seqfold 0.9.0__tar.gz → 0.10.2__tar.gz

seqfold-0.10.2/.github/workflows/release.yml

@@ -0,0 +1,309 @@
+# This file is autogenerated by maturin v1.13.3
+# To update, run
+#
+#    maturin generate-ci github --pytest -o .github/workflows/release.yml
+#
+# Builds + tests wheels on every push/PR; publishes to PyPI on tag push.
+name: Release
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+  # Publishing a GitHub Release is the single source of truth for a release:
+  # the version is taken from the release tag and the wheels go to PyPI.
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Mainstream glibc targets with working test emulation. Other arches
+        # (s390x/ppc64le/32-bit) install from the sdist.
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+      - uses: astral-sh/setup-uv@v7
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        shell: bash
+        run: |
+          set -e
+          uv venv .venv
+          source .venv/bin/activate
+          uv pip install seqfold --no-index --no-deps --find-links dist --reinstall
+          uv pip install seqfold pytest
+          pytest
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') && matrix.platform.target != 'ppc64' }}
+        uses: uraimo/run-on-arch-action@v3
+        with:
+          arch: ${{ matrix.platform.target }}
+          # ubuntu22.04 provides the aarch64 image used to run the emulated tests.
+          distro: ubuntu22.04
+          githubToken: ${{ github.token }}
+          install: |
+            apt-get update
+            apt-get install -y --no-install-recommends python3 python3-venv
+          run: |
+            set -e
+            python3 -m venv .venv
+            source .venv/bin/activate
+            pip install pytest
+            pip install seqfold --no-index --no-deps --find-links dist --force-reinstall
+            pip install seqfold
+            pytest
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        run: |
+          set -e
+          docker run --rm -v ${{ github.workspace }}:/io -w /io alpine:latest sh -c '
+            apk add py3-pip py3-virtualenv
+            python3 -m virtualenv .venv
+            source .venv/bin/activate
+            pip install seqfold --no-index --no-deps --find-links dist --force-reinstall
+            pip install seqfold pytest
+            pytest
+          '
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') }}
+        uses: uraimo/run-on-arch-action@v3
+        with:
+          arch: ${{ matrix.platform.target }}
+          distro: alpine_latest
+          githubToken: ${{ github.token }}
+          install: |
+            apk add py3-virtualenv
+          run: |
+            set -e
+            python3 -m virtualenv .venv
+            source .venv/bin/activate
+            pip install seqfold --no-index --no-deps --find-links dist --force-reinstall
+            pip install seqfold pytest
+            pytest
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # 32-bit Windows (x86) is dropped: setup-python can't reliably provide
+        # 32-bit CPython 3.13, and it's a legacy target with ~no users. Those
+        # install from the sdist.
+        platform:
+          - runner: windows-2025
+            target: x64
+            python_arch: x64
+          - runner: windows-11-arm
+            target: aarch64
+            python_arch: arm64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+          architecture: ${{ matrix.platform.python_arch }}
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+      - uses: astral-sh/setup-uv@v7
+      - name: pytest
+        shell: bash
+        run: |
+          set -e
+          uv venv .venv
+          source .venv/Scripts/activate
+          uv pip install seqfold --no-index --no-deps --find-links dist --reinstall
+          uv pip install seqfold pytest
+          pytest
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - runner: macos-15-intel
+            target: x86_64
+          - runner: macos-latest
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+      - uses: astral-sh/setup-uv@v7
+      - name: pytest
+        run: |
+          set -e
+          uv venv .venv
+          source .venv/bin/activate
+          uv pip install seqfold --no-index --no-deps --find-links dist --reinstall
+          uv pip install seqfold pytest
+          pytest
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
+    needs: [linux, musllinux, windows, macos, sdist]
+    # Dedicated publishing environment. Configure it under repo Settings ->
+    # Environments (and name it as the PyPI trusted publisher's "Environment").
+    # Add required reviewers there to gate who can actually publish to PyPI.
+    environment: pypi
+    permissions:
+      # Mint the OIDC token PyPI trusted publishing exchanges (no API token).
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v7
+      - name: Generate artifact attestation
+        uses: actions/attest@v4
+        with:
+          subject-path: 'wheels-*/*'
+      - name: Install uv
+        if: ${{ github.event_name == 'release' }}
+        uses: astral-sh/setup-uv@v7
+      # No token: uv uses GitHub OIDC trusted publishing (id-token: write above).
+      - name: Publish to PyPI
+        if: ${{ github.event_name == 'release' }}
+        run: uv publish --trusted-publishing always 'wheels-*/*'

seqfold-0.10.2/.gitignore

@@ -0,0 +1,147 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# 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
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# vscode settings
+.vscode
+
+# .c/.html files during build
+seqfold/*.c
+seqfold/*.html
+
+# Rust / maturin build artifacts
+/target
+.venv/
+
+# development/test files
+/data/dna
+*.stats
+
+
+.DS_Store

seqfold-0.10.2/Cargo.lock

@@ -0,0 +1,191 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 4
+
+[[package]]
+name = "crossbeam-deque"
+version = "0.8.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9dd111b7b7f7d55b72c0a6ae361660ee5853c9af73f70c3c2ef6858b950e2e51"
+dependencies = [
+ "crossbeam-epoch",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-epoch"
+version = "0.9.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e"
+dependencies = [
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-utils"
+version = "0.8.21"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d0a5c400df2834b80a4c3327b3aad3a4c4cd4de0629063962b03235697506a28"
+
+[[package]]
+name = "either"
+version = "1.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91622ff5e7162018101f2fea40d6ebf4a78bbe5a49736a2020649edf9693679e"
+
+[[package]]
+name = "heck"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
+
+[[package]]
+name = "libc"
+version = "0.2.186"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68ab91017fe16c622486840e4c83c9a37afeff978bd239b5293d61ece587de66"
+
+[[package]]
+name = "once_cell"
+version = "1.21.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9f7c3e4beb33f85d45ae3e3a1792185706c8e16d043238c593331cc7cd313b50"
+
+[[package]]
+name = "portable-atomic"
+version = "1.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c33a9471896f1c69cecef8d20cbe2f7accd12527ce60845ff44c153bb2a21b49"
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.106"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8fd00f0bb2e90d81d1044c2b32617f68fcb9fa3bb7640c23e9c748e53fb30934"
+dependencies = [
+ "unicode-ident",
+]
+
+[[package]]
+name = "pyo3"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cd274650b21d4bfc26a0a47587962c1edb425f69287324355cd040c3ea66071c"
+dependencies = [
+ "libc",
+ "once_cell",
+ "portable-atomic",
+ "pyo3-build-config",
+ "pyo3-ffi",
+ "pyo3-macros",
+]
+
+[[package]]
+name = "pyo3-build-config"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5e2a7d2f0d013342f295c048ad19237add5154a55b1c5a254c0ec93d4109078"
+dependencies = [
+ "target-lexicon",
+]
+
+[[package]]
+name = "pyo3-ffi"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ca85c467da1bbc8d866eea5deff9cf29ea5f7785054a17da36e65bda9c05845b"
+dependencies = [
+ "libc",
+ "pyo3-build-config",
+]
+
+[[package]]
+name = "pyo3-macros"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ac53762fd065daa3194dd09337a38bd793a188100fd1a9304c4ab312d901771"
+dependencies = [
+ "proc-macro2",
+ "pyo3-macros-backend",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "pyo3-macros-backend"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4ca3a1557399783172dc5bf39cfca835157732532cba56b71d2292161e53b362"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "quote"
+version = "1.0.45"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "41f2619966050689382d2b44f664f4bc593e129785a36d6ee376ddf37259b924"
+dependencies = [
+ "proc-macro2",
+]
+
+[[package]]
+name = "rayon"
+version = "1.12.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fb39b166781f92d482534ef4b4b1b2568f42613b53e5b6c160e24cfbfa30926d"
+dependencies = [
+ "either",
+ "rayon-core",
+]
+
+[[package]]
+name = "rayon-core"
+version = "1.13.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "22e18b0f0062d30d4230b2e85ff77fdfe4326feb054b9783a3460d8435c8ab91"
+dependencies = [
+ "crossbeam-deque",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "seqfold"
+version = "0.10.2"
+dependencies = [
+ "pyo3",
+ "rayon",
+ "smallvec",
+]
+
+[[package]]
+name = "smallvec"
+version = "1.15.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "67b1b7a3b5fe4f1376887184045fcf45c69e92af734b7aaddc05fb777b6fbd03"
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+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e665b8803e7b1d2a727f4023456bbbbe74da67099c585258af0ad9c5013b9b99"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "target-lexicon"
+version = "0.13.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "adb6935a6f5c20170eeceb1a3835a49e12e19d792f6dd344ccc76a985ca5a6ca"
+
+[[package]]
+name = "unicode-ident"
+version = "1.0.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6e4313cd5fcd3dad5cafa179702e2b244f760991f45397d14d4ebf38247da75"

seqfold-0.10.2/Cargo.toml

@@ -0,0 +1,34 @@
+[package]
+name = "seqfold"
+# Dev default only. Releases take the version from the GitHub Release tag, which
+# the CI injects here before building (see DEVELOPMENT.md). pyproject.toml reads
+# this via `dynamic = ["version"]`.
+version = "0.10.2"
+edition = "2021"
+description = "Predict the minimum free energy structure of nucleic acids"
+license = "MIT"
+repository = "https://github.com/Lattice-Automation/seqfold"
+readme = "README.md"
+
+[lib]
+name = "seqfold"
+crate-type = ["cdylib", "rlib"]
+
+[features]
+# Enables the PyO3 extension module. Off by default so `cargo test` exercises
+# the pure-Rust engine without linking libpython.
+python = ["dep:pyo3"]
+
+[dependencies]
+# abi3-py38: build a single stable-ABI wheel that works on CPython 3.8+,
+# instead of a separate wheel per Python minor version.
+pyo3 = { version = "0.29", features = ["extension-module", "abi3-py38"], optional = true }
+# Data-parallel fill of the DP matrix (one task per cell on each anti-diagonal).
+rayon = "1.10"
+# Inline storage for the small per-cell basepair lists (no heap alloc for the
+# common 0-1 element case).
+smallvec = "1"
+
+[profile.release]
+lto = true
+codegen-units = 1