From ea27937439c9db88421772c45bada8f2befddeb9 Mon Sep 17 00:00:00 2001
From: Philip Delff <philip@delff.dk>
Date: Sat, 17 Aug 2024 20:06:49 -0400
Subject: [PATCH 1/2] including ext

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index e70f568e..94c4ab54 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,7 +55,6 @@ vignettes/*\.R
 inst/examples/nonmem/modelfit_dir*
 inst/examples/nonmem/trashed_*
 inst/examples/nonmem/backup_*
-inst/examples/nonmem/*\.ext
 inst/examples/nonmem/*\.phi
 inst/examples/nonmem/xgxr001dir/backup_*
 tests_manual/testthat/testOutput

From 55ce2d8072b55ad4859c3b790b36f51b2afa1998 Mon Sep 17 00:00:00 2001
From: Philip Delff <philip@delff.dk>
Date: Sun, 18 Aug 2024 09:11:18 -0400
Subject: [PATCH 2/2] fix tests, quiet merge in NMreadExt()

---
 R/NMreadExt.R                                 |   2 +-
 .../testthat/testReference/NMdataConf_01.rds  | Bin 368 -> 378 bytes
 .../testthat/testReference/NMdataConf_02.rds  | Bin 366 -> 375 bytes
 tests/testthat/testReference/NMreadExt_01.rds | Bin 761 -> 814 bytes
 tests/testthat/testReference/NMreadExt_02.rds | Bin 1760 -> 1807 bytes
 tests/testthat/testReference/NMreadExt_03.rds | Bin 2422 -> 2479 bytes
 tests/testthat/testReference/NMreadExt_04.rds | Bin 1643 -> 1691 bytes
 tests/testthat/testReference/NMreadExt_05.rds | Bin 1821 -> 1871 bytes
 tests/testthat/testReference/NMrelate_02.rds  | Bin 1913 -> 0 bytes
 tests/testthat/test_NMdataConf.R              |  59 ++----------------
 tests/testthat/test_NMreadExt.R               |  15 ++++-
 tests/testthat/test_NMrelate.R                |   6 ++
 12 files changed, 23 insertions(+), 59 deletions(-)
 delete mode 100644 tests/testthat/testReference/NMrelate_02.rds

diff --git a/R/NMreadExt.R b/R/NMreadExt.R
index 931438d3..4a6245af 100644
--- a/R/NMreadExt.R
+++ b/R/NMreadExt.R
@@ -210,7 +210,7 @@ NMreadExt <- function(file,return,as.fun,modelname,col.model,auto.ext,tableno="m
         
         tab.blocks
 
-        pars <- mergeCheck(pars,tab.blocks,by=cc(par.type,i),all.x=T)
+        pars <- mergeCheck(pars,tab.blocks,by=cc(par.type,i),all.x=T,quiet=TRUE)
         pars[abs(i-j)>(blocksize-1),(c("iblock","blocksize")):=list(NA,NA)]
 
         pars[par.type%in%c("OMEGA","SIGMA")&i==j&is.na(iblock),iblock:=i]
diff --git a/tests/testthat/testReference/NMdataConf_01.rds b/tests/testthat/testReference/NMdataConf_01.rds
index 42c514e4f37921f161519f58708f8faea7d076ee..da4314deb197c6783e3ee72a7cf4d62f70d80351 100644
GIT binary patch
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diff --git a/tests/testthat/testReference/NMdataConf_02.rds b/tests/testthat/testReference/NMdataConf_02.rds
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diff --git a/tests/testthat/testReference/NMreadExt_01.rds b/tests/testthat/testReference/NMreadExt_01.rds
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GIT binary patch
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diff --git a/tests/testthat/testReference/NMreadExt_02.rds b/tests/testthat/testReference/NMreadExt_02.rds
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diff --git a/tests/testthat/testReference/NMreadExt_04.rds b/tests/testthat/testReference/NMreadExt_04.rds
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diff --git a/tests/testthat/testReference/NMrelate_02.rds b/tests/testthat/testReference/NMrelate_02.rds
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diff --git a/tests/testthat/test_NMdataConf.R b/tests/testthat/test_NMdataConf.R
index c4ea4ea6..7df968c9 100644
--- a/tests/testthat/test_NMdataConf.R
+++ b/tests/testthat/test_NMdataConf.R
@@ -2,6 +2,7 @@ context("NMdataConf")
 
 NMdataConf(reset=TRUE)
 
+    ## can't compare functions
 dropFuns <- function(x){
     x$as.fun <- NULL
     x$file.mod <- NULL
@@ -24,7 +25,7 @@ test_that("defaults",{
     expect_equal_to_reference(defaults,fileRef)
 
     ## compareCols(readRDS(fileRef),defaults)
-
+    
 })
 
 test_that("reset",{
@@ -36,20 +37,6 @@ test_that("reset",{
 
     defaults <- dropFuns(defaults)
     defaults2 <- dropFuns(defaults2)
-    ## defaults$as.fun <- NULL
-    ## defaults$file.mod <- NULL
-    ## defaults$file.cov <- NULL
-    ## defaults$file.ext <- NULL
-    ## defaults$file.phi <- NULL
-    ## defaults$file.shk <- NULL
-    ## defaults$modelname <- NULL
-    ## defaults2$as.fun <- NULL
-    ## defaults2$file.mod <- NULL
-    ## defaults2$file.cov <- NULL
-    ## defaults2$file.ext <- NULL
-    ## defaults2$file.phi <- NULL
-    ## defaults2$file.shk <- NULL
-    ## defaults2$modelname <- NULL
     
     
     expect_equal(defaults,defaults2)
@@ -96,21 +83,6 @@ test_that("change fun in globalenv does not affect NMdataConf()",{
     defaults <- dropFuns(defaults)
     defaults2 <- dropFuns(defaults2)
     
-    ## defaults$as.fun <- NULL
-    ## defaults$file.mod <- NULL
-    ## defaults$file.cov <- NULL
-    ## defaults$file.ext <- NULL
-    ## defaults$file.phi <- NULL
-    ## defaults$file.shk <- NULL
-    ## defaults$modelname <- NULL
-    ## defaults2$as.fun <- NULL
-    ## defaults2$file.mod <- NULL
-    ## defaults2$file.cov <- NULL
-    ## defaults2$file.ext <- NULL
-    ## defaults2$file.phi <- NULL
-    ## defaults2$file.shk <- NULL
-    ## defaults2$modelname <- NULL
-    
     expect_equal(defaults,defaults2)
 })
 
@@ -143,22 +115,6 @@ test_that("change fun in globalenv does not affect NMdataConf()",{
     defaults <- dropFuns(defaults)
     defaults2 <- dropFuns(defaults2)
     
-    ## defaults$as.fun <- NULL
-    ## defaults$file.mod <- NULL
-    ## defaults$file.cov <- NULL
-    ## defaults$file.ext <- NULL
-    ## defaults$file.phi <- NULL
-    ## defaults$file.shk <- NULL
-    ## defaults$modelname <- NULL
-
-    ## defaults2$as.fun <- NULL
-    ## defaults2$file.mod <- NULL
-    ## defaults2$file.cov <- NULL
-    ## defaults2$file.ext <- NULL
-    ## defaults2$file.phi <- NULL
-    ## defaults2$file.shk <- NULL
-    ## defaults2$modelname <- NULL
-    
     expect_equal(defaults,defaults2)
 })
 
@@ -173,17 +129,10 @@ test_that("deprecated use.rds",{
     NMdataConf(formats.read=c("csv"))
     new <- NMdataConf()
 
-    ## can't compare functions
-    new$as.fun <- NULL
-    new$file.cov <- NULL
-    new$file.ext <- NULL
-    new$file.mod <- NULL
-    new$file.phi <- NULL
-    new$file.shk <- NULL
-    new$modelname <- NULL
+    new <- dropFuns(new)
     
     expect_equal_to_reference(new,fileRef)
-    compareCols(readRDS(fileRef),new)
+    ## compareCols(readRDS(fileRef),new)
 })
 
 test_that("reset removes unknown",{
diff --git a/tests/testthat/test_NMreadExt.R b/tests/testthat/test_NMreadExt.R
index d1e77de2..ad4ef0af 100644
--- a/tests/testthat/test_NMreadExt.R
+++ b/tests/testthat/test_NMreadExt.R
@@ -31,6 +31,7 @@ test_that("basic - all",{
     if(F){
         ref <- readRDS(fileRef)
         compareCols(ref,res)
+        compareCols(ref$pars,res$pars)
     }
 
 })
@@ -46,6 +47,7 @@ test_that("basic - all from multiple models",{
     if(F){
         ref <- readRDS(fileRef)
         compareCols(ref,res)
+        compareCols(ref$pars,res$pars)
     }
 
 })
@@ -61,9 +63,8 @@ test_that("muref - all",{
 
     if(F){
         ref <- readRDS(fileRef)
-        res
-        ref
-        
+        compareCols(ref,res)
+        compareCols(ref$pars,res$pars)
     }
 
 
@@ -76,6 +77,14 @@ test_that("muref SAEM - all",{
 
     res <- NMreadExt(file=file.ext,as.fun="data.table",return="all")
     expect_equal_to_reference(res,fileRef)
+
+    if(F){
+        ref <- readRDS(fileRef)
+        compareCols(ref,res)
+        compareCols(ref$pars,res$pars)
+    }
+
+
 })
 
 test_that("muref SAEM - tableno options",{
diff --git a/tests/testthat/test_NMrelate.R b/tests/testthat/test_NMrelate.R
index 8e8a708e..acf56083 100644
--- a/tests/testthat/test_NMrelate.R
+++ b/tests/testthat/test_NMrelate.R
@@ -48,6 +48,12 @@ test_that("merge with NMreadExt results",{
     )
 
     expect_equal_to_reference(res,fileRef)
+
+    if(F){
+        ref <- readRDS(fileRef)
+        compareCols(ref$ext.nofix,   res$ext.nofix)
+
+}
     
 })