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Merge pull request #23 from camilogarciabotero/dev
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Refactor ORF main type, update entire writting API and other general changes
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camilogarciabotero authored Jan 10, 2024
2 parents 0aac328 + 6ce48ff commit c0105b8
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13 changes: 10 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -6,9 +6,16 @@ The format is based on Keep a Changelog and this project adheres to Semantic Ver

## [UNRELEASED](https://github.com/camilogarciabotero/GeneFinder.jl/compare/v0.0.10...main)

- Add `write_gff` methods.
- Clean up comments and docs.
- Add `iscoding` method.

## [0.2.0]

- A more stable ORF type that asserts for incorrect ORFs.
- Extended `Base.getindex` method to better handle ORF enabling: `seq[orf]` regardless of the ORF strand.
- The `write_*` API is much more stable and its been rewriten to handle IOStreams and `IOBuffers` as well.
- The new `record_orfs_fna` and `record_orfs_faa` methods intearact with the FASTX interface.
- Codebase has been reduced. Direct String manipulation is not enabled for `findorfs` and `get_*` methods.
- Docstrings have been updated following method updates.
- Better tests and now `Aqua.jl` is used for several tests as well.

## [0.1.0]

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187 changes: 3 additions & 184 deletions Manifest.toml
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Expand Up @@ -2,40 +2,20 @@

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9 changes: 3 additions & 6 deletions Project.toml
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@@ -1,27 +1,24 @@
name = "GeneFinder"
uuid = "2bc6ee46-2158-4f5a-a720-91cb2d7cee64"
authors = ["Camilo García-Botero"]
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2 comments on commit c0105b8

@camilogarciabotero
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@JuliaRegistrator register

Release notes:

Breaking changes

  • A more stable ORF type that asserts for incorrect ORFs.
  • Extended Base.getindex method to better handle ORF enabling: seq[orf] regardless of the ORF strand.
  • The write_* API is much more stable and its been rewriten to handle IOStreams and IOBuffers as well.
  • The new record_orfs_fna and record_orfs_faa methods intearact with the FASTX interface.
  • Codebase has been reduced. Direct String manipulation is not enabled for findorfs and get_* methods.
  • Docstrings have been updated following method updates.
  • Better tests and now Aqua.jl is used for several tests as well.

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Registration pull request created: JuliaRegistries/General/98659

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.0 -m "<description of version>" c0105b8b20e12b7cf6ef0cdfec7f7f8f3e483949
git push origin v0.2.0

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