Merge pull request #9 from gdalle/update_hmms

Update to HiddenMarkovModels v0.6

Project.toml

@@ -1,15 +1,15 @@
 name = "PeriodicHiddenMarkovModels"
 uuid = "4873b48c-7fd1-4fb6-93c5-649b25bdde2e"
 authors = ["David Métivier <[email protected]> and contributors"]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
 HiddenMarkovModels = "84ca31d5-effc-45e0-bfda-5a68cd981f47"
 StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
 
 [compat]
-julia = "1.10"
+julia = "1.10, 1.11"
 ArgCheck = "2.3"
 StatsAPI = "1.6"
-HiddenMarkovModels = "0.5"
+HiddenMarkovModels = "0.6"

src/PeriodicHiddenMarkovModels.jl

@@ -4,6 +4,7 @@ using ArgCheck: @argcheck
 import HiddenMarkovModels as HMMs
 import StatsAPI
 using HiddenMarkovModels
+using HiddenMarkovModels: AbstractVectorOrNTuple
 
 export
     # utilities.jl

src/fit.jl

@@ -3,19 +3,19 @@ function StatsAPI.fit!(
     fb_storage::HMMs.ForwardBackwardStorage,
     obs_seq::AbstractVector,
     n2t::AbstractVector;
-    seq_ends::AbstractVector{Int},
+    seq_ends::AbstractVectorOrNTuple{Int},
 ) where {T}
     (; γ, ξ) = fb_storage
     L, N = period(hmm), length(hmm)
-    
+
     hmm.init .= zero(T)
     for l in 1:L
         hmm.trans[l] .= zero(T)
     end
-    for k in eachindex(seq_ends)
+    @views for k in eachindex(seq_ends)
         t1, t2 = HMMs.seq_limits(seq_ends, k)
         hmm.init .+= γ[:, t1]
-        n2t_k = view(n2t, t1:t2)
+        n2t_k = n2t[t1:t2]
 
         for l in 1:L
             hmm.trans[l] .+= sum(ξ[first(parentindices(n2t_k))[findall(n2t_k .== l)]])
@@ -27,9 +27,9 @@ function StatsAPI.fit!(
     end
     for l in 1:L
         times_l = Int[]
-        for k in eachindex(seq_ends)
+        @views for k in eachindex(seq_ends)
             t1, t2 = HMMs.seq_limits(seq_ends, k)
-            n2t_k = view(n2t, t1:t2)
+            n2t_k = n2t[t1:t2]
             append!(times_l, first(parentindices(n2t_k))[findall(n2t_k .== l)])
         end
         for i in 1:N
@@ -40,4 +40,4 @@ function StatsAPI.fit!(
         @assert HMMs.valid_hmm(hmm, l)
     end
     return nothing
-end
+end