hstrat-surface-concept
Algorithm development for lightweight fixed-length recency-proportional hereditary stratigraphy data structure
Science Score: 67.0%
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
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.2%) to scientific vocabulary
Repository
Algorithm development for lightweight fixed-length recency-proportional hereditary stratigraphy data structure
Basic Info
- Host: GitHub
- Owner: mmore500
- License: mit
- Language: Python
- Default Branch: master
- Size: 3.29 GB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 15
- Releases: 6
Metadata Files
README.md
Hereditary Stratigraphic Surface (hsurf) Concept
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hsurf provides efficient, constant-space downsampling of data streams via DStream algorithms, with applications including heredity stratigraphic phylogenetic inference over distributed digital evolution populations.
- Free software: MIT license
Installation
python3 -m pip install "git+https://github.com/mmore500/hstrat-surface-concept.git@v1.0.2#egg=hsurf"
To set up locally,
bash
git clone --single-branch https://github.com/mmore500/hstrat-surface-concept.git
cd hstrat-surface-concept
./submodules.sh
Documentation
Slide deck & graphics for this project are at https://hopth.ru/ce.
Some notes are in the template manuscript skeleton in tex/, which is built via GitHub actions and can be downloaded as an artifact.
See binder for usage examples.
Roadmap
This repository hosts prototype code for algorithm development of a lightweight fixed-length hereditary stratigraphy data structure.
Code here is designed for use in conjunction with the mainline hstrat and downstream packages.
Long-term, code in this repository will migrate to the hstrat and downstream packages and this will remain only to ensure records (and reproducibility) of prototype work.
Citing
If pecking contributes to a scientific publication, please cite it as
Matthew Andres Moreno. (2024). mmore500/hstrat-surface-concept. Zenodo. https://zenodo.org/doi/10.5281/zenodo.10779240
bibtex
@software{moreno2024hsurf,
author = {Matthew Andres Moreno},
title = {mmore500/hstrat-surface-concept},
month = mar,
year = 2024,
publisher = {Zenodo},
doi = {10.5281/zenodo.10779240},
url = {https://zenodo.org/doi/10.5281/zenodo.10779240}
}
Consider also citing hstrat. And don't forget to leave a star on GitHub!
Credits
This package was created with Cookiecutter and the mmore500/cookiecutter-dishtiny-project project template.
Owner
- Name: Matthew Andres Moreno
- Login: mmore500
- Kind: user
- Location: East Lansing, MI
- Company: @devosoft
- Website: mmore500.github.io
- Twitter: MorenoMathewA
- Repositories: 43
- Profile: https://github.com/mmore500
doctoral student, Computer Science and Engineering at Michigan State University
Citation (CITATION.cff)
cff-version: 1.0.2 message: "If you use this software, please cite it as below. Also consider citing the mainline hstrat package." title: 'hstrat-surface-concept: Python software protyping fixed-buffer hereditary stratigraphy instrumentation' abstract: "hsurf provides efficient, constant-space instrumentation for heredity stratigraphic phylogenetic inference over distributed digital evolution populations." authors: - family-names: Moreno given-names: Matthew Andres orcid: 0000-0003-4726-4479 date-released: 2024-03-04 doi: https://zenodo.org/doi/10.5281/zenodo.10779240 license: MIT repository-code: https://github.com/mmore500/hstrat-surface-concept url: "https://github.com/mmore500/hstrat-surface-concept"
GitHub Events
Total
- Issues event: 43
- Issue comment event: 30
- Push event: 523
- Create event: 19
Last Year
- Issues event: 43
- Issue comment event: 30
- Push event: 523
- Create event: 19
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 86
- Total pull requests: 32
- Average time to close issues: 28 days
- Average time to close pull requests: 6 days
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.38
- Average comments per pull request: 0.19
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 24
- Pull requests: 0
- Average time to close issues: 7 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mmore500 (113)
- connoryang1 (2)
- joeymsu (1)
Pull Request Authors
- mmore500 (69)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- JamesIves/github-pages-deploy-action 4.0.0 composite
- actions/checkout v2 composite
- actions/setup-node v3 composite
- actions/upload-artifact v2 composite
- docker/build-push-action v1 composite
- fregante/setup-git-user v1 composite
- mmore500/docker-texlive-full sha-ea45eb5 build
- 115 dependencies
- breathe ==4.19.2
- coverxygen ==1.5.0
- exhale ==0.2.3
- myst-parser ==0.12.9
- sphinx ==3.1.2
- sphinx-rtd-theme ==0.5.0
- sphinxemoji ==0.1.8
- Deprecated ==1.2.13
- IPython ==7.31.1
- Jinja2 <3.1
- black ==22.10.0
- hstrat ==1.7.4
- interval_search ==0.3.1
- isort ==5.12.0
- matplotlib ==3.6.2
- nb-clean ==2.4.0
- nbconvert ==7.6.0
- nbmetalog ==0.2.6
- numpy ==1.23.5
- opytional ==0.1.0
- pandas ==1.5.2
- pytest ==7.2.2
- pytest-xdist ==3.2.1
- ruff ==0.0.260
- scipy ==1.10.1
- seaborn ==0.12.1
- teeplot ==0.5.0
- tqdm ==4.64.1
- 115 dependencies