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Open Source Science

https://github.com/4dnucleome/partsegcore-compiled-backend

https://github.com/4dnucleome/partsegcore-compiled-backend

Science Score: 39.0%

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
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: 4DNucleome
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 954 KB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 0
  • Open Issues: 5
  • Releases: 0
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License

Readme.md

PartSegCorecompiledbackend

Contributions Wheels PyPI version Anaconda-Server Badge Python Version Documentation Status Publication DOI

This is a package with all cython/c++ backend for ParSeg

Current release extracted from PartSegCore module to avoid building multiple wheels for the main package and speedup tests.

This package requires libomp for build. On linux it can be installed with apt install libomp-dev or yum install libomp-devel. On macOS it can be installed with brew install libomp.

As clang version created on macOS do not have native openmp brew do not set libomp as default visible. If you install libomp with brew and want to build package from source you need to set OMP variable to libomp location.

For example:

bash export OMP="$(brew --prefix libomp)" pip install .

As currently there is no wheel for macOS ARM64 it is required to build package from source.

Development in Clion

To install Python build dependencies, run:

bash pip install scikit-build-core cython cython-cmake numpy setuptools-scm

Then, install the package in development mode:

bash pip install --no-build-isolation --config-settings=editable.rebuild=true\ -Cbuild-dir=build -ve .

vendor FindCython.cmake from cython-cmake to cmake directory.

bash mkdir cmake && cython-cmake vendor cmake

Set CUSTOM_MODULE_PATH environment variable to full path to cmake directory.

Set it in Settings → Build, Execution, Deployment → CMake → Environment

Cite as

Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021). https://doi.org/10.1186/s12859-021-03984-1

Owner

  • Name: 4DNucleome
  • Login: 4DNucleome
  • Kind: organization

GitHub Events

Total
  • Watch event: 1
  • Delete event: 28
  • Issue comment event: 39
  • Push event: 112
  • Pull request review comment event: 35
  • Pull request review event: 53
  • Pull request event: 57
  • Create event: 32
Last Year
  • Watch event: 1
  • Delete event: 28
  • Issue comment event: 39
  • Push event: 112
  • Pull request review comment event: 35
  • Pull request review event: 53
  • Pull request event: 57
  • Create event: 32

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 24
  • Total Committers: 1
  • Avg Commits per committer: 24.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Grzegorz Bokota b****b@g****m 24

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 109
  • Average time to close issues: N/A
  • Average time to close pull requests: 17 days
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.98
  • Merged pull requests: 72
  • Bot issues: 0
  • Bot pull requests: 59
Past Year
  • Issues: 0
  • Pull requests: 45
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.82
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 29
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • Czaki (50)
  • dependabot[bot] (32)
  • pre-commit-ci[bot] (27)
Top Labels
Issue Labels
Pull Request Labels
dependencies (32) github_actions (11)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 9,058 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 24
  • Total maintainers: 1
pypi.org: partsegcore-compiled-backend

PartSegCore compiled backend,

  • Versions: 22
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 9,058 Last month
Rankings
Downloads: 3.6%
Dependent packages count: 4.7%
Average: 18.3%
Dependent repos count: 21.7%
Forks count: 29.8%
Stargazers count: 31.9%
Maintainers (1)
massad
Last synced: 10 months ago
conda-forge.org: partsegcore-compiled-backend
  • Versions: 2
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 46.0%
Stargazers count: 60.1%
Forks count: 61.1%
Last synced: 11 months ago

Dependencies

.github/workflows/wheels.yml actions
  • actions/checkout v3 composite
  • actions/download-artifact v2 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • pypa/cibuildwheel v2.11.4 composite
  • pypa/gh-action-pypi-publish master composite
pyproject.toml pypi
setup.py pypi