Bump cogent3 from 2024.2.5a1 to 2024.5.7a1

[dependabot]

Bumps cogent3 from 2024.2.5a1 to 2024.5.7a1.

Changelog

Sourced from cogent3's changelog.

Changes in release "2024.5.7a1"

Contributors

• @​KatherineCaley for reviewing PRs and code contributions related to SeqView taking on a more prominent role in recording history of operations on sequences.
• First-time contributions from @​Yutong-Shao, @​Zongjing-Han, @​yantonglu, @​ShunyiYang, @​KyleSu12, @​Ruizhe-wang, @​Firimp 🎉
• Adopted suggested documentation example proposed by Lizhaozhe123, with some amendments, for the trim_stop_codons app.
• Multiple contributions from @​GavinHuttley
• @​rmcar17 identified and fixed a bug 🚀!
• @​rmcar17 addressed deprecation of using end as a column name
• Implementation of plug-in support 🏗️ by @​khiron
• We had many contributors to project maintenance, making the contributor experience better 🎉!! @​rmcar17, @​GavinHuttley @​fredjaya reviewed PR's 🛠️🚀 @​khiron, @​KatherineCaley, @​YapengLang, @​fredjaya, @​rmcar17 and @​GavinHuttley all commented on Issues. @​khiron, @​fredjaya and @​rmcar17 contributed to general maintenance tasks, including developer docs and troubleshooting infrastructure issues.

ENH

• Annotation databases are now preserved after renaming sequences. This is made possible because SeqView has the seqid attribute which is preserved and is independent of the name of the enclosing Sequence.
• Sequence.parent_coordinates() now returns information related to its parent. For example, we have a sequence with name "1" which we then sliced and rename the slice to "gene". Calling gene.parent_coordinates() would return "1", slice start, slice end, strand.
• methods on likelihood function objects that work with continuous-time Markov models no longer fail if the model also has discrete-time edges. These include lf.get_lengths_as_ens(), lf.get_annotated_tree(), lf.get_paralinear_metric().
• Added new lf.get_ens_tree(). This returns trees with the expected number of substitutions as the branch length. On discrete-time edges the branch length is set to None. Think of this tree as the true "evolutionary tree". Thanks to Von Bing Yap for suggesting this!
• Plugin support that will allow 3rd-party developers to add their custom functionality to the cogent3 pipeline as first class apps
• The new IndelMap class uses numpy arrays to store information about gap locations for aligned sequences. This will greatly reduce the memory overhead for aligned sequences. The class also provides explicit methods for inter-converting between sequence and alignment coordinates. An important difference to the original Map implementation is that IndelMap is memoryless, meaning the history of slice operations is now fully delegated to the SeqView class.

... (truncated)

Commits

• 69a668d Merge pull request #1857 from GavinHuttley/develop
• 10fd7e6 REL: updated changelog for release
• 57a26e5 DEV: update version to 2024.5.7a1
• 57e605d Merge pull request #1856 from GavinHuttley/develop
• 76710c6 DEV: acknowledge contributors to project
• 4c292a8 Merge pull request #1855 from cogent3/dependabot/pip/plotly-5.22.0
• ad40cdf Bump plotly from 5.21.0 to 5.22.0
• b5e9501 STY: pre-commit linting with black and isort
• 6027f82 Merge pull request #1836 from cogent3/dependabot/pip/black-24.4.2
• d031943 Merge pull request #1851 from YapengLang/feature/issue-1636
• Additional commits viewable in compare view

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[coveralls]

Pull Request Test Coverage Report for Build 9055827293

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 100.0%

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Totals
Change from base Build 8964233522:	0.0%
Covered Lines:	415
Relevant Lines:	415

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💛 - Coveralls