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
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Repository
Useful Genomic Tools
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
UsefulGnom
Python package for viral genomic analysis utilities.
Usage
python
import usefulgnom as ug
Setting up the repository
To build the package and maintain dependencies, we use Poetry. In particular, it's good to install it and become familiar with its basic functionalities by reading the documentation.
To set up the environment (together with development tools), run:
bash
$ poetry install --with dev
$ poetry run pre-commit install
Then, you will be able to run tests:
bash
$ poetry run pytest
... or check the types:
bash
$ poetry run pyright
Alternatively, you may prefer to work with the right Python environment using:
bash
$ poetry shell
$ pytest
Existing code quality checks
The code quality checks run on GitHub can be seen in
- .github/workflows/test.yml for the python package CI/CD,
- .github/workflows/test-snake.yml for the snakemake workflow CI.
We are using:
- Ruff to lint the code.
- Black to format the code.
- Pyright to check the types.
- Pytest to run the unit tests code and workflows.
- Interrogate to check the documentation.
- Snakefmt to format snakemake workflows.
Workflow
We use Feature Branch Workflow, in which modifications of the code should happen via small pull requests.
We recommend submitting small pull requests and starting with drafts outlining proposed changes.
Currently Implemented
- Calulating Base Coverage Depth and Mutation Statistics, adapoted from @AugusteRi
- Calulating Amplicon Coverage, adapoted from @dr-david
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
Total
- Pull request review event: 2
Last Year
- Pull request review event: 2
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gordon J. Köhn | g****n@k****t | 94 |
| Gordon J. Koehn | k****g@b****h | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
Dependencies
- actions/cache v2 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- snok/install-poetry v1 composite
- actions/cache v2 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- psf/black stable composite
- snok/install-poetry v1 composite
- black ^23.1.0 develop
- interrogate ^1.5.0 develop
- mkdocs-gen-files ^0.4.0 develop
- mkdocs-literate-nav ^0.6.0 develop
- mkdocs-material ^9.1.6 develop
- mkdocstrings ^0.21.2 develop
- pre-commit ^3.1.0 develop
- pyright ^1.1.309 develop
- pytest ^7.2.1 develop
- pytest-cov ^4.0.0 develop
- pytest-xdist ^3.2.0 develop
- ruff ^0.0.253 develop
- matplotlib ^3.9.2
- pandas ^2.2.2
- python ^3.12
- seaborn ^0.13.2