Merge pull request #17 from usgs-coupled/master

Sync develop with master

.github/workflows/cmake.yml

@@ -5,6 +5,9 @@ on:
   pull_request:
     branches: [ master ]
 
+  schedule:
+    - cron:  '15 14 4,11,18,25 * *'
+
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
@@ -56,7 +59,7 @@ jobs:
         arch: x64
 
     - name: CTest
-      run: ctest -S ctest.cmake -V --output-on-failure
+      run: ctest -S ctest.cmake -V --output-on-failure --timeout 900
 
     - name: Upload results
       uses: actions/upload-artifact@v3
@@ -75,9 +78,18 @@ jobs:
           repository: usgs-coupled-subtrees/phreeqc3-HTMLversion
           ref: master
 
+      - name: cache htmlhelp
+        id: cache-htmlhelp
+        uses: actions/cache@v3
+        with:
+          path: "C:/Program Files (x86)/HTML Help Workshop"
+          key: ${{ runner.os }}-htmlhelp
+
       - name: install htmlhelp
+        if: steps.cache-htmlhelp.outputs.cache-hit != 'true'
+        timeout-minutes: 5
         run: |
-          curl -L -O http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe
+          curl -L -O --max-time 120 http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe
           cmd /c start /wait .\htmlhelp.exe /q /c /t:$(Get-Location)\tmp
           $file = "$(Get-Location)\tmp\htmlhelp.inf"
           (Get-Content $file) | Foreach-Object { $_ `
@@ -158,6 +170,11 @@ jobs:
           needs: roxygen2, pkgbuild, check
           working-directory: R/phreeqc
 
+      - name: Display sessionInfo()
+        run: sessionInfo()
+        working-directory: R/phreeqc
+        shell: Rscript {0}
+
       - name: roxygen2::roxygenise()
         run: roxygen2::roxygenise()
         working-directory: R/phreeqc
@@ -181,6 +198,7 @@ jobs:
           name: cran
           path: ${{ github.workspace }}/R/phreeqc/check/phreeqc_*.tar.gz
 
+
   # r-build:
   #   needs: [init]
   #   runs-on: ubuntu-latest
@@ -214,6 +232,7 @@ jobs:
   #         name: cran
   #         path: ${{github.workspace}}/R/phreeqc_*.tar.gz
 
+
   # r-valgrind:
   #   needs: [r-build]
   #   runs-on: ubuntu-latest
@@ -259,6 +278,7 @@ jobs:
   #         name: valgrind
   #         path: ${{github.workspace}}/R/valgrind.full.out
 
+
   distcheck:
     needs: [init, chm]
     runs-on: ubuntu-latest

.gitignore

@@ -211,4 +211,5 @@ doc/RELEASE
 /unit/x64
 
 # builds (folders beginning with _ (underscore)
-/_*
+**/_*/**
+**/.vshistory/**

phreeqc3-examples/CMakeLists.txt

@@ -275,12 +275,18 @@ add_test(NAME examples.ex22
 COMMAND $<TARGET_FILE:phreeqc> ${PROJECT_SOURCE_DIR}/examples/ex22 ex22.out ${PROJECT_SOURCE_DIR}/database/phreeqc.dat ex22.log
 )
 
-# these take more than 600 seconds
-set(SKIP
+# Note when setting labels we can't use the following:
+#   set_tests_properties(${test} PROPERTIES LABELS "pitzer")
+# since it will overwrite any existing labels already set
+
+# long_debug
+# > 600 seconds Debug
+set(LONG_DEBUG
   examples.ex21
 )
 
-# disable tests that take too long
-foreach(test ${SKIP})
-  set_tests_properties(${test} PROPERTIES DISABLED TRUE)
+# label tests that take too long
+foreach(test ${LONG_DEBUG})
+  set_property(TEST ${test} APPEND PROPERTY LABELS "long_debug")
+  set_property(TEST ${test} APPEND PROPERTY LABELS "long_memcheck")
 endforeach()

src/phreeqcpp/PBasic.cpp

@@ -3610,7 +3610,7 @@ factor(struct LOC_exec * LINK)
 
 		std::string std_num;
 		{
-			snprintf(token, sizeof(token), "%*.*e", length, width, nmbr);
+			snprintf(token, max_length, "%*.*e", length, width, nmbr);
 			std_num = token;
 		}
 
@@ -3653,7 +3653,7 @@ factor(struct LOC_exec * LINK)
 
 		std::string std_num;
 		{
-			snprintf(token, sizeof(token), "%*.*f", length, width, nmbr);
+			snprintf(token, max_length, "%*.*f", length, width, nmbr);
 			std_num = token;
 		}
 

src/phreeqcpp/basicsubs.cpp

@@ -2097,7 +2097,6 @@ match_elts_in_species(const char *name, const char *mytemplate)
 	 * write out string
 	 */
 	token[0] = '\0';
-	assert(MAX_LENGTH == sizeof(token1));
 	for (i = 0; i < count_match_tokens; i++)
 	{
 		strcat(token, match_vector[i].first.c_str());