Tooling

.github/workflows/ci.yml

@@ -5,9 +5,20 @@ on:
     tags: [v*]
   pull_request:
 jobs:
+  format:
+    name: Runic formatting check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - run: julia -e 'using Pkg; Pkg.add("Runic")'
+      - run: julia -m Runic --check src/ test/
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
       fail-fast: false
       matrix:
@@ -19,25 +30,23 @@ jobs:
           - macOS-latest
         arch:
           - x64
+        include:
+          - version: 'nightly'
+            experimental: true
+          - version: '1'
+            experimental: false
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+        continue-on-error: true
+      - uses: codecov/codecov-action@v4
+        continue-on-error: true # re-enable after v1.0
         with:
           file: lcov.info

codecov.yml

@@ -0,0 +1,7 @@
+# Re-enable status checks after v1.0 coverage baseline is established
+coverage:
+  status:
+    project:
+      enabled: no
+    patch:
+      enabled: no

docs/Project.toml

@@ -5,3 +5,6 @@ Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Microbiome = "3bd8f0ae-a0f2-5238-a5af-e1b399a4940c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[compat]
+Documenter = "1"

docs/make.jl

@@ -2,19 +2,21 @@ using Documenter, Microbiome, Microbiome.Dictionaries
 
 makedocs(
     sitename = "Microbiome.jl",
-    strict=:doctest,
+    warnonly = [:missing_docs, :cross_references],
+    doctest = false, # doctests disabled until outputs are updated for v1.0
     pages = [
         "Home" => "index.md",
         "Samples and features" => "samples_features.md",
         "Profiles and Communities" => "profiles.md",
         "Diversity measures" => "diversity.md",
     ],
-    authors = "Kevin Bonham, PhD <kbonham@wellesley.edu",
+    authors = "Kevin Bonham, PhD <kbonham@wellesley.edu>",
     format = Documenter.HTML(
         prettyurls = get(ENV, "CI", nothing) == "true",
-        edit_link="main",
-        canonical="http://docs.ecojulia.org/BiobakeryUtils.jl/stable/")
-        )
+        edit_link = "main",
+        canonical = "https://docs.ecojulia.org/Microbiome.jl/stable/",
+    ),
+)
 
 deploydocs(
     repo = "github.com/EcoJulia/Microbiome.jl.git",

docs/src/profiles.md

@@ -405,7 +405,7 @@ CommunityProfile
 samples
 features
 samplenames
-**featurenames**
+featurenames
 commjoin
 relativeabundance
 relativeabundance!

docs/src/samples_features.md

@@ -224,7 +224,6 @@ Metabolite("other name", missing, missing, missing)
 
 ```@docs
 MicrobiomeSample
-metadata
 ```
 
 ```@docs

src/Microbiome.jl

@@ -2,68 +2,68 @@ module Microbiome
 
 # Samples and Features
 export MicrobiomeSample,
-       Taxon,
-       GeneFunction,
-       Metabolite,
-       set!,
-       unset!,
-       insert!,
-       delete!,
-       name,
-       taxrank,
-       hasrank,
-       taxon,
-       hastaxon,
-       genefunction,
-       commonname,
-       masscharge,
-       retentiontime
+    Taxon,
+    GeneFunction,
+    Metabolite,
+    set!,
+    unset!,
+    insert!,
+    delete!,
+    name,
+    taxrank,
+    hasrank,
+    taxon,
+    hastaxon,
+    genefunction,
+    commonname,
+    masscharge,
+    retentiontime
 
 # EcoBase Translations
 export abundances,
-       nfeatures,
-       featurenames,
-       getfeature,
-       nsamples,
-       samplenames,
-       getsample,
-       AbstractFeature,
-       AbstractSample
-    #    featureabundances,
-    #    sampleabundances
+    nfeatures,
+    featurenames,
+    getfeature,
+    nsamples,
+    samplenames,
+    getsample,
+    AbstractFeature,
+    AbstractSample
+#    featureabundances,
+#    sampleabundances
 
 # Profiles
 export CommunityProfile,
-       featuretype,
-       features,
-       samples,
-       ranks,
-       rankfilter,
-       profiletype,
-       featuretotals,
-       sampletotals,
-       commjoin
-   
+    featuretype,
+    features,
+    samples,
+    ranks,
+    rankfilter,
+    profiletype,
+    featuretotals,
+    sampletotals,
+    commjoin
+
 # Abundances
 export present,
-       prevalence,
-       relativeabundance!,
-       relativeabundance,
-       prevalence_filter
+    prevalence,
+    relativeabundance!,
+    relativeabundance,
+    prevalence_filter
 #     filterabund
 
 # Diversity
 export ginisimpson,
-       shannon,
-       ginisimpson!,
-       shannon!,
-       present,
-       prevalence,
-       braycurtis,
-       jaccard,
-       hellinger,
-       pcoa
-       
+    shannon,
+    ginisimpson!,
+    shannon!,
+    present,
+    prevalence,
+    braycurtis,
+    jaccard,
+    hellinger,
+    pcoa
+
 using Statistics
 using SparseArrays
 using EcoBase

src/diversity.jl

@@ -9,7 +9,7 @@ When called on an `AbstractAbundanceTable`,
 returns a 1 x nsamples matrix with 1 entry per sample.
 See also [`shannon!`](@ref).
 """
-function shannon(v::Union{AbstractVector{T}, AbstractSparseMatrix{T}}) where T<:Real
+function shannon(v::Union{AbstractVector{T}, AbstractSparseMatrix{T}}) where {T <: Real}
     total = sum(v)
     logtotal = log(total)
     # The iszero condition is necessary to prevent log(0)
@@ -29,7 +29,7 @@ If `overwrite=false` (the default), uses `insert!` to perform this operation,
 so an error will be thrown if any sample already contains a `:shannon` entry.
 Otherwise, uses `set!`.
 """
-function shannon!(abt::AbstractAbundanceTable; overwrite=false)
+function shannon!(abt::AbstractAbundanceTable; overwrite = false)
     func! = overwrite ? set! : insert!
     for s in samples(abt)
         col = abt[:, s]
@@ -48,7 +48,7 @@ When called on an `AbstractAbundanceTable`,
 returns a 1 x nsamples matrix with 1 entry per sample.
 See also [`ginisimpson!`](@ref).
 """
-function ginisimpson(v::Union{AbstractVector{T}, AbstractSparseMatrix{T}}) where T<:Real
+function ginisimpson(v::Union{AbstractVector{T}, AbstractSparseMatrix{T}}) where {T <: Real}
     total = sum(v)
     return 1 - sum(x -> x^2, v) / (total^2)
 end
@@ -66,7 +66,7 @@ If `overwrite=false` (the default), uses `insert!` to perform this operation,
 so an error will be thrown if any sample already contains a `:ginisimpson` entry.
 Otherwise, uses `set!`.
 """
-function ginisimpson!(abt::AbstractAbundanceTable; overwrite=false)
+function ginisimpson!(abt::AbstractAbundanceTable; overwrite = false)
     func! = overwrite ? set! : insert!
     for s in samples(abt)
         col = abt[:, s]
@@ -81,26 +81,26 @@ end
 
 Returns a pairwise Bray-Curtis dissimilarity matrix.
 """
-braycurtis(abt::AbstractAbundanceTable) = pairwise(BrayCurtis(), collect(abundances(abt)), dims=2)
+braycurtis(abt::AbstractAbundanceTable) = pairwise(BrayCurtis(), collect(abundances(abt)), dims = 2)
 
 """
     jaccard(abt::AbstractAbundanceTable)
 
 Returns a pairwise Jaccard distance matrix.
 """
-jaccard(abt::AbstractAbundanceTable) = pairwise(Jaccard(), collect(abundances(abt)), dims=2)
+jaccard(abt::AbstractAbundanceTable) = pairwise(Jaccard(), collect(abundances(abt)), dims = 2)
 
 """
     hellinger(abt::AbstractAbundanceTable)
 
 Returns a pairwise Hellinger distance matrix.
 """
-hellinger(abt::AbstractAbundanceTable) = pairwise(HellingerDist(), collect(abundances(abt)), dims=2)
+hellinger(abt::AbstractAbundanceTable) = pairwise(HellingerDist(), collect(abundances(abt)), dims = 2)
 
 """
     pcoa(abt::AbstractAbundanceTable, f=braycurtis) 
 
 Returns eigenvectors from fitting `MDS` to a distance metric generated by `f`,
 by default `braycurtis`.
 """
-pcoa(abt::AbstractAbundanceTable, f=braycurtis) = fit(MDS, f(abt), distances = true)
+pcoa(abt::AbstractAbundanceTable, f = braycurtis) = fit(MDS, f(abt), distances = true)

src/ecobase.jl

@@ -28,4 +28,4 @@ const samplenames = EcoBase.placenames
 const getsample = EcoBase.placeoccurrences
 
 abstract type AbstractFeature <: EcoBase.AbstractThings end
-abstract type AbstractSample <: EcoBase.AbstractPlaces{Nothing} end
+abstract type AbstractSample <: EcoBase.AbstractPlaces{Nothing} end

src/features.jl

@@ -1,16 +1,16 @@
 name(as::AbstractFeature) = as.name
 
 const _ranks = (
-    domain     = 0,
-    kingdom    = 1,
-    phylum     = 2,
-    class      = 3,
-    order      = 4,
-    family     = 5,
-    genus      = 6,
-    species    = 7,
+    domain = 0,
+    kingdom = 1,
+    phylum = 2,
+    class = 3,
+    order = 4,
+    family = 5,
+    genus = 6,
+    species = 7,
     subspecies = 8,
-    strain     = 9
+    strain = 9,
 )
 
 const _shortranks = (
@@ -23,7 +23,7 @@ const _shortranks = (
     g = :genus,
     s = :species,
     t = :subspecies,
-    u = missing
+    u = missing,
 )
 
 """
@@ -51,16 +51,16 @@ See also [`taxon`](@ref Microbiome.taxon).
 struct Taxon <: AbstractFeature
     name::String
     rank::Union{Missing, Symbol}
-    
+
     Taxon(s::AbstractString, ::Missing) = new(s, missing)
-    Taxon(s::AbstractString, rank::Symbol) = in(rank, keys(_ranks)) ? 
-                                                        new(s, rank)  :
-                                                        error("Invalid rank $rank, must be one of $(keys(_ranks))")
+    Taxon(s::AbstractString, rank::Symbol) = in(rank, keys(_ranks)) ?
+        new(s, rank) :
+        error("Invalid rank $rank, must be one of $(keys(_ranks))")
 end
 
 Taxon(n::AbstractString, rank::Int) = 0 <= rank <= 9 ?
-                                            Taxon(n, keys(_ranks)[rank+1]) :
-                                            error("Invalid rank $rank, must be one of $_ranks")
+    Taxon(n, keys(_ranks)[rank + 1]) :
+    error("Invalid rank $rank, must be one of $_ranks")
 Taxon(n::AbstractString) = Taxon(n, missing)
 
 function Base.String(t::Taxon)
@@ -239,7 +239,7 @@ Accessor function for the `rt` field of a [`Metabolite`](@ref).
 retentiontime(m::Metabolite) = m.rt
 
 @testset "Metabolites" begin
-    m1 = Metabolite("name", "common", 1., 1.)
+    m1 = Metabolite("name", "common", 1.0, 1.0)
     @test name(m1) == "name"
     @test commonname(m1) == "common"
     @test masscharge(m1) == 1