From noreply at r-forge.r-project.org  Fri Aug  1 05:35:57 2025
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  1 Aug 2025 05:35:57 +0200 (CEST)
Subject: [CHNOSZ-commits] r933 - in pkg/CHNOSZ: . R inst inst/tinytest
Message-ID: <20250801033557.23CB11859A6@r-forge.r-project.org>

Author: jedick
Date: 2025-08-01 05:35:56 +0200 (Fri, 01 Aug 2025)
New Revision: 933

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/mosaic.R
   pkg/CHNOSZ/README.md
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/tinytest/test-mosaic.R
Log:
Fix mosaic() to form H2O


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2025-07-25 06:06:38 UTC (rev 932)
+++ pkg/CHNOSZ/DESCRIPTION	2025-08-01 03:35:56 UTC (rev 933)
@@ -1,4 +1,4 @@
-Date: 2025-07-25
+Date: 2025-08-01
 Package: CHNOSZ
 Version: 2.2.0-3
 Title: Thermodynamic Calculations and Diagrams for Geochemistry

Modified: pkg/CHNOSZ/R/mosaic.R
===================================================================
--- pkg/CHNOSZ/R/mosaic.R	2025-07-25 06:06:38 UTC (rev 932)
+++ pkg/CHNOSZ/R/mosaic.R	2025-08-01 03:35:56 UTC (rev 933)
@@ -47,7 +47,7 @@
   if(length(stable) == 2) {
     # Use only predominant basis species for mosaic stacking 20220723
     stable2.orig <- stable2 <- stable[[2]]
-    # Why c(1, ?
+    # Why c(1, ...) ?
     # The first basis species should always be included (because it has to be swapped out for the others)
     istable2 <- sort(unique(c(1, as.numeric(stable2))))
     for(i in seq_along(istable2)) stable2[stable2.orig == istable2[i]] <- i
@@ -152,6 +152,7 @@
     }
     put.basis(allbases[i, ], thislogact)
     # Load the formed species using the current basis
+    species(delete = TRUE)
     species(species0$ispecies, species0$logact)
 
     # If mosaic() changes variables on the diagram, argument names for affinity() also have to be changed 20230809

Modified: pkg/CHNOSZ/README.md
===================================================================
--- pkg/CHNOSZ/README.md	2025-07-25 06:06:38 UTC (rev 932)
+++ pkg/CHNOSZ/README.md	2025-08-01 03:35:56 UTC (rev 933)
@@ -1,5 +1,5 @@
 <!-- badges: start -->
-[![CRAN/METACRAN Version](https://img.shields.io/cran/v/CHNOSZ?label=CRAN&color=4bc51e)](https://cran.r-project.org/package=CHNOSZ)
+[![CRAN status](https://www.r-pkg.org/badges/version/CHNOSZ)](https://CRAN.R-project.org/package=CHNOSZ)
 [![R-CMD-check](https://github.com/jedick/CHNOSZ/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jedick/CHNOSZ/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2025-07-25 06:06:38 UTC (rev 932)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-08-01 03:35:56 UTC (rev 933)
@@ -22,6 +22,8 @@
       \item \code{label.plot()} and \code{label.figure()} now handle
       logarithmic scales for x and y axes.
 
+      \item Fix bug preventing \code{mosaic()} from being used to form \H2O.
+
     }
 
 }

Modified: pkg/CHNOSZ/inst/tinytest/test-mosaic.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-mosaic.R	2025-07-25 06:06:38 UTC (rev 932)
+++ pkg/CHNOSZ/inst/tinytest/test-mosaic.R	2025-08-01 03:35:56 UTC (rev 933)
@@ -152,3 +152,17 @@
 #title(main = "A(single basis species) - A(all basis species)")
 #legend("topleft", legend = describe.reaction(s1$reaction))
 expect_equivalent(as.numeric(Adiff), rep(0, length(Adiff)), info = info)
+
+# Test added on 20250801
+info <- "mosaic() can be used to form H2O"
+# This wasn't working because a call to species(1) (for the species index of H2O)
+# failed to replace pre-existing specie definition (for the basis species).
+# Now mosaic() uses species(delete = TRUE) to always start with a new species definition.
+basis(c("H3PO4", "H4P2O7", "O2", "H+"))
+bases <- list(
+  c("H3PO4", "H2PO4-", "HPO4-2", "PO4-3"),
+  c("H4P2O7", "H3P2O7-", "H2P2O7-2", "HP2O7-3", "P2O7-4")
+)
+species("H2O")
+m <- mosaic(bases)
+expect_identical(m$A.species$species$name, "water", info = info)