BioJulia / FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.
https://biojulia.dev
MIT License
61 stars 20 forks source link

Make BioSequences a weak dependency #93

Closed jakobnissen closed 1 year ago

jakobnissen commented 1 year ago

In the upcoming Julia 1.9 release, Julia supports weak depencies which allow deps to be supported, but not required. With this change, on Julia 1.9, BioSequences is not automatically loaded when FASTX is. This allows BioSequences (and its deps) to be not be loaded when FASTX is, reducing loading time by about 1/3.

Closes #90

codecov[bot] commented 1 year ago

Codecov Report

Base: 90.78% // Head: 89.64% // Decreases project coverage by -1.14% :warning:

Coverage data is based on head (76ae872) compared to base (617e7c1). Patch coverage: 63.33% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #93 +/- ## ========================================== - Coverage 90.78% 89.64% -1.15% ========================================== Files 14 15 +1 Lines 662 676 +14 ========================================== + Hits 601 606 +5 - Misses 61 70 +9 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `89.64% <63.33%> (-1.15%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | Coverage Δ | | |---|---|---| | [src/FASTX.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL0ZBU1RYLmps) | `92.98% <ø> (+1.67%)` | :arrow_up: | | [src/fasta/fasta.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL2Zhc3RhL2Zhc3RhLmps) | `100.00% <ø> (ø)` | | | [src/fastq/fastq.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL2Zhc3RxL2Zhc3RxLmps) | `100.00% <ø> (ø)` | | | [src/fastq/record.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL2Zhc3RxL3JlY29yZC5qbA==) | `94.94% <ø> (ø)` | | | [ext/BioSequencesExt.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-ZXh0L0Jpb1NlcXVlbmNlc0V4dC5qbA==) | `57.69% <57.69%> (ø)` | | | [src/fasta/record.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL2Zhc3RhL3JlY29yZC5qbA==) | `82.14% <100.00%> (ø)` | | | [src/workload.jl](https://codecov.io/gh/BioJulia/FASTX.jl/pull/93/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL3dvcmtsb2FkLmps) | `100.00% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia)

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jakobnissen commented 1 year ago

This is ready to go (failure is coverage issues). I'm leaving it up for a bit to decide if it's worth it.