[CHNOSZ-commits] r955 - in pkg/CHNOSZ: . R inst/tinytest man

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2026-01-07 11:25:43 +0100 (Wed, 07 Jan 2026)
New Revision: 955

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/inst/tinytest/test-util.data.R
   pkg/CHNOSZ/man/util.data.Rd
Log:
Add tests for util.data.R


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2026-01-07 09:21:10 UTC (rev 954)
+++ pkg/CHNOSZ/DESCRIPTION	2026-01-07 10:25:43 UTC (rev 955)
@@ -1,6 +1,6 @@
 Date: 2026-01-07
 Package: CHNOSZ
-Version: 2.2.0-21
+Version: 2.2.0-22
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2026-01-07 09:21:10 UTC (rev 954)
+++ pkg/CHNOSZ/R/util.data.R	2026-01-07 10:25:43 UTC (rev 955)
@@ -6,7 +6,7 @@
 #source("util.data.R")
 #source("util.character.R")
 
-thermo.refs <- function(key = NULL, keep.duplicates = FALSE) {
+thermo.refs <- function(key = NULL, keep.duplicates = FALSE, browser = getOption("browser")) {
   ## Return references for thermodynamic data.
   ## 20110615 browse.refs() first version
   ## 20170212 thermo.refs() remove browsing (except for table of all sources)
@@ -128,8 +128,8 @@
     .cat("</table></body></html>")
     ### End adaptation from print.findFn
     # Show table in browser
-    browseURL(File)
-    cat("thermo.refs: table of references is shown in browser\n")
+    browseURL(File, browser = browser)
+    message("thermo.refs: table of references is shown in browser")
   } else if(is.character(key)) {
     # Return citation information for the given source(s)
     # We omit the [S92] in "HDNB78 [S92]" etc.

Modified: pkg/CHNOSZ/inst/tinytest/test-util.data.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-util.data.R	2026-01-07 09:21:10 UTC (rev 954)
+++ pkg/CHNOSZ/inst/tinytest/test-util.data.R	2026-01-07 10:25:43 UTC (rev 955)
@@ -137,3 +137,29 @@
 #   temperatures and pressures of saturated and aromatic high molecular weight solid and liquid 
 #   hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. 
 #   Geochim. Cosmochim. Acta 62, 3591--3636. https://doi.org/10.1016/S0016-7037(97)00345-1
+
+# Tests added on 20260107
+
+info <- "thermo.refs() creates HTML table without error"
+# Create the HTML but divert the output to a NULL connection
+expect_silent(thermo.refs(browser = sink), info = info)
+# Turn off the connection
+sink()
+
+info <- "thermo.refs() returns reference for source key"
+expect_equal(thermo.refs("HDNB78")$key, "HDNB78", info = info)
+
+info <- "thermo.refs() returns reference for species index"
+expect_equal(thermo.refs(info("SiO2"))$key, "SHS89", info = info)
+
+info <- "thermo.refs() returns references for subcrt() species output"
+expect_equal(thermo.refs(subcrt("carrollite"))$key, "HDR+24", info = info)
+
+info <- "thermo.refs() returns references for subcrt() reaction output"
+expect_equal(thermo.refs(subcrt(c("oxygen", "O2"), c(-1, 1)))$key, c("WEP+82", "SHS89", "Kel60"), info = info)
+
+info <- "check.OBIGT() runs without error"
+expect_silent(out <- check.OBIGT(), info = info)
+
+info <- "dumpdata() runs without error"
+expect_silent(dd <- dumpdata(), info = info)

Modified: pkg/CHNOSZ/man/util.data.Rd
===================================================================
--- pkg/CHNOSZ/man/util.data.Rd	2026-01-07 09:21:10 UTC (rev 954)
+++ pkg/CHNOSZ/man/util.data.Rd	2026-01-07 10:25:43 UTC (rev 955)
@@ -14,7 +14,7 @@
 }
 
 \usage{
-  thermo.refs(key = NULL, keep.duplicates = FALSE)
+  thermo.refs(key = NULL, keep.duplicates = FALSE, browser = getOption("browser"))
   check.EOS(eos, model, prop, return.difference = TRUE)
   check.GHS(ghs, return.difference = TRUE)
   check.OBIGT()
@@ -26,6 +26,7 @@
 \arguments{
   \item{key}{character, numeric, or list; bibliographic reference key(s)}
   \item{keep.duplicates}{logical, keep duplicated references?}
+  \item{browser}{character, name of browser to use (see \code{\link{browseURL}})}
   \item{eos}{dataframe, equations-of-state parameters in the format of \code{thermo()$OBIGT}}
   \item{model}{character, thermodynamic model (see \code{\link{thermo}})}
   \item{prop}{character, property of interest (\samp{Cp} or \samp{V})}