https://github.com/biocore/improved-octo-waddle
Balanced parentheses succinct data structure in Python
Science Score: 59.0%
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
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: plos.org -
✓Committers with academic emails
3 of 4 committers (75.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary
Keywords from Contributors
Repository
Balanced parentheses succinct data structure in Python
Basic Info
- Host: GitHub
- Owner: biocore
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: master
- Size: 1.69 MB
Statistics
- Stars: 7
- Watchers: 5
- Forks: 8
- Open Issues: 19
- Releases: 11
Metadata Files
README.md
Improved Octo Waddle
An implementation of the balanced parentheses tree structure as described by Cordova and Navarro.
Install notes
Installation is a two step procedure right now due to the chicken and egg problem of requiring numpy and cython for setup.py to execute. The package is named iow in pypi as "bp" was taken at time of registration.
$ conda create --name bp python=3.8
$ conda activate bp
$ conda install numpy cython
$ pip install iow
Developer notes
If pulling the source, please note that we use a submodule and Github does not by default bring it down. After a clone, please run:
$ git submodule update --init --recursive
Fragment insertion
BP supports the jplace format. Fragments can be inserted using either fully-resolved or multifurcation mode to resolve multiple placements to the same edge. In fully resolved, the edge placed against is broken N times where N is the number of fragments on the edge. In multifurcation, a new node is constructed as the average of the distal length for the N fragments, and a separate multifurcation node is added which encompasses the placed fragments.
Important: the multifurcation mode support is GPL licensed code. Support for that mode is in a fork of this repository, see improved-octo-waddle-gpl.
Insertions can be handled by the command line following install:
``` $ bp placement --help Usage: bp placement [OPTIONS]
Options: --placements PATH jplace formatted data [required] --output PATH Where to write the resulting newick [required]
--method [fully-resolved|multifurcating] Whether to fully resolve or multifurcate [required]
--help Show this message and exit. ```
Note that the multifurcating support relies on GPL code derived from the Genesis project. To use this method, please install iow-gpl.
Owner
- Name: biocore
- Login: biocore
- Kind: organization
- Location: Cyberspace
- Website: http://biocore.github.io/
- Repositories: 76
- Profile: https://github.com/biocore
Collaboratively developed bioinformatics software.
GitHub Events
Total
- Create event: 2
- Release event: 1
- Issues event: 2
- Watch event: 1
- Issue comment event: 6
- Push event: 8
- Pull request review event: 1
- Pull request review comment event: 1
- Pull request event: 5
- Fork event: 2
Last Year
- Create event: 2
- Release event: 1
- Issues event: 2
- Watch event: 1
- Issue comment event: 6
- Push event: 8
- Pull request review event: 1
- Pull request review comment event: 1
- Pull request event: 5
- Fork event: 2
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 175
- Total Committers: 4
- Avg Commits per committer: 43.75
- Development Distribution Score (DDS): 0.389
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel McDonald | d****d@u****u | 107 |
| Daniel McDonald | m****t@c****u | 64 |
| esayyari | e****i@u****u | 3 |
| Daniel McDonald | m****t@D****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 36
- Total pull requests: 26
- Average time to close issues: 11 months
- Average time to close pull requests: 3 months
- Total issue authors: 7
- Total pull request authors: 4
- Average comments per issue: 0.75
- Average comments per pull request: 1.27
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Issue authors: 2
- Pull request authors: 2
- Average comments per issue: 2.5
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- wasade (26)
- mortonjt (3)
- fedarko (2)
- ElDeveloper (2)
- esayyari (1)
- satishskamath (1)
- antgonza (1)
Pull Request Authors
- wasade (26)
- fedarko (2)
- constellation99 (2)
- esayyari (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 394 last-month
- Total docker downloads: 93,681
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Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 3
(may contain duplicates) - Total versions: 13
- Total maintainers: 1
pypi.org: iow
Balanced parentheses
- Homepage: https://github.com/biocore/improved-octo-waddle
- Documentation: https://iow.readthedocs.io/
- License: bsd-3-clause
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Latest release: 1.0.8
published 11 months ago
Rankings
Maintainers (1)
pypi.org: iow-gpl
Balanced parentheses
- Homepage: https://github.com/biocore/improved-octo-waddle
- Documentation: https://iow-gpl.readthedocs.io/
- License: bsd-3-clause
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Latest release: 1.0.6
published about 3 years ago
Rankings
Maintainers (1)
Dependencies
- cython *
- flake8 *
- nose *
- numpy *
- scikit-bio *
- click *
- cython *
- nose *
- numpy *
- pandas *
- scikit-bio *
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish release/v1 composite