metaseed 0.14.0__tar.gz

metaseed-0.14.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Report a bug to help us improve
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Description
+
+A clear description of the bug.
+
+## Steps to Reproduce
+
+1. Go to '...'
+2. Click on '...'
+3. See error
+
+## Expected Behavior
+
+What you expected to happen.
+
+## Actual Behavior
+
+What actually happened.
+
+## Environment
+
+- OS: [e.g., macOS 14, Ubuntu 22.04]
+- Python version: [e.g., 3.11.5]
+- Metaseed version: [e.g., 0.6.0]
+- Browser (if UI issue): [e.g., Chrome 120]
+
+## Error Messages
+
+```
+Paste any error messages here
+```
+
+## Additional Context
+
+Any other relevant information.

metaseed-0.14.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest a new feature
+title: ''
+labels: enhancement
+assignees: ''
+---
+
+## Problem
+
+Describe the problem this feature would solve.
+
+## Proposed Solution
+
+Describe your proposed solution.
+
+## Alternatives Considered
+
+Any alternative solutions you've considered.
+
+## Use Case
+
+How would you use this feature?
+
+## Additional Context
+
+Any other relevant information, mockups, or examples.

metaseed-0.14.0/.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+
+Brief description of the changes.
+
+## Related Issues
+
+Fixes #(issue number)
+
+## Type of Change
+
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Breaking change
+- [ ] Documentation update
+
+## Checklist
+
+- [ ] Tests pass locally
+- [ ] Pre-commit hooks pass
+- [ ] Documentation updated (if applicable)
+- [ ] Changes are backward compatible (or breaking changes documented)
+
+## Testing
+
+Describe how the changes were tested.

metaseed-0.14.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+# Least privilege: CI only needs to read the repo.
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4.3.0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86 # v5.4.2
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        # dcat (rdflib) is needed so mypy sees real types for dcat/serialize.py;
+        # the other extras are just httpx, already pulled in by dev.
+        run: uv sync --extra dev --extra dcat
+
+      - name: Run linting
+        run: uv run ruff check .
+
+      - name: Check formatting
+        # Gate formatting in CI, not only in the pre-commit hook. Without this,
+        # drift is invisible to anyone who commits without the hook installed --
+        # which is how main reached 18 non-compliant files before #147.
+        run: uv run ruff format --check .
+
+      - name: Run type checking
+        run: uv run mypy src/metaseed
+
+      - name: Run tests with coverage
+        # Exclude network-marked tests: they hit live third-party services
+        # (e.g. the EBI/MetaboLights API), so an external outage would fail CI
+        # for unrelated changes. Exclude selenium-marked tests: they drive a real
+        # browser and run in the dedicated `selenium` job below. This matches the
+        # project's pre-push hook.
+        run: |
+          uv run pytest \
+            -m "not selenium and not network" \
+            --cov=src/metaseed \
+            --cov-report=xml \
+            --cov-fail-under=78 \
+            -q
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@0565863a31f2c772f9f0395002a31e3f06189574 # v5.4.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false
+
+  selenium:
+    runs-on: ubuntu-latest
+    # Advisory: the browser suite drives a real headless Chrome, so occasional
+    # flakiness must never block a merge. ubuntu-latest ships Chrome, and
+    # Selenium Manager (selenium>=4.20) resolves the driver; the tests start
+    # their own uvicorn server, so no extra service setup is needed.
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4.3.0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86 # v5.4.2
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --extra dev --extra dcat
+
+      - name: Run Selenium tests (headless Chrome)
+        # --timeout caps any hung browser so a stuck test cannot stall the job.
+        run: uv run pytest -m selenium tests/test_ui -q --timeout=180
+
+  audit:
+    runs-on: ubuntu-latest
+    # Advisory: a newly-disclosed CVE in a transitive dependency must not block
+    # an unrelated PR — the vulnerability DB updates independently of this code.
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4.3.0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86 # v5.4.2
+
+      - name: Set up Python
+        # Use uv-managed CPython (ships ensurepip), so uvx can build pip-audit's
+        # isolated environment.
+        run: uv python install 3.12
+
+      - name: Audit dependencies for known vulnerabilities
+        # Audit the full locked closure — base + all extras + dev group — so a CVE
+        # in an optional adapter dep (metaseed[pride], dcat, …) is caught too.
+        run: |
+          uv export --format requirements-txt --no-emit-project --no-hashes --all-extras \
+            | uvx --python 3.12 pip-audit --requirement /dev/stdin

metaseed-0.14.0/.github/workflows/docs.yml

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+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - '.github/workflows/docs.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+
+      - name: Install Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Build presentation
+        run: |
+          cd docs/slides
+          quarto render index.qmd
+
+      - name: Build documentation
+        run: uv run mkdocs build --strict
+
+      - name: Copy presentation to site
+        run: |
+          mkdir -p site/slides
+          cp -r docs/slides/index.html docs/slides/images site/slides/
+          # embed-resources renders a self-contained index.html; index_files
+          # only exists when resources are not embedded.
+          [ -d docs/slides/index_files ] && cp -r docs/slides/index_files site/slides/ || true
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

metaseed-0.14.0/.github/workflows/release.yml

@@ -0,0 +1,78 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Need full history for hatch-vcs
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Install dependencies
+        # Must match the CI gate's extras, not just its markers: tests/test_seek
+        # imports rdflib, so `--extra dev` alone fails at collection and the
+        # release never reaches the publish job.
+        run: uv sync --extra dev --extra dcat --extra seek
+
+      - name: Run tests
+        # Match the CI gate: exclude network-marked tests. They hit live third-party
+        # APIs (EBI/MetaboLights) and flake for unrelated reasons, so a release must
+        # never be blocked by an external outage (per CLAUDE.md "Local must match CI").
+        run: |
+          uv run python -m pytest tests/ \
+            -m "not selenium and not network" \
+            --ignore=tests/test_ui/test_selenium.py \
+            --ignore=tests/test_ui/test_spec_builder_selenium.py \
+            --ignore=tests/test_ui/test_validation_selenium.py \
+            --ignore=tests/test_ui/selenium/ \
+            -q
+
+      - name: Build package
+        run: uv build
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          generate_release_notes: true
+
+      - name: Upload dist for the publish job
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    # Publishes to PyPI via Trusted Publishing (OIDC): no API token is stored in
+    # the repo. Requires a matching publisher on PyPI for this repo + workflow +
+    # environment. Runs only after the release job's tests and build succeed.
+    needs: release
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # mint the short-lived OIDC token PyPI verifies
+    steps:
+      - name: Download the built distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

metaseed-0.14.0/.gitignore

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+# Python
+__pycache__/
+
+# Generated version file (hatch-vcs)
+src/metaseed/_version.py
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+
+# UV
+.uv/
+# uv.lock is committed for reproducible dev/CI builds and Dependabot scanning.
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.nox/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Jupyter
+.ipynb_checkpoints/
+
+# Documentation
+site/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Environment
+.env
+.env.local
+*.local
+
+# Logs
+*.log
+
+# Type checking
+.mypy_cache/
+.pytype/

metaseed-0.14.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        exclude: ^mkdocs\.yml$
+      - id: check-toml
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: check-merge-conflict
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Keep in step with the ruff version resolved in uv.lock. When the two drift,
+    # the hook and CI format the same code differently and every toolchain bump
+    # produces a repo-wide reformat commit.
+    rev: v0.15.22
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, .]
+        pass_filenames: false
+      - id: ruff-format
+        args: [.]
+        pass_filenames: false
+
+  - repo: local
+    hooks:
+      - id: vulture
+        name: vulture dead code
+        entry: uv run vulture
+        language: system
+        types: [python]
+        args: [src/, --min-confidence=80]
+        pass_filenames: false
+
+      - id: mypy
+        name: mypy type check
+        entry: uv run python -m mypy src/metaseed
+        language: system
+        types: [python]
+        pass_filenames: false
+
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.27.0
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: run tests before push
+        entry: uv run python -m pytest -x -q --tb=short -n auto -m "not network and not selenium"
+        language: system
+        stages: [pre-push]
+        pass_filenames: false
+        always_run: true

metaseed-0.14.0/.python-version

@@ -0,0 +1 @@
+3.12