crevice 0.1.1__tar.gz

crevice-0.1.1/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: CREVICE crashed, produced malformed output, or behaved differently from its documentation.
+labels: [bug]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting. Please give enough detail for someone else to reproduce the problem.
+        If you think a *scientific result* is wrong (e.g. a radius or volume), that is welcome too:
+        say what you expected and why, and which parameters you used.
+  - type: input
+    id: version
+    attributes:
+      label: CREVICE version or commit
+      description: Output of `python -c "import crevice; print(crevice.__version__)"`, or the Git commit.
+    validations:
+      required: true
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: Operating system, Python version, and `python -m pip freeze` (or at least NumPy, SciPy, MDAnalysis, Matplotlib and Gemmi versions).
+      render: text
+    validations:
+      required: true
+  - type: textarea
+    id: command
+    attributes:
+      label: Exact command or code
+      description: The complete command line or a minimal Python snippet.
+      render: shell
+    validations:
+      required: true
+  - type: textarea
+    id: input
+    attributes:
+      label: Input
+      description: PDB accession, or how to obtain the structure/trajectory. Attach a minimal file if it can be shared.
+    validations:
+      required: true
+  - type: textarea
+    id: observed
+    attributes:
+      label: What happened
+      description: Full error traceback or the unexpected output.
+      render: text
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: What you expected
+    validations:
+      required: true

crevice-0.1.1/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+# Contact links (for example GitHub Discussions) need the repository's absolute
+# URL; add a contact_links list here once it is known.

crevice-0.1.1/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature or method request
+description: Suggest a new analysis, option, output or documentation improvement.
+labels: [enhancement]
+body:
+  - type: textarea
+    id: problem
+    attributes:
+      label: Scientific or practical problem
+      description: What question are you trying to answer, and what is missing today?
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed behaviour
+      description: Commands, parameters or outputs you would like. Mention related tools (HOLE, HOLLOW, CAVER, MDAnalysis, ...) if relevant.
+    validations:
+      required: true
+  - type: textarea
+    id: validation
+    attributes:
+      label: How could it be checked?
+      description: Analytic controls, reference data or comparators that would show the feature works. It is fine to say you do not know.
+  - type: dropdown
+    id: contribute
+    attributes:
+      label: Would you like to help implement it?
+      options:
+        - "Not at this time"
+        - "Yes, with guidance"
+        - "Yes, I can open a pull request"

crevice-0.1.1/.github/PULL_REQUEST_TEMPLATE.md

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+## Summary
+
+<!-- What does this change and why? Link related issues. -->
+
+## Type of evidence
+
+<!-- Tick all that apply; see "Scientific honesty conventions" in CONTRIBUTING.md. -->
+
+- [ ] Software/synthetic tests only
+- [ ] Real-system observations (inputs and parameters listed below)
+- [ ] Native viewer run and output inspected (name the viewer and version)
+- [ ] Documentation only
+
+## Checks
+
+- [ ] `python -m pytest -q -rs tests`
+      Result (passed / skipped / failed) and every skip reason:
+- [ ] Existing numerical results are unchanged, **or** the change is intended and
+      before/after values are shown below
+- [ ] `CHANGELOG.md` `[Unreleased]` updated
+- [ ] User documentation updated where behaviour changed
+- [ ] No absolute local paths, personal data or large binary files added
+
+## Evidence and limitations
+
+<!-- Exact commands, inputs (with sources), what was inspected, what was not
+checked and anything left unfinished. See "Reporting evidence for a change" in
+CONTRIBUTING.md. -->

crevice-0.1.1/.github/constraints/minimum.txt

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+# Oldest supported releases of CREVICE's required runtime libraries.
+# Used by the CI "minimum-versions" job: pip install -c this-file '.[test]'.
+# Keep in sync with [project].dependencies lower bounds in pyproject.toml
+# (tests/test_packaging.py enforces this).
+numpy==1.26.4
+scipy==1.11.4
+MDAnalysis==2.7.0
+matplotlib==3.8.0
+scikit-image==0.22.0

crevice-0.1.1/.github/workflows/release.yml

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+name: Release to PyPI
+
+# Publishing a GitHub Release whose tag is vX.Y.Z (matching __version__ in
+# src/crevice/__init__.py) builds, tests and uploads that version to PyPI.
+# Running the workflow manually ("Run workflow") uploads the current commit's
+# build to TestPyPI instead, as a dry run. Uploads use PyPI Trusted Publishing
+# (OpenID Connect), so no API token is stored in the repository; see
+# https://docs.pypi.org/trusted-publishers/ for the one-time PyPI and TestPyPI setup.
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build and test the distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.12'
+      - name: Install the package with test dependencies
+        run: python -m pip install ".[test]" build twine
+      - name: Check the release tag matches the package version
+        if: github.event_name == 'release'
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          version=$(python -c "import re, pathlib; print(re.search(r'__version__ = \"([^\"]+)\"', pathlib.Path('src/crevice/__init__.py').read_text()).group(1))")
+          tag_version="${TAG#v}"
+          normalized=$(python -c "from packaging.version import Version; import sys; print(Version(sys.argv[1]))" "$tag_version")
+          echo "tag=$TAG package=$version"
+          if [ "$normalized" != "$version" ]; then
+            echo "::error::Release tag $TAG does not match __version__ $version"
+            exit 1
+          fi
+      - name: Run the test suite
+        run: python -m pytest -q -rs tests
+      - name: Build sdist and wheel
+        run: python -m build --outdir dist
+      - name: Check distribution metadata
+        run: python -m twine check --strict dist/*
+      - uses: actions/upload-artifact@v7
+        with:
+          name: distributions
+          path: dist/
+
+  publish-pypi:
+    name: Upload to PyPI
+    if: github.event_name == 'release'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/crevice/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          name: distributions
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-testpypi:
+    name: Upload to TestPyPI (manual dry run)
+    if: github.event_name == 'workflow_dispatch'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/crevice/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          name: distributions
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true

crevice-0.1.1/.github/workflows/tests.yml

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+name: Scientific and Packaging Checks
+
+# Software checks only: passing CI is not real-system or functional validation.
+on:
+  push:
+    branches: [main]
+    tags: ['v*']
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  OMP_NUM_THREADS: '1'
+  OPENBLAS_NUM_THREADS: '1'
+  PIP_DISABLE_PIP_VERSION_CHECK: '1'
+  MPLBACKEND: Agg
+
+jobs:
+  test:
+    name: tests (Python ${{ matrix.python }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Keep in step with requires-python and the classifiers in pyproject.toml.
+        python: ['3.10', '3.11', '3.12', '3.13']
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: Install CREVICE with required and test dependencies
+        run: python -m pip install '.[test]'
+      - name: Record environment
+        run: |
+          mkdir -p ci-artifacts
+          python -m pip freeze > ci-artifacts/pip-freeze.txt
+      - name: Regression suite
+        run: >-
+          python -m pytest -q -rs tests
+          --junitxml=ci-artifacts/pytest.xml
+      - uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: tests-python-${{ matrix.python }}
+          path: ci-artifacts/
+
+  minimum-versions:
+    name: tests (oldest supported NumPy/SciPy/MDAnalysis/Matplotlib)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.10'
+          cache: pip
+          cache-dependency-path: |
+            pyproject.toml
+            .github/constraints/minimum.txt
+      - name: Install with the declared lower bounds pinned
+        run: python -m pip install -c .github/constraints/minimum.txt '.[test]'
+      - name: Record environment
+        run: |
+          mkdir -p ci-artifacts
+          python -m pip freeze > ci-artifacts/pip-freeze.txt
+      - name: Regression suite
+        run: >-
+          python -m pytest -q -rs tests
+          --junitxml=ci-artifacts/pytest.xml
+      - uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: tests-minimum-versions
+          path: ci-artifacts/
+
+  build:
+    name: sdist and wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.12'
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: Install build tools
+        run: python -m pip install build twine
+      # Without --sdist/--wheel, `build` makes the sdist and then builds the
+      # wheel from that sdist, so this also proves the sdist is buildable.
+      - name: Build sdist and wheel
+        run: python -m build --outdir dist
+      - name: Check distribution metadata
+        run: python -m twine check --strict dist/*
+      - name: List sdist contents
+        run: tar -tzf dist/*.tar.gz | sort > dist/sdist-contents.txt
+      - name: Install the wheel in a fresh environment and smoke-test it
+        run: |
+          wheel=$(ls dist/*.whl)
+          test "$(echo "$wheel" | wc -l)" -eq 1
+          python scripts/check_wheel.py "$wheel" --report dist/wheel-check.json
+      - uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: distributions
+          path: dist/
+
+  docs:
+    name: documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.12'
+          cache: pip
+          cache-dependency-path: |
+            pyproject.toml
+            docs/requirements.txt
+      - name: Install CREVICE and the documentation requirements
+        run: python -m pip install . -r docs/requirements.txt
+      # Warnings are errors. The API pages import crevice from src/, and the
+      # intersphinx inventories are fetched over the network.
+      - name: Build the HTML documentation
+        run: python -m sphinx -W --keep-going -b html docs docs/_build/html
+      # External link checking is informational only: publisher sites often
+      # refuse automated requests, so it must not block CI.
+      - name: Check external links (non-blocking)
+        continue-on-error: true
+        run: python -m sphinx -b linkcheck docs docs/_build/linkcheck
+      - uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: documentation-html
+          path: |
+            docs/_build/html/
+            docs/_build/linkcheck/output.txt

crevice-0.1.1/.gitignore

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+# Python and tooling caches
+__pycache__/
+*.py[cod]
+.pytest_cache/
+*.egg-info/
+build/
+/dist/
+
+# Local environments
+/.venv/
+/.venv-*/
+
+# CREVICE's default structure cache (--cache-dir) and local viewer toolchains
+/.crevice/
+
+# Output written by the examples and quick-start commands
+/results/

crevice-0.1.1/.readthedocs.yaml

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+# Read the Docs configuration for the CREVICE documentation site.
+# No hosted build has been run yet; only local and CI-equivalent builds are verified.
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt