cylindra
cylindra is a GUI-integrated cryo-ET image analysis tool for cylindrical periodic
structures such as microtubules.
→ Documentation
Installation
- Use
pip
pip install cylindra[recommended] -U
- From source
If you install from the source, you'll need Rust to compile a part of the code.
git clone https://github.com/hanjinliu/cylindra.git
cd cylindra
pip install -e .[recommended]
Usage
Launch GUI
-
From shell
cylindra
-
From a Python interpreter
from cylindra import start # launch a napari viewer with a cylindra dock widget. ui = start()
Command line interface
cylindra is implemented with some basic command line interface (CLI).
cylindra --help
Implemented Functions
- Automatic/manual fitting of splines to cylindrical structures in 3D.
- Analyze lattice structures (such as lattice spacing and skew angle) using Cylindric Fourier transformation.
- Automatic determination of polarity, protofilament number etc.
- Monomer mapping along splines for subtomogram averaging and alignment.
- Microtubule seam search with or without binding proteins.
- Subtomogram alignment with 2D constraint.
- Tomogram simulation of cylindric structures.
- Efficient manual picking along cylindrical structures.
Prerequisite and Recommendations
- Python ≥ 3.12. This project follows spec-0000.
- Sufficient memory size. Most of the intense calculations are done out-of-core
using
dask, so that you can even run on 8-GB memory PC in many cases. However, larger memory size will make parallel processing more efficient. ≥32 GB is recommended. - Images should be loaded from SSD. Raw image stacks are loaded lazily in most of the processes. Loading from HDD will slow down many analyses as well. In the latest version, you can use "Cache image on SSD" option to directly analyze tomograms stored in HDD.
Issues
If you encountered any bugs or have any requests, feel free to report an issue. (We'll appreciate if you find some methods are over-fitted to microtubules and do not work well on other cylindric structures)
For better reproducibility, please copy your environments from Others > cylindra info
and the recorded macro from Others > Macro > Show macro.
Citation
If you find cylindra useful in your work, please consider citing our paper.
Heterogeneous local structures of the microtubule lattice revealed by cryo-ET and non-averaging analysis
Hanjin Liu, Hiroshi Yamaguchi, Masahide Kikkawa, Tomohiro Shima
bioRxiv 2024.04.30.591984; doi: https://doi.org/10.1101/2024.04.30.591984
1 maintainer
Metadata
1 maintainer
Release files for cylindra 1.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| cylindra-1.3.0.tar.gz | 15.1 MB | Without provenance | Details for cylindra-1.3.0.tar.gz |
Built distributions (wheels)
Total release size: 68.8 MB
Release files / cylindra-1.3.0.tar.gz
| Download URL | cylindra-1.3.0.tar.gz |
|---|---|
| Size | 15.1 MB |
| Tags | Source |
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maturin/1.16.0
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Release files / cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_s390x.manylinux_2_17_s390x.whl |
|---|---|
| Size | 1.2 MB |
| Tags | Linux glibc 2.17+ IBM System/390x PyPy 3.12 PyPy 3.12 8.0 |
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Release files / cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
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| Tags | Linux glibc 2.17+ PowerPC 64-le PyPy 3.12 PyPy 3.12 8.0 |
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Release files / cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_armv7l.manylinux_2_17_armv7l.whl
| Download URL | cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_armv7l.manylinux_2_17_armv7l.whl |
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Release files / cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | cylindra-1.3.0-pp312-pypy312_pp80-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
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| Tags | CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ x86-64 |
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| Download URL | cylindra-1.3.0-cp315-cp315t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
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Release files / cylindra-1.3.0-cp315-cp315t-manylinux1_i686.manylinux_2_5_i686.whl
| Download URL | cylindra-1.3.0-cp315-cp315t-manylinux1_i686.manylinux_2_5_i686.whl |
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| Tags | CPython 3.15 CPython 3.15 free-threading Linux glibc 2.5+ x86-32 |
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Release files / cylindra-1.3.0-cp315-cp315-win_amd64.whl
| Download URL | cylindra-1.3.0-cp315-cp315-win_amd64.whl |
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| Download URL | cylindra-1.3.0-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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| Tags | CPython 3.15 Linux glibc 2.17+ x86-64 |
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| Download URL | cylindra-1.3.0-cp315-cp315-manylinux2014_s390x.manylinux_2_17_s390x.whl |
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| Download URL | cylindra-1.3.0-cp315-cp315-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
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| Download URL | cylindra-1.3.0-cp315-cp315-manylinux2014_armv7l.manylinux_2_17_armv7l.whl |
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| Size | 1.1 MB |
| Tags | CPython 3.15 Linux glibc 2.17+ ARMv7l |
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| Download URL | cylindra-1.3.0-cp314-cp314t-manylinux2014_s390x.manylinux_2_17_s390x.whl |
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| Tags | CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ IBM System/390x |
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| Tags | CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ PowerPC 64-le |
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| Download URL | cylindra-1.3.0-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
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| Tags | CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARM64 |
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| Download URL | cylindra-1.3.0-cp314-cp314-win_amd64.whl |
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Release files / cylindra-1.3.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
| Download URL | cylindra-1.3.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.14 Linux glibc 2.17+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | cylindra-1.3.0-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.14 Linux glibc 2.17+ IBM System/390x |
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SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | cylindra-1.3.0-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.14 Linux glibc 2.17+ PowerPC 64-le |
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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 |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp314-cp314-manylinux2014_armv7l.manylinux_2_17_armv7l.whl
| Download URL | cylindra-1.3.0-cp314-cp314-manylinux2014_armv7l.manylinux_2_17_armv7l.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.14 Linux glibc 2.17+ ARMv7l |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | cylindra-1.3.0-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.14 Linux glibc 2.17+ 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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp314-cp314-manylinux1_i686.manylinux_2_5_i686.whl
| Download URL | cylindra-1.3.0-cp314-cp314-manylinux1_i686.manylinux_2_5_i686.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.14 Linux glibc 2.5+ 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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp314-cp314-macosx_10_12_x86_64.whl
| Download URL | cylindra-1.3.0-cp314-cp314-macosx_10_12_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.14 macOS 10.12+ 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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-win_amd64.whl
| Download URL | cylindra-1.3.0-cp313-cp313-win_amd64.whl |
|---|---|
| Size | 984.4 kB |
| Tags | CPython 3.13 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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
| Download URL | cylindra-1.3.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.13 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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | cylindra-1.3.0-cp313-cp313-manylinux2014_s390x.manylinux_2_17_s390x.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.13 Linux glibc 2.17+ IBM System/390x |
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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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | cylindra-1.3.0-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.13 Linux glibc 2.17+ PowerPC 64-le |
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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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-manylinux2014_armv7l.manylinux_2_17_armv7l.whl
| Download URL | cylindra-1.3.0-cp313-cp313-manylinux2014_armv7l.manylinux_2_17_armv7l.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.13 Linux glibc 2.17+ 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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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | cylindra-1.3.0-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.13 Linux glibc 2.17+ 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-manylinux1_i686.manylinux_2_5_i686.whl
| Download URL | cylindra-1.3.0-cp313-cp313-manylinux1_i686.manylinux_2_5_i686.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.13 Linux glibc 2.5+ 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp313-cp313-macosx_10_12_x86_64.whl
| Download URL | cylindra-1.3.0-cp313-cp313-macosx_10_12_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.13 macOS 10.12+ 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-win_amd64.whl
| Download URL | cylindra-1.3.0-cp312-cp312-win_amd64.whl |
|---|---|
| Size | 983.9 kB |
| Tags | CPython 3.12 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-win32.whl
| Download URL | cylindra-1.3.0-cp312-cp312-win32.whl |
|---|---|
| Size | 924.6 kB |
| Tags | CPython 3.12 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
| Download URL | cylindra-1.3.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.12 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | cylindra-1.3.0-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ IBM System/390x |
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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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | cylindra-1.3.0-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
|---|---|
| Size | 1.3 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ PowerPC 64-le |
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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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-manylinux2014_armv7l.manylinux_2_17_armv7l.whl
| Download URL | cylindra-1.3.0-cp312-cp312-manylinux2014_armv7l.manylinux_2_17_armv7l.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | cylindra-1.3.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-manylinux1_i686.manylinux_2_5_i686.whl
| Download URL | cylindra-1.3.0-cp312-cp312-manylinux1_i686.manylinux_2_5_i686.whl |
|---|---|
| Size | 1.2 MB |
| Tags | CPython 3.12 Linux glibc 2.5+ x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Release files / cylindra-1.3.0-cp312-cp312-macosx_10_12_x86_64.whl
| Download URL | cylindra-1.3.0-cp312-cp312-macosx_10_12_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.12 macOS 10.12+ 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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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
maturin/1.16.0
|
Security for cylindra 1.3.0
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