A multithreaded python wrapper for rust bindings of minimap2.
Project description
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_batch
to 50 milliseconds, with 6 attempts. Each attempt will double the previous back off time. - Improved error handling for
map_batch
, now will raise aRuntimeError
if the backoff time is exceeded. Also prevented loggingInternal error returning data, the receiver iterator has finished. sending on a disconnected channel 2870
to stderr excessively. - Added tests for mapping more than 50000 reads, using
back_off=True
andback_off=False
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BLAKE2b-256 | fed803ca34c108449a85df3142c5d3e92f7eff0ac94530e1f73aba629d813ea8 |
Hashes for mappy_rs-0.0.7-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 69ef5e13bfbdfff71eb164611ecee2b99f5e24273324e7e1c1c135374a828dbb |
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MD5 | 22ee6260dbb51ffc3875bf6459fc9179 |
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BLAKE2b-256 | 115a9ebd888d6d6f7ded3ba8daedf7ff2a3202011d53e671ed61f8701f218ded |
Hashes for mappy_rs-0.0.7-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 58dc220c69c9559a13981b216cfef7aa32d00f90bbdaf5cf9d5b8a6595e99cb8 |
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MD5 | 315f0715cab5aee32fec41d585f77d41 |
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BLAKE2b-256 | 11fb0aa767355d34a3798e3166807f29bbf4c344c13af4a79a3ef7a0a60e7e56 |
Hashes for mappy_rs-0.0.7-cp311-cp311-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 9e631ebd336175e51ea24d0527c3ae1f680761764a2eba8abe70f47df7e095f6 |
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MD5 | 7055d88c06443e1de712158b1270b36e |
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BLAKE2b-256 | 16a71bdbdf0d8627808b879e8e7a74536cbffc0d85413252e8a4b633beb00014 |
Hashes for mappy_rs-0.0.7-cp311-cp311-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | bd28f9def43fa00dcba2b81f2c2fd73a92139d13cb310303b89fb2fb5f6db448 |
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MD5 | 0d750de60507113f39d5b6e2782f8693 |
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BLAKE2b-256 | bae78b4548d5854e03cf1e667ab89620614109184629f130299db066b62cc191 |
Hashes for mappy_rs-0.0.7-cp311-cp311-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 390a275f7bb3cb6f942557b4e6568bbe4a1c23d4cc9b4e39350aa860a8dd7bcf |
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MD5 | 1091296060887269b208905337282fab |
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BLAKE2b-256 | fb25af11fb904aa61159eb27c568133185bbefb605366fbb980cd95d94cdf6be |
Hashes for mappy_rs-0.0.7-cp310-cp310-musllinux_1_2_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2552e9d2f91ebc41611999696b5995fe04758247473866aec2c0f3b3cf837301 |
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MD5 | e33436a0d7d2c56c3a7fe791fdd2a391 |
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BLAKE2b-256 | 766b82b450dd2d8277c6a10772f98185ba3ecd241310df5967ee49fa5d33a7bc |
Hashes for mappy_rs-0.0.7-cp310-cp310-musllinux_1_2_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2ff5af4d2060e1bcf37257d6451cbc5c997fc809d327cbc8db50405bc9a367ba |
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MD5 | 91bc788d93587a8f405892e2ee260008 |
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BLAKE2b-256 | ec5bd2d25917bad66035477392a2bb4fc6fb2d5ad05be9f40aeae743fc5ef2ec |
Hashes for mappy_rs-0.0.7-cp310-cp310-musllinux_1_2_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b9de76c2bbcaaf9ca7880a42f5c22f9d4c3bf290acd9abf4162c1af4c93454d2 |
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MD5 | b15cef9f5d5ae43aded5994997d27f5b |
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BLAKE2b-256 | 3898420c94d0642410792e41dd6347b6ffc7b839e9b2e01d5b54e58ac8cea0bf |
Hashes for mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 408055b692370861191517970757847c5361b4d95f64f9fccf03aada83710357 |
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MD5 | 955c70b3487186d76cc7ff7f7c09d621 |
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BLAKE2b-256 | 27e88adff644d59b52de5de045332b5fa463cc032608839e26363df43241591c |
Hashes for mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 64f089214d3fc2df08e78ad626847bddc85768fbd109ed1b458ccbbaddebd281 |
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MD5 | b88ad17de96a5dea4868447b1e372f11 |
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BLAKE2b-256 | 80a99a0f10ce8d88f0810364e5fd8ea80b35e9b8419dccbc075fb1823cbc510c |
Hashes for mappy_rs-0.0.7-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5c8fd468b145d11f6616f974c9e2faa976ca262de317fd190bc5e75bbc18eee3 |
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MD5 | 87ba87ddb0b24c1decf3bdd8fdef0efb |
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BLAKE2b-256 | b3f7d9a33aefd066a49aa46ddd5254c430e59f595656f4310549434e2fc42e8a |
Hashes for mappy_rs-0.0.7-cp310-cp310-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d166309a98c8301e5e248c68bf5518d8714ccbe74aa425368da65ceb99995079 |
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MD5 | de3b078e0acf3430b8241f64aceb21ec |
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BLAKE2b-256 | 28edd6d743092d1f8965b67527c57d3f1eb65e8fa5926a04791a1f896eba4a5d |
Hashes for mappy_rs-0.0.7-cp310-cp310-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d9c40d13762009b068cb5f72640d91c30ccc931046d4571d48ab19e0787b08a0 |
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MD5 | 804c27832f62ad5756f9b4e41b7ecca5 |
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BLAKE2b-256 | 8feb73d551c97769047bb83f0c8cf79bddce74a5a2cddb8b2c03afb0d2b74234 |
Hashes for mappy_rs-0.0.7-cp310-cp310-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a3332daedb73950ebe062ea9445e0a1fc55d6d73a5f4ffd4d32c93dda1347da9 |
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MD5 | 733166c4205546e2d81de6ae771f8e1c |
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BLAKE2b-256 | 6b1468b9f9f18f181b63b945af868949daa97a94c29cb339a7832cd8c020b181 |
Hashes for mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 802890b091ea25aa2038b48a145f1f90b77369dbe958282891bccc03f0d6b5b3 |
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MD5 | 52017da72599692c126326d9445032fc |
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BLAKE2b-256 | a5edd1169a6dc96a5748cb26c8d954b9185032b8ca0eccceab0078a642eee9f9 |
Hashes for mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5d6ba835bd0140a405e588c0308c142c55ea056bc7c879066601b32016f90b47 |
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MD5 | 068e62d76ef55d63dfb05fff860c0418 |
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BLAKE2b-256 | cddab54a352def4d5469df2dba4fb8bb5f0d0d189ea0822946f1a91fbef2f3a5 |
Hashes for mappy_rs-0.0.7-cp39-cp39-musllinux_1_2_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8efcae6e035659fb5a1467ac4389a17cf8265de989581d5791c6f689352cce61 |
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MD5 | fb8c27964041c37037cc7dfb96bedcbf |
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BLAKE2b-256 | bcc5ff93eb76431eb72f8149a9f3a5ac50bd878b38cfe810a1d835053a60336b |
Hashes for mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c82752c90728a5e4704bb39b9916f3db01ff9e667beaebf0087517d2516db66e |
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MD5 | e5167974820f06c6fa7f67a57986ddf2 |
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BLAKE2b-256 | 9cf50047541c371689e60238367437d2a827c2176e7a3c07e7fcf60586ac797e |
Hashes for mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 460f58c1a0dab73b2b5bf41bd63b761f516c30f48393c91556c5ca6bd1b19ab9 |
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MD5 | e0595c0474afc3cf2387efe622097129 |
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BLAKE2b-256 | 12a8cdc73ca541bd170a923e9752b4caf6708fe3dae8f73daed9309fabd29ca5 |
Hashes for mappy_rs-0.0.7-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c6d91699c4bd0177b10644db8bf40d3ea10206ee4d6092f924a5921e1b764be2 |
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MD5 | 55da5fbcec53f7e84909d01e14726fb1 |
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BLAKE2b-256 | e10c330695b995348984fda38f5d0bfb7dec14176fc66cfd6b08c5dbbcf898f6 |
Hashes for mappy_rs-0.0.7-cp39-cp39-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | dd0ae6237d04c7bb0ef13644cbc91c5c9d64ec1a4a2c741c381144835e13003b |
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MD5 | 8fbad0cc082177fdf313bebbbff333f7 |
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BLAKE2b-256 | 482a50f561350aed256b78c2d9795e8387825ca41e33d2032918ca179e273387 |
Hashes for mappy_rs-0.0.7-cp39-cp39-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 64dff8ec70dcbf3d689caaa8e6b18aeac9c098732d0637dade88ceca02fdba12 |
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MD5 | 2f92fda1e075b6e62e9763a3a20dc69b |
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BLAKE2b-256 | 2a089445fc7fe317fcb79738e3479cc0674226340c05677da3cc68c9a3e4be6e |
Hashes for mappy_rs-0.0.7-cp39-cp39-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f80f1c84871b895b46cc2d1668780c8614d7f7e51fac205510f40b813ad605cf |
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MD5 | 9d4e9b07a388f3d1e0b32ba03c4d1a9f |
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BLAKE2b-256 | c38e1f912b237bcce785b78a870d40bb5ce4108926550c9edcf4321de125b4a5 |
Hashes for mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8763a27864269d70815f05a845e6ce73c77a30f13aaeb80d6233194436b5de12 |
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MD5 | b5dabd414c985bde7b9ed87c33518466 |
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BLAKE2b-256 | 2d6247d85295c56c7f9a3b5f6ee41694f6eb810ddc73587e5c192e055f3d0171 |
Hashes for mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 96f0b5ab2c384662fcecb9b05125afb8269999d7922f0b67a06e871f405adcac |
|
MD5 | 3c82ed98e0d31e582e053db8e4f57124 |
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BLAKE2b-256 | c848f070e03ed370b591c17efbbb3e68ff90e9aad97ef21a55b84ba83a59be3a |
Hashes for mappy_rs-0.0.7-cp38-cp38-musllinux_1_2_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 56795fbeb372fb9880aa5d95678650cef3e27909e1788a9096fc786e289811ea |
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MD5 | 01dc230eda2d76f73b5bbe6af8ad82fa |
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BLAKE2b-256 | 54c272909da4140b4888b951885944f9615e2ab371bae74085686f963f55fb9a |
Hashes for mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 632d39f4e9c9d720370bc384b86289a2b8acff79f57c70e7b0c694cbcd8096df |
|
MD5 | c38e89a6a099435a239cc762314d6990 |
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BLAKE2b-256 | 95a557ff6c5e92d288914cab687a50836194e54b362669f9b17eaa1b15c648c3 |
Hashes for mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 259af58b2a67ee87ffb65b4800aa185192446d2aa615f8eba0363f67641348de |
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MD5 | 671d7fe000d3e6511f73f29a53a6d7c2 |
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BLAKE2b-256 | 9b0ca999b47da6706c906849b7c56004857f92b2633ca7040cfceedf4a725168 |
Hashes for mappy_rs-0.0.7-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b48980e6cce185e5618646a45fa1ed4e3af9a430fbee1943c768251c356b5ee5 |
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MD5 | 0ad72bbb443de343f21f42b69e1b3267 |
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BLAKE2b-256 | 2b2938985f30555669510befbc7229e32f31e34d5bca7de2a22d32ae6cd15ba9 |
Hashes for mappy_rs-0.0.7-cp38-cp38-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 551104d48f9d190b800939a607ad083242673f37468c5269b0293d58f1537f23 |
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MD5 | 20261ee4bcefdde21342f3fb7bb9a985 |
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BLAKE2b-256 | df63fe55035cee29c8c384bcfe0a7cf27a1ce2d9b3df999da92b38ad8d651423 |
Hashes for mappy_rs-0.0.7-cp38-cp38-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 643aab18f94857d85c5730082ad1dbe604ea3248512a3667c28c4c98bb49a0b7 |
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MD5 | 5764f275725f8c96ff93451fdb5d18d0 |
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BLAKE2b-256 | 701c844a6201224a6ee76f1f65ae2552dfdd62755e17f28d3c2506fcf597b831 |
Hashes for mappy_rs-0.0.7-cp38-cp38-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e353dbea215cece9e85855712dcd7a0980450e253f065d17525a09239d82bebe |
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MD5 | 705006be5dec1f2154ff7416f456c9a9 |
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BLAKE2b-256 | a7c7771d8bd06a5ff6cae5f21a5f6505978902b8eed6d448f6e96bd933558edd |