automesh 0.2.9__tar.gz

automesh-0.2.9/.github/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+Don't be a jerk!

automesh-0.2.9/.github/CONTRIBUTING.md

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+# Contributing
+
+Contributors can open issues or create pull requests.
+
+## Issues
+
+Contributors can open new issues on the GitHub repository [here](https://github.com/autotwin/automesh/issues). An issue can either report an existing bug, or request a new feature. Contributors should ensure that their candidate issue does not match an existing open issue before opening it. If a closely-related but incomplete open issue exists, contributors should comment on the existing open issue.
+
+### Bug Reports
+
+A new bug report can be opened [here](https://github.com/autotwin/automesh/issues/new?template=bug_report.md).
+
+### Feature Requests
+
+A new feature request can be opened [here](https://github.com/autotwin/automesh/issues/new?template=feature_request.md). Feature requests that are deemed feasible will be considered by the developers, and could even be addressed by a contributor through a pull request. Feature requests that are deemed infeasible will likely be denied.
+
+## Pull Requests
+
+Contributors can propose changes to the code in the repository by creating a pull request as follows:
+
+- Fork the base repository [here](https://github.com/autotwin/automesh/fork).
+- Clone the forked repository, make changes, and push them back to the fork.
+- Create a pull request between the base and forked repositories [here](https://github.com/autotwin/automesh/pulls).
+- Wait for the pull request to be either approved or dismissed. Approval and subsequent merging of pull requests is contingent upon:
+
+  - The tests are all passing, resulting in a high (desirably, complete) code coverage, and any changes are properly tested.
+  - The documentation is successfully built, and any changes are properly documented.
+  - The changes provide an appropriate and substantial improvement to the repository.

automesh-0.2.9/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**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.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

automesh-0.2.9/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**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.

automesh-0.2.9/.github/SECURITY.md

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+# Security Policy
+
+## Reporting a Vulnerability
+
+If there are any vulnerabilities, do not hesitate to report them, but please report them privately.

automesh-0.2.9/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "cargo"
+    directory: "/"
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

automesh-0.2.9/.github/pull_request_template.md

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+# Pull Request Template
+
+This template should be used for making any pull requests.
+
+## Goal
+
+Here, describe the goal of the pull request, i.e. what does it seek to address? Does this pull request fix an existing bug, or create a new feature? Why are the changes proposed by this pull request necessary?
+
+## Specifics
+
+Here, describe the specific changes to the repository suggested by this pull request. Which modules/methods/etc. were added or edited, and why? Have any new dependencies been introduced, and why?
+
+## Verification
+
+Here, describe steps taken to verify that the pull request is up to the standards of the repository. Were the suggested changes fully documented and tested, and do they match the existing code style? How exactly was this verification completed?

automesh-0.2.9/.github/workflows/book.yml

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+name: Book
+on:
+  pull_request:
+    branches: main
+  push:
+    branches: main
+env:
+  CARGO_TERM_COLOR: always
+jobs:
+  mdbook:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - uses: actions-rs/toolchain@v1
+        with:
+          default: true
+          toolchain: stable
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: automesh
+        run: cargo install --path .
+      - name: mdbook
+        run: cargo install mdbook mdbook-cmdrun mdbook-katex
+      - name: rust
+        run: cargo build --release
+      - name: maturin
+        run: pip install maturin
+      - name: install
+        run: maturin build --release --features python
+      - name: python
+        run: pip install --find-links=target/wheels/ automesh
+      - name: test
+        run: mdbook test --library-path target/release/deps/
+      - name: build
+        run: mdbook build
+      - name: move
+        run: mkdir -p _site/ && cp -r book/build/* _site/
+      - name: upload
+        uses: actions/upload-pages-artifact@v3
+  deploy:
+    if: github.event_name != 'pull_request'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    needs: mdbook
+    permissions:
+      id-token: write
+      pages: write
+    runs-on: ubuntu-latest
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

automesh-0.2.9/.github/workflows/bump.yml

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+name: Bump
+on:
+  release:
+    types: published
+jobs:
+  bump:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - name: bump
+        id: bump
+        run: |
+          VERSION=$(cargo tree | grep automesh | cut -d " " -f 2 | cut -d "v" -f 2)
+          MAJOR_MINOR=$(echo $VERSION | rev | cut -d "." -f 2- | rev)
+          PATCH=$(echo $VERSION | rev | cut -d "." -f 1)
+          BUMP=$(( $PATCH + 1))
+          BUMPED_VERSION=$(echo $MAJOR_MINOR"."$BUMP)
+          BUMP_BRANCH=$(echo "bump-$VERSION-to-$BUMPED_VERSION")
+          echo "bump_branch=$BUMP_BRANCH" >> $GITHUB_OUTPUT
+          sed -i "s/version = \"$VERSION\"/version = \"$BUMPED_VERSION\"/" Cargo.toml
+          git config --global user.email "bump"
+          git config --global user.name "bump"
+          git add Cargo.toml
+          git commit -m "Bumping version from $VERSION to $BUMPED_VERSION."
+          git branch $BUMP_BRANCH
+          git checkout $BUMP_BRANCH
+          git push --set-upstream origin $BUMP_BRANCH
+      - name: pr
+        uses: rematocorp/open-pull-request-action@v1
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          from-branch: ${{ steps.bump.outputs.bump_branch }}
+          to-branch: ${{ github.event.repository.default_branch }}
+          repository-owner: autotwin
+          repository: ${{ github.event.repository.name }}

automesh-0.2.9/.github/workflows/python.yml

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+name: Python
+on:
+  pull_request:
+    branches: main
+  release:
+    types: published
+jobs:
+  test:
+    if: github.event_name != 'release'
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+    - uses: actions-rs/toolchain@v1
+      with:
+        components: clippy
+        default: true
+        toolchain: stable
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: clippy
+      run: cargo clippy --features python -- -D warnings
+    - name: maturin
+      run: pip install maturin
+    - name: build
+      run: maturin build --release --features python
+    - name: install
+      run: pip install --find-links=target/wheels/ automesh[dev]
+    - name: pycodestyle
+      run: pycodestyle --verbose .
+    - name: pytest
+      run: pytest --verbose
+  source:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - name: Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          default: true
+          toolchain: stable
+      - name: python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.13
+      - name: requirements
+        run: pip install build maturin twine
+      - name: source
+        run: python -m build . --sdist
+      - name: check
+        run: twine check dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+  wheel:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions-rs/toolchain@v1
+      with:
+        default: true
+        toolchain: stable
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: requirements
+      run: pip install build maturin twine
+    - name: foo
+      if: matrix.os == 'macos-latest'
+      run: brew uninstall --ignore-dependencies xz
+    - name: wheel
+      run: maturin build --release --features python
+    - name: check
+      run: twine check target/wheels/*
+    - uses: actions/upload-artifact@v4
+      with:
+        name: ${{ matrix.os }}-${{ matrix.python-version }}-dist
+        path: target/wheels
+  twine:
+    needs: [source, wheel]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v4
+    - uses: actions/setup-python@v5
+      with:
+        check-latest: true
+        python-version: 3.13
+    - name: requirements
+      run: pip install twine
+    - name: wheels
+      run: mv ./*-dist*/*.whl dist/
+    - name: ppload
+      if: github.event_name == 'release'
+      run: twine upload -u __token__ -p ${{ secrets.PYPI_TOKEN }} dist/*

automesh-0.2.9/.github/workflows/rust.yml

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+name: Rust
+on:
+  pull_request:
+    branches: main
+  release:
+    types: published
+env:
+  CARGO_TERM_COLOR: always
+jobs:
+  bench:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: nightly
+      - uses: actions/setup-python@v5
+        with:
+          check-latest: true
+          python-version: 3.13
+      - name: numpy
+        run: pip install numpy
+      - name: pillow
+        run: pip install pillow
+      - name: block
+        run: ./benches/block.sh
+      - name: bench
+        run: rustup run nightly cargo bench
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - name: cleanup
+        run: rm -fr book/ sandbox/ tests/
+      - name: package
+        run: cargo package
+      - name: login
+        if: github.event_name == 'release'
+        run: cargo login ${{ secrets.CRATES_IO_TOKEN }}
+      - name: publish
+        if: github.event_name == 'release'
+        run: cargo publish
+  test:
+    if: github.event_name != 'release'
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        toolchain:
+          - beta
+          - stable
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - uses: actions-rs/toolchain@v1
+        with:
+          components: clippy, rustfmt
+          default: true
+          toolchain: ${{ matrix.toolchain }}
+      - name: build
+        run: cargo build --release
+      - name: clippy
+        run: cargo clippy -- -D warnings
+      - name: clippy
+        run: cargo clippy --tests
+      - name: doc
+        run: cargo rustdoc --release -- --html-in-header docs/katex.html
+      - name: fmt
+        run: cargo fmt --all -- --check
+      - name: test
+        run: cargo test --release

automesh-0.2.9/.gitignore

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+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# ignore input/output files by default
+*.csv
+*.e
+*.exo
+*.g
+*.inp
+*.mesh
+*.npy
+*.vtk
+
+# ignore build binaries
+*.so
+
+# ignore macOS database files
+.DS_Store
+
+# ignore virtual environment
+.venv/
+
+# Generated by Cargo
+# will have compiled files and executables
+debug/
+target/
+
+# Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
+# More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
+Cargo.lock
+
+# These are backup files generated by rustfmt
+**/*.rs.bk
+
+# MSVC Windows builds of rustc generate these, which store debugging information
+*.pdb
+
+**.whl
+*.vscode
+**__pycache__
+**.pytest_cache
+book/build/
+benches/block/

automesh-0.2.9/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: check-yaml
+    -   id: check-added-large-files
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/backplane/pre-commit-rust-hooks
+    rev: v1.1.0
+    hooks:
+    -   id: clippy
+        args: ['--', '-D',  'warnings']
+    # -   id: clippy
+    #     name: cargo clippy --tests
+    #     args: ['--tests', '--', '-D',  'warnings']
+    -   id: clippy
+        name: cargo clippy --features python
+        args: ['--features', 'python', '--', '-D',  'warnings']
+    -   id: fmt
+# -   repo: https://github.com/psf/black
+#     rev: 24.8.0  # Use the latest version
+#     hooks:
+#     -   id: black
+#         args: [--line-length=79]
+-   repo: local
+    hooks:
+    -   id: pycodestyle
+        name: pycodestyle
+        entry: pycodestyle tests
+        language: system
+        pass_filenames: false

automesh-0.2.9/.readthedocs.yaml

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+version: 2
+build:
+  os: ubuntu-lts-latest
+  tools:
+    python: "latest"
+    rust: "latest"
+  commands:
+    - pip install cmake maturin[patchelf] pdoc
+    - maturin build --features python --release
+    - pip install --find-links=target/wheels/ automesh
+    - mkdir -p $READTHEDOCS_OUTPUT/html/
+    - pdoc automesh --logo "https://github.com/autotwin/automesh/blob/main/docs/logo.png?raw=true" --math --no-show-source --output-dir $READTHEDOCS_OUTPUT/html/ --template-directory docs/
+    - VERSION=$(cargo tree | grep automesh | cut -d " " -f 2 | cut -d "v" -f 2) && sed -i "s/automesh latest/automesh $VERSION/" $READTHEDOCS_OUTPUT/html/automesh.html

automesh-0.2.9/.zenodo.json

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+{
+    "title": "automesh",
+    "creators": [
+      {
+        "name": "Chad B. Hovey",
+        "affiliation": "Sandia National Laboratories",
+        "orcid": "0000-0003-0915-5765"
+      },
+      {
+        "name": "Michael R. Buche",
+        "affiliation": "Sandia National Laboratories",
+        "orcid": "0000-0003-1892-0502"
+      }
+    ],
+    "license": "GPL-3.0",
+    "upload_type": "software"
+}

automesh-0.2.9/CITATION.cff

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+cff-version: 1.2.0
+title: automesh
+message: 'If you use this software, please cite it as below.'
+type: software
+authors:
+  - family-names: Hovey
+    given-names: Chad B.
+    orcid: 'https://orcid.org/0000-0003-1892-0502'
+    email: chovey@sandia.gov
+    affiliation: Sandia National Laboratories
+  - family-names: Buche
+    given-names: Michael R.
+    orcid: 'https://orcid.org/0000-0003-0915-5765'
+    email: mrbuche@sandia.gov
+    affiliation: Sandia National Laboratories
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.13845433
+repository-code: 'https://github.com/autotwin/automesh'
+url: 'https://autotwin.github.io/automesh'
+abstract: Automatic mesh generation.
+license: MIT