signac

Manage large and heterogeneous data spaces on the file system.

https://github.com/glotzerlab/signac

Science Score: 62.0%

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

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
  • Academic publication links
  • Committers with academic emails
    16 of 40 committers (40.0%) from academic institutions
  • Institutional organization owner
    Organization glotzerlab has institutional domain (glotzerlab.engin.umich.edu)
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary

Keywords

data data-management database reproducibility

Keywords from Contributors

physics polygons computational-geometry geometry polyhedra shapes histogram mesh transformers tk
Last synced: 6 months ago · JSON representation ·

Repository

Manage large and heterogeneous data spaces on the file system.

Basic Info
Statistics
  • Stars: 135
  • Watchers: 12
  • Forks: 37
  • Open Issues: 10
  • Releases: 15
Topics
data data-management database reproducibility
Created about 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Codeowners Governance

README.md

signac - simple data management

Affiliated with NumFOCUS PyPI conda-forge GitHub Actions RTD License PyPI-downloads Twitter GitHub Stars

The signac framework helps users manage and scale file-based workflows, facilitating data reuse, sharing, and reproducibility.

It provides a simple and robust data model to create a well-defined indexable storage layout for data and metadata. This makes it easier to operate on large data spaces, streamlines post-processing and analysis and makes data collectively accessible.

Resources

Installation

The recommended installation method for signac is through conda or pip. The software is tested for Python 3.8+ and is built for all major platforms.

To install signac via the conda-forge channel, execute:

bash conda install -c conda-forge signac

To install signac via pip, execute:

bash pip install signac

Detailed information about alternative installation methods can be found in the documentation.

Quickstart

The framework facilitates a project-based workflow. Set up a new project:

bash $ mkdir my_project $ cd my_project $ signac init

and access the project handle:

```python

project = signac.get_project() ```

Testing

You can test this package by executing:

bash $ python -m pytest tests/

Acknowledgment

When using signac as part of your work towards a publication, we would really appreciate that you acknowledge signac appropriately. We have prepared examples on how to do that here. Thank you very much!

The signac framework is a NumFOCUS Affiliated Project.

Owner

  • Name: Glotzer Group
  • Login: glotzerlab
  • Kind: organization
  • Location: University of Michigan

We develop molecular simulation tools to study the self-assembly of complex materials and explore matter at the nanoscale.

Citation (CITATION.cff)

# YAML 1.2
---
cff-version: "1.0.3"
title: signac
version: 2.3.0
abstract: |
    The signac framework helps users manage and scale file-based workflows, facilitating data
    reuse, sharing, and reproducibility. It provides a simple and robust data model to create
    a well-defined indexable storage layout for data and metadata. This makes it easier to
    operate on large data spaces, streamlines post-processing and analysis and makes data
    collectively accessible.
authors:
  -
    family-names: Adorf
    given-names: "Carl Simon"
    affiliation: "University of Michigan"
    orcid: "https://orcid.org/0000-0003-4962-2495"
  -
    family-names: Ramasubramani
    given-names: Vyas
    affiliation: "University of Michigan"
    orcid: "https://orcid.org/0000-0001-5181-9532"
  -
    family-names: Dice
    given-names: "Bradley D."
    affiliation: "University of Michigan"
    orcid: "https://orcid.org/0000-0002-9983-0770"
  -
    family-names: Henry
    given-names: Mike
    affiliation: "Boise State University"
    orcid: "https://orcid.org/0000-0002-3870-9993"
  -
    family-names: Butler
    given-names: Brandon
    affiliation: "University of Michigan"
    orcid: "https://orcid.org/0000-0001-7739-7796"
  -
    family-names: Kerr
    given-names: "Corwin B."
    affiliation: "University of Michigan"
    orcid: "https://orcid.org/0000-0003-0776-2596"
  -
    family-names: Dodd
    given-names: "Paul M."
    affiliation: "University of Michigan"
  -
    family-names: Glotzer
    given-names: "Sharon C."
    affiliation: "University of Michigan"
    orcid: "https://orcid.org/0000-0002-7197-0085"
keywords:
  - python
  - "data management"
  - reproducibility
  - sharability
  - workflow
  - "scientific computing"
license: "http://www.opensource.org/licenses/BSD-3-Clause"
message: >
  Development and deployment supported by MICCoM, as part of the Computational
  Materials Sciences Program funded by the U.S. Department of Energy, Office of
  Science, Basic Energy Sciences, Materials Sciences and Engineering Division,
  under Subcontract No. 6F-30844. Project conceptualization and implementation
  supported by the National Science Foundation, Award # DMR 1409620.
repository-code: https://github.com/glotzerlab/signac
references:
  - type: article
  - authors:
    -
      family-names: Adorf
      given-names: "Carl Simon"
      affiliation: "University of Michigan"
      orcid: "https://orcid.org/0000-0003-4962-2495"
    -
      family-names: Dodd
      given-names: "Paul M."
      affiliation: "University of Michigan"
    -
      family-names: Ramasubramani
      given-names: Vyas
      affiliation: "University of Michigan"
      orcid: "https://orcid.org/0000-0001-5181-9532"
    -
      family-names: Glotzer
      given-names: "Sharon C."
      affiliation: "University of Michigan"
      orcid: "https://orcid.org/0000-0002-7197-0085"
  - title: "Simple data and workflow management with the signac framework"
  - journal: "Comput. Mater. Sci."
  - volume: 146
  - number: C
  - year: 2018
  - pages: 9
  - doi: "10.1016/j.commatsci.2018.01.035"
...

GitHub Events

Total
  • Create event: 24
  • Release event: 1
  • Issues event: 4
  • Watch event: 4
  • Delete event: 25
  • Issue comment event: 25
  • Push event: 47
  • Pull request review comment event: 5
  • Pull request review event: 14
  • Pull request event: 47
  • Fork event: 1
Last Year
  • Create event: 24
  • Release event: 1
  • Issues event: 4
  • Watch event: 4
  • Delete event: 25
  • Issue comment event: 25
  • Push event: 47
  • Pull request review comment event: 5
  • Pull request review event: 14
  • Pull request event: 47
  • Fork event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 2,380
  • Total Committers: 40
  • Avg Commits per committer: 59.5
  • Development Distribution Score (DDS): 0.329
Past Year
  • Commits: 39
  • Committers: 6
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.513
Top Committers
Name Email Commits
Carl Simon Adorf c****f@u****u 1,597
dependabot[bot] 4****] 265
Bradley Dice b****e@b****m 246
Vyas Ramasubramani v****i@g****m 121
pre-commit-ci[bot] 6****] 19
Corwin Kerr c****r@u****u 18
Joshua A. Anderson j****r@u****u 14
Vishav Sharma 4****1 14
Tim Moore t****3@g****m 12
Alyssa Travitz 3****z 11
Brandon Butler b****r@u****u 8
Paul Dodd p****d@u****u 8
Mike Henry m****y@b****u 5
Abhavya Chandra a****a@i****n 4
Hardik Ojha 4****o 4
Mike Henry 1****y 4
Onkar Mahapatra 7****7 3
Ali Malek p****k@g****m 2
AlainKadar 7****r 2
Kelly Wang 4****g 2
Jens Glaser j****r@u****u 2
xadams x****s@u****u 1
tommy-waltmann 5****n 1
Glotzpeep G****p@h****g 1
HPCClass Admin e****2@c****u 1
Tim Moore m****t@u****u 1
slowglow 7****w 1
shandave 7****e 1
rskye144 5****4 1
jennyfothergill 3****l 1
and 10 more...

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 30
  • Total pull requests: 237
  • Average time to close issues: 8 months
  • Average time to close pull requests: 23 days
  • Total issue authors: 13
  • Total pull request authors: 13
  • Average comments per issue: 4.37
  • Average comments per pull request: 1.46
  • Merged pull requests: 215
  • Bot issues: 2
  • Bot pull requests: 156
Past Year
  • Issues: 2
  • Pull requests: 56
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: 5 days
  • Issue authors: 2
  • Pull request authors: 5
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.89
  • Merged pull requests: 44
  • Bot issues: 1
  • Bot pull requests: 43
Top Authors
Issue Authors
  • vyasr (10)
  • bdice (5)
  • cbkerr (4)
  • csadorf (2)
  • Yijia-Jiang (1)
  • arosen93 (1)
  • sagnik (1)
  • joaander (1)
  • dependabot[bot] (1)
  • bc118 (1)
  • mikemhenry (1)
  • tommy-waltmann (1)
  • pre-commit-ci[bot] (1)
Pull Request Authors
  • dependabot[bot] (141)
  • bdice (24)
  • vyasr (18)
  • cbkerr (16)
  • pre-commit-ci[bot] (15)
  • joaander (9)
  • b-butler (4)
  • csadorf (4)
  • janbridley (2)
  • javierbg (1)
  • slowglow (1)
  • mikemhenry (1)
  • kidrahahjo (1)
Top Labels
Issue Labels
pinned (6) enhancement (5) documentation (4) good first issue (3) stale (2) proposal (2) refactor (1) requires-1.x-deprecation (1) doc-style (1) dependencies (1) python (1)
Pull Request Labels
dependencies (141) python (49) github_actions (22) refactor (8) enhancement (5) bug (4) good first issue (2) pinned (2) expertise-needed (1)

Dependencies

pyproject.toml pypi
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doc/requirements.txt pypi
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requirements/requirements-test-optional.txt pypi
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  • ruamel.yaml ==0.17.21
  • tables ==3.7.0
  • zarr ==2.11.3
requirements/requirements-test.txt pypi
  • coverage ==6.4.1
  • pytest ==7.1.2
  • pytest-cov ==3.0.0
  • pytest-xdist ==2.5.0
requirements.txt pypi
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