oxli
oxli is a powerful Rust library with a simple Python interface for counting k-mers in genomic sequencing data.
Use oxli to bring fast kmer counting and comparison operations to your Python projects.
This library is written on top of the sourmash rust library, and the underlying code for dealing with sequence data is well tested.
Installation
Quick setup
oxli is available on conda-forge for Linux, Mac OS X, and Windows for Python versions 3.10, 3.11, and 3.12:
conda install oxli
This will install the oxli library for Python.
For developers
You can also try building oxli yourself and using it in development mode:
# Setup conda development env
mamba env create -f environment.yml -n oxli
# Install oxli in dev mode
pip install -e '.[test]'
Getting Started
See the the oxli Wiki for documentation on the Python API.
Basic Usage
Initialise a new KmerCountTable
# Import oxli
from oxli import KmerCountTable
# Create new count table
kct = KmerCountTable(ksize=4) # Count 4-mers
Adding k-mer counts.
# Add single k-mer with count()
kct.count("AAAA")
>>> 1
# Increment count
kct.count("AAAA")
>>> 2
# Forward and Reverse complement counted together
kct.count("TTTT")
>>> 3
# Add many k-mers from a longer sequence with consume
kct.consume("GGGGGGGGGG") # 7 x 4-mers of 'GGGG'
Lookup counts by k-mer.
# Retrieve kmer counts
kct.get('GGGG') # Count for GGGG/CCCC
>>> 7
kct.get('AAAA') #Count for AAAA/TTTT
>>> 3
Extracting k-mers from files.
# Screed for FASTA/FASTQ parsing
import screed
# Create new table
counts = KmerCountTable(ksize=21)
# Read fasta records and extract k-mers
for record in screed.open('doc/example.fa'):
counts.consume(record.sequence)
>>> 349910
What's the history here?
First, oxli is channeling khmer, a package written by @ctb and many others. You shouldn't be too surprised to see useful functionality from khmer making an appearance in oxli.
The khmer package was useful for inspecting large collections of k-mers, but was hard to maintain and evolve.
In ~2016 @ctb's lab more or less switched over to developing sourmash, which was initially built on a similar tech stack to khmer (Python & C++).
At some point, @luizirber rewrote the sourmash C++ code into Rust.
This forced @ctb to learn Rust to maintain sourmash.
@ctb then decided he liked Rust an awful lot, and missed some of the khmer functionality.
And, voila! oxli was born.
Authors
Author: C. Titus Brown (@ctb), ctbrown@ucdavis.edu
with with miscellaneous features by @Adamtaranto
2 maintainers
Release files for oxli 0.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| oxli-0.3.0.tar.gz | 143.8 kB | Details |
Built distributions (wheels)
Total release size:92.2 MB
Release files / oxli-0.3.0.tar.gz
| Download URL | oxli-0.3.0.tar.gz |
|---|---|
| Size | 143.8 kB |
| Tags | Source |
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Release files / oxli-0.3.0-pp310-pypy310_pp73-musllinux_1_2_x86_64.whl
| Download URL | oxli-0.3.0-pp310-pypy310_pp73-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 2.0 MB |
| Tags | Linux musl 1.2+ x86-64 PyPy 3.10 PyPy 3.10 7.3 |
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| Download URL | oxli-0.3.0-pp310-pypy310_pp73-musllinux_1_2_i686.whl |
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| Tags | Linux musl 1.2+ x86-32 PyPy 3.10 PyPy 3.10 7.3 |
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Yes |
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maturin/1.7.1
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Release files / oxli-0.3.0-cp311-none-win_amd64.whl
| Download URL | oxli-0.3.0-cp311-none-win_amd64.whl |
|---|---|
| Size | 1.4 MB |
| Tags | CPython 3.11 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Yes |
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maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-none-win32.whl
| Download URL | oxli-0.3.0-cp311-none-win32.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.11 Windows x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Yes |
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maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-musllinux_1_2_x86_64.whl
| Download URL | oxli-0.3.0-cp311-cp311-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-musllinux_1_2_i686.whl
| Download URL | oxli-0.3.0-cp311-cp311-musllinux_1_2_i686.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-musllinux_1_2_armv7l.whl
| Download URL | oxli-0.3.0-cp311-cp311-musllinux_1_2_armv7l.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.11 Linux musl 1.2+ ARMv7l |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-musllinux_1_2_aarch64.whl
| Download URL | oxli-0.3.0-cp311-cp311-musllinux_1_2_aarch64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.11 Linux musl 1.2+ ARM64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | oxli-0.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | oxli-0.3.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ IBM System/390x |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
| Download URL | oxli-0.3.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ PowerPC 64-le |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | oxli-0.3.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | oxli-0.3.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 1.7 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ ARMv7l |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | oxli-0.3.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 1.7 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | oxli-0.3.0-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 1.4 MB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp311-cp311-macosx_10_12_x86_64.whl
| Download URL | oxli-0.3.0-cp311-cp311-macosx_10_12_x86_64.whl |
|---|---|
| Size | 1.7 MB |
| Tags | CPython 3.11 macOS 10.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-none-win_amd64.whl
| Download URL | oxli-0.3.0-cp310-none-win_amd64.whl |
|---|---|
| Size | 1.4 MB |
| Tags | CPython 3.10 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-none-win32.whl
| Download URL | oxli-0.3.0-cp310-none-win32.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.10 Windows x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-musllinux_1_2_x86_64.whl
| Download URL | oxli-0.3.0-cp310-cp310-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-musllinux_1_2_i686.whl
| Download URL | oxli-0.3.0-cp310-cp310-musllinux_1_2_i686.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-musllinux_1_2_armv7l.whl
| Download URL | oxli-0.3.0-cp310-cp310-musllinux_1_2_armv7l.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.10 Linux musl 1.2+ ARMv7l |
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SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-musllinux_1_2_aarch64.whl
| Download URL | oxli-0.3.0-cp310-cp310-musllinux_1_2_aarch64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.10 Linux musl 1.2+ ARM64 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | oxli-0.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | oxli-0.3.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl |
|---|---|
| Size | 2.0 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ IBM System/390x |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
| Download URL | oxli-0.3.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ PowerPC 64-le |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | oxli-0.3.0-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | oxli-0.3.0-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 1.7 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARMv7l |
|
SHA-256 checksum How to use checksums |
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|
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | oxli-0.3.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 1.7 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
Release files / oxli-0.3.0-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | oxli-0.3.0-cp310-cp310-macosx_11_0_arm64.whl |
|---|---|
| Size | 1.4 MB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
maturin/1.7.1
|
