automatic formatting

triggered by @stelmo on PR #696

src/io/show/BalancedGrowthCommunityModel.jl

@@ -1,7 +1,13 @@
 function Base.show(io::Base.IO, ::MIME"text/plain", cm::CommunityMember)
-    println(io, "A $(typeof(cm.model)) community member with $(n_reactions(cm.model)) reactions, $(n_metabolites(cm.model)) metabolites, and abundance $(cm.abundance*100)%.")
+    println(
+        io,
+        "A $(typeof(cm.model)) community member with $(n_reactions(cm.model)) reactions, $(n_metabolites(cm.model)) metabolites, and abundance $(cm.abundance*100)%.",
+    )
 end
 
 function Base.show(io::Base.IO, ::MIME"text/plain", cm::BalancedGrowthCommunityModel)
-    println(io, "A balanced growth community model comprised of $(length(cm.members)) underlying models.")
+    println(
+        io,
+        "A balanced growth community model comprised of $(length(cm.members)) underlying models.",
+    )
 end

src/reconstruction/ObjectModel.jl

@@ -282,7 +282,8 @@ function add_biomass_metabolite(
 
     m.reactions = copy(model.reactions)
     m.reactions[biomass_rxn_id] = copy(model.reactions[biomass_rxn_id])
-    m.reactions[biomass_rxn_id].metabolites = copy(model.reactions[biomass_rxn_id].metabolites)
+    m.reactions[biomass_rxn_id].metabolites =
+        copy(model.reactions[biomass_rxn_id].metabolites)
     m.reactions[biomass_rxn_id].metabolites[biomass_metabolite_id] = 1.0
 
     m

src/types/misc/BalancedGrowthCommunityModel.jl

@@ -39,7 +39,12 @@ $(TYPEDSIGNATURES)
 A helper function to find the index of the appropriate model. Assumes each `id`
 is delimited by `#` that separates the model ID prefix and the original id.
 """
-function access_community_member(cm::BalancedGrowthCommunityModel, id::String, accessor::Function; default=nothing)
+function access_community_member(
+    cm::BalancedGrowthCommunityModel,
+    id::String,
+    accessor::Function;
+    default = nothing,
+)
     id_split = split(id, "#")
     idx = findfirst(startswith(first(id_split)), m.id for m in cm.members)
     isnothing(idx) && return default # can only access inside community member

src/types/models/BalancedGrowthCommunityModel.jl

@@ -91,7 +91,8 @@ respective underlying [`CommunityMember`](@ref) appended as a prefix with the
 delimiter `#`. The environmental metabolites have no prefix.
 """
 function Accessors.metabolites(cm::BalancedGrowthCommunityModel)
-    mets = [add_community_prefix(m, mid) for m in cm.members for mid in metabolites(m.model)]
+    mets =
+        [add_community_prefix(m, mid) for m in cm.members for mid in metabolites(m.model)]
     return [mets; "ENV_" .* get_env_mets(cm)]
 end
 
@@ -256,14 +257,14 @@ Return the semantically meaningful reactions of the model.
 Accessors.n_fluxes(cm::BalancedGrowthCommunityModel) =
     sum(n_fluxes(m.model) for m in cm.members) + length(get_env_mets(cm)) + 1
 
-#= 
+#=
 This loops implements the rest of the accssors through access_community_member.
 Since most of the environmental reactions are generated programmtically, they
 will not have things like annotations etc. For this reason, these methods will
-only work if they access something inside the community members. 
+only work if they access something inside the community members.
 =#
 for (func, def) in (
-    (:reaction_gene_association, nothing), 
+    (:reaction_gene_association, nothing),
     (:reaction_subsystem, nothing),
     (:reaction_stoichiometry, nothing),
     (:metabolite_formula, nothing),
@@ -280,6 +281,7 @@ for (func, def) in (
     (:gene_name, nothing),
 )
     @eval begin # TODO add docstrings somehow
-        Accessors.$func(cm::BalancedGrowthCommunityModel, id::String) = access_community_member(cm, id, $func; default=$def)
+        Accessors.$func(cm::BalancedGrowthCommunityModel, id::String) =
+            access_community_member(cm, id, $func; default = $def)
     end
 end

test/types/BalancedGrowthCommunityModel.jl

@@ -66,10 +66,7 @@
         members = [cm1, cm2],
         env_met_flux_bounds = Dict("Ae" => (-10, 10)),
     )
-    @test contains(
-        sprint(show, MIME("text/plain"), cm),
-        "balanced growth",
-    )
+    @test contains(sprint(show, MIME("text/plain"), cm), "balanced growth")
 
     @test issetequal(
         reactions(cm),