[CHNOSZ-commits] r663 - in pkg/CHNOSZ: . R inst tests/testthat

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

Author: jedick
Date: 2021-03-23 00:43:04 +0100 (Tue, 23 Mar 2021)
New Revision: 663

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/inst/TODO
   pkg/CHNOSZ/tests/testthat/test-info.R
Log:
Improve messages output by info()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2021-03-22 12:48:39 UTC (rev 662)
+++ pkg/CHNOSZ/DESCRIPTION	2021-03-22 23:43:04 UTC (rev 663)
@@ -1,6 +1,6 @@
-Date: 2021-03-21
+Date: 2021-03-22
 Package: CHNOSZ
-Version: 1.4.0-32
+Version: 1.4.0-33
 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/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2021-03-22 12:48:39 UTC (rev 662)
+++ pkg/CHNOSZ/R/info.R	2021-03-22 23:43:04 UTC (rev 663)
@@ -144,12 +144,9 @@
     mystate <- thermo$OBIGT$state[ispecies.out]
     ispecies.other <- ispecies[!ispecies %in% ispecies.out]
     otherstates <- thermo$OBIGT$state[ispecies.other]
-    # for minerals (cr), use the word "phase"; otherwise, use "state" 20190209
-    word <- "state"
-    # substitute the mineral name for "cr" 20190121
-    if(mystate == "cr" | sum(otherstates=="cr") > 1) {
-      word <- "phase"
-      otherstates[otherstates=="cr"] <- thermo$OBIGT$name[ispecies.other[otherstates=="cr"]]
+    # For non-aqueous species, list other substances (isomers) in the same state 20210321
+    if(mystate != "aq" & sum(otherstates==mystate) > 0) {
+      otherstates[otherstates==mystate] <- thermo$OBIGT$name[ispecies.other[otherstates==mystate]]
     }
     transtext <- othertext <- ""
     # we count, but don't show the states for phase transitions (cr2, cr3, etc)
@@ -159,14 +156,19 @@
       ntrans <- sum(istrans)
       if(ntrans == 1) transtext <- paste(" with", ntrans, "phase transition")
       else if(ntrans > 1) transtext <- paste(" with", ntrans, "phase transitions")
-      # if it's not already in the species name, substitute the mineral name for "cr" 20190121
-      if(species != thermo$OBIGT$name[ispecies.out]) mystate <- thermo$OBIGT$name[ispecies.out]
     }
-    otherstates <- otherstates[!istrans]
-    if(length(otherstates) == 1) othertext <- paste0("; other available ", word, " is ", otherstates)
-    if(length(otherstates) > 1) othertext <- paste0("; other available ", word, "s are ", paste(otherstates, collapse=", "))
+    myname <- NULL
+    if(mystate != "aq") {
+      # If it's not already in the species name, append the substance name 20210323
+      myname <- thermo$OBIGT$name[ispecies.out]
+      if(species == myname) myname <- NULL
+    }
+    otherstates <- unique(otherstates[!istrans])
+    if(length(otherstates) == 1) othertext <- paste0("; also available in ", otherstates)
+    if(length(otherstates) > 1) othertext <- paste0("; also available in ", paste(otherstates, collapse=", "))
     if(transtext != "" | othertext != "") {
       starttext <- paste0("info.character: found ", species, "(", mystate, ")")
+      if(!is.null(myname)) starttext <- paste0(starttext, " [", myname, "]")
       message(starttext, transtext, othertext)
     }
   }

Modified: pkg/CHNOSZ/inst/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO	2021-03-22 12:48:39 UTC (rev 662)
+++ pkg/CHNOSZ/inst/TODO	2021-03-22 23:43:04 UTC (rev 663)
@@ -37,13 +37,6 @@
 a2 <- affinity(iprotein = 1)
 expect_equal(a1$values, a2$values)
 
-[20210122] Fix incorrect states in messages:
-> subcrt("C10H22")
-info.character: found C10H22(decane); other available phases are gas, gas, gas, liq, liq, liq
-> subcrt("C10H22", "liq")
-info.character: found C10H22(liq); other available states are liq, liq
-
-
 [20210212]
 
 - Fix formatting of messages from palply() (seen with read.fasta())

Modified: pkg/CHNOSZ/tests/testthat/test-info.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-info.R	2021-03-22 12:48:39 UTC (rev 662)
+++ pkg/CHNOSZ/tests/testthat/test-info.R	2021-03-22 23:43:04 UTC (rev 663)
@@ -4,8 +4,8 @@
   expect_equal(info.character("acetate", "cr"), NA)
   expect_message(info.character("acetate", "cr"), "only 'aq' is available")
   expect_message(info.character("methane", "cr"), "only 'gas' 'liq' are available")
-  expect_message(info.character("methane"), "other available state is liq")
-  expect_message(info.character("SiO2", "cr"), "other available phases are")
+  expect_message(info.character("methane"), "also available in liq")
+  expect_message(info.character("SiO2", "cr"), "also available in.*quartz")
   expect_message(info.character("chalcocite"), "found chalcocite\\(cr\\) with 2 phase transitions")
   # H2O is a special case
   expect_equal(info.character("H2O", "aq"), info.character("H2O", "liq"))