signac-flow

Workflow management for signac-managed data spaces.

https://github.com/glotzerlab/signac-flow

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
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DOI references
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Academic publication links
✓
Committers with academic emails
18 of 43 committers (41.9%) from academic institutions
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Institutional organization owner
Organization glotzerlab has institutional domain (glotzerlab.engin.umich.edu)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary

Keywords

python signac workflow

Keywords from Contributors

data-management reproducibility polygon computational-geometry shapes geometry polyhedra physics molecular-simulation molecular-dynamics-simulation

Last synced: 6 months ago · JSON representation ·

Repository

Workflow management for signac-managed data spaces.

Basic Info

Host: GitHub
Owner: glotzerlab
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://signac.readthedocs.io/
Size: 4.95 MB

Statistics

Stars: 48
Watchers: 12
Forks: 38
Open Issues: 51
Releases: 28

Archived

Topics

python signac workflow

Created about 7 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codeowners

README.md

[!IMPORTANT]

signac-flow is no longer maintained.

Switch to row.

signac-flow - manage workflows with signac

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

The signac-flow tool provides the basic components to set up simple to complex workflows for projects managed by the signac framework. That includes the definition of data pipelines, execution of data space operations and the submission of operations to high-performance super computers.

Resources

Framework documentation: Examples, tutorials, topic guides, and package Python APIs.
Package documentation: API reference for the signac-flow package.
Discussion board: Ask the signac-flow user community for help.

Installation

The recommended installation method for signac-flow is through conda or pip. The software is tested for Python versions 3.6+ and is built for all major platforms.

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

bash conda install -c conda-forge signac-flow

To install signac-flow via pip, execute:

bash pip install signac-flow

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

Testing

You can test this package by executing

$ python -m pytest tests/

within the repository root directory.

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-flow
version: 0.29.0
abstract: |
    The signac-flow tool provides the basic components to set up simple to complex workflows for projects as part of the signac framework. That includes the definition of data pipelines, execution of data space operations and the submission of operations to high-performance super computers.
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
  - shareability
  - 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-flow
...

GitHub Events

Total

Watch event: 1
Delete event: 15
Issue comment event: 5
Push event: 17
Pull request review event: 3
Pull request event: 32
Fork event: 1
Create event: 17

Last Year

Watch event: 1
Delete event: 15
Issue comment event: 5
Push event: 17
Pull request review event: 3
Pull request event: 32
Fork event: 1
Create event: 17

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,350
Total Committers: 43
Avg Commits per committer: 31.395
Development Distribution Score (DDS): 0.513

Past Year

Commits: 26
Committers: 3
Avg Commits per committer: 8.667
Development Distribution Score (DDS): 0.346

Top Committers

Name	Email	Commits
Carl Simon Adorf	c**f@u**u	658
Bradley Dice	b**e@b**m	183
dependabot[bot]	4****]	132
Vyas Ramasubramani	v**b@u**u	121
Brandon Butler	b**r@u**u	73
Hardik Ojha	4****o	44
Joshua A. Anderson	j**r@u**u	22
pre-commit-ci[bot]	6****]	18
Corwin Kerr	c**r@u**u	16
Pengji	z**j@u**u	11
Paul Dodd	p**d@u**u	9
Jens Glaser	j**r@u**u	6
Mike Henry	m**y@b**u	5
Alyssa Travitz	3****z	5
Tim Moore	m**c@u**u	5
Kelly Wang	4****g	3
Abhavya Chandra	a**a@i**n	2
Andrei Berceanu	b****u	2
Ben Swerdlow	b**d@u**u	2
Ignacio Blanco Varela	8****0	2
Javier Barbero	j**5@g**m	2
Matt Thompson	m**n@v**u	2
Mike Henry	1****y	2
Shannon Moran	m**e@u**u	2
vishav1771	4****1	2
Charlotte Shiqi Zhao	5****2	2
Ramanish Singh	4****h	2
Rose K. Cersonsky	4****s	2
yuanzhou0827	4****7	1
shandave	7****e	1
and 13 more...

Committer Domains (Top 20 + Academic)

umich.edu: 13 g.clemson.edu: 1 br006.pvt.bridges.psc.edu: 1 vanderbilt.edu: 1 iitgn.ac.in: 1 boisestate.edu: 1 bradleydice.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 40
Total pull requests: 202
Average time to close issues: 9 months
Average time to close pull requests: 30 days
Total issue authors: 18
Total pull request authors: 16
Average comments per issue: 4.55
Average comments per pull request: 1.86
Merged pull requests: 169
Bot issues: 1
Bot pull requests: 103

Past Year

Issues: 1
Pull requests: 31
Average time to close issues: N/A
Average time to close pull requests: 12 days
Issue authors: 1
Pull request authors: 2
Average comments per issue: 0.0
Average comments per pull request: 0.29
Merged pull requests: 21
Bot issues: 1
Bot pull requests: 31

View more stats

Top Authors

Issue Authors

kidrahahjo (6)
b-butler (5)
joaander (5)
bdice (4)
javierbg (3)
cbkerr (2)
vyasr (2)
zhangyemayapro (2)
rosecers (1)
justinGilmer (1)
csadorf (1)
CalCraven (1)
syjlee (1)
tommy-waltmann (1)
rayasare (1)

Pull Request Authors

dependabot[bot] (118)
b-butler (46)
joaander (22)
pre-commit-ci[bot] (15)
bdice (14)
cbkerr (10)
vyasr (5)
kidrahahjo (5)
csadorf (3)
rayasare (2)
iblanco11981870 (2)
melodyyzh (1)
rosecers (1)
javierbg (1)
tabedzki (1)

Top Labels

Issue Labels

bug (7) good first issue (6) cluster submission (5) enhancement (2)

Pull Request Labels

dependencies (118) python (46) github_actions (24) bug (4) environments (3) enhancement (2) cluster submission (2) groups (1) GSoC (1) aggregation (1)

Packages

Total packages: 2
Total downloads:
- pypi 1,281 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 27
(may contain duplicates)
Total versions: 78
Total maintainers: 7

pypi.org: signac-flow

Simple workflow management for signac projects.

Homepage: https://signac.io
Documentation: https://docs.signac.io
License: BSD 3-Clause License for the software signac-flow. Copyright (c) 2017, The Regents of the University of Michigan All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Latest release: 0.29.0
published almost 2 years ago

Versions: 47
Dependent Packages: 0
Dependent Repositories: 11
Downloads: 1,281 Last month

Rankings

Dependent repos count: 4.4%

Forks count: 6.6%

Average: 8.4%

Stargazers count: 9.5%

Dependent packages count: 10.1%

Downloads: 11.4%

Maintainers (7)

b-butler bdice csadorf mmh vramasub cbkerr tcmoore3

Last synced: 6 months ago

conda-forge.org: signac-flow

The signac-flow tool provides the basic components to setup simple to complex workflows for signac projects. That includes the definition of data pipelines, execution of data space operations and the submission of operations to high-performance super computers.

Homepage: https://signac.io
License: BSD-3-Clause
Latest release: 0.22.0
published over 3 years ago

Versions: 31
Dependent Packages: 0
Dependent Repositories: 16

Rankings

Dependent repos count: 8.9%

Forks count: 30.3%

Average: 33.0%

Stargazers count: 41.2%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

.github/workflows/publish-packages.yml actions

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

.github/workflows/run-pytest.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite

doc/requirements.txt pypi

sphinx >=4.0.0
sphinx_rtd_theme >=1.0.0
sphinxcontrib-programoutput *

pyproject.toml pypi

cloudpickle >=1.6.0
deprecation >=2.0.0
jinja2 >=3.0.0
jsonschema >=3.0.0
signac >=1.8.0
tqdm >=4.60.0

requirements/requirements-dev.txt pypi

click >=7.0 development
pre-commit ==3.0.4 development
ruamel.yaml >=0.16.12 development

requirements/requirements-test.txt pypi

click ==8.1.3 test
coverage ==7.1.0 test
pytest ==7.2.1 test
pytest-cov ==4.0.0 test
ruamel.yaml ==0.17.21 test

requirements.txt pypi

cloudpickle >=1.6.0
deprecation >=2.0.0
jinja2 >=3.0.0
jsonschema >=3.0.0
signac >=1.8.0
tqdm >=4.60.0

.github/workflows/deploy-pypi.yml actions

.github/workflows/deploy-test-pypi.yml actions