ATrieGC
A python/c++ module to store large amount of sequences and look at hamming distance clustering. Should be a lot faster than the naive method (measuring every hamming distances between pairs).
Installation
After cloning the git repository:
pip3 install atriegc
Usage
Working with the nucleotide alphabet
import atriegc
tr = atriegc.TrieNucl()
tr.insert("AAAATGC")
tr.insert("ATAATGC")
tr.insert("TTTTTGC")
max_hamming_distance = 1
print(tr.neighbours("AAATTGC", max_hamming_distance))
print(tr.clusters(max_hamming_distance))
Working with the amino acid alphabet
Where aminoacid are indicated with capital letters.
tr = atriegc.TrieAA()
tr.insert("CARGKYSPATFDSW")
Working with a generic alphabet
The alphabet should be passed as a string which lists all the possible characters of the alphabet
tr = atriegc.Trie("abcdef")
1 maintainer
Metadata
1 maintainer
Release files for atriegc 0.0.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| atriegc-0.0.4.tar.gz | 15.9 kB | Details |
Built distributions (wheels)
Total release size: 59.0 MB
Release files / atriegc-0.0.4.tar.gz
| Download URL | atriegc-0.0.4.tar.gz |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp310-cp310-musllinux_1_2_x86_64.whl
| Download URL | atriegc-0.0.4-cp310-cp310-musllinux_1_2_x86_64.whl |
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| Size | 2.2 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 |
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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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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp310-cp310-musllinux_1_2_i686.whl
| Download URL | atriegc-0.0.4-cp310-cp310-musllinux_1_2_i686.whl |
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| Size | 2.3 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-32 |
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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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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | atriegc-0.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 1.3 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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SHA-256 checksum How to use checksums |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | atriegc-0.0.4-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl |
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| Size | 1.3 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-32 |
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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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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | atriegc-0.0.4-cp310-cp310-macosx_11_0_arm64.whl |
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| Size | 100.3 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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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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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp310-cp310-macosx_10_9_x86_64.whl
| Download URL | atriegc-0.0.4-cp310-cp310-macosx_10_9_x86_64.whl |
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| Size | 102.7 kB |
| Tags | CPython 3.10 macOS 10.9+ x86-64 |
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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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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-win_amd64.whl
| Download URL | atriegc-0.0.4-cp39-cp39-win_amd64.whl |
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| Size | 89.8 kB |
| Tags | CPython 3.9 Windows x86-64 |
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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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No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-win32.whl
| Download URL | atriegc-0.0.4-cp39-cp39-win32.whl |
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| Size | 81.9 kB |
| Tags | CPython 3.9 Windows x86-32 |
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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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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-musllinux_1_2_x86_64.whl
| Download URL | atriegc-0.0.4-cp39-cp39-musllinux_1_2_x86_64.whl |
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| Size | 2.2 MB |
| Tags | CPython 3.9 Linux musl 1.2+ x86-64 |
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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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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-musllinux_1_2_i686.whl
| Download URL | atriegc-0.0.4-cp39-cp39-musllinux_1_2_i686.whl |
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| Size | 2.3 MB |
| Tags | CPython 3.9 Linux musl 1.2+ x86-32 |
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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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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | atriegc-0.0.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 1.3 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
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SHA-256 checksum How to use checksums |
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No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | atriegc-0.0.4-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl |
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| Size | 1.3 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-32 |
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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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No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp39-cp39-macosx_11_0_arm64.whl
| Download URL | atriegc-0.0.4-cp39-cp39-macosx_11_0_arm64.whl |
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| Size | 100.5 kB |
| Tags | CPython 3.9 macOS 11.0+ ARM64 |
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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? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp39-cp39-macosx_10_9_x86_64.whl
| Download URL | atriegc-0.0.4-cp39-cp39-macosx_10_9_x86_64.whl |
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| Size | 102.8 kB |
| Tags | CPython 3.9 macOS 10.9+ x86-64 |
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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? |
No |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp38-cp38-win_amd64.whl
| Download URL | atriegc-0.0.4-cp38-cp38-win_amd64.whl |
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| Size | 89.7 kB |
| Tags | CPython 3.8 Windows x86-64 |
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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? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp38-cp38-win32.whl
| Download URL | atriegc-0.0.4-cp38-cp38-win32.whl |
|---|---|
| Size | 81.7 kB |
| Tags | CPython 3.8 Windows x86-32 |
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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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No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp38-cp38-musllinux_1_2_x86_64.whl
| Download URL | atriegc-0.0.4-cp38-cp38-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 2.2 MB |
| Tags | CPython 3.8 Linux musl 1.2+ x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp38-cp38-musllinux_1_2_i686.whl
| Download URL | atriegc-0.0.4-cp38-cp38-musllinux_1_2_i686.whl |
|---|---|
| Size | 2.3 MB |
| Tags | CPython 3.8 Linux musl 1.2+ x86-32 |
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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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No |
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twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | atriegc-0.0.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
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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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No |
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twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | atriegc-0.0.4-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-32 |
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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? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp38-cp38-macosx_11_0_arm64.whl
| Download URL | atriegc-0.0.4-cp38-cp38-macosx_11_0_arm64.whl |
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| Size | 100.3 kB |
| Tags | CPython 3.8 macOS 11.0+ ARM64 |
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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? |
No |
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twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp38-cp38-macosx_10_9_x86_64.whl
| Download URL | atriegc-0.0.4-cp38-cp38-macosx_10_9_x86_64.whl |
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| Size | 102.6 kB |
| Tags | CPython 3.8 macOS 10.9+ x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp37-cp37m-win_amd64.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-win_amd64.whl |
|---|---|
| Size | 90.2 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Windows x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp37-cp37m-win32.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-win32.whl |
|---|---|
| Size | 82.9 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Windows x86-32 |
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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? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp37-cp37m-musllinux_1_2_x86_64.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-musllinux_1_2_x86_64.whl |
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| Size | 2.2 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux musl 1.2+ x86-64 |
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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? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp37-cp37m-musllinux_1_2_i686.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-musllinux_1_2_i686.whl |
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| Size | 2.3 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux musl 1.2+ x86-32 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
|
Release files / atriegc-0.0.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-64 |
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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? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-32 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp37-cp37m-macosx_10_9_x86_64.whl
| Download URL | atriegc-0.0.4-cp37-cp37m-macosx_10_9_x86_64.whl |
|---|---|
| Size | 102.2 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc macOS 10.9+ x86-64 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-win_amd64.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-win_amd64.whl |
|---|---|
| Size | 90.1 kB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Windows x86-64 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-win32.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-win32.whl |
|---|---|
| Size | 82.7 kB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Windows x86-32 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-musllinux_1_2_x86_64.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 2.2 MB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Linux musl 1.2+ x86-64 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-musllinux_1_2_i686.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-musllinux_1_2_i686.whl |
|---|---|
| Size | 2.3 MB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Linux musl 1.2+ x86-32 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Linux glibc 2.17+ x86-64 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Linux glibc 2.17+ x86-32 |
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twine/5.1.1 CPython/3.12.5
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Release files / atriegc-0.0.4-cp36-cp36m-macosx_10_9_x86_64.whl
| Download URL | atriegc-0.0.4-cp36-cp36m-macosx_10_9_x86_64.whl |
|---|---|
| Size | 101.8 kB |
| Tags | CPython 3.6 CPython 3.6 pymalloc macOS 10.9+ x86-64 |
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twine/5.1.1 CPython/3.12.5
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