diff --git a/.LSAN_suppr.txt b/.LSAN_suppr.txt new file mode 100644 index 000000000..6384b856e --- /dev/null +++ b/.LSAN_suppr.txt @@ -0,0 +1,7 @@ +# Suppression of memory leaks +# https://github.com/google/sanitizers/wiki/AddressSanitizerLeakSanitizer#suppressions + +# These are known leaks that await fixing + +# https://github.com/DrylandEcology/SOILWAT2/issues/205 +leak:SW_VPD_construct diff --git a/.travis.yml b/.travis.yml index d29b209b0..52147db7e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,13 +1,44 @@ language: cpp +# We want to run the `*_severe` debug and test targets; thus, we need +# to enable ptrace capability for (L/A)SAN which is currently not possible +# with container-based builds on travis-ci +# TODO: revert to `sudo: false` once the following are fixed/made possible +# - https://github.com/google/sanitizers/issues/764 +# - https://github.com/travis-ci/travis-ci/issues/9033 +sudo: required + +matrix: + fast_finish: true + +# We want to run the `*_severe` debug and test targets; thus, we need +# g++ >= 4.9 and clang++ >= 3.5 compiler: - clang - gcc +addons: + apt: + sources: + - ubuntu-toolchain-r-test + packages: + - gcc-4.9 + - g++-4.9 + +before_install: + - if [[ $CXX = g++ ]]; then export CXX="g++-4.9" CC="gcc-4.9"; fi + script: - - export CPPFLAGS=-DSWDEBUG && make cleaner bint_run - - make cleaner cov test_run + # compile and run optimized binary + - make clean bin bint_run + # compile and run debug binary + - make clean bin_debug_severe bint_run + # compile and run (severe) unit tests + - ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe test_run + # determine code coverage of unit tests + - make clean cov test_run after_success: - bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports" - - make cleaner + # clean up + - make clean diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 000000000..94a9ed024 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index efa887fd0..4ccb16fd5 100644 --- a/README.md +++ b/README.md @@ -49,6 +49,16 @@ You can help us in different ways: [pull request](https://github.com/DrylandEcology/SOILWAT2/pulls) +__Compilation__: + * Requirements: + - the `gcc` or `clang/llvm` toolchains + - `gcc >= v4.9` and `clang >= v3.3` for the `*_severe` test/debug targets + - POSIX- or GNU-compliant `make` + - On Windows OS: an installation of `cygwin` + * Build with `make` (see `make help` to print information about all + available targets) + + __SOILWAT2 code is used as part of three applications__: * stand-alone (code flag `SOILWAT` is defined if neither `STEPWAT` nor `RSOILWAT` exist), @@ -75,17 +85,27 @@ __Tests, documentation, and code__ form a trinity * Note: `SOILWAT2` is written in C whereas `GoogleTest` is a C++ framework. * Run unit tests locally on the command-line with ``` - make test # compiles the unit-test binary/executable (with `-DSWDEBUG`) - make test_run # executes the unit-test binary - make cleaner + 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 ``` * Development/feature branches can only be merged into master if they pass - all checks + all checks on `appveyor` and `travis` continuous integration servers, i.e., + run the following locally to prepare a pull-request or commit to be reviewed + ``` + make clean bin_debug_severe bint_run + make clean test_severe test_run + ``` + * Note that you may want/need to exclude known memory leaks from severe + testing (see https://github.com/DrylandEcology/SOILWAT2/issues/205): + ``` + ASAN_OPTIONS=detect_leaks=1 LSAN_OPTIONS=suppressions=.LSAN_suppr.txt make clean test_severe test_run + ``` * Informal and local integration tests example: 1. Before coding, run `testing/` and produce reference output ``` git checkout master - make cleaner bint_run + make bin bint_run cp -r testing/Output testing/Output_ref ``` 2. Develop your code and keep "testing/Output_ref" locally, i.e., don't @@ -93,7 +113,7 @@ __Tests, documentation, and code__ form a trinity 3. Regularly, e.g., before finalizing a commit, check that new code produces identical output (that is unless you work on output...) ``` - make cleaner bint_run + make bin bint_run diff testing/Output/ testing/Output_ref/ -qs ``` @@ -116,19 +136,21 @@ __Tests, documentation, and code__ form a trinity ... } ``` - * Clean, compile and run SOILWAT2-standalone in debugging mode with, e.g., + * Clean, compile and run optimized SOILWAT2-standalone in debugging mode + with, e.g., ``` - make cleaner bint_run CPPFLAGS=-DSWDEBUG + make bin bint_run CPPFLAGS=-DSWDEBUG ``` - * Alternatively, you can use the pre-configured debugging targets - `bin_debug` and `bind`, for instance, with + * Alternatively and potentially preferably, you can use the pre-configured + debugging targets + `bin_debug` and `bin_debug_severe`, for instance, with ``` - make cleaner bind bint_run + make bin_debug_severe bint_run ``` * If **valgrind** is installed, then you can call the target `bind_valgrind` (see description in `makefile`) with ``` - make cleaner bind_valgrind + make bind_valgrind ```
diff --git a/SW_Carbon.h b/SW_Carbon.h index 342999779..2119733ac 100644 --- a/SW_Carbon.h +++ b/SW_Carbon.h @@ -5,30 +5,40 @@ * @date 23 January 2017 */ #ifndef CARBON - #define CARBON /**< A macro that only lets the variables in @f SW_Carbon.h be defined once. */ +#define CARBON /**< A macro that only lets the variables in @f SW_Carbon.h be defined once. */ - #include "SW_Defines.h" +#include "SW_Defines.h" - /** - * @brief The main structure holding all CO2-related data. - */ - typedef struct { - int - use_wue_mult, /**< A boolean integer indicating if WUE multipliers should be calculated. */ - use_bio_mult; /**< A boolean integer indicating if biomass multipliers should be calculated. */ +#ifdef __cplusplus +extern "C" { +#endif + +/** + * @brief The main structure holding all CO2-related data. + */ +typedef struct { + int + use_wue_mult, /**< A boolean integer indicating if WUE multipliers should be calculated. */ + use_bio_mult; /**< A boolean integer indicating if biomass multipliers should be calculated. */ - char - scenario[64]; /**< A 64-char array holding the scenario name for which we are extracting CO2 data from the carbon.in file. */ + char + scenario[64]; /**< A 64-char array holding the scenario name for which we are extracting CO2 data from the carbon.in file. */ - double - ppm[MAX_NYEAR]; /**< A 1D array holding atmospheric CO2 concentration values (units ppm) that are indexed by calendar year. Is typically only populated for the years that are being simulated. `ppm[index]` is the CO2 value for the calendar year `index + 1` */ + double + ppm[MAX_NYEAR]; /**< A 1D array holding atmospheric CO2 concentration values (units ppm) that are indexed by calendar year. Is typically only populated for the years that are being simulated. `ppm[index]` is the CO2 value for the calendar year `index + 1` */ - } SW_CARBON; +} SW_CARBON; + +/* Function Declarations */ +void SW_CBN_construct(void); +void SW_CBN_deconstruct(void); +void SW_CBN_read(void); +void calculate_CO2_multipliers(void); + + +#ifdef __cplusplus +} +#endif - /* Function Declarations */ - void SW_CBN_construct(void); - void SW_CBN_deconstruct(void); - void SW_CBN_read(void); - void calculate_CO2_multipliers(void); #endif diff --git a/SW_Control.h b/SW_Control.h index 349977363..60ed43874 100644 --- a/SW_Control.h +++ b/SW_Control.h @@ -18,6 +18,10 @@ #ifndef SW_CONTROL_H #define SW_CONTROL_H +#ifdef __cplusplus +extern "C" { +#endif + void SW_CTL_init_model(const char *firstfile); void SW_CTL_clear_model(Bool full_reset); void SW_CTL_obtain_inputs(void); @@ -29,4 +33,9 @@ void SW_CTL_run_current_year(void); void SW_CTL_SetMemoryRefs(void); #endif + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Defines.h b/SW_Defines.h index 3e063b37d..88df69c1b 100644 --- a/SW_Defines.h +++ b/SW_Defines.h @@ -17,11 +17,15 @@ /********************************************************/ #ifndef SOILW_DEF_H - #define SOILW_DEF_H +#define SOILW_DEF_H #include /* for atan() in tanfunc() below */ #include "generic.h" +#ifdef __cplusplus +extern "C" { +#endif + /* Not sure if this parameter is variable or a consequence of algebra, * but it's different in the FORTRAN version than in the ELM doc. * If deemed to need changing, might as well recompile rather than @@ -150,4 +154,9 @@ typedef enum { eF, /* file management */ eOUT /* output */ } ObjType; + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Files.h b/SW_Files.h index a96e3dc13..9f0873b82 100644 --- a/SW_Files.h +++ b/SW_Files.h @@ -14,7 +14,11 @@ /********************************************************/ /********************************************************/ #ifndef SW_FILES_H - #define SW_FILES_H +#define SW_FILES_H + +#ifdef __cplusplus +extern "C" { +#endif #define SW_NFILES 23 @@ -43,4 +47,9 @@ void SW_CSV_F_INIT(const char *s); void SW_F_SetMemoryRefs(void); #endif + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Flow.h b/SW_Flow.h index 4c425e643..1b0380037 100644 --- a/SW_Flow.h +++ b/SW_Flow.h @@ -1,3 +1,18 @@ +#ifndef SW_FLOW_H +#define SW_FLOW_H + + +#ifdef __cplusplus +extern "C" { +#endif + void SW_FLW_construct(void); void SW_FLW_deconstruct(void); void SW_Water_Flow(void); + + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/SW_Flow_lib.h b/SW_Flow_lib.h index 18a82dcec..50f5988bb 100644 --- a/SW_Flow_lib.h +++ b/SW_Flow_lib.h @@ -37,6 +37,10 @@ #ifndef SW_WATERSUBS_H #define SW_WATERSUBS_H +#ifdef __cplusplus +extern "C" { +#endif + /* Standing crop can only intercept so much precip * This is the limiter used inside stdcrop_intercepted() */ @@ -179,4 +183,9 @@ void soil_temperature_today(double *ptr_dTime, double deltaX, double sT1, double int nRgr, double sTempR[], double oldsTempR[], double vwcR[], double wpR[], double fcR[], double bDensityR[], double csParam1, double csParam2, double shParam, Bool *ptr_stError); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Main_lib.c b/SW_Main_lib.c index 2fea9f1f3..09deaa644 100644 --- a/SW_Main_lib.c +++ b/SW_Main_lib.c @@ -36,7 +36,7 @@ /* --------------------------------------------------- */ /* see generic.h and filefuncs.h for more info on these vars */ -char inbuf[1024]; /* buffer used by input statements */ +char inbuf[MAX_FILENAMESIZE]; /* buffer used by input statements */ char errstr[MAX_ERROR]; /* used to compose an error msg */ FILE *logfp; /* file handle for logging messages */ int logged; /* boolean: true = we logged a msg */ @@ -62,7 +62,7 @@ void usage(void) { sw_error(0, "%s", s1); } -char _firstfile[1024]; +char _firstfile[MAX_FILENAMESIZE]; void init_args(int argc, char **argv) { /* =================================================== */ diff --git a/SW_Markov.h b/SW_Markov.h index 1cf818a6e..1a5641e8d 100644 --- a/SW_Markov.h +++ b/SW_Markov.h @@ -13,6 +13,10 @@ #ifndef SW_MARKOV_H #define SW_MARKOV_H +#ifdef __cplusplus +extern "C" { +#endif + typedef struct { /* pointers to arrays of probabilities for each day saves some space */ @@ -42,4 +46,10 @@ void SW_MKV_today(TimeInt doy, RealD *tmax, RealD *tmin, RealD *rain); void SW_MKV_SetMemoryRefs( void); #endif + +#ifdef __cplusplus +} +#endif + #endif + diff --git a/SW_Model.h b/SW_Model.h index 46a791b30..43cc9278b 100644 --- a/SW_Model.h +++ b/SW_Model.h @@ -23,6 +23,10 @@ #include "Times.h" #include "SW_Defines.h" +#ifdef __cplusplus +extern "C" { +#endif + typedef struct { TimeInt /* controlling dates for model run */ startyr, /* beginning year for model run */ @@ -54,4 +58,9 @@ void SW_MDL_deconstruct(void); void SW_MDL_new_year(void); void SW_MDL_new_day(void); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Output.c b/SW_Output.c index 793183173..634d64cb6 100644 --- a/SW_Output.c +++ b/SW_Output.c @@ -1826,6 +1826,8 @@ int SW_OUT_read_onekey(OutKey k, OutSum sumtype, char period[], int first, last = 366; #ifndef RSOILWAT strcpy(period, "YR"); + #else + if (period) {} // avoid `-Wunused-parameter` #endif } else if ((k == eSW_AllVeg || k == eSW_ET || k == eSW_AllWthr || k == eSW_AllH2O)) diff --git a/SW_Output.h b/SW_Output.h index 1a546bf9a..bcf8acf2d 100644 --- a/SW_Output.h +++ b/SW_Output.h @@ -37,6 +37,10 @@ #include "SW_Weather.h" #include "SW_VegProd.h" +#ifdef __cplusplus +extern "C" { +#endif + // Array-based output: #if defined(RSOILWAT) || defined(STEPWAT) @@ -343,4 +347,9 @@ void get_co2effects_SXW(OutPeriod pd); void SW_OUT_SetMemoryRefs(void); #endif + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Output_mock.c b/SW_Output_mock.c index 347625d61..0ffcd9749 100644 --- a/SW_Output_mock.c +++ b/SW_Output_mock.c @@ -72,8 +72,8 @@ IntUS ncol_OUT[SW_OUTNKEYS]; // Mock definitions -char const *key2str[] = {}; -char const *pd2longstr[] = {}; +char const *key2str[] = {"SW_MISSING"}; +char const *pd2longstr[] = {"SW_MISSING"}; diff --git a/SW_Output_outarray.h b/SW_Output_outarray.h index 1f7cdabc3..fd4bbd939 100644 --- a/SW_Output_outarray.h +++ b/SW_Output_outarray.h @@ -16,6 +16,11 @@ #ifndef SW_OUTPUT_ARRAY_H #define SW_OUTPUT_ARRAY_H +#ifdef __cplusplus +extern "C" { +#endif + + /** iOUT returns the index to the `i`-th column for time period `pd` in an output array that is organized by columns where `i` is base0 and `pd` is `OutPeriod`. The index order has to match up with column names as @@ -48,4 +53,9 @@ void setGlobalSTEPWAT2_OutputVariables(void); #endif +#ifdef __cplusplus +} +#endif + + #endif diff --git a/SW_Output_outtext.h b/SW_Output_outtext.h index a0b675670..2ca7a642a 100644 --- a/SW_Output_outtext.h +++ b/SW_Output_outtext.h @@ -16,6 +16,10 @@ #ifndef SW_OUTPUT_TXT_H #define SW_OUTPUT_TXT_H +#ifdef __cplusplus +extern "C" { +#endif + typedef struct { Bool make_soil[SW_OUTNPERIODS], make_regular[SW_OUTNPERIODS]; @@ -59,4 +63,9 @@ void write_headers_to_csv(OutPeriod pd, FILE *fp_reg, FILE *fp_soil, Bool does_a void find_TXToutputSoilReg_inUse(void); void SW_OUT_close_files(void); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Site.h b/SW_Site.h index 6129528ab..5b84d6901 100644 --- a/SW_Site.h +++ b/SW_Site.h @@ -49,6 +49,10 @@ #include "SW_Defines.h" +#ifdef __cplusplus +extern "C" { +#endif + typedef unsigned int LyrIndex; @@ -149,4 +153,9 @@ LyrIndex _newlayer(void); void SW_SIT_SetMemoryRefs(void); #endif + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Sky.h b/SW_Sky.h index 900327f16..9ed016f30 100644 --- a/SW_Sky.h +++ b/SW_Sky.h @@ -18,9 +18,13 @@ #ifndef SW_SKY_H #define SW_SKY_H - #include "SW_Times.h" +#ifdef __cplusplus +extern "C" { +#endif + + typedef struct { RealD cloudcov [MAX_MONTHS], /* monthly cloud cover (frac) */ windspeed [MAX_MONTHS], /* windspeed (m/s) */ @@ -40,4 +44,9 @@ void SW_SKY_read(void); void SW_SKY_init(double scale_sky[], double scale_wind[], double scale_rH[], double scale_transmissivity[]); void SW_SKY_construct(void); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_SoilWater.h b/SW_SoilWater.h index 416bcae00..1378afa2b 100644 --- a/SW_SoilWater.h +++ b/SW_SoilWater.h @@ -41,6 +41,10 @@ #ifndef SW_SOILWATER_H #define SW_SOILWATER_H +#ifdef __cplusplus +extern "C" { +#endif + #include "generic.h" #include "SW_Defines.h" #include "SW_Times.h" @@ -153,4 +157,9 @@ void SW_WaterBalance_Checks(void); void SW_SWC_SetMemoryRefs(void); #endif + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Times.h b/SW_Times.h index 4919ffa30..401c6d199 100644 --- a/SW_Times.h +++ b/SW_Times.h @@ -33,6 +33,11 @@ #include "Times.h" +#ifdef __cplusplus +extern "C" { +#endif + + /*---------------------------------------------------------------*/ typedef enum { Yesterday, Today @@ -55,4 +60,9 @@ typedef struct { * containing the start/end years. */ + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_VegEstab.h b/SW_VegEstab.h index 8b86b1de2..2c984a6ce 100644 --- a/SW_VegEstab.h +++ b/SW_VegEstab.h @@ -21,6 +21,11 @@ #include "../ST_defines.h" #endif +#ifdef __cplusplus +extern "C" { +#endif + + /* indices to bars[] */ #define SW_GERM_BARS 0 #define SW_ESTAB_BARS 1 @@ -122,4 +127,9 @@ void _echo_VegEstab(void); */ + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_VegProd.h b/SW_VegProd.h index dc6cb2602..2346d7896 100644 --- a/SW_VegProd.h +++ b/SW_VegProd.h @@ -37,6 +37,11 @@ #include "SW_Defines.h" /* for tanfunc_t*/ #include "Times.h" // for MAX_MONTHS +#ifdef __cplusplus +extern "C" { +#endif + + #define BIO_INDEX 0 /**< An integer representing the index of the biomass multipliers in the VegType#co2_multipliers 2D array. */ #define WUE_INDEX 1 /**< An integer representing the index of the WUE multipliers in the VegType#co2_multipliers 2D array. */ @@ -131,4 +136,9 @@ void apply_biomassCO2effect(double* new_biomass, double *biomass, double multipl void _echo_VegProd(void); void get_critical_rank(void); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/SW_Weather.h b/SW_Weather.h index 2b89368bb..4b4b79133 100644 --- a/SW_Weather.h +++ b/SW_Weather.h @@ -27,6 +27,11 @@ #include "SW_Times.h" #include "SW_Defines.h" +#ifdef __cplusplus +extern "C" { +#endif + + /* missing values may be different than with other things */ #define WTH_MISSING 999. @@ -96,4 +101,9 @@ void SW_WTH_clear_runavg_list(void); void SW_WTH_SetMemoryRefs(void); #endif + +#ifdef __cplusplus +} +#endif + #endif diff --git a/Times.h b/Times.h index 23964ecbb..eefa365a6 100644 --- a/Times.h +++ b/Times.h @@ -43,6 +43,11 @@ #include #include "generic.h" +#ifdef __cplusplus +extern "C" { +#endif + + /*---------------------------------------------------------------*/ #define MAX_MONTHS 12 #define MAX_WEEKS 53 @@ -118,4 +123,9 @@ Bool isleapyear(const TimeInt year); void interpolate_monthlyValues(double monthlyValues[], double dailyValues[]); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/appveyor.yml b/appveyor.yml index cb002caf6..109a27ea8 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -9,8 +9,14 @@ install: - git submodule update --init --recursive # to run your custom scripts instead of automatic MSBuild +# Note: appveyor doesn't have sanitizers -> cannot run *_severe test targets build_script: - set PATH=%PATH%;c:\cygwin\bin - - set CPPFLAGS=-DSWDEBUG && make cleaner bint_run - - make cleaner testci test_run - - make cleaner + # compile and run optimized binary + - make clean bin bint_run + # compile and run debug binary + - make clean bin_debug bint_run + # compile and run unit tests + - make clean test test_run + # clean up + - make clean diff --git a/filefuncs.h b/filefuncs.h index 3faa810f0..e7635d235 100644 --- a/filefuncs.h +++ b/filefuncs.h @@ -11,6 +11,9 @@ #include "generic.h" +#ifdef __cplusplus +extern "C" { +#endif /*************************************************** * Function definitions @@ -30,4 +33,9 @@ void LogError(FILE *fp, const int mode, const char *fmt, ...); extern char inbuf[]; /* declare in main, use anywhere */ + +#ifdef __cplusplus +} +#endif + #endif diff --git a/generic.h b/generic.h index f68ad32de..1fd94ad97 100644 --- a/generic.h +++ b/generic.h @@ -49,6 +49,11 @@ #include #endif + +#ifdef __cplusplus +extern "C" { +#endif + /*************************************************** * Basic definitions ***************************************************/ @@ -248,5 +253,10 @@ extern errstr[]; #define strdup(x) sw_strdup(x) #endif + +#ifdef __cplusplus +} +#endif + #define GENERIC_H #endif diff --git a/makefile b/makefile index ef7b21fd7..34ce79e4c 100644 --- a/makefile +++ b/makefile @@ -1,25 +1,35 @@ -#----------------------------------------------------------------------------------- +#------------------------------------------------------------------------------- # commands explanations -#----------------------------------------------------------------------------------- -# make bin compile the binary executable using optimizations -# make bint same as 'make bin' plus moves a copy of the binary to the +#------------------------------------------------------------------------------- +# help display the top of this file, i.e., print explanations +# +# make all (synonym to 'bin'): compile the binary executable using +# optimizations +# make bint same as 'make bin' plus move a copy of the binary to the # 'testing/' folder -# make bint_run same as 'make bint' plus executes the binary in the testing/ folder +# make bint_run same as 'make bint' plus execute the binary in testing/ +# # make lib create SOILWAT2 library -# make test compile unit tests in 'test/ folder with googletest -# make testci compile unit tests with less severe flags due to older compiler versions in 'test/ folder with googletest -# make test_run run unit tests (in a previous step compiled with 'make test' or 'make testci') +# +# make test compile unit tests in 'test/ folder (with googletest) +# make test_severe compile unit tests with severe flags in 'test/' +# make test_run run unit tests (in a previous step compiled with 'make test' +# or 'make test_severe') +# # make bin_debug compile the binary executable in debug mode -# make bind same as 'make bin_debug' plus moves a copy of the binary to the -# 'testing/' folder -# make bind_valgrind same as 'make bind' plus runs valgrind on the debug binary in the testing/ folder +# make bin_debug_severe same as 'make bin_debug' but with severe flags +# make bind_valgrind same as 'make bind' plus run valgrind on the debug +# binary in the testing/ folder +# # make cov same as 'make test' but with code coverage support -# make cov_run run unit tests and gcov on each source file (in a previous step -# compiled with 'make cov') -# make cleaner delete all of the o files, test files, libraries, and the binary exe +# make cov_run run unit tests and gcov on each source file (in a previous +# step compiled with 'make cov') +# +# make clean (synonym to 'cleaner'): delete all of the o files, test +# files, libraries, and the binary exe(s) # make test_clean delete test files and libraries # make cov_clean delete files associated with code coverage -#----------------------------------------------------------------------------------- +#------------------------------------------------------------------------------- uname_m = $(shell uname -m) @@ -44,30 +54,36 @@ lib_target_cov = lib$(target_cov).a # RM = rm use_c11 = -std=c11 +use_gnu11 = -std=gnu11 # gnu11 required for googletest on Windows/cygwin use_gnu++11 = -std=gnu++11 # gnu++11 required for googletest on Windows/cygwin #------ FLAGS # Diagnostic warning/error messages warning_flags = -Wall -Wextra -warning_flags_bin = $(warning_flags) -Wpedantic -Werror +# Don't use 'warning_flags_severe*' for production builds and rSOILWAT2 +warning_flags_severe = $(warning_flags) -Wpedantic -Werror +warnings_flags_severe_cxx = $(warning_flags_severe) -Wno-error + # TODO: address underlying problems so that we can eliminate `-Wno-error`: + # - compiler warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated (https://github.com/DrylandEcology/SOILWAT2/issues/208) + # - compiler warning: variable length arrays (https://github.com/DrylandEcology/SOILWAT2/issues/214) # Instrumentation options for debugging and testing instr_flags = -fstack-protector-all -instr_flags_severe = -D_FORTIFY_SOURCE=2 -Wno-macro-redefined \ - -fsanitize=undefined -fsanitize=address +instr_flags_severe = $(instr_flags) -fsanitize=undefined -fsanitize=address # -fstack-protector-strong (gcc >= v4.9) # (gcc >= 4.0) -D_FORTIFY_SOURCE: lightweight buffer overflow protection to some memory and string functions # (gcc >= 4.8; llvm >= 3.1) -fsanitize=address: replaces `mudflap` run time checker; https://github.com/google/sanitizers/wiki/AddressSanitizer + # (gcc >= 4.9; llvm >= 3.3) -fsanitize=undefined # Precompiler and compiler flags and options sw_CPPFLAGS = $(CPPFLAGS) sw_CFLAGS = $(CFLAGS) -sw_CXXFLAGS = $(CXXFLAGS) -Wno-error=deprecated # TODO: clang++: "treating 'c' input as 'c++' when in C++ mode" +sw_CXXFLAGS = $(CXXFLAGS) -bin_flags = -O2 +bin_flags = -O2 -fno-stack-protector debug_flags = -g -O0 -DSWDEBUG -cov_flags = -coverage +cov_flags = -O0 -coverage # Linker flags and libraries # order of libraries is important for GNU gcc (libSOILWAT2 depends on libm) @@ -83,28 +99,25 @@ gtest_LDLIBS = -l$(gtest) #------ CODE FILES -sources = $(sw_sources) SW_Main_lib.c SW_VegEstab.c SW_Control.c generic.c \ +sources_core = SW_Main_lib.c SW_VegEstab.c SW_Control.c generic.c \ rands.c Times.c mymemory.c filefuncs.c SW_Files.c SW_Model.c \ SW_Site.c SW_SoilWater.c SW_Markov.c SW_Weather.c SW_Sky.c \ - SW_Output.c SW_Output_get_functions.c\ SW_VegProd.c SW_Flow_lib.c SW_Flow.c SW_Carbon.c -objects = $(sources:.c=.o) + +sources_lib = $(sw_sources) $(sources_core) SW_Output.c SW_Output_get_functions.c +objects_lib = $(sources_lib:.c=.o) # Unfortunately, we currently cannot include 'SW_Output.c' because # - cannot increment expression of enum type (e.g., OutKey, OutPeriod) # - assigning to 'OutKey' from incompatible type 'int' # ==> instead, we use 'SW_Output_mock.c' which provides mock versions of the # public functions (but will result in some compiler warnings) -sources_tests = SW_Main_lib.c SW_VegEstab.c SW_Control.c generic.c \ - rands.c Times.c mymemory.c filefuncs.c SW_Files.c SW_Model.c \ - SW_Site.c SW_SoilWater.c SW_Markov.c SW_Weather.c SW_Sky.c \ - SW_Output_mock.c \ - SW_VegProd.c SW_Flow_lib.c SW_Flow.c SW_Carbon.c -objects_tests = $(sources_tests:.c=.o) +sources_lib_test = $(sources_core) SW_Output_mock.c +objects_lib_test = $(sources_lib_test:.c=.o) -bin_sources = SW_Main.c SW_Output_outtext.c # SOILWAT2-standalone -bin_objects = $(bin_sources:.c=.o) +sources_bin = SW_Main.c SW_Output_outtext.c # SOILWAT2-standalone +objects_bin = $(sources_bin:.c=.o) gtest = gtest @@ -121,84 +134,72 @@ bin : $(target) lib : $(lib_target) $(lib_target) : - $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(bin_flags) $(warning_flags_bin) \ - $(use_c11) -c $(sources) + $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(bin_flags) $(warning_flags) \ + $(use_c11) -c $(sources_lib) -@$(RM) -f $(lib_target) - $(AR) -rcs $(lib_target) $(objects) - -@$(RM) -f $(objects) + $(AR) -rcs $(lib_target) $(objects_lib) + -@$(RM) -f $(objects_lib) $(lib_target_test) : - $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warning_flags) \ - $(instr_flags) $(use_gnu++11) -c $(sources_tests) + $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags) \ + $(instr_flags) $(use_gnu11) -c $(sources_lib_test) -@$(RM) -f $(lib_target_test) - $(AR) -rcs $(lib_target_test) $(objects_tests) - -@$(RM) -f $(objects_tests) + $(AR) -rcs $(lib_target_test) $(objects_lib_test) + -@$(RM) -f $(objects_lib_test) -$(lib_target_severe) : - $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warning_flags) \ - $(instr_flags_severe) $(use_gnu++11) -c $(sources_tests) +$(lib_target_severe) : # needs CXX because of '*_severe' flags which must match test binary build + $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warnings_flags_severe_cxx) \ + $(instr_flags_severe) $(use_gnu++11) -c $(sources_lib_test) -@$(RM) -f $(lib_target_severe) - $(AR) -rcs $(lib_target_severe) $(objects_tests) - -@$(RM) -f $(objects_tests) + $(AR) -rcs $(lib_target_severe) $(objects_lib_test) + -@$(RM) -f $(objects_lib_test) -$(lib_target_cov) : +$(lib_target_cov) : # needs CXX because of 'coverage' flags which must match test binary build $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warning_flags) \ - $(instr_flags) $(cov_flags) $(use_gnu++11) -c $(sources_tests) + $(instr_flags) $(cov_flags) $(use_gnu++11) -c $(sources_lib_test) -@$(RM) -f $(lib_target_cov) - $(AR) -rcs $(lib_target_cov) $(objects_tests) - -@$(RM) -f $(objects_tests) + $(AR) -rcs $(lib_target_cov) $(objects_lib_test) + -@$(RM) -f $(objects_lib_test) $(target) : $(lib_target) - $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(bin_flags) $(warning_flags_bin) \ + $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(bin_flags) $(warning_flags) \ $(use_c11) \ - -o $(target) $(bin_sources) $(target_LDLIBS) $(sw_LDFLAGS) + -o $(target) $(sources_bin) $(target_LDLIBS) $(sw_LDFLAGS) -bin_debug : - $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags) \ - $(instr_flags_severe) $(use_c11) -c $(sources_tests) +bin_debug_severe : + $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags_severe) \ + $(instr_flags_severe) $(use_c11) -c $(sources_lib_test) -@$(RM) -f $(lib_target_severe) - $(AR) -rcs $(lib_target_severe) $(objects_tests) - -@$(RM) -f $(objects_tests) + $(AR) -rcs $(lib_target_severe) $(objects_lib_test) + -@$(RM) -f $(objects_lib_test) - $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags) \ + $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags_severe) \ $(instr_flags_severe) $(use_c11) \ - -o $(target) $(bin_sources) $(severe_LDLIBS) $(sw_LDFLAGS) - -bin_debug_ci : - $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags) \ - $(instr_flags) $(use_c11) -c $(sources_tests) - - -@$(RM) -f $(lib_target_test) - $(AR) -rcs $(lib_target_test) $(objects_tests) - -@$(RM) -f $(objects_tests) + -o $(target) $(sources_bin) $(severe_LDLIBS) $(sw_LDFLAGS) +bin_debug : $(lib_target_test) $(CC) $(sw_CPPFLAGS) $(sw_CFLAGS) $(debug_flags) $(warning_flags) \ $(instr_flags) $(use_c11) \ - -o $(target) $(bin_sources) $(test_LDLIBS) $(sw_LDFLAGS) + -o $(target) $(sources_bin) $(test_LDLIBS) $(sw_LDFLAGS) .PHONY : bint -bint : bin +bint : cp $(target) testing/$(target) .PHONY : bint_run bint_run : bint ./testing/$(target) -d ./testing -f files.in -.PHONY : bind -bind : bin_debug - cp $(target) testing/$(target) - .PHONY : bind_valgrind -bind_valgrind : bin_debug_ci - cp $(target) testing/$(target) +bind_valgrind : bin_debug bint valgrind -v --track-origins=yes --leak-check=full ./testing/$(target) -d ./testing -f files.in @@ -216,13 +217,13 @@ $(lib_gtest) : @$(AR) -r $(lib_gtest) gtest-all.o -test : $(lib_gtest) $(lib_target_severe) - $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warning_flags) \ +test_severe : $(lib_gtest) $(lib_target_severe) + $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warnings_flags_severe_cxx) \ $(instr_flags_severe) $(use_gnu++11) \ -isystem ${GTEST_DIR}/include -pthread \ test/*.cc -o $(bin_test) $(gtest_LDLIBS) $(severe_LDLIBS) $(sw_LDFLAGS) -testci : $(lib_gtest) $(lib_target_test) +test : $(lib_gtest) $(lib_target_test) $(CXX) $(sw_CPPFLAGS) $(sw_CXXFLAGS) $(debug_flags) $(warning_flags) \ $(instr_flags) $(use_gnu++11) \ -isystem ${GTEST_DIR}/include -pthread \ @@ -248,7 +249,7 @@ cov_run : cov .PHONY : clean1 clean1 : - -@$(RM) -f $(objects) $(bin_objects) + -@$(RM) -f $(objects_lib) $(objects_bin) .PHONY : clean2 clean2 : @@ -264,7 +265,7 @@ test_clean : -@$(RM) -f gtest-all.o $(lib_gtest) $(bin_test) -@$(RM) -f $(lib_target_test) $(lib_target_severe) $(lib_target_cov) -@$(RM) -fr *.dSYM - -@$(RM) -f $(objects_tests) + -@$(RM) -f $(objects_lib_test) .PHONY : cov_clean cov_clean : @@ -276,3 +277,9 @@ cleaner : clean1 clean2 bint_clean test_clean cov_clean .PHONY : clean clean : cleaner + + + +.PHONY : help +help : + less makefile diff --git a/memblock.h b/memblock.h index 0fbfe1c67..2fa7b8fd6 100644 --- a/memblock.h +++ b/memblock.h @@ -8,6 +8,10 @@ #include #include +#ifdef __cplusplus +extern "C" { +#endif + #define bGarbage 0xCC /*typedef unsigned char byte*/ typedef signed char flag; @@ -52,4 +56,9 @@ flag fValidPointer(void *pv, size_t size); #define fPtrLessEq(pLeft, pRight) ((pLeft) <= (pRight)) #define fPtrGrtrEq(pLeft, pRight) ((pLeft) >= (pRight)) + +#ifdef __cplusplus +} +#endif + #endif diff --git a/myMemory.h b/myMemory.h index fde206984..bdfdbc2e8 100644 --- a/myMemory.h +++ b/myMemory.h @@ -13,6 +13,11 @@ #include "memblock.h" #endif +#ifdef __cplusplus +extern "C" { +#endif + + char *Str_Dup(const char *s); /* return pointer to malloc'ed dup of s */ void *Mem_Malloc(size_t size, const char *funcname); void *Mem_Calloc(size_t nobjs, size_t size, const char *funcname); @@ -21,4 +26,9 @@ void Mem_Free(void *block); void Mem_Set(void *block, byte c, size_t n); void Mem_Copy(void *dest, const void *src, size_t n); + +#ifdef __cplusplus +} +#endif + #endif diff --git a/rands.c b/rands.c index 32c41d4ea..7e8528fe1 100644 --- a/rands.c +++ b/rands.c @@ -13,6 +13,7 @@ long _randseed = 0L; #ifdef RSOILWAT #include // for the random number generators + #include // for rnorm() #endif @@ -328,7 +329,7 @@ double RandNorm(double mean, double stddev) { #ifdef RSOILWAT GetRNGstate(); - y = norm_rand(); + y = rnorm(mean, stddev); PutRNGstate(); #else diff --git a/rands.h b/rands.h index 014b6869d..ce0c9b716 100644 --- a/rands.h +++ b/rands.h @@ -13,6 +13,10 @@ #include #include +#ifdef __cplusplus +extern "C" { +#endif + /*************************************************** * Basic definitions ***************************************************/ @@ -52,5 +56,10 @@ float RandBeta(float aa, float bb); #define RandUni RandUni_good #endif + +#ifdef __cplusplus +} +#endif + #define RANDS_H #endif diff --git a/test/sw_maintest.cc b/test/sw_maintest.cc index e63e3852c..6b012dae3 100644 --- a/test/sw_maintest.cc +++ b/test/sw_maintest.cc @@ -48,11 +48,13 @@ const char * masterfile_test = "files.in"; // relative to 'dir_test' // Global variables which are defined in SW_Main_lib.c: -extern char errstr[]; -extern FILE *logfp; -extern int logged; -extern Bool QuietMode, EchoInits; -extern char _firstfile[]; +// We need to redefine them here because they are not included in the library +char inbuf[MAX_FILENAMESIZE]; +char errstr[MAX_ERROR]; +FILE *logfp; +int logged; +Bool QuietMode, EchoInits; +char _firstfile[MAX_FILENAMESIZE]; @@ -81,9 +83,9 @@ int main(int argc, char **argv) { res = RUN_ALL_TESTS(); //--- Take down SOILWAT2 variables - SW_SIT_clear_layers(); - SW_WTH_clear_runavg_list(); + SW_CTL_clear_model(swTRUE); // de-allocate all memory //--- Return output of 'RUN_ALL_TESTS()', see https://github.com/google/googletest/blob/master/googletest/docs/FAQ.md#my-compiler-complains-about-ignoring-return-value-when-i-call-run_all_tests-why return res; } + diff --git a/test/test_SW_SoilWater.cc b/test/test_SW_SoilWater.cc index 4d8f29f46..79bf44e98 100644 --- a/test/test_SW_SoilWater.cc +++ b/test/test_SW_SoilWater.cc @@ -22,6 +22,8 @@ extern SW_SITE SW_Site; extern SW_VEGPROD SW_VegProd; namespace{ + float tol = 1e-6; + // Test the 'SW_SoilWater' function 'SW_VWCBulkRes' TEST(SWSoilWaterTest, SWVWCBulkRes){ //declare mock INPUTS @@ -61,8 +63,9 @@ namespace{ SW_SWC_adjust_snow(temp_min, temp_max, ppt, &rain, &snow, &snowmelt); EXPECT_EQ(rain, 1); EXPECT_EQ(snow, 0); - Reset_SOILWAT2_after_UnitTest(); + // Reset to previous global states + Reset_SOILWAT2_after_UnitTest(); } // Test the 'SW_SoilWater' function 'SW_SWCbulk2SWPmatric' @@ -77,7 +80,6 @@ namespace{ swcBulk = 999; res = SW_SWCbulk2SWPmatric(fractionGravel, swcBulk, n); EXPECT_EQ(res, 0.0); - Reset_SOILWAT2_after_UnitTest(); // test swp val swcBulk = 4; @@ -89,38 +91,45 @@ namespace{ RealD resExpect = .00013310902; // did math by hand to get this value RealD actualExpectDiff = fabs(res - resExpect); EXPECT_LT(actualExpectDiff, .0002); + + // Reset to previous global states + Reset_SOILWAT2_after_UnitTest(); } // Test the 'SW_SoilWater' function 'SW_SWPmatric2VWCBulk' TEST(SWSoilWaterTest, SWSWPmatric2VWCBulk){ // set up mock variables - RealD fractionGravel = .1; + RealD fractionGravel; RealD swpMatric = 15.0; RealD p; RealD tExpect; RealD t; - RealD actualExpectDiff; RealD psisMatric = 18.608013; RealD binverseMatric = 0.188608; RealD thetaMatric = 41.37; - RealD testNumber; + + int i; LyrIndex n = 0; + SW_Site.lyr[n]->thetasMatric = thetaMatric; - SW_Site.lyr[n]->psisMatric = psisMatric; - SW_Site.lyr[n]->bMatric = binverseMatric; - - // run tests for gravel fractions on the interval [.05, .8], step .05 - for(testNumber = 1; testNumber <= 16; testNumber++){ - fractionGravel = (testNumber / 20); - p = powe(psisMatric / (swpMatric * BARCONV), binverseMatric); - tExpect = thetaMatric * p * 0.01 * (1 - fractionGravel); + SW_Site.lyr[n]->psisMatric = psisMatric; + SW_Site.lyr[n]->bMatric = binverseMatric; + + p = thetaMatric * 0.01 * \ + powe(psisMatric / (swpMatric * BARCONV), binverseMatric); + + // run tests for gravel fractions on the interval [.0, .8], step .05 + for (i = 0; i <= 16; i++) + { + fractionGravel = i / 20.; + tExpect = p * (1 - fractionGravel); t = SW_SWPmatric2VWCBulk(fractionGravel, swpMatric, n); - actualExpectDiff = fabs(t - tExpect); // Tolerance for error since division with RealD introcuces some error - EXPECT_LT(actualExpectDiff, 0.0000001); - + EXPECT_NEAR(t, tExpect, tol); } + + // Reset to previous global states Reset_SOILWAT2_after_UnitTest(); } }