Merge pull request #38 from huddlej/add-gamma-cli-test

Fix error with CLI when specifying the gamma parameter value by reverting type of gamma parameter from Real to Float64
PierreBarrat · Sep 14, 2023 · 22cd328 · 22cd328
2 parents e9d43b6 + 0b19dff
commit 22cd328
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diff --git a/src/cli.jl b/src/cli.jl
@@ -37,7 +37,7 @@ We suggest two sets of defaults for running TreeKnit. `--better-trees` will prod
 	nwk_file1::AbstractString, nwk_file2::AbstractString, nwk_files::AbstractString...;
 	# options
 	outdir::AbstractString = "treeknit_results",
-	gamma::Real = OptArgs().γ,
+	gamma::Float64 = OptArgs().γ,
 	seq_lengths::AbstractString = join([string(i) for i in repeat([1], 2+ length(nwk_files))], " "),
 	n_mcmc_it::Int = OptArgs().nMCMC,
 	rounds::Int = 1,

diff --git a/test/command_line_tests.sh b/test/command_line_tests.sh
@@ -12,7 +12,7 @@ else
 fi 
 
 export PATH="$HOME/.julia/bin:$PATH"
-treeknit test/NYdata/tree_ha.nwk test/NYdata/tree_na.nwk --auspice-view
+treeknit test/NYdata/tree_ha.nwk test/NYdata/tree_na.nwk --auspice-view --gamma 2
 OUT=$?
 if [ "$OUT" != 0 ]; then
     rm -r treeknit_results