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[CHANGED] added a dependency to doc optional extras
REL: bumped release to 2024.11.8a3
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.2 to 0.7.3. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.7.2...0.7.3) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
DOC: update intro and add link to preprint
Bump ruff from 0.7.2 to 0.7.3
Reviewer's Guide by SourceryThis PR updates the project's documentation, dependencies, and version number. The main changes include a significant revision of the README.md description to better reflect the project's capabilities and purpose, along with minor version updates for dependencies and the package itself. No diagrams generated as the changes look simple and do not need a visual representation. File-Level Changes
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Hey @GavinHuttley - I've reviewed your changes and they look great!
Here's what I looked at during the review
- 🟡 General issues: 1 issue found
- 🟢 Security: all looks good
- 🟢 Testing: all looks good
- 🟢 Complexity: all looks good
- 🟡 Documentation: 1 issue found
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
| @@ -50,7 +50,7 @@ test = [ | |||
| "pytest", | |||
| "pytest-cov", | |||
| "pytest-xdist", | |||
| "ruff==0.7.2", | |||
| "ruff==0.7.3", | |||
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suggestion: Consider consolidating the duplicated Ruff dependency specification
The Ruff dependency is currently specified with the same version in both test and dev dependencies. Consider moving it to a shared dependency list or using dependency inheritance to avoid potential maintenance issues.
| `diverse_seq` provides tools for selecting a representative subset of sequences from a larger collection. It is an alignment-free method which scales linearly with the number of sequences. It identifies the subset of sequences that maximize diversity as measured using Jensen-Shannon divergence. `diverse_seq` provides a command-line tool (`dvs`) and plugins to the Cogent3 app system (prefixed by `dvs_`) allowing users to embed code in their own scripts. The command-line tools can be run in parallel. | ||
| `diverse-seq` implements computationally efficient alignment-free algorithms that enable efficient prototyping for phylogenetic workflows. It can accelerate parameter selection searches for sequence alignment and phylogeny estimation by identifying a subset of sequences that are representative of the diversity in a collection. We show that selecting representative sequences with an entropy measure of *k*-mer frequencies correspond well to sampling via conventional genetic distances. The computational performance is linear with respect to the number of sequences and can be run in parallel. Applied to a collection of 10.5k whole microbial genomes on a laptop took ~8 minutes to prepare the data and 4 minutes to select 100 representatives. `diverse-seq` can further boost the performance of phylogenetic estimation by providing a seed phylogeny that can be further refined by a more sophisticated algorithm. For ~1k whole microbial genomes on a laptop, it takes ~1.8 minutes to estimate a bifurcating tree from mash distances. | ||
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| You can read more about the methods implemented in `diverse_seq` in the preprint [here](https://biorxiv.org/cgi/content/short/2024.11.10.622877v1). |
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issue (documentation): Inconsistent package name formatting between diverse-seq and diverse_seq
Consider using a consistent name throughout the documentation to avoid confusion. If the different forms are intentional (e.g., project name vs package name), please clarify this.
Pull Request Test Coverage Report for Build 11785962632Warning: This coverage report may be inaccurate.This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.
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Summary by Sourcery
Enhance the README with a comprehensive description of the 'diverse_seq' tool's capabilities and update the 'ruff' dependency version in the build configuration. Add 'statsmodels' to the documentation dependencies.
Enhancements:
Build: