PopGen.jl Versions Save

PopGen v0.9.4

Diff since v0.9.3

PopGen v0.9.3

Diff since v0.9.2

PopGen v0.9.1

Diff since v0.9.0

Closed issues:

• [feature] replace ProgressMeter with Term.jl ProgressBar (#96)

Merged pull requests:

• CompatHelper: bump compat for MultivariateStats to 0.10, (keep existing compat) (#108) (@github-actions[bot])

PopGen v0.9.0

⚠️⚠️ Breaking Changes

• PopGenCore.jl compat restricted to latest version (very breaking changes)

• kinship methods

  • returns NamedMatrix if no bootstrapping
  • returns DataFrame if bootstrapping

• pairwisefst methods use method = Name instead of method = "Name"

  • fewer keystrokes
  • autocompletion!

✨✨ New Things

• new clustering methods wrapped in generic cluster function:
  • kmedoids
  • hierarchical clustering
  • fuzzy c-means
  • dbscan
• write to Baypass format files
• read/write PLINK (ped)
• t-SNE analysis

⚡⚡ Improvements

• kinship
  • substantially improved speed
  • substantially decreased RAM usage (orders of magnitude)
• pairwisefst
  • better API
  • faster and fewer allocations
• better biallelic conditionals
• a lot of internal functions have been optimized for speed and fewer allocations (PopGenCore.jl)

🐛🐛 Bug fixes

• absolute path eliding in file reading info
• a bunch more I forgot to write down

Diff since v0.8.0

Merged pull requests:

• add more clustering methods (#99) (@pdimens)
• add cluster() wrapper (#100) (@pdimens)

PopGen v0.8.0

⚠️⚠️ Breaking Changes

• dropped support for Julia <v1.6
  • new count methods we use aren't supported by previous versions

✨✨ New Things

• k-means clustering using Kmeans++ via kmeans()
• Principcal Component Analysis via pca()
• new deps Clustering.jl and MultivariateStats.jl
• Jason and Pavel both completed their doctorates!

⚡⚡ Improvements

• allele matrix creation methods (internal) have >50% fewer LOC and are >2x faster!

🐛🐛 Bug fixes

• none, I think

Diff since v0.7.1

Merged pull requests:

• Pca (#97) (@pdimens)
• CompatHelper: add new compat entry for Clustering at version 0.14, (keep existing compat) (#98) (@github-actions[bot])

PopGen v0.7.1

Diff since v0.7.0

Closed issues:

• permutations for fst shuffle indices and return views (#94)

No changed, linked with zenodo

Full Changelog: https://github.com/BioJulia/PopGen.jl/compare/v0.7.0...0.7.1

PopGen v0.7.0

Diff since v0.6.5

⚠️⚠️ Breaking Changes

• all PopData functionality moved to separate package PopGenCore.jl
• PopGen.jl reexports functions from PopGenCore.jl for familiar functionality
• .meta and .loci have been renamed .metadata and .genodata
• .metadata is no longer a DataFrame and instead a new PopDataInfo type
• latitude and longitude columns no longer mandatory and omitted in cases where not used

⚡⚡ Improvements

• PopData can be indexed like a DataFrame and it will return a brand new PopData!
• PopDataInfo is self-updating (in most cases)
• preliminary plink .bed file importing (not writing, yet)
• show for PopData is now smaller and cleaner
• INFO text for data importing now elides abs paths longer than the terminal width
• VCF/BCF support no longer lazy loaded
• VCF/BCF uses VariantCallFormat.jl now (instead of GeneticVariations.jl)
• VCF/BCF uses different GZ library for decompression
• try...catch blocks used in file io for faster file reading and fewer lines of code

🐛🐛 Bug fixes

• super slow structure io on larger files

Closed issues:

• [feature] Split file IO into separate package (#82)
• [feature] remove release branch (#83)
• [feature] speed up fst permutations (#84)
• [feature] locus-by-locus pairwise FST (#87)

Merged pull requests:

• CompatHelper: add new compat entry for "NaturalSort" at version "1" (#80) (@github-actions[bot])
• CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#90) (@github-actions[bot])
• CompatHelper: add new compat entry for PopGenCore at version 0.2, (keep existing compat) (#91) (@github-actions[bot])

PopGen v0.6.5

Diff since v0.6.4

Closed issues:

• [feature] Compatibility with DataFrames v1 (#71)
• [feature] add NaturalSort.jl as dep (#74)
• [bug] isbiallelic(::PopData) returns incorrect answer (#75)
• [bug] PopData.meta.name incorrectly typed from vcf import (#76)
• [feature] consolidate file import info text (#77)
• [bug] export keep and keep! (#78)

Merged pull requests:

• CompatHelper: bump compat for "MultipleTesting" to "0.5" (#73) (@github-actions[bot])
• push 0.6.5 to release (#79) (@pdimens)

PopGen v0.6.4

• updates compat to use DataFrames.jl 1.x

Diff since v0.6.3

Merged pull requests:

• CompatHelper: bump compat for "DataFrames" to "1.0" (#68) (@github-actions[bot])
• CompatHelper: bump compat for "Distributions" to "0.25" (#69) (@github-actions[bot])
• CompatHelper: bump compat for "DataFrames" to "1.1" (#70) (@github-actions[bot])
• add DataFrames 1.x compat (#72) (@pdimens)