https://github.com/databio/pypiper
Python toolkit for building restartable pipelines
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓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
7 of 18 committers (38.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.9%) to scientific vocabulary
Keywords
bioinformatics
bioinformatics-pipeline
pipeline
python
python-toolkit
Keywords from Contributors
ngs
pipeline-submission-engine
reproducibility
Last synced: 5 months ago
·
JSON representation
Repository
Python toolkit for building restartable pipelines
Basic Info
- Host: GitHub
- Owner: databio
- License: bsd-2-clause
- Language: Python
- Default Branch: master
- Homepage: http://pypiper.databio.org
- Size: 1.63 MB
Statistics
- Stars: 45
- Watchers: 15
- Forks: 9
- Open Issues: 56
- Releases: 33
Topics
bioinformatics
bioinformatics-pipeline
pipeline
python
python-toolkit
Created almost 11 years ago
· Last pushed 12 months ago
Metadata Files
Readme
Contributing
License
Support
README.md
Pypiper
A lightweight python toolkit for gluing together restartable, robust shell pipelines. Learn more in the documentation.
Owner
- Name: Databio
- Login: databio
- Kind: organization
- Location: University of Virginia
- Website: https://databio.org
- Repositories: 88
- Profile: https://github.com/databio
Solving problems in computational biology
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 1
- Watch event: 3
- Push event: 5
- Pull request event: 2
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 1
- Watch event: 3
- Push event: 5
- Pull request event: 2
- Fork event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| nsheff | n****f | 492 |
| Vince Reuter | v****r@g****m | 338 |
| Michal Stolarczyk | s****3@g****m | 66 |
| Andre Rendeiro | a****o@g****m | 36 |
| Donald Campbell | 1****r | 31 |
| jklughammer | j****r@c****t | 15 |
| Charles Dietz | c****z@c****t | 12 |
| Khoroshevskyi | s****0@g****m | 9 |
| mfarlik | m****k@c****t | 5 |
| jpsmith5 | j****h@v****u | 4 |
| Florian Halbritter | f****r | 2 |
| fhalbritter | f****r@c****t | 2 |
| Nikolaus Fortelny | n****y@n****t | 2 |
| Nikolaus Fortelny | n****y@n****t | 2 |
| Andreas Schoenegger | a****r@c****t | 1 |
| Murat Tugrul | m****l@g****m | 1 |
| Paul Datlinger | p****r@c****t | 1 |
| hussainzaidi | h****i@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 118
- Total pull requests: 31
- Average time to close issues: 7 months
- Average time to close pull requests: about 2 months
- Total issue authors: 11
- Total pull request authors: 5
- Average comments per issue: 2.22
- Average comments per pull request: 1.48
- Merged pull requests: 30
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 44 minutes
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- vreuter (50)
- nsheff (41)
- donaldcampbelljr (8)
- stolarczyk (5)
- zhangzhen (2)
- jpsmith5 (2)
- nfortelny (1)
- wilfriedguiblet (1)
- jklughammer (1)
- afrendeiro (1)
- Rob-murphys (1)
Pull Request Authors
- vreuter (14)
- nsheff (10)
- donaldcampbelljr (9)
- khoroshevskyi (3)
- fhalbritter (1)
Top Labels
Issue Labels
enhancement (19)
question (18)
bug (13)
docs (6)
likely-solved (5)
priority-low (5)
brainstorming (5)
priority-high (3)
platform-specific (2)
tests (2)
macOS (1)
house-of-cards (1)
version-specific (1)
known-issue (1)
PyPI (1)
API (1)
deprecation (1)
design (1)
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 34,185 last-month
- Total docker downloads: 27,138
-
Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 11
(may contain duplicates) - Total versions: 29
- Total maintainers: 5
pypi.org: piper
A lightweight python toolkit for gluing together restartable, robust command line pipelines
- Homepage: https://github.com/databio/pypiper/
- Documentation: https://piper.readthedocs.io/
- License: BSD2
-
Latest release: 0.14.4
published 12 months ago
Rankings
Docker downloads count: 1.4%
Downloads: 2.6%
Dependent repos count: 4.4%
Dependent packages count: 4.7%
Average: 5.8%
Stargazers count: 10.1%
Forks count: 11.4%
Maintainers (4)
Last synced:
7 months ago
spack.io: py-piper
A lightweight python toolkit for gluing together restartable, robust shell pipelines.
- Homepage: https://github.com/databio/pypiper
- License: []
-
Latest release: 0.12.3
published about 3 years ago
Rankings
Dependent repos count: 0.0%
Average: 19.2%
Stargazers count: 23.5%
Forks count: 25.4%
Dependent packages count: 28.1%
Maintainers (1)
Last synced:
6 months ago
Dependencies
requirements/requirements-docs.txt
pypi
- markdown-include *
- mkdocs >=1.0
- piper *
- pydoc-markdown *
requirements/requirements-ngstk.txt
pypi
- numpy *
- pandas *
- pysam *
- yacman *
requirements/requirements-plot.txt
pypi
- matplotlib *
- scipy *
- seaborn *
requirements/requirements-pypiper.txt
pypi
- attmap >=0.12.5
- logmuse >=0.2.4
- pandas *
- psutil *
- ubiquerg >=0.4.5
- yacman *
requirements/requirements-test.txt
pypi
- coveralls >=1.1 test
- hypothesis * test
- mock ==2.0.0 test
- pytest >=4.2.1 test
- pytest-cov ==2.6.1 test
- pytest-remotedata * test
- veracitools * test