remove uses of metadata() (#107)

Co-authored-by: Kevin Bonham <[email protected]>

Project.toml

@@ -4,7 +4,7 @@ keywords = ["microbiology", "microbiome", "biology", "metagenomics"]
 license = "MIT"
 desc = "Convenience functions for working with the bioBakery"
 authors = ["kescobo <[email protected]>", "annelle-abatoni <[email protected]>", "anikaluo <[email protected]>", "Vanja Klepac-Ceraj <[email protected]>"]
-version = "0.6"
+version = "0.7.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -18,7 +18,7 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 [compat]
 CSV = "0.8, 0.9, 0.10"
 Conda = "1.5"
-Microbiome = "0.9"
+Microbiome = "0.9.4,0.10"
 Reexport = "0.2, 1"
 ReTest = "0.3"
 Tables = "1.2.1"

docs/src/metaphlan.md

@@ -317,7 +317,7 @@ SRS014459, SRS014464, SRS014470...SRS014476, SRS014494
 
 
 
-julia> metadata(mps3)
+julia> get(mps3)
 6-element Vector{NamedTuple{(:sample, :STSite, :filename), Tuple{String, String, String}}}:
  (sample = "SRS014459", STSite = "Stool", filename = "SRS014459-Stool_profile.tsv")
  (sample = "SRS014464", STSite = "Anterior_nares", filename = "SRS014464-Anterior_nares_profile.tsv")
@@ -396,7 +396,7 @@ but there are [many other options](https://juliahub.com/ui/Search?q=plotting&typ
 
 julia> using CairoMakie
 
-julia> sites = [m.STSite for m in metadata(mps3)]
+julia> sites = [m.STSite for m in get(mps3)] # or get(m, :STSite)
 6-element Vector{String}:
  "Stool"
  "Anterior_nares"

src/humann.jl

@@ -231,7 +231,7 @@ from a `CommunityProfile` with metadata attached to the samples.
 or a vector of symbols.
 """
 function write_pcl(path, comm::CommunityProfile; usemetadata=:all)
-    coltab = Tables.columntable(metadata(comm))
+    coltab = Tables.columntable(get(comm))
     if usemetadata == :all
         usemetadata = collect(keys(coltab))
         popfirst!(usemetadata)
@@ -269,7 +269,7 @@ function humann_barplot(comm::CommunityProfile, outpath; kwargs...)
     write_pcl(tmp, comm)
 
     cmd = ["humann_barplot", "--i", tmp, "-o", outpath,
-            "--last-metadata", string(last(keys(first(metadata(comm)))))]
+            "--last-metadata", string(last(keys(first(get(comm)))))]
 
     add_cli_kwargs!(cmd, kwargs; optunderscores=false)
     run(Cmd(cmd))