v0.7.0

BiobakeryUtils v0.7.0

Diff since v0.6.0

Closed issues:

• Kevin adds some database installations to the Microbiome.jl tutorial (#102)
• Remove mentions of "compiled" from docstrings (#103)

Merged pull requests:

• Juliacon code demo (#101) (@annelle-abatoni)
• updates to tutorial (#104) (@kescobo)
• delete compiles/d (#105) (@anikaluo)
• fix test sizes (#106) (@kescobo)
• Change compat to microbiome 10, remove metadata() (#107) (@kescobo)

v0.6.0

BiobakeryUtils v0.6.0

Diff since v0.5.5

Merged pull requests:

• Update for compatibility with Microbiome 0.9 (breaking) (#99) (@kescobo)

v0.5.5

BiobakeryUtils v0.5.5

Diff since v0.5.4

Merged pull requests:

• Kneaddata (#98) (@kescobo)

v0.5.4

BiobakeryUtils v0.5.4

Diff since v0.5.3

Merged pull requests:

• Correcting the environment name, and this 2nd note is something that … (#95) (@adRn-s)
• Correcting URLs (#96) (@adRn-s)
• Some other documentation fixes (#97) (@kescobo)

v0.5.3

BiobakeryUtils v0.5.3

Diff since v0.5.2

v0.5.2

BiobakeryUtils v0.5.2

Diff since v0.5.1

v0.5.1

BiobakeryUtils v0.5.1

Diff since v0.5.0

Closed issues:

• slice = gfs_strat["UniRef90_D0TRR5", :] (#91)

Merged pull requests:

• Typos (#93) (@kescobo)

v0.5.0

BiobakeryUtils v0.5.0

Diff since v0.4.0

Closed issues:

• Add Microbiome.jl 0.7 constructors (#22)
• Metadata import into microbial communities (#24)
• Add Doc strings to documentation files in the right places (#27)
• Fixe biobakery link in README (#29)
• Make sure all DataFrames - returning functions switch to comm profile (#30)
• make rm_strat! actually do something (#31)
• Remove panphlan_calcs for now (#32)
• use more descriptive argument names (eg. elt) (#33)
• can findclade be modified so that it also takes taxa numbers as arguments, not just symbol? (#34)
• Tutorials/Documentation (#48)
• Metaphlan: Broken Link (#54)
• Deprecate permanova in favor of hydra (#55)
• Use Conda.jl to add humann to CI so we can test those functions (#58)
• Add docs for filter patterns (#61)
• add quotes around path for install_devs (#67)
• Fix round-tripping of humann tables (#70)
• potential markdown typo (#73)
• function docs formatting in tutorial (#74)
• spec not defined (#76)
• images not displayed (#77)
• Metaphlan Tutorial Ref Links (#78)
• create a "troubleshooting section" (#83)
• Error - no method matching taxon(::SubString) (#84)

Merged pull requests:

• Updating Microbiome.jl 0.7.0 (#21) (@annelle-abatoni)
• remove panphlan (#35) (@anikaluo)
• fix biobakery link (#37) (@anikaluo)
• Additional findclade methods (#38) (@anikaluo)
• Metaphlan docs (#40) (@anikaluo)
• Metaphlan Profiles Function (#42) (@anikaluo)
• adding rm_strat (#47) (@annelle-abatoni)
• taxfilter & taxfilter! documentation (#49) (@annelle-abatoni)
• Tutorial (#50) (@anikaluo)
• Changing DataFrame to AbstractDataFrame in humann2.jl (#51) (@annelle-abatoni)
• change contributing link (#56) (@anikaluo)
• V3docs (#57) (@kescobo)
• Humann profiles (#59) (@kescobo)
• change CommProfile names (#60) (@anikaluo)
• remove DataFrames dependency (#62) (@kescobo)
• Metaphlan and Humann tutorials (#63) (@kescobo)
• Conda test (#65) (@kescobo)
• Fix tests (#66) (@kescobo)
• fix docstring for install_deps (#68) (@kescobo)
• Metaphlan Tutorials (#69) (@kescobo)
• Tutorial refinements (#71) (@kescobo)
• typos in metaphlan tutorial (#72) (@anikaluo)
• Adding authors (#80) (@annelle-abatoni)
• use docs build action (#81) (@kescobo)
• Issue jubilee (#82) (@kescobo)
• add troubleshooting section (#83) (#85) (@kescobo)
• fix branch name in GHA (#86) (@kescobo)
• nprocs-> nproc (#87) (@kescobo)
• Ecojulia transfer (#88) (@kescobo)
• update deps (#89) (@kescobo)
• Cli fix (#90) (@kescobo)
• Cli fix (#92) (@kescobo)

v0.4.0

BiobakeryUtils v0.4.0

Diff since v0.3.3

Closed issues:

• taxfilter should keep unclassifieds (#13)

Merged pull requests:

• rework metaphlan to expose taxon parsing (#17) (@kescobo)
• try to fix github action (#18) (@kescobo)

v0.3.3

BiobakeryUtils v0.3.3

Diff since v0.3.2

Merged pull requests:

• update DataFrames dep (#15) (@kescobo)