DrylandEcology · dschlaep · Oct 24, 2023 · Aug 26, 2023 · Aug 26, 2023 · Aug 27, 2023
diff --git a/.github/workflows/main_nix.yml b/.github/workflows/main_nix.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Run binary (with sanitizers)
       # Apple clang does not support "AddressSanitizer: detect_leaks" (at least as of clang-1200.0.32.29)
       if: ${{ runner.os != 'macOS' }}
-      run: make clean bin_leaks
+      run: make clean bin_sanitizer
 
     - name: Unit tests (shuffle and repeat 3x)
       run: make clean test_rep3rnd
@@ -47,7 +47,7 @@ jobs:
     - name: Severe unit tests (with sanitizers)
       # Apple clang does not support "AddressSanitizer: detect_leaks" (at least as of clang-1200.0.32.29)
       if: ${{ runner.os != 'macOS' }}
-      run: make clean test_leaks
+      run: make clean test_sanitizer
 
 
   check_code_coverage:
@@ -60,7 +60,7 @@ jobs:
         submodules: recursive
 
     - name: Generate coverage report
-      run: CC=gcc CXX=g++ GCOV=gcov make clean clean_cov cov
+      run: CXX=g++ GCOV=gcov make clean clean_cov cov
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,30 @@
 # NEWS
 
+# SOILWAT2 v7.2.0
+* Simulation output remains the same as the previous version.
+
+* SOILWAT2 now handles errors more gracefully (#346; @N1ckP3rsl3y, @dschlaep).
+    * Code no longer crashes on error immediately (except for STEPWAT2).
+    * Code stores messages of warnings and error status.
+    * All functions now check for errors and return early
+      (after cleaning up memory).
+
+* SOILWAT2 now defines its own structure for random numbers (#373; @dschlaep).
+  This allows to hide implementation details, i.e., STEPWAT2 will no
+  longer need to interact directly with `pcg` and rSOILWAT2 will no longer
+  depend on `pcg` which it never has used.
+
+* New `sw_strtok()` is thread-safe and replaces not thread-safe `strtok()`
+  (#376; @N1ckP3rsl3y).
+
+* Obsolete code in DEBUG_MEM* sections is removed (#369; @dschlaep).
+
+
 # SOILWAT2 v7.1.0
 * Simulation output remains the same as the previous version.
 
-* Prepare for SOILWAT2 to become thread-safe and reentrant (#346; @N1ckP3rsl3y)
+* Prepare for SOILWAT2 to become thread-safe and reentrant
+  (#346; @N1ckP3rsl3y, @dschlaep)
     * Definition clarifications
         * Thread-safe - Multiple threads (a future SOILWAT2 development)
           will not influence each other unintentionally. Here, we implemented

diff --git a/README.md b/README.md
@@ -95,9 +95,9 @@ A full code documentation may be built, see [here](#get_documentation).
 <a name="compile"></a>
 ### Compilation
   * Requirements:
-    - the `gcc` or `clang/llvm` toolchains compliant with `C11`
-      - for unit tests (using `googletest`), additionally,
-        - `g++ >= v5.0` or `clang++ >= v5.0` compliant with `C++11`
+    - the `gcc` or `clang/llvm` toolchains compliant with `C99`
+      - for unit tests (using `googletest`)
+        - toolchains compliant with `C++14`
         - `POSIX API`
     - GNU-compliant `make`
     - On Windows OS: an installation of `cygwin`
@@ -113,7 +113,13 @@ A full code documentation may be built, see [here](#get_documentation).
     available targets), for instance,
     ```{.sh}
         cd SOILWAT2/
-        make bin
+        make
+    ```
+
+    You can use a specific compiler, e.g.,
+    ```{.sh}
+        CC=gcc make
+        CC=clang make
     ```
 <br>
 
@@ -208,9 +214,9 @@ causes some complications, see `makefile`.
 
 Run unit tests locally on the command-line with
 ```{.sh}
-      make test test_run         # compiles and executes the unit-tests
-      make test_severe test_run  # compiles/executes with strict/severe flags
-      make clean                 # cleans build artifacts
+      make test_run              # compiles and executes the tests
+      make test_severe           # compiles/executes with strict/severe flags
+      make clean_test            # cleans build artifacts
 ```
 
 
@@ -308,24 +314,31 @@ Currently, the following is implemented:
 
 __Continous integration checks__
 
-Development/feature branches can only be merged into master if they pass
-all checks on the continuous integration servers.
-Running the following tests locally helps to increase chances that
-they will work well on the servers as well:
+Development/feature branches can only be merged into the main branch and
+released if they pass all checks on the continuous integration servers
+(see `.github/workflows/`).
+
+Please run the "severe", "sanitizer", and "leak" targets locally
+(see also `tools/check_SOILWAT2.sh`)
 ```{.sh}
-      make clean bin_debug_severe bint_run
-      make clean test_severe test_run
+      make clean_build bin_debug_severe
+      make clean_test test_severe
 ```
 
 <br>
 
-__Sanitizer__
+__Sanitizers & leaks__
 
-Running tests with the `severe` targets may require excluding known memory leaks
-(see [issue #205](https://github.com/DrylandEcology/SOILWAT2/issues/205)):
+Run the simulation and tests with the `leaks` program, For instance,
+```{.sh}
+      make clean_build bin_leaks
+      make clean_test test_leaks
+```
 
+Run the simulation and tests with sanitizers. For instance,
 ```{.sh}
-      ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe test_run
+      make clean_build bin_sanitizer
+      make clean_test test_sanitizer
 ```
 
 The address sanitizer may not work correctly and/or fail when used with the
@@ -343,7 +356,7 @@ This can be fixed, for instance, with the following steps
 
 ```{.sh}
       # build test executable with clang and leak detection
-      CC=clang CXX=clang++ ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe
+      CXX=clang++ ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe
 
       # check faulty library path
       otool -L sw_test
@@ -386,21 +399,14 @@ This can be fixed, for instance, with the following steps
     with, e.g.,
 
 ```{.sh}
-    make bin bint_run CPPFLAGS=-DSWDEBUG
+    make bin_run CPPFLAGS=-DSWDEBUG
 ```
 
   * Alternatively, use the pre-configured debugging targets
     `bin_debug` and `bin_debug_severe`, for instance, with
 
 ```{.sh}
-    make bin_debug_severe bint_run
-```
-
-  * If **valgrind** is installed, then call the target `bind_valgrind`
-    (see description in `makefile`) with
-
-```
-    make bind_valgrind
+    make bin_debug_severe
 ```
 
 <br>

diff --git a/doc/additional_pages/A_SOILWAT2_user_guide.md b/doc/additional_pages/A_SOILWAT2_user_guide.md
@@ -39,15 +39,13 @@ on your side.
 
 ### Minimal requirements
   - on any platform:
-    - to compile the `SOILWAT2` executable
-      - `C11` compliant [gcc][] or [clang/llvm][] toolchains;
-        ideally, `gcc >= v4.9` or `clang >= v3.3`
-    - to compile the `SOILWAT2` unit tests (using `googletest`)
-      - `C++11` compliant [gcc][] or [clang/llvm][] toolchains;
-        where `gcc >= v5.0` or `clang >= v5.0`
+    - to compile the `SOILWAT2` simulation program
+      - `C99` compliant [gcc][] or [clang/llvm][] toolchains
+    - to compile the `SOILWAT2` tests program (using `googletest`)
+      - `C++14` compliant [gcc][] or [clang/llvm][] toolchains
+         (see [googletest cxx support](https://github.com/google/oss-policies-info/blob/main/foundational-cxx-support-matrix.md));
       - `POSIX API` (needs to be activated on `cygwin`, see `makefile`)
-    - POSIX- [make](https://pubs.opengroup.org/onlinepubs/9699919799/) or
-      GNU-compliant [make](https://www.gnu.org/software/make/)
+    - GNU-compliant [make](https://www.gnu.org/software/make/)
     - [git][] to download the code from the `github` repository
   - additionally, on Windows OS:
     - a `*nix` emulator, e.g., an installation of [cygwin][] or [docker][]
@@ -56,7 +54,7 @@ on your side.
     - having agreed to the xcode license (run `xcodebuild -license`)
     - or, alternatively, the full [xcode][] installation
   - optional:
-    - [doxygen][] (ideally `>= v1.8.17`) and
+    - [doxygen][] (ideally `>= v1.9.3`) and
       a minimal `latex` installation (see below)
       to generate a local copy of the documentation
 
@@ -111,7 +109,7 @@ on your side.
   * Compile an executable binary, e.g.,
 ```{.sh}
     cd SOILWAT2/
-    make bin
+    make
 ```
 
 <br>
@@ -141,7 +139,7 @@ on your side.
 ```
     or, equivalently,
 ```{.sh}
-    make bin
+    make
     bin/SOILWAT2 -d ./tests/example -f files.in
 ```
 

diff --git a/include/SW_Control.h b/include/SW_Control.h
@@ -28,6 +28,7 @@ extern "C" {
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
+void SW_CTL_init_ptrs(SW_ALL* sw, char *InFiles[]);
 void SW_CTL_setup_model(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
                         PATH_INFO* PathInfo, LOG_INFO* LogInfo);
 void SW_CTL_clear_model(Bool full_reset, SW_ALL* sw, PATH_INFO* PathInfo);
@@ -39,10 +40,6 @@ void SW_CTL_main(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
 void SW_CTL_run_current_year(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
                              LOG_INFO* LogInfo);
 
-#ifdef DEBUG_MEM
-void SW_CTL_SetMemoryRefs(SW_OUTPUT SW_Output[]);
-#endif
-
 
 #ifdef __cplusplus
 }

diff --git a/include/SW_Defines.h b/include/SW_Defines.h
@@ -22,6 +22,11 @@
 #include <math.h>  /* >= C99; for: atan(), isfinite() */
 #include "include/generic.h"
 
+#if !defined(RSOILWAT) /* rSOILWAT2 uses R's RNGs */
+#include "external/pcg/pcg_basic.h" // see https://github.com/imneme/pcg-c-basic
+#endif
+
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -97,6 +102,12 @@ extern "C" {
 #define MAX_FILENAMESIZE 512
 #define MAX_PATHSIZE 2048
 
+/* Maximum number of messages to store in LOG_INFO */
+#define MAX_MSGS 10
+
+/* Maximum number of characters for a single message in LOG_INFO */
+#define MAX_LOG_SIZE 300
+
 /* this could be defined by STEPWAT */
 #ifndef DFLT_FIRSTFILE
   #define DFLT_FIRSTFILE "files.in"
@@ -245,6 +256,17 @@ typedef unsigned int TimeInt;
 typedef unsigned int LyrIndex;
 typedef signed char flag;
 
+
+/* =================================================== */
+/*                   RNG structs                    */
+/* --------------------------------------------------- */
+#if defined(RSOILWAT)
+typedef int sw_random_t; /* not used by rSOILWAT2; it uses instead R's RNG */
+#else
+typedef pcg32_random_t sw_random_t;
+#endif
+
+
 #ifdef __cplusplus
 }
 #endif

diff --git a/include/SW_Files.h b/include/SW_Files.h
@@ -53,15 +53,12 @@ typedef enum {
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
 void SW_F_read(PATH_INFO* PathInfo, LOG_INFO* LogInfo);
-void SW_F_construct(char *InFiles[], const char *firstfile, char _ProjDir[],
+void SW_F_init_ptrs(char *InFiles[]);
+void SW_F_construct(const char *firstfile, char _ProjDir[],
 					LOG_INFO *LogInfo);
 void SW_F_deconstruct(char *InFiles[]);
 void SW_CSV_F_INIT(const char *s, LOG_INFO* LogInfo);
 
-#ifdef DEBUG_MEM
-void SW_F_SetMemoryRefs(void);
-#endif
-
 
 #ifdef __cplusplus
 }

diff --git a/include/SW_Main_lib.h b/include/SW_Main_lib.h
@@ -16,10 +16,12 @@ extern "C" {
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
-void sw_init_args(int argc, char **argv, Bool *QuietMode,
+void sw_init_args(int argc, char **argv,
 	Bool *EchoInits, char **_firstfile, LOG_INFO* LogInfo);
 void sw_print_version(void);
-void sw_check_log(Bool QuietMode, LOG_INFO* LogInfo);
+void sw_fail_on_error(LOG_INFO* LogInfo);
+void sw_init_logs(FILE* logInitPtr, LOG_INFO* LogInfo);
+void sw_write_warnings(LOG_INFO* LogInfo);
 
 #ifdef __cplusplus
 }

diff --git a/include/SW_Markov.h b/include/SW_Markov.h
@@ -22,6 +22,7 @@ extern "C" {
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
+void SW_MKV_init_ptrs(SW_MARKOV* SW_Markov);
 void SW_MKV_construct(unsigned long rng_seed, SW_MARKOV* SW_Markov,
 					  LOG_INFO* LogInfo);
 void SW_MKV_deconstruct(SW_MARKOV* SW_Markov);
@@ -33,10 +34,6 @@ void SW_MKV_setup(SW_MARKOV* SW_Markov, unsigned long Weather_rng_seed,
 void SW_MKV_today(SW_MARKOV* SW_Markov, TimeInt doy0, TimeInt year,
 			RealD *tmax, RealD *tmin, RealD *rain, LOG_INFO* LogInfo);
 
-#ifdef DEBUG_MEM
-void SW_MKV_SetMemoryRefs( void);
-#endif
-
 
 #ifdef __cplusplus
 }

diff --git a/include/SW_Output.h b/include/SW_Output.h
@@ -126,6 +126,7 @@ extern char const *styp2str[];
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
+void SW_OUT_init_ptrs(SW_ALL* sw);
 void SW_OUT_construct(Bool make_soil[], Bool make_regular[],
 		SW_OUTPUT_POINTERS* SW_OutputPtrs, SW_OUTPUT* SW_Output,
 		LyrIndex n_layers, SW_GEN_OUT *GenOutput);
@@ -152,8 +153,8 @@ void SW_OUT_flush(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
 				  LOG_INFO* LogInfo);
 void _collect_values(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
 		Bool bFlush_output, TimeInt tOffset, LOG_INFO* LogInfo);
-void _echo_outputs(SW_ALL* sw, LOG_INFO* LogInfo);
-void _echo_all_inputs(SW_ALL* sw, LOG_INFO* LogInfo);
+void _echo_outputs(SW_ALL* sw);
+void _echo_all_inputs(SW_ALL* sw);
 
 void find_OutPeriods_inUse(SW_GEN_OUT* GenOutput, SW_OUTPUT* SW_Output);
 Bool has_OutPeriod_inUse(OutPeriod pd, OutKey k, IntUS used_OUTNPERIODS,
@@ -306,11 +307,6 @@ void get_biomass_SXW(OutPeriod pd, SW_ALL* sw);
 #endif
 
 
-#ifdef DEBUG_MEM
-	void SW_OUT_SetMemoryRefs(SW_OUTPUT SW_Output[]);
-#endif
-
-
 #ifdef __cplusplus
 }
 #endif

diff --git a/include/SW_Site.h b/include/SW_Site.h
@@ -240,7 +240,7 @@ void SW_SIT_read(SW_SITE* SW_Site, char *InFiles[],
 				 SW_CARBON* SW_Carbon, LOG_INFO* LogInfo);
 void SW_SIT_init_run(SW_VEGPROD* SW_VegProd, SW_SITE* SW_Site,
 					LOG_INFO* LogInfo);
-void _echo_inputs(SW_SITE* SW_Site, LOG_INFO* LogInfo);
+void _echo_inputs(SW_SITE* SW_Site);
 
 /* these used to be in Layers */
 void SW_LYR_read(SW_SITE* SW_Site, char *InFiles[], LOG_INFO* LogInfo);
@@ -255,10 +255,6 @@ void set_soillayers(SW_VEGPROD* SW_VegProd, SW_SITE* SW_Site,
 void derive_soilRegions(SW_SITE* SW_Site, int nRegions,
 						RealD *regionLowerBounds, LOG_INFO* LogInfo);
 
-#ifdef DEBUG_MEM
-	void SW_SIT_SetMemoryRefs(void);
-#endif
-
 
 #ifdef __cplusplus
 }