Project TOML file #63
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With the IO submodules removed in #64, there is no longer any need for Automa as a dependency.
Version 2 of BioSequences is dropping the IO submodules, and so BufferedStreams is no longer needed.
Codecov Report
@@ Coverage Diff @@
## version2 #63 +/- ##
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+ Coverage 73.73% 81.21% +7.48%
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Files 47 47
Lines 1938 2316 +378
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+ Hits 1429 1881 +452
+ Misses 509 435 -74
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Do you have plans to merge this version into master, so that projects using |
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I was going to leave master as it is until the version2 branch is in a state I am happy with, at which point master will be updated and a V2.X of BioSequences, with a new API and sequence types will be released. The work for BioSequences v2.0 is not far from completion now: one or two weeks should do it with the time I have available. As far as I can tell, BioSequences 1.1 using REQUIRE hasn't been causing any issues, I've been developing and releasing packages that use Project.toml and BioSequences without an issue so far. |
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Oh it makes complete sense. I was under the impression that "A package with a project file cannot depend on one without a project file" (from here). But this may not be a problem for packages that were in METADATA before the switch to the General registry, as all these packages are in there, and with their own uuid. Sorry for the trouble. Looking forward to BioSequences v2.0! |
* Rename types in BioSequences (#53) * Add unsafe_setindex for more Base.setindex methods (#54) * Move and generalise sequence transformation methods (#56) * Reworked random LongSequence generation (#55) * Remove IO submodules (#62) * Remove the ABIF submodule * Project TOML file (#63) * Remove Automa * Replace BioCore with BioGenerics * SkipmerFactory (#57) * Add findnext, findprev and each methods for functions * Refactor naive counting and gc_counting and add counting manual page * Update transforms to work for BigMers and actually test BigMers * Redux the bit-parallel mismatch counter methods * Add a paired sequence bitpar function compiler * Match counter redux * Ambiguous site counting redux * Gap site counting redux * Certain site counting redux * Remove old site counting system and document the new one * Remove redundant gc_count function for LongSequences * Redux the mer iteration interface and add sections to the manual
This PR removes any dependencies no longer used by the BioSequences module, and will replace the REQUIRE file with a Project.toml