oxidane 0.2.0__tar.gz

oxidane-0.2.0/.github/workflows/python.yml

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+name: Test the Python bindings
+
+# Linux only by default; macOS and Windows too when run by hand, on a tag, or
+# on a pull request labelled full-ci. scripts/ci-local.sh runs the same tests.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, labeled]
+    paths-ignore: ['**.md', 'docs/**', 'assets/**', 'LICENSE']
+  push:
+    branches: [main]
+    tags: ['v*']
+    paths-ignore: ['**.md', 'docs/**', 'assets/**', 'LICENSE']
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+jobs:
+  python:
+    if: github.event.action != 'labeled' || github.event.label.name == 'full-ci'
+    strategy:
+      fail-fast: false
+      matrix:
+        include: >-
+          ${{ fromJSON((github.event_name == 'workflow_dispatch' || startsWith(github.ref, 'refs/tags/') || contains(github.event.pull_request.labels.*.name, 'full-ci'))
+          && '[{"os":"ubuntu-latest","python":"3.9"},{"os":"ubuntu-latest","python":"3.14"},{"os":"macos-latest","python":"3.12"},{"os":"windows-latest","python":"3.12"}]'
+          || '[{"os":"ubuntu-latest","python":"3.9"},{"os":"ubuntu-latest","python":"3.14"}]') }}
+    runs-on: ${{ matrix.os }}
+    env:
+      CARGO_BUILD_JOBS: "1"
+      RAYON_NUM_THREADS: "1"
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Install Rust
+        run: rustup toolchain install stable --profile minimal
+      - uses: astral-sh/setup-uv@v10.3.0
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Build and install the local bindings and test dependencies
+        run: uv sync --locked --project bindings/python --extra notebook
+      - name: Test the API and notebook display
+        run: uv run --no-sync --project bindings/python pytest bindings/python/tests

oxidane-0.2.0/.github/workflows/release.yml

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+name: Test and package the library
+
+# Linux only on pull requests; macOS and Windows too when run by hand, on a
+# tag, or on a pull request labelled full-ci. scripts/ci-local.sh runs the same
+# checks.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, labeled]
+    paths-ignore: ['**.md', 'docs/**', 'assets/**', 'LICENSE']
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}
+    if: github.event.action != 'labeled' || github.event.label.name == 'full-ci'
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: >-
+          ${{ fromJSON((github.event_name == 'workflow_dispatch' || startsWith(github.ref, 'refs/tags/') || contains(github.event.pull_request.labels.*.name, 'full-ci'))
+          && '["ubuntu-latest","macos-latest","windows-latest"]' || '["ubuntu-latest"]') }}
+    env:
+      # Debug info in every example and test binary fills the Linux runner's disk.
+      CARGO_PROFILE_DEV_DEBUG: "0"
+      CARGO_INCREMENTAL: "0"
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Install Rust
+        run: rustup toolchain install stable --profile minimal
+      - uses: Swatinem/rust-cache@v2
+      - name: Check every target
+        run: cargo +stable check --locked --all-features --all-targets
+      - name: Run library, regression and documentation tests
+        run: cargo +stable test --locked --all-features
+
+  release:
+    name: Draft a source release
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Install Rust
+        run: rustup toolchain install stable --profile minimal
+      - name: Archive the tagged library and verify its contents
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          set -euo pipefail
+          package_version=$(cargo +stable metadata --no-deps --format-version 1 | jq -r '.packages[] | select(.name == "oxidane") | .version')
+          test "$RELEASE_TAG" = "v$package_version"
+          release_name="oxidane-$package_version"
+          archive_path="$RUNNER_TEMP/$release_name.tar.gz"
+          git archive --format=tar --prefix="$release_name/" HEAD | gzip -n > "$archive_path"
+          tar -xzf "$archive_path" -C "$RUNNER_TEMP"
+          cargo +stable check --locked --all-features --all-targets --manifest-path "$RUNNER_TEMP/$release_name/Cargo.toml"
+          (
+            cd "$RUNNER_TEMP"
+            sha256sum "$release_name.tar.gz" > "$release_name.tar.gz.sha256"
+          )
+          echo "RELEASE_ARCHIVE=$archive_path" >> "$GITHUB_ENV"
+      - name: Create a draft with the source and its checksum
+        env:
+          GH_TOKEN: ${{ github.token }}
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          gh release create "$RELEASE_TAG" \
+            "$RELEASE_ARCHIVE" "$RELEASE_ARCHIVE.sha256" \
+            --verify-tag --draft --generate-notes --title "$RELEASE_TAG"

oxidane-0.2.0/.github/workflows/wheels.yml

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+name: Build the Python wheels
+
+# Only when run by hand (Actions tab, "Run workflow"), on a tag, or on a pull
+# request labelled full-ci; scripts/ci-local.sh builds the same wheels locally.
+# A v* tag uploads the wheels and sdist to PyPI; a manual run can upload them
+# to TestPyPI instead. Both use trusted publishing, so no token is stored.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, labeled]
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+    inputs:
+      testpypi:
+        description: Upload the build to TestPyPI
+        type: boolean
+        default: false
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  wheel:
+    name: Wheel for ${{ matrix.name }}
+    if: >-
+      github.event_name != 'pull_request'
+      || (contains(github.event.pull_request.labels.*.name, 'full-ci')
+          && (github.event.action != 'labeled' || github.event.label.name == 'full-ci'))
+    runs-on: ${{ matrix.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: Linux x86-64, runner: ubuntu-latest, target: x86_64, manylinux: '2014', image: 'python:3.12-slim', platform: linux/amd64 }
+          - { name: Linux ARM64, runner: ubuntu-latest, target: aarch64, manylinux: '2014', image: 'python:3.12-slim', platform: linux/arm64 }
+          - { name: Linux x86-64 musl, runner: ubuntu-latest, target: x86_64, manylinux: musllinux_1_2, image: 'python:3.12-alpine', platform: linux/amd64 }
+          - { name: Linux ARM64 musl, runner: ubuntu-latest, target: aarch64, manylinux: musllinux_1_2, image: 'python:3.12-alpine', platform: linux/arm64 }
+          - { name: macOS Intel, runner: macos-15-intel, target: x86_64, native: true }
+          - { name: macOS Apple silicon, runner: macos-latest, target: aarch64, native: true }
+          - { name: Windows x64, runner: windows-latest, target: x64, native: true }
+          - { name: Windows ARM64, runner: windows-latest, target: aarch64 }
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+      - name: Build an abi3 wheel
+        uses: PyO3/maturin-action@v1
+        with:
+          working-directory: bindings/python
+          target: ${{ matrix.target }}
+          manylinux: ${{ matrix.manylinux || 'auto' }}
+          args: --release --locked --out dist
+      - name: Set up emulation for the Linux test container
+        if: matrix.platform == 'linux/arm64'
+        uses: docker/setup-qemu-action@v3
+      - name: Install the wheel and normalize a file (Linux container)
+        if: matrix.image
+        run: |
+          docker run --rm --platform ${{ matrix.platform }} -v "$PWD/bindings/python:/io" -w /tmp ${{ matrix.image }} sh -euc '
+            pip install --quiet /io/dist/*.whl
+            printf "id,smiles\n1,Oc1ccccn1\n" > in.csv
+            oxidane-normalize in.csv out.csv -s smiles
+            grep -q "O=c1\[nH\]cccc1" out.csv
+            python -c "import oxidane as ox; assert ox.canonical_tautomer(\"Oc1ccccn1\") == \"O=c1[nH]cccc1\""'
+      - name: Install the wheel and normalize a file
+        if: matrix.native
+        run: |
+          python -m venv "$RUNNER_TEMP/venv"
+          if [ -d "$RUNNER_TEMP/venv/Scripts" ]; then bin="$RUNNER_TEMP/venv/Scripts"; else bin="$RUNNER_TEMP/venv/bin"; fi
+          "$bin/python" -m pip install --quiet bindings/python/dist/*.whl
+          cd "$RUNNER_TEMP"
+          printf 'id,smiles\n1,Oc1ccccn1\n' > in.csv
+          "$bin/oxidane-normalize" in.csv out.csv -s smiles
+          grep -q 'O=c1\[nH\]cccc1' out.csv
+          "$bin/python" -c 'import oxidane as ox; assert ox.canonical_tautomer("Oc1ccccn1") == "O=c1[nH]cccc1"'
+      - uses: actions/upload-artifact@v5
+        with:
+          name: wheel-${{ matrix.runner }}-${{ matrix.target }}-${{ matrix.manylinux || 'native' }}
+          path: bindings/python/dist/*.whl
+
+  sdist:
+    name: Source distribution
+    needs: wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - uses: PyO3/maturin-action@v1
+        with:
+          working-directory: bindings/python
+          command: sdist
+          args: --out dist
+      - uses: actions/upload-artifact@v5
+        with:
+          name: sdist
+          path: bindings/python/dist/*.tar.gz
+
+  wheels:
+    name: All wheels in one download
+    needs: [wheel, sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v6
+        with:
+          path: dist
+          merge-multiple: true
+      - run: ls -l dist
+      - uses: actions/upload-artifact@v5
+        with:
+          name: oxidane-python-wheels
+          path: dist/*
+
+  publish:
+    name: Publish to ${{ startsWith(github.ref, 'refs/tags/v') && 'PyPI' || 'TestPyPI' }}
+    needs: wheels
+    if: >-
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v'))
+      || (github.event_name == 'workflow_dispatch' && inputs.testpypi)
+    runs-on: ubuntu-latest
+    environment:
+      name: ${{ startsWith(github.ref, 'refs/tags/v') && 'pypi' || 'testpypi' }}
+      url: ${{ startsWith(github.ref, 'refs/tags/v') && 'https://pypi.org/p/oxidane' || 'https://test.pypi.org/p/oxidane' }}
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Check that the tag matches the package versions
+        if: startsWith(github.ref, 'refs/tags/v')
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          set -euo pipefail
+          for manifest in Cargo.toml bindings/python/Cargo.toml bindings/python/pyproject.toml; do
+            version=$(sed -n 's/^version = "\(.*\)"$/\1/p' "$manifest" | head -1)
+            echo "$manifest: $version"
+            test "$RELEASE_TAG" = "v$version"
+          done
+      - uses: actions/download-artifact@v6
+        with:
+          name: oxidane-python-wheels
+          path: dist
+      - run: ls -l dist
+      - name: Upload to PyPI
+        if: startsWith(github.ref, 'refs/tags/v')
+        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Upload to TestPyPI
+        if: "!startsWith(github.ref, 'refs/tags/v')"
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

oxidane-0.2.0/.gitignore

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+target/
+src/test_io.sh
+git_pusher.sh
+__pycache__/
+.DS_Store
+flamegraph.sh
+# Written by the ignored canonicalization benchmark
+tests/wrong_smiles.txt
+
+# Local working notes, not for publication
+notes/
+manuscript/
+publication/
+examples/publication.rs

oxidane-0.2.0/CITATION.cff

@@ -0,0 +1,18 @@
+cff-version: 1.2.0
+message: "If you use oxidane, please cite it as below."
+title: "oxidane: a cheminformatics toolkit in Rust"
+type: software
+license: MIT
+repository-code: "https://github.com/um-univie/oxidane"
+version: 0.2.0
+authors:
+  - family-names: Uhlir
+    given-names: Manuel
+    affiliation: "University of Vienna"
+keywords:
+  - cheminformatics
+  - Rust
+  - SMILES
+  - canonicalization
+  - tautomers
+  - conformer generation

oxidane-0.2.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,18 @@
+# Code of Conduct
+
+This project adopts the [Contributor Covenant, version 2.1](https://www.contributor-covenant.org/version/2/1/code_of_conduct/).
+
+We are committed to a harassment-free experience for everyone, regardless of
+age, body size, visible or invisible disability, ethnicity, sex
+characteristics, gender identity and expression, level of experience,
+education, socio-economic status, nationality, personal appearance, race,
+religion, or sexual identity and orientation.
+
+Be respectful and constructive in issues, pull requests and discussions.
+Harassment, personal attacks and publishing others' private information are
+not tolerated.
+
+Report unacceptable behaviour to the maintainers at <manuel.uhlir@univie.ac.at>.
+Reports are handled confidentially. Maintainers may remove comments, commits
+or contributions that violate this code, and may ban contributors temporarily
+or permanently.

oxidane-0.2.0/CONTRIBUTING.md

@@ -0,0 +1,40 @@
+# Contributing to oxidane
+
+Bug reports, questions and pull requests are welcome.
+
+## Reporting problems
+
+Open an issue at <https://github.com/um-univie/oxidane/issues>. For a wrong
+chemical result, include the input (SMILES, SMARTS or a minimal SDF), what
+oxidane returned, what you expected, and if possible what RDKit or another
+toolkit returns. State the oxidane version or commit.
+
+## Development setup
+
+```sh
+git clone https://github.com/um-univie/oxidane
+cd oxidane
+cargo test --locked --all-features
+```
+
+Python bindings live in `bindings/python` and are built with maturin:
+
+```sh
+cd bindings/python
+uv run maturin develop
+uv run pytest
+```
+
+## Pull requests
+
+- Branch from `main`; keep a pull request to one change.
+- Add a test for every bug fix and new feature. Chemistry fixes should include
+  the molecule that exposed the problem.
+- Run `cargo fmt`, `cargo clippy --all-targets --all-features` and
+  `cargo test --locked --all-features` before pushing.
+- Code derived from other projects must be license-compatible with MIT and
+  recorded in `THIRD_PARTY.md`.
+
+## Code of conduct
+
+This project follows the [Code of Conduct](CODE_OF_CONDUCT.md).