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Mappy-rs
A multi-threaded minimap2 aligner for python. Built for readfish compatibility.
Heavily leaning on and inspired by Joeseph Guhlin's minimap2-rs repository. They also have a more heavily featured python client, which also provides multithreaded alignment. This client provides a more simple streaming interface for use in pipelines.
pip install mappy-rs
Developers
Start with some Docs on Py03 - https://pyo3.rs/latest/
If you wish to contribute, have a look at CONTRIBUTING.md
In order to build an importable module:
python -m venv .env
source -m .env/bin/activate
pip install ".[tests]"
To run the tests:
# Python
pytest
# Rust
cargo t --no-default-features
Then in your python shell of choice:
import mappy_rs
aligner = mappy_rs.Aligner("resources/test/test.mmi")
The current iteration of mappy-rs serves as a drop in for mappy, implementing all the same methods. However if this is the use case, you may well be better off using mappy, as the extra level of Rust between your python and C++ may well add slightly slower performance.
Multithreading
In order to use multi threading, one must first enable it.
import mappy_rs
aligner = mappy_rs.Aligner("resources/test/test.mmi")
# Use 10 threads
aligner.enable_threading(10)
Enabling threading makes the map_batch method available.
This method requires a list or iterable of dictionaries, which can have any number of keys and depth, but must contain the key seq with a string value in the top-level dictionary.
Currently, the maximum batch size to be iterated in one call is 20000.
For example:
import mappy_rs
aligner = mappy_rs.Aligner("resources/test/test.mmi")
aligner.enable_threading(10)
seqs = [
{"seq": "ACGTAGCATCGAGACTACGA", "Other_random_key": "banter"},
{"seq": "ACGTAGCATCGAGACTACGA", "Other_random_key": "banter"},
]
for (mapping, data) in aligner.map_batch(seqs):
print(list(mapping))
print(data)
Benchmarks
A simple benchmark against classic mappy, and mappy_rs with incrementing numbers of threads, run on a 2018 Macbook.
Device
| Property | Value |
|---|---|
| Model Name | MacBook Pro |
| Model Identifier | MacBookPro15,2 |
| Processor Name | Quad-Core Intel Core i7 |
| Processor Speed | 2.7 GHz |
| Number of Processors | 1 |
| Total Number of Cores | 4 |
| L2 Cache (per Core) | 256 KB |
| L3 Cache | 8 MB |
| Hyper-Threading Technology | Enabled |
| Memory | 16 GB |
Results
| Name (time in s) | Min | Max | Mean | StdDev | Median | IQR | Outliers | OPS | Rounds | Iterations |
|---|---|---|---|---|---|---|---|---|---|---|
| test_benchmark_multi[5] | 26.8900 (1.0) | 30.0969 (1.0) | 28.0622 (1.0) | 1.2614 (1.0) | 27.9017 (1.0) | 1.6081 (1.35) | 1;0 | 0.0356 (1.0) | 5 | 1 |
| test_benchmark_multi[4] | 28.5573 (1.06) | 43.4543 (1.44) | 32.3371 (1.15) | 6.2815 (4.98) | 29.7480 (1.07) | 5.2148 (4.37) | 1;1 | 0.0309 (0.87) | 5 | 1 |
| test_benchmark_multi[3] | 31.6497 (1.18) | 36.9986 (1.23) | 33.5103 (1.19) | 2.0542 (1.63) | 32.8415 (1.18) | 1.9576 (1.64) | 1;0 | 0.0298 (0.84) | 5 | 1 |
| test_benchmark_multi[2] | 43.2616 (1.61) | 86.3859 (2.87) | 53.8572 (1.92) | 18.3339 (14.53) | 45.9328 (1.65) | 14.6382 (12.26) | 1;1 | 0.0186 (0.52) | 5 | 1 |
| test_classic_mappy[mappy_al] | 78.5566 (2.92) | 82.8876 (2.75) | 79.6177 (2.84) | 1.8343 (1.45) | 78.8350 (2.83) | 1.1938 (1.0) | 1;1 | 0.0126 (0.35) | 5 | 1 |
| test_classic_mappy[mappy_al_rs] | 83.7239 (3.11) | 87.9675 (2.92) | 85.4424 (3.04) | 1.6806 (1.33) | 85.6335 (3.07) | 2.3310 (1.95) | 2;0 | 0.0117 (0.33) | 5 | 1 |
| test_benchmark_multi[1] | 84.8418 (3.16) | 94.0907 (3.13) | 86.7404 (3.09) | 4.1096 (3.26) | 84.8749 (3.04) | 2.4310 (2.04) | 1;1 | 0.0115 (0.32) | 5 | 1 |
Changelog
0.0.6
- Lowered backoff time for
map_batchto 50 milliseconds, with 6 attempts. Each attempt will double the previous back off time. - Improved error handling for
map_batch, now will raise aRuntimeErrorif the backoff time is exceeded. Also prevented loggingInternal error returning data, the receiver iterator has finished. sending on a disconnected channel 2870to stderr excessively. - Added tests for mapping more than 50000 reads, using
back_off=Trueandback_off=False
1 maintainer
Metadata
1 maintainer
Release files for mappy-rs 0.0.7
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Source distribution (sdist)
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| mappy_rs-0.0.7.tar.gz | 1.3 MB | Details |
Built distributions (wheels)
Total release size: 52.3 MB
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Release files / mappy_rs-0.0.7-pp38-pypy38_pp73-musllinux_1_2_aarch64.whl
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Release files / mappy_rs-0.0.7-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / mappy_rs-0.0.7-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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Release files / mappy_rs-0.0.7-pp38-pypy38_pp73-macosx_11_0_arm64.whl
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Release files / mappy_rs-0.0.7-pp38-pypy38_pp73-macosx_10_12_x86_64.whl
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Release files / mappy_rs-0.0.7-pp38-pypy38_pp73-macosx_10_7_x86_64.whl
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Release files / mappy_rs-0.0.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / mappy_rs-0.0.7-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
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Release files / mappy_rs-0.0.7-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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Release files / mappy_rs-0.0.7-cp312-cp312-macosx_11_0_arm64.whl
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Release files / mappy_rs-0.0.7-cp312-cp312-macosx_10_12_x86_64.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-musllinux_1_2_x86_64.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-musllinux_1_2_armv7l.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-musllinux_1_2_aarch64.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-macosx_11_0_arm64.whl
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Release files / mappy_rs-0.0.7-cp311-cp311-macosx_10_12_x86_64.whl
File added late
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Release files / mappy_rs-0.0.7-cp311-cp311-macosx_10_7_x86_64.whl
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Release files / mappy_rs-0.0.7-cp310-cp310-musllinux_1_2_x86_64.whl
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Release files / mappy_rs-0.0.7-cp310-cp310-musllinux_1_2_aarch64.whl
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Release files / mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
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| Size | 973.2 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARMv7l |
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maturin/1.2.3
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Release files / mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 883.7 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 |
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maturin/1.2.3
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Release files / mappy_rs-0.0.7-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | mappy_rs-0.0.7-cp310-cp310-macosx_11_0_arm64.whl |
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| Size | 395.3 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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maturin/1.2.3
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Release files / mappy_rs-0.0.7-cp310-cp310-macosx_10_12_x86_64.whl
File added late
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While project maintainers occasionally add legitimate files to an existing release, late additions can also indicate a security compromise.
We recommend inspecting the release file before installing.
| Download URL | mappy_rs-0.0.7-cp310-cp310-macosx_10_12_x86_64.whl |
|---|---|
| Size | 385.9 kB |
| Tags | CPython 3.10 macOS 10.12+ x86-64 |
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maturin/1.6.0
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Release files / mappy_rs-0.0.7-cp310-cp310-macosx_10_7_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp310-cp310-macosx_10_7_x86_64.whl |
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| Size | 414.5 kB |
| Tags | CPython 3.10 macOS 10.7+ x86-64 |
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maturin/1.2.3
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Release files / mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_x86_64.whl |
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| Size | 986.9 kB |
| Tags | CPython 3.9 Linux musl 1.2+ x86-64 |
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No |
| Uploaded via |
maturin/1.2.3
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Release files / mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_armv7l.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_armv7l.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.9 Linux musl 1.2+ ARMv7l |
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No |
| Uploaded via |
maturin/1.2.3
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Release files / mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_aarch64.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_aarch64.whl |
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| Size | 991.4 kB |
| Tags | CPython 3.9 Linux musl 1.2+ ARM64 |
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No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 835.6 kB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
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No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 973.7 kB |
| Tags | CPython 3.9 Linux glibc 2.17+ ARMv7l |
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No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 884.3 kB |
| Tags | CPython 3.9 Linux glibc 2.17+ ARM64 |
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No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp39-cp39-macosx_11_0_arm64.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-macosx_11_0_arm64.whl |
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| Size | 396.4 kB |
| Tags | CPython 3.9 macOS 11.0+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp39-cp39-macosx_10_12_x86_64.whl
File added late
This file was uploaded more than 14 days after the first file in this release.
While project maintainers occasionally add legitimate files to an existing release, late additions can also indicate a security compromise.
We recommend inspecting the release file before installing.
| Download URL | mappy_rs-0.0.7-cp39-cp39-macosx_10_12_x86_64.whl |
|---|---|
| Size | 386.4 kB |
| Tags | CPython 3.9 macOS 10.12+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.6.0
|
Release files / mappy_rs-0.0.7-cp39-cp39-macosx_10_7_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp39-cp39-macosx_10_7_x86_64.whl |
|---|---|
| Size | 415.3 kB |
| Tags | CPython 3.9 macOS 10.7+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_x86_64.whl |
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| Size | 987.0 kB |
| Tags | CPython 3.8 Linux musl 1.2+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_armv7l.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_armv7l.whl |
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| Size | 1.1 MB |
| Tags | CPython 3.8 Linux musl 1.2+ ARMv7l |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_aarch64.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_aarch64.whl |
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| Size | 991.6 kB |
| Tags | CPython 3.8 Linux musl 1.2+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 835.7 kB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 973.8 kB |
| Tags | CPython 3.8 Linux glibc 2.17+ ARMv7l |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 883.8 kB |
| Tags | CPython 3.8 Linux glibc 2.17+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-macosx_11_0_arm64.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-macosx_11_0_arm64.whl |
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| Size | 396.7 kB |
| Tags | CPython 3.8 macOS 11.0+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
Release files / mappy_rs-0.0.7-cp38-cp38-macosx_10_12_x86_64.whl
File added late
This file was uploaded more than 14 days after the first file in this release.
While project maintainers occasionally add legitimate files to an existing release, late additions can also indicate a security compromise.
We recommend inspecting the release file before installing.
| Download URL | mappy_rs-0.0.7-cp38-cp38-macosx_10_12_x86_64.whl |
|---|---|
| Size | 386.9 kB |
| Tags | CPython 3.8 macOS 10.12+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.6.0
|
Release files / mappy_rs-0.0.7-cp38-cp38-macosx_10_7_x86_64.whl
| Download URL | mappy_rs-0.0.7-cp38-cp38-macosx_10_7_x86_64.whl |
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| Size | 415.9 kB |
| Tags | CPython 3.8 macOS 10.7+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.2.3
|
