BioJulia/BioSequences.jl: v3.0.0

Diff since v2.0.5

Closed issues:

• getindex not defined for arrays (#61)
• Problems installing BioSequences package (#71)
• Performance review before release (#86)
• julia 1.5: Time for views of a sequence? (#102)
• Erroneous reverse_complement behaviour? (#110)
• Slicing ReferenceSequences (#114)
• Failed push! adds empty bases (#115)
• Future of subsequences (#118)
• Demultiplexer fails for Levenshtein distance > 1 (#124)
• One-hot encoding of sequences (#130)
• Spring cleanup for v3 (#138)
• Fixup tests before v3 (#139)
• Check interfaces, remove NotImplemented errors (#140)
• Streamline find functions to behave like Base's (#141)
• [speculative] Remove BioSequence(::Integer)? (#142)
• Disallow construction of k-mers from integers (#145)
• Move to upcoming release of BioSymbols (#148)
• Add trait "iscomplete" to Alphabet (#151)
• ERROR: UndefVarError: FASTA not defined (#152)
• Export RE.Regex, and make constructors easier. (#167)
• approxsearch and approxrsearch should return Union{Nothing, T} (#175)
• Default to dynamic allocation for string literals (#180)
• No version for Julia 1.6.1 (#185)
• No version for Julia 1.6.1 (#186)
• errors in docs: random kmers (#195)
• Don't recommend users engage in type piracy with stringbyte (#198)
• Include comparison example (#199)

Merged pull requests:

• Implement range slices over kmers (#112) (@cjprybol)
• Update links for this pull request template (#113) (@cjprybol)
• Fix push! (#116) (@jakobnissen)
• Fix StackOverflow error on Kmer instatiation (#117) (@jakobnissen)
• Remove LongSequence copy-on-write (#119) (@jakobnissen)
• Add sequence view (#120) (@jakobnissen)
• Remove Kmers (#121) (@SabrinaJaye)
• CompatHelper: bump compat for "StableRNGs" to "1.0" (#122) (@github-actions[bot])
• Make same-type conversion noop (#123) (@jakobnissen)
• Fix ReferenceSequence slicing bug (#125) (@lhnguyen-vn)
• Allow hamming circle around N (#126) (@tp2750)
• Fix reversing seq with unused data (#128) (@jakobnissen)
• Refactor translation (#131) (@jakobnissen)
• Deprecate minhash (#132) (@jakobnissen)
• Move some indexing logic from LongSequence to BioSequence (#133) (@jakobnissen)
• Add join and join! for BioSequence (#134) (@jakobnissen)
• Fix typo in genetic code show (#136) (@jakobnissen)
• Change semantics of find to match Base (#144) (@jakobnissen)
• Remove the constructor LongSequence{A}(::Integer) (#146) (@jakobnissen)
• Remove conversion to/from integers and kmers, and direct instantiatio… (#147) (@jakobnissen)
• Re-add construction between integer/kmer (#149) (@jakobnissen)
• Remove ConditionIterator (#150) (@jakobnissen)
• Remove financial backing and Gitter from README (#153) (@jakobnissen)
• Remove @sprintf dependency. (#156) (@SabrinaJaye)
• Remove BioGenerics dependency (#157) (@SabrinaJaye)
• Remove Combinatorics dependency (#158) (@SabrinaJaye)
• Remove IndexableBitVector dependency (#159) (@SabrinaJaye)
• Update user manual (#160) (@SabrinaJaye)
• Update interface to version 3. (#161) (@jakobnissen)
• Change sequence type aliases (#163) (@SabrinaJaye)
• Add fast equality for BioSequence (#164) (@jakobnissen)
• Add findfirst method for BioSymbol (#166) (@jakobnissen)
• Export RE.Regex and RE.RegexMatch as BioRegex and BioRegexMatch (#169) (@jakobnissen)
• Approximate search now returns nothing when no match is found (#176) (@jakobnissen)
• Remove undefined exports (#177) (@jakobnissen)
• Fix doctests after type alias renaming (#181) (@jakobnissen)
• Fix documenter warnings about broken links (#183) (@jakobnissen)
• Remove dependency on StableRNGs (#188) (@jakobnissen)
• Search API redo (#190) (@SabrinaJaye)
• Improve docstrings and changelog slightly (#191) (@jakobnissen)
• Add workflow for downstream tests (#192) (@CiaranOMara)
• Improve docstrings (#193) (@jakobnissen)
• Add parsing of BioSequence, simplify some printing (#194) (@jakobnissen)
• Remove sequence conversion to/from String and Vector (#196) (@jakobnissen)
• Fix REPL blocks in docs (#197) (@jakobnissen)
• Rename stringbyte and avoid pirating BioSymbols (#200) (@jakobnissen)
• Clarify comparison to sequences in docs (#201) (@jakobnissen)
• Add has_interface function (#202) (@jakobnissen)
• WIP: Test bonanza for v3 (#203) (@jakobnissen)
• Fix issues from v3/master merge (#207) (@jakobnissen)
• Fix bugs in minimal Alphabet interface example (#208) (@jakobnissen)