && sudo apt-get install -y wkhtmltopdf
+
+      - name: Run pytest
+        run: uv run --dev pytest --cov --test-group-count 8 --test-group=${{ matrix.group }} --test-group-random-seed=12345 --rootdir=/home/runner/work/scout
+
+      - name: Upload coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage${{ matrix.group }}
+          path: .coverage
+          include-hidden-files: true
+
+  coverage:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+      - name: Install deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install coverage
+      - name: Download all artifacts
+        # Download and combine coverage1, coverage2, etc.
+        uses: actions/download-artifact@v4
+      - name: Run coverage
+        run: |
+          coverage combine coverage*/.coverage*
+          coverage report
+          coverage xml
+      - uses: codecov/codecov-action@v4
+        env:
+            CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

scout_browser-4.94/.github/workflows/validate_internal_docs_links.yml

@@ -0,0 +1,13 @@
+name: Validate internal documentation links
+
+"on": [pull_request]
+
+jobs:
+    tests:
+        name: mkdocs serve strict
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v3
+            - name: launch mkdocs in strict mode
+              run: uv run --only-group docs mkdocs build --strict

scout_browser-4.94/.github/workflows/vulture.yml

@@ -0,0 +1,23 @@
+name: "Vulture - Find unused code"
+on:
+  - pull_request
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: vulture
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Find changed Python files
+        id: files
+        uses: Ana06/get-changed-files@v2.2.0
+        with:
+          filter: "*.py"
+
+      - name: Scavenge
+        uses: anaynayak/python-vulture-action@v1.0
+        id: vulture
+        with:
+          vulture-args: --min-confidence 80 --ignore-names cls,args,kwargs,real_variant_database ${{steps.files.outputs.all}}
+        continue-on-error: true

scout_browser-4.94/.github/workflows/woke.yml

@@ -0,0 +1,15 @@
+name: woke
+on:
+  - pull_request
+jobs:
+  woke:
+    name: Non-inclusive language check with woke
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: woke
+        uses: get-woke/woke-action@v0
+        with:
+          fail-on-error: false

scout_browser-4.94/.gitignore

@@ -0,0 +1,88 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+dist/
+
+# Environments
+
+venv/
+
+# Pycharm
+.idea/
+
+# Installer logs
+pip-log.txt
+
+# Mac OSX
+.DS_Store
+.icloud
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+.cache/
+.pytest_cache/
+pytest.ini
+
+# si
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+*.sublime-*
+dev/
+.vagrant/
+htmlcov/
+provision/roles/
+.env
+*.ipynb
+.vscode/
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Sphinx/MkDocs
+docs/_build/
+site/
+
+# Flask
+instance
+
+# Node.js
+node_modules/
+_book/
+
+# Textmate
+.tm_properties
+
+# Linters
+pylintrc
+
+# Other
+/local
+scripts/local
+*sqlite
+
+#Docker
+volumes
+
+# Emacs (Just so I don't have to see them green in Atom ;-)
+*~
+*#