[CHNOSZ-commits] r727 - in pkg/CHNOSZ: . R inst inst/tinytest

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

Author: jedick
Date: 2022-06-08 15:58:00 +0200 (Wed, 08 Jun 2022)
New Revision: 727

Added:
   pkg/CHNOSZ/inst/tinytest/test-util.expression.R
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.expression.R
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/tinytest/test-util.R
Log:
Make expr.species() recognize non-integer coefficients


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2022-06-04 05:29:26 UTC (rev 726)
+++ pkg/CHNOSZ/DESCRIPTION	2022-06-08 13:58:00 UTC (rev 727)
@@ -1,6 +1,6 @@
-Date: 2022-06-04
+Date: 2022-06-08
 Package: CHNOSZ
-Version: 1.9.9-19
+Version: 1.9.9-20
 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.expression.R
===================================================================
--- pkg/CHNOSZ/R/util.expression.R	2022-06-04 05:29:26 UTC (rev 726)
+++ pkg/CHNOSZ/R/util.expression.R	2022-06-08 13:58:00 UTC (rev 727)
@@ -324,18 +324,19 @@
   ## like makeup(), but split apart the formula based on
   ## numbers (subscripts); don't scan for elemental symbols 20171018
   # if there are no numbers or charge, return the formula as-is
-  if(! (grepl("[0-9]", formula) | grepl("\\+[0-9]?$", formula) | grepl("-[0-9]?$", formula))) return(formula)
+  # Change [0-9]? to [\\.0-9]* (recognize decimal point in numbers, recognize charge longer than one digit) 20220608
+  if(! (grepl("[\\.0-9]", formula) | grepl("\\+[\\.0-9]*$", formula) | grepl("-[\\.0-9]*$", formula))) return(formula)
   # first split off charge
   # (assume that no subscripts are signed)
   Z <- 0
-  hascharge <- grepl("\\+[0-9]?$", formula) | grepl("-[0-9]?$", formula)
+  hascharge <- grepl("\\+[\\.0-9]*$", formula) | grepl("-[\\.0-9]*$", formula)
   if(hascharge) {
     # for charge, we match + or - followed by zero or more numbers at the end of the string
-    if(grepl("\\+[0-9]?$", formula)) {
+    if(grepl("\\+[\\.0-9]*$", formula)) {
       fsplit <- strsplit(formula, "+", fixed=TRUE)[[1]]
       if(is.na(fsplit[2])) Z <- 1 else Z <- as.numeric(fsplit[2])
     }
-    if(grepl("-[0-9]?$", formula)) {
+    if(grepl("-[\\.0-9]*$", formula)) {
       fsplit <- strsplit(formula, "-")[[1]]
       # for formula=="H-citrate-2", unsplit H-citrate
       if(length(fsplit) > 2) {
@@ -349,10 +350,10 @@
   }
   # to get strings, replace all numbers with placeholder (#), then split on that symbol
   # the outer gsub is to replace multiple #'s with one
-  numhash <- gsub("#+", "#", gsub("[0-9]", "#", formula))
+  numhash <- gsub("#+", "#", gsub("[\\.0-9]", "#", formula))
   strings <- strsplit(numhash, "#")[[1]]
   # to get coefficients, replace all characters (non-numbers) with placeholder, then split
-  charhash <- gsub("#+", "#", gsub("[^0-9]", "#", formula))
+  charhash <- gsub("#+", "#", gsub("[^\\.0-9]", "#", formula))
   coeffs <- strsplit(charhash, "#")[[1]]
   # if the first coefficient is empty, remove it
   if(coeffs[1]=="") coeffs <- tail(coeffs, -1) else {

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2022-06-04 05:29:26 UTC (rev 726)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2022-06-08 13:58:00 UTC (rev 727)
@@ -124,6 +124,10 @@
       Stacking 2 is bounded by a thick orange line, instead of just the
       border shared with bornite.
 
+      \item Improve handling of non-integer coefficients in
+      \code{expr.species()}. The result for FeS1.33 was previously equivalent
+      to FeS[.33] but is now shown correctly as FeS[1.33].
+
     }
   }
 

Modified: pkg/CHNOSZ/inst/tinytest/test-util.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-util.R	2022-06-04 05:29:26 UTC (rev 726)
+++ pkg/CHNOSZ/inst/tinytest/test-util.R	2022-06-08 13:58:00 UTC (rev 727)
@@ -34,9 +34,6 @@
 testGHS <- GHS("H2O", G = 0, H = 0)
 expect_equal(as.numeric(testGHS[1, 3]), testent[2], info = info)
   
-info <- "expr.species() produces expected errors"
-expect_error(expr.species(c("H2O", "CO2")), "more than one species", info = info)
-
 info <- "[P|T|E].units() do not accept invalid units"
 expect_error(P.units("X"), "units of pressure must be either bar or MPa", info = info)
 expect_error(T.units("X"), "units of temperature must be either C or K", info = info)

Added: pkg/CHNOSZ/inst/tinytest/test-util.expression.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-util.expression.R	                        (rev 0)
+++ pkg/CHNOSZ/inst/tinytest/test-util.expression.R	2022-06-08 13:58:00 UTC (rev 727)
@@ -0,0 +1,14 @@
+# Load default settings for CHNOSZ
+reset()
+
+info <- "expr.species() produces expected errors"
+expect_error(expr.species(c("H2O", "CO2")), "more than one species", info = info)
+
+# 20220608
+info <- "expr.species() handles non-integer coefficients"
+es <- expr.species("FeS1.33")
+expect_equal(es[[length(es)]], "1.33")
+
+info <- "expr.species() handles non-integer charge"
+es <- expr.species("FeS+1.33")
+expect_equal(es[[length(es)]], "+1.33")