up compats, corrects tests, and bump version because behavior is slig…

…htly different now that GLM drops colliear columns by default

Project.toml

@@ -1,6 +1,6 @@
 name = "HurdleDMR"
 uuid = "f9e53bcf-9449-548a-a5fe-a83e43094f75"
-version = "1.3.3"
+version = "1.4.0"
 
 [deps]
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -19,16 +19,16 @@ StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [compat]
-GLM = "1.5"
+GLM = "1.8"
 LambertW = "0.4"
-Lasso = "0.6"
-LoggingExtras = "0.4"
+Lasso = "0.7"
+LoggingExtras = "1.0"
 Missings = "1.0"
 OrderedCollections = "1.1, 1.2, 1.3, 1.4"
 StatsBase = "0.33"
 StatsModels = "0.6"
 Tables = "1.4"
-julia = "0.7, 1"
+julia = "1"
 
 [extras]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

test/hdmr.jl

@@ -324,10 +324,6 @@ coefsHppos4, coefsHpzero4 = coef(hdmrcoefs4)
 @test coefsHpzero4[:,3] == zeros(p+1)
 @test HurdleDMR.includelinX(hdmrcoefs4) == includel
 
-if M == InclusionRepetition
-    @info("Testing hdmr degenerate cases. The 12 following warnings by workers are expected ...")
-end
-
 zcounts = Matrix(deepcopy(counts))
 Random.seed!(13)
 for I = eachindex(zcounts)
@@ -380,13 +376,7 @@ coefsHppos3, coefsHpzero3 = coef(hdmrcoefs3)
 @test HurdleDMR.includelinX(hdmrcoefs3) == includel
 
 # hurdle dmr parallel remote cluster
-if M == Hurdle
-    hdmrcoefs4 = fit(HDMRPaths{M},covars, zcounts; parallel=false, testargs...)
-else
-    rx = Regex("fit\\($M...\\) failed for countsj")
-    warnings = [(:warn, rx) for i=1:4]
-    hdmrcoefs4 = @test_logs(warnings..., fit(HDMRPaths{M},covars, zcounts; parallel=false, testargs...))
-end
+hdmrcoefs4 = fit(HDMRPaths{M},covars, zcounts; parallel=false, testargs...)
 coefsHppos4, coefsHpzero4 = coef(hdmrcoefs4)
 @test coefsHppos ≈ coefsHppos4
 @test coefsHpzero ≈ coefsHpzero4

test/inrep.jl

@@ -302,8 +302,12 @@ coefsJpos, coefsJzero = coef(inrep;select=AllSeg())
 ydeg = zero(y)
 ydeg[1] = 2
 ydeg[2] = 3
-increpglm = @test_logs (:warn, r"failed to fit truncated counts model to positive") fit(InclusionRepetition,GeneralizedLinearModel,[ones(size(X,1)) X],ydeg; showwarnings=true)
-
+# should fail to fit positives model with dropcollinear=false (GLM<1.8.1 behavior)
+increpglm1 = @test_logs (:warn, r"failed to fit truncated counts model to positive") fit(InclusionRepetition,GeneralizedLinearModel,[ones(size(X,1)) X],ydeg; showwarnings=true, dropcollinear=false)
+# should be able to fit positives model with dropcollinear=true (default GLM>=1.8.1 behavior)
+increpglm2 = fit(InclusionRepetition,GeneralizedLinearModel,[ones(size(X,1)) X],ydeg; showwarnings=true)
+@test coef(increpglm1)[1] != coef(increpglm2)[1]
+@test coef(increpglm1)[2] ≈ coef(increpglm2)[2]
 
 # degenerate positive counts data case 1 without >1
 y0or1 = deepcopy(y)

test/runtests.jl

@@ -17,7 +17,7 @@ include("helpers.jl")
 include("dmr.jl")
 include("hdmr.jl")
 @static if !Sys.iswindows()
-    # NOTE: we don't run tests on windows because the randomly fail due to mmap() throwing:
+    # NOTE: we don't run tests on windows because they randomly fail due to mmap() throwing:
     # LoadError: could not create mapping view: The operation completed successfully.
     include("multicounts.jl")
 end