guanaco

https://github.com/rosalindfranklininstitute/guanaco

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
2 of 2 committers (100.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary

Last synced: 11 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: rosalindfranklininstitute
License: gpl-3.0
Language: Python
Default Branch: master
Size: 12.7 MB

Statistics

Stars: 1
Watchers: 0
Forks: 1
Open Issues: 4
Releases: 15

Fork of jmp1985/guanaco

Created over 5 years ago · Last pushed 12 months ago

Metadata Files

Readme License

README.md

guanaco

Python library for doing 3D CTF correction

Installation

In order to build this package, the following dependencies are required:

The CUDA toolkit
FFTW

To install from the github repository do the following

sh export CUDACXX=${PATH_TO_CUDA}/bin/nvcc python -m pip install git+https://github.com/rosalindfranklininstitute/guanaco.git@master

To install from source, clone this repository. The repository has a submodule for pybind11 so after cloning the repository run

sh git submodule update --init --recursive

Then do the following:

sh export CUDACXX=${PATH_TO_CUDA}/bin/nvcc python -m pip install .

If you would like to run the tests then, clone this repository and then do the following:

sh export CUDACXX=${PATH_TO_CUDA}/bin/nvcc python -m pip install .[test]

Installation for developers

To install for development, clone this repository and then do the following:

sh export CUDACXX=${PATH_TO_CUDA}/bin/nvcc python -m pip install -e .

Testing

To run the tests, follow the installation instructions for developers and then do the following:

sh pytest

Usage

To do a tomographic reconstruction with no CTF correction do something do the following

sh guanaco -i images.mrc -o rec.mrc -d gpu

To correct all images with the same single defocus something do the following

sh guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7

To correct all images with the same defocus range something do the following

sh guanaco -i images.mrc -o rec.mrc -d gpu --df=20000 --Cs=2.7 --ndf=10

Issues

Please use the GitHub issue tracker to submit bugs or request features.

License

Distributed under the terms of the GPLv3 license, guanaco is free and open source software.

Owner

Name: Rosalind Franklin Institute
Login: rosalindfranklininstitute
Kind: organization
Email: info@rfi.ac.uk
Location: UK

Website: https://rfi.ac.uk
Repositories: 32
Profile: https://github.com/rosalindfranklininstitute

The Rosalind Franklin Institute is dedicated to transforming life science through interdisciplinary research and technology development

GitHub Events

Total

Release event: 2
Push event: 10
Create event: 1

Last Year

Release event: 2
Push event: 10
Create event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 128
Total Committers: 2
Avg Commits per committer: 64.0
Development Distribution Score (DDS): 0.008

Past Year

Commits: 9
Committers: 1
Avg Commits per committer: 9.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
James Parkhurst	j**t@d**k	127
DimitriosBellos	D**s@r**k	1

Committer Domains (Top 20 + Academic)

rfi.ac.uk: 1 diamond.ac.uk: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time

Total issues: 4
Total pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: 5 days
Total issue authors: 2
Total pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.5
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jmp1985 (3)
DimitriosBellos (1)

Pull Request Authors

DimitriosBellos (2)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 112 last-month

Total dependent packages: 2
Total dependent repositories: 1
Total versions: 14
Total maintainers: 1

pypi.org: guanaco

3D CTF correction

Documentation: https://guanaco.readthedocs.io/
License: gpl-3.0
Latest release: 0.3.4
published 12 months ago

Versions: 14
Dependent Packages: 2
Dependent Repositories: 1
Downloads: 112 Last month

Rankings

Dependent packages count: 4.7%

Downloads: 14.0%

Average: 20.4%

Dependent repos count: 21.8%

Forks count: 22.6%

Stargazers count: 38.8%

Maintainers (1)

james_2002uk

Last synced: 12 months ago

Dependencies

.github/workflows/conda.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/python-package.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/python-publish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

conda/environment.yaml conda

anaconda-client
conda-build
conda-verify
cudatoolkit-dev
python 3.9.*

requirements.txt pypi

cmake *
mock *
ninja *
pytest *
pytest-cov *
scipy *
setuptools *
wheel *

setup.py pypi

mrcfile *