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Open Source Science

https://github.com/ccpem/caked

https://github.com/ccpem/caked

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: ccpem
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 5.46 MB
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 0
  • Open Issues: 8
  • Releases: 3
Created over 2 years ago · Last pushed 12 months ago
Metadata Files
Readme Contributing License Code of conduct

README.md

CAKED

Actions Status PyPI version PyPI platforms

A package to load tomograms and subtomograms from different sources into a PyTorch DataLoader class.

The DiskDataLoader and DiskDataset classes were initially developed for Affinity-VAE by Marjan Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith (@crangelsmith). These authors have also prepared and curated the corresponding test data.

Installation

bash python -m venv env source env/bin/activate python -m pip install --upgrade pip python -m pip install caked

From source:

bash git clone https://github.com/alan-turing-institute/CAKED cd CAKED python -m pip install .

Usage

Contributing

See CONTRIBUTING.md for instructions on how to contribute.

License

Distributed under the terms of the MIT license.

This packaged was based on this very useful and well built project template.

Owner

  • Name: CCP-EM
  • Login: ccpem
  • Kind: organization

Collaborative Computational Project for Electron cryo-Microscopy

GitHub Events

Total
  • Release event: 3
  • Watch event: 1
  • Member event: 1
  • Push event: 6
  • Pull request review event: 1
  • Pull request event: 5
  • Create event: 5
Last Year
  • Release event: 3
  • Watch event: 1
  • Member event: 1
  • Push event: 6
  • Pull request review event: 1
  • Pull request event: 5
  • Create event: 5

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 18
  • Total pull requests: 20
  • Average time to close issues: 6 days
  • Average time to close pull requests: 7 days
  • Total issue authors: 3
  • Total pull request authors: 5
  • Average comments per issue: 0.39
  • Average comments per pull request: 0.5
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 days
  • Issue authors: 0
  • Pull request authors: 4
  • Average comments per issue: 0
  • Average comments per pull request: 0.17
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mooniean (2)
Pull Request Authors
  • mooniean (9)
  • JatGreer (5)
  • jolaem (3)
  • dependabot[bot] (3)
  • hllelli2 (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (3) disk (1)

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3.1.4 composite
  • pre-commit/action v3.0.0 composite
pyproject.toml pypi
  • mrcfile *
  • numpy *
  • pandas *
  • pyarrow *
  • scipy *
  • torch *
  • torchvision *