Build(deps-py): Update maturin requirement from <1.12.0,>=1 to >=1,<1.13.0 in the dependencies group (#3902)
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Updates the requirements on maturin to permit the latest version. Updates
maturinto 1.12.2Release notes
Sourced from maturin's releases.
v1.12.2
What's Changed
- fix: allow absolute paths for
--sbom-includeby@messensein PyO3/maturin#3004Full Changelog: https://github.com/PyO3/maturin/compare/v1.12.1...v1.12.2
Changelog
Sourced from maturin's changelog.
1.12.2
- Fix: allow absolute paths for
--sbom-include(#3004)1.12.1
- Replace addnab/docker-run-action with direct docker run command
- Add
--sbom-includeCLI argument for additional SBOM files (#2999)- Fix: resolve include patterns relative to python-source for sdist and wheel (#3000)
- Feat: log external shared libraries and their dependents before patchelf
- Feat: support including
OUT_DIRassets in wheel builds (#3001)- Add test case for uniffi with multiple crates (#2839)
1.12.0
- Use pypi compatibility validation for own CI (#2929)
- Update toml crates for toml 1.1 support (#2934)
- Use a single location for MSRV (#2936)
- Fix editable install for binary projects with Python modules (#2938)
- Release to crates.io only after the builds passed (#2939)
- Use
mymindstorm/setup-emsdk@v14in generated GitHub Actions workflow (#2941)- Use trusted publishing for crates.io (#2943)
- Filter linked_paths by KIND and linked_libs (#2949)
- Update bytes to 1.11.1 (#2960)
- Normalize wheel distribution names to match the PyPA spec (#2954)
- Allow build loongarch64 and riscv64 for musllinux (#2963)
- Strip excluded cargo targets in sdist (#2964)
- Normalize wheel
RECORDpaths (on Windows) (#2965)- Bump MSRV to 1.88.0 (#2966)
- Support MATURIN_STRIP env var and --strip true/false to override pyproject.toml (#2968)
- Fix: copy bin artifacts before auditwheel repair to avoid rerun failures (#2969)
- Fix: rewrite python-source in pyproject.toml when building sdist (#2972)
- Fix: resolve wheel include patterns relative to project root (#2973)
- Fix: always include workspace Cargo.toml in sdist (#2974)
- Refactor: simplify source_distribution.rs (#2976)
- Feat: support PEP 735 dependency groups in develop command (#2978)
- Fix license file handling for workspace-level license files (#2970)
- Support PEP 739 build-details.json when cross compiling (#2979)
- Fix .libs directory name for namespace packages (#2981)
- Fix: exclude duplicate python source files from sdist for workspace members (#2982)
- Fix: remove default-members from workspace Cargo.toml in sdist (#2983)
- Fix: correctly filter workspace members in sdist by directory path (#2984)
- Feat: Add PEP 770 SBOM support (#2980)
- Error when python-source is set but Python module is missing (#2986)
- Feat: add auditwheel SBOM for grafted shared libraries (#2985)
- Fix sdist duplicate README error when readme is in both Cargo.toml and pyproject.toml (#2987)
- Fix: support python-source pointing outside Rust source directory (#2988)
- Relax ziglang dependency version requirement (#2990)
- Stop adding link-native-libraries flag by default in Emscripten platform in latest Rust (#2991)
- Fix docker build github workflow
... (truncated)
Commits
adb2906Release v1.12.26473568fix: allow absolute paths for--sbom-include(#3004)e772489Release v1.12.10672082add test case for uniffi with multiple crates (#2839)f201566feat: support includingOUT_DIRassets in wheel builds (#3001)66b4869feat: log external shared libraries and their dependents before patchelf8f8f9f7fix: resolve include patterns relative to python-source for sdist and wheel (...1688a73netlify: update mdbook to 0.5.2aefe09dAdd--sbom-includeCLI argument for additional SBOM files (#2999)8a688caDocument SBOM support in user guide- Additional commits viewable in compare view
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sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
Usage:
sourmash 1.0 is published on JOSS; please cite that paper if you use sourmash (
doi: 10.21105/joss.06830):.The latest major release is sourmash v4, which has several command-line and Python incompatibilities with previous versions. Please visit our migration guide to upgrade!
sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes:
FracMinHashsketching, which enables accurate comparisons (including ANI) between data sets of different sizessourmash gather, a combinatorial k-mer approach for more accurate metagenomic profilingPlease see the sourmash publications for details.
The name is a riff off of Mash, combined with @ctb’s love of whiskey. (Sour mash is used in making whiskey.)
Maintainers: C. Titus Brown (@ctb), Luiz C. Irber, Jr (@luizirber), and N. Tessa Pierce-Ward (@bluegenes).
sourmash was initially developed by the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine, and now includes contributions from the global research and developer community.
Installation
We recommend using conda-forge to install sourmash:
This will install the latest stable version of sourmash 4.
You can also use pip to install sourmash:
A quickstart tutorial is available.
Requirements
sourmash runs under Python 3.11 and later on Windows, Mac OS X, and Linux. The base requirements are screed, cffi, numpy, matplotlib, and scipy. Conda will install everything necessary, and is our recommended installation method (see below).
Installation with conda
conda-forge is a community maintained channel for the conda package manager. installing conda, you can install sourmash by running:
which will install the latest released version.
Support
For questions, please open an issue on Github, or ask in our chat.
Development
Development happens on github at sourmash-bio/sourmash.
sourmash is developed in Python and Rust, and you will need a Rust environment to build it; see the developer notes for our suggested development setup.
After installation,
sourmashis the main command-line entry point; run it withpython -m sourmash, or dopip install -e /path/to/repoto do a developer install in a virtual environment.The
sourmash/directory contains the Python library and command-line interface code.The
src/core/directory contains the Rust library implementing core functionality.Tests require py.test and can be run with
make test.Please see the developer notes for more information on getting set up with a development environment.
CTB Jan 2024