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dependabot[bot]

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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⚠️ Dependabot is rebasing this PR ⚠️

Rebasing might not happen immediately, so don’t worry if this takes some time.

Note: if you make any changes to this PR yourself, they will take precedence over the rebase.


⚠️ Dependabot is rebasing this PR ⚠️

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Note: if you make any changes to this PR yourself, they will take precedence over the rebase.


Updates the requirements on maturin to permit the latest version. Updates maturin to 1.12.2

Release notes

Sourced from maturin's releases.

v1.12.2

What's Changed

Full 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-include CLI 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_DIR assets 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@v14 in 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 RECORD paths (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
  • adb2906 Release v1.12.2
  • 6473568 fix: allow absolute paths for --sbom-include (#3004)
  • e772489 Release v1.12.1
  • 0672082 add test case for uniffi with multiple crates (#2839)
  • f201566 feat: support including OUT_DIR assets in wheel builds (#3001)
  • 66b4869 feat: log external shared libraries and their dependents before patchelf
  • 8f8f9f7 fix: resolve include patterns relative to python-source for sdist and wheel (...
  • 1688a73 netlify: update mdbook to 0.5.2
  • aefe09d Add --sbom-include CLI argument for additional SBOM files (#2999)
  • 8a688ca Document SBOM support in user guide
  • Additional commits viewable in compare view

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13天前2337次提交

sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

Project Status: Active – The project has reached a stable, usable state and is being actively developed. License: 3-Clause BSD Documentation Gitter

DOI pyOpenSci

Bioconda install PyPI Conda Platforms Debian Testing Debian Unstable

Python 3.11 Python 3.12 Python 3.13 Build Status codecov

Usage:

sourmash sketch dna *.fq.gz
sourmash compare *.sig -o distances.cmp -k 31
sourmash plot distances.cmp

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:

  • FracMinHash sketching, which enables accurate comparisons (including ANI) between data sets of different sizes
  • sourmash gather, a combinatorial k-mer approach for more accurate metagenomic profiling

Please 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:

conda install -c conda-forge sourmash-minimal

This will install the latest stable version of sourmash 4.

You can also use pip to install sourmash:

pip 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:

$ conda create -n sourmash_env -c conda-forge sourmash-minimal
$ conda activate sourmash_env
$ sourmash --help

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, sourmash is the main command-line entry point; run it with python -m sourmash, or do pip install -e /path/to/repo to 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

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