Rel 1.1.0

Author: goedman

.github/workflows/CI.yml

@@ -7,7 +7,7 @@ on:
   pull_request:
 
 env:
-  JULIA_CMDSTAN_HOME: "/home/worker/cmdstan-2.26.0/"
+  JULIA_CMDSTAN_HOME: "/home/worker/cmdstan-2.27.0/"
 
 jobs:
   test:
@@ -41,13 +41,13 @@ jobs:
           OLDWD=`pwd`
           cd ~
           pwd
-          wget https://github.com/stan-dev/cmdstan/releases/download/v2.26.0/cmdstan-2.26.0.tar.gz
-          tar -xzpf cmdstan-2.26.0.tar.gz
+          wget https://github.com/stan-dev/cmdstan/releases/download/v2.27.0/cmdstan-2.27.0.tar.gz
+          tar -xzpf cmdstan-2.27.0.tar.gz
           ls -lia .
           make -C $JULIA_CMDSTAN_HOME build
           cd $OLDWD
         env:
-          JULIA_CMDSTAN_HOME: "/home/runner/cmdstan-2.26.0/"
+          JULIA_CMDSTAN_HOME: "/home/runner/cmdstan-2.27.0/"
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
@@ -66,7 +66,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
         env:
-          JULIA_CMDSTAN_HOME: "/home/runner/cmdstan-2.26.0/"
+          JULIA_CMDSTAN_HOME: "/home/runner/cmdstan-2.27.0/"
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.num_threads == 1
       - uses: codecov/codecov-action@v1

Project.toml

@@ -1,7 +1,7 @@
 name = "ParetoSmoothedImportanceSampling"
 uuid = "98f080ec-61e2-11eb-1c7b-31ea1097256f"
-authors = ["@alvaro1101, Rob J Goedman <goedman@icloud.com"]
-version = "1.0.0"
+authors = ["@alvaro1101, Rob J Goedman <goedman@icloud.com>"]
+version = "1.1.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -17,11 +17,10 @@ StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-CSV = "0.8"
-DataFrames = "0.22, 1.0"
-Distributions = "0.24, 0.25"
+CSV = "0.9"
+DataFrames = "1.2"
+Distributions = "0.25"
 JSON = "0.21"
-StanSample = "3.0"
 StatsFuns = "0.9"
 StatsPlots = "0.14"
 julia = "1"

test/test_demo_wells.jl

@@ -1,7 +1,8 @@
 using ParetoSmoothedImportanceSampling
-using StanSample, StatsFuns
+using Statistics, StatsFuns
 using Printf
 using JSON
+using StanSample
 using Test
 
 ProjDir = @__DIR__
@@ -22,7 +23,7 @@ data1 = (p = m, N = n, y = Int.(y), x = x)
 # Fit the model in Stan
 rc1 = stan_sample(sm1; data=data1)
 if success(rc1)
-    nt1 = read_samples(sm1)
+    nt1 = read_samples(sm1, :namedtuple)
 
     # Compute LOO and standard error
     log_lik = nt1.log_lik'
@@ -52,7 +53,7 @@ data2 = (p = m, N = n, y = Int.(y), x = x2)
 rc2 = stan_sample(sm1; data=data2)
 
 if success(rc2)
-    nt2 = read_samples(sm1)
+    nt2 = read_samples(sm1, :namedtuple)
     # Compute LOO and standard error
     log_lik = nt2.log_lik'
     loo2, loos2, pk2 = psisloo(log_lik)
@@ -95,7 +96,7 @@ for cvi in 1:3
     # Fit the model in Stan
     rc3 = stan_sample(sm3; data=standatacv)
     if success(rc3)
-        nt3 = read_samples(sm3)
+        nt3 = read_samples(sm3, :namedtuple)
         # Compute LOO and standard error
         log_likt = nt3.log_likt'
         local n_sam, n_obs = size(log_likt)