signac
Manage large and heterogeneous data spaces on the file system.
Science Score: 62.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓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
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○Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Manage large and heterogeneous data spaces on the file system.
Basic Info
- Host: GitHub
- Owner: glotzerlab
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://signac.readthedocs.io/
- Size: 7.44 MB
Statistics
- Stars: 135
- Watchers: 12
- Forks: 37
- Open Issues: 10
- Releases: 15
Topics
Metadata Files
README.md
signac - simple data management
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
- Framework documentation: Examples, tutorials, topic guides, and package Python APIs.
- Package documentation: API reference for the signac package.
- Discussion board: Ask the signac user community for help.
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
- Website: https://glotzerlab.engin.umich.edu
- Repositories: 33
- Profile: https://github.com/glotzerlab
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
Top Committers
| Name | 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... | ||
Committer Domains (Top 20 + Academic)
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
Pull Request Labels
Dependencies
- filelock >=3.0
- packaging >=15.0
- tqdm >=4.10.0
- sphinx >=4.0.0
- sphinx_rtd_theme >=1.0.0
- sphinxcontrib-programoutput *
- h5py ==3.7.0
- numpy ==1.22.4
- pandas ==1.4.2
- pymongo ==4.1.1
- redis ==4.3.1
- ruamel.yaml ==0.17.21
- tables ==3.7.0
- zarr ==2.11.3
- coverage ==6.4.1
- pytest ==7.1.2
- pytest-cov ==3.0.0
- pytest-xdist ==2.5.0
- filelock >=3.0
- packaging >=15.0
- tqdm >=4.10.0
- actions/checkout v3 composite
- actions/download-artifact v2 composite
- actions/setup-python v4 composite
- actions/upload-artifact v2 composite
- pypa/gh-action-pypi-publish release/v1 composite
- supercharge/mongodb-github-action 1.7.0 composite
- supercharge/redis-github-action 1.4.0 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- codecov/codecov-action v2 composite
- supercharge/mongodb-github-action 1.7.0 composite
- supercharge/redis-github-action 1.4.0 composite