Unit tests, modelrunner, debug and archive all pass now.

CASAL2/source/Observations/Age/ProportionsAtLength.cpp

@@ -319,8 +319,8 @@ void ProportionsAtLength::DoBuild() {
 // I *think* this is duplicating the selectivity over all categories, if only one is given in the observation block 
   LOG_FINE() << "category_counter = " << category_counter;
   LOG_FINE() << "Listing categories (combined?):";
-  for (unsigned category_index = 0; category_index < category_labels_.size(); ++category_index) {
-    LOG_FINE() << "Combined category " << category_index << " = " << category_labels_[category_index];
+  for (unsigned combined_category_index = 0; combined_category_index < category_labels_.size(); ++combined_category_index) {
+    LOG_FINE() << "Combined category " << combined_category_index << " = " << category_labels_[combined_category_index];
   }
   LOG_FINE() << "Number of categories: " << category_labels_.size();
 //  if (selectivities_.size() == 1 && category_labels_.size() != 1) {
@@ -380,7 +380,7 @@ void ProportionsAtLength::Execute() {
     Double start_value = 0.0;
     Double end_value   = 0.0;
     Double final_value = 0.0;
-	Double category_index = 0.0;
+	unsigned category_index = 0;
 
     /**
      * Loop through the 2 combined categories building up the

CASAL2/source/Version.h

@@ -4,10 +4,10 @@
 #define VERSION "24.10 (2024-10-08)"
 #define SOURCE_REPOS "[email protected]:SamikDatta/CASAL2.git:fix_capped_selectivity"
 #define VERSION_NUMBER "24.10"
-#define SOURCE_CONTROL_REVISION 971860f228ddd35825fe4ad1f6446a082062d8d7
+#define SOURCE_CONTROL_REVISION 6289afd73d3a6166504d23a1d7fec6c6b72f63e4
 #define SOURCE_CONTROL_DATE "2024-10-08"
 #define SOURCE_CONTROL_YEAR "2024"
 #define SOURCE_CONTROL_MONTH "October"
-#define SOURCE_CONTROL_TIME "05:47:59"
-#define SOURCE_CONTROL_VERSION "2024-10-08 05:47:59 UTC (rev. 971860f22)"
+#define SOURCE_CONTROL_TIME "21:01:32"
+#define SOURCE_CONTROL_VERSION "2024-10-08 21:01:32 UTC (rev. 6289afd73)"
 #endif

Documentation/UserManual/Version.tex

@@ -2,9 +2,9 @@
 \newcommand{\Version}{24.10 (2024-10-08)}
 \newcommand{\SourceRepos}{[email protected]:SamikDatta/CASAL2.git:fix_capped_selectivity}
 \newcommand{\VersionNumber}{24.10}
-\newcommand{\SourceControlRevision}{971860f228ddd35825fe4ad1f6446a082062d8d7}
+\newcommand{\SourceControlRevision}{6289afd73d3a6166504d23a1d7fec6c6b72f63e4}
 \newcommand{\SourceControlDateDoc}{2024-10-08}
 \newcommand{\SourceControlYearDoc}{2024}
 \newcommand{\SourceControlMonthDoc}{October}
-\newcommand{\SourceControlTimeDoc}{05:47:59}
-\newcommand{\SourceControlVersion}{2024-10-08 05:47:59 UTC (rev. 971860f22)}
+\newcommand{\SourceControlTimeDoc}{21:01:32}
+\newcommand{\SourceControlVersion}{2024-10-08 21:01:32 UTC (rev. 6289afd73)}

R-libraries/Version.R

@@ -2,9 +2,9 @@
 Version<-"24.10 (2024-10-08)"
 SourceRepos<-"[email protected]:SamikDatta/CASAL2.git:fix_capped_selectivity"
 VersionNumber<-"24.10"
-SourceControlRevision<-"971860f228ddd35825fe4ad1f6446a082062d8d7"
+SourceControlRevision<-"6289afd73d3a6166504d23a1d7fec6c6b72f63e4"
 SourceControlDateDoc<-"2024-10-08"
 SourceControlYearDoc<-"2024"
 SourceControlMonthDoc<-"October"
-SourceControlTimeDoc<-"05:47:59"
-SourceControlVersion<-"2024-10-08 05:47:59 UTC (rev. 971860f22)"
+SourceControlTimeDoc<-"21:01:32"
+SourceControlVersion<-"2024-10-08 21:01:32 UTC (rev. 6289afd73)"

TestModels/LIN_tc/estimate_betadiff.err

@@ -1,6 +1,4 @@
 
-[INFO] Setting the random number seed to 20
-[INFO] Estimable parameters were set from the input configuration files
 [WARNING] At line 47 in Observation.csl2 the table obs : The sum of the values for year 1990 was 0.9999 and do not sum to 1.0
 [WARNING] At line 47 in Observation.csl2 the table obs : The sum of the values for year 1993 was 0.9998 and do not sum to 1.0
 [WARNING] At line 47 in Observation.csl2 the table obs : The sum of the values for year 1994 was 0.9999 and do not sum to 1.0
@@ -912,5 +910,4 @@ finished main minimiser loop
 Successful convergence in optimise
 [INFO] Assert Passed: The Assert with label 'ObjectiveFunction' for the Objective Function had value 2296.97 and 2296.97 was expected.
 [INFO] Completed
-[INFO] Total CPU time: -89.2414 hours
-[INFO] Total elapsed time: 2 seconds
+[INFO] Total elapsed time: 3 seconds

TestModels/LIN_tc/estimate_betadiff.log

@@ -1,48 +1,46 @@
-Environment: User=Casal2 ([email protected]:casal2/casal2)
-Call: /opt/casal2/casal2/BuildSystem/Casal2/casal2 -e -g 20 -c config_betadiff.csl2 
-Date: Sun May 26 22:10:38 2024
+Casal2 ([email protected]:NIWAFisheriesModelling/CASAL2.git:add_mig_ss3)
+Call: C:\Users\dattas\Documents\CASAL2\BuildSystem/Casal2/casal2.exe -e -g 20 -c config_betadiff.csl2 
+Date: Wed Oct 09 11:00:57 2024
 Seed: 20
-Version: v24.05 (2024-05-26)
+Version: v24.10 (2024-10-02)
 Copyright (c) 2017-2024, NIWA (www.niwa.co.nz)
-root
- Machine=thoth (Linux 6.8.8-1-default x86_64)
- PID=23950
+Environment: User=dattas Machine=NIWA-1022446 OS=Windows_NT PID=23136
 
 
 *partition[state1]
 year: 1972
 time_step: Dec_Aug
 values {dataframe_with_row_labels}
 category 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
-male 23260874.844909 16517179.350706 12160454.690762 9247178.189888 7238201.875357 5814166.346700 4779614.628199 4011304.911897 3429387.991501 2980826.954591 2596782.186602 2237089.555294 1904089.988397 1599643.380839 1325047.491795 1080976.050511 867442.430752 683794.149101 528741.549288 400421.410237 296493.050779 214261.131635 509324.680440
-female 23260874.844909 16517179.350706 12160454.690762 9247178.189888 7238201.875357 5814166.346700 4779614.628199 4011304.911897 3429387.991501 2980826.954591 2596782.186602 2237089.555294 1904089.988397 1599643.380839 1325047.491795 1080976.050511 867442.430752 683794.149101 528741.549288 400421.410237 296493.050779 214261.131635 509324.680440
+male 23260874.844910 16517179.350707 12160454.690762 9247178.189888 7238201.875357 5814166.346701 4779614.628199 4011304.911897 3429387.991501 2980826.954591 2596782.186602 2237089.555294 1904089.988396 1599643.380839 1325047.491795 1080976.050511 867442.430752 683794.149101 528741.549288 400421.410237 296493.050779 214261.131635 509324.680440
+female 23260874.844910 16517179.350707 12160454.690762 9247178.189888 7238201.875357 5814166.346701 4779614.628199 4011304.911897 3429387.991501 2980826.954591 2596782.186602 2237089.555294 1904089.988396 1599643.380839 1325047.491795 1080976.050511 867442.430752 683794.149101 528741.549288 400421.410237 296493.050779 214261.131635 509324.680440
 *end
 
 *partition[state2]
 year: 1972
 time_step: Sep_Nov
 values {dataframe_with_row_labels}
 category 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
-male 0.000000 21352734.721381 15299927.289502 11355719.778550 8697903.653626 6852434.325498 5536225.994747 4574736.456165 3857166.730800 3311285.735630 2879794.211263 2501770.602888 2148742.604714 1822935.890245 1526072.762365 1259295.354556 1023109.740777 817357.103631 641216.803991 493244.103468 371442.503533 273367.409739 662775.143442
-female 0.000000 21352734.721381 15299927.289502 11355719.778550 8697903.653626 6852434.325498 5536225.994747 4574736.456165 3857166.730800 3311285.735630 2879794.211263 2501770.602888 2148742.604714 1822935.890245 1526072.762365 1259295.354556 1023109.740777 817357.103631 641216.803991 493244.103468 371442.503533 273367.409739 662775.143442
+male 0.000000 21352734.721382 15299927.289502 11355719.778550 8697903.653627 6852434.325498 5536225.994747 4574736.456165 3857166.730800 3311285.735630 2879794.211263 2501770.602888 2148742.604714 1822935.890245 1526072.762365 1259295.354556 1023109.740777 817357.103630 641216.803991 493244.103468 371442.503533 273367.409739 662775.143442
+female 0.000000 21352734.721382 15299927.289502 11355719.778550 8697903.653627 6852434.325498 5536225.994747 4574736.456165 3857166.730800 3311285.735630 2879794.211263 2501770.602888 2148742.604714 1822935.890245 1526072.762365 1259295.354556 1023109.740777 817357.103630 641216.803991 493244.103468 371442.503533 273367.409739 662775.143442
 *end
 
 *partition[state1]
 year: 2018
 time_step: Dec_Aug
 values {dataframe_with_row_labels}
 category 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
-male 23166379.111709 17116276.699535 12234856.831120 8053855.511927 7928562.733123 6749727.324782 4941106.844677 4889320.054517 3336544.795077 3493357.306140 2355406.162758 1779128.275752 1300672.379941 1198476.736746 980764.381909 643239.058128 515444.775398 457978.302818 439721.435000 376711.683920 259084.881637 182721.348452 227777.924571
-female 23167525.677952 17119886.400305 12242622.246415 8068024.469335 7956758.658503 6781102.637607 4962888.348235 4905658.956549 3341723.524037 3489619.923448 2345841.922178 1766374.298895 1288034.814954 1184537.685702 967696.690930 633562.496514 506901.070366 449994.305438 431965.153151 369853.603272 254210.882764 179043.707839 219482.129038
+male 23166379.111710 17116276.699535 12234856.831121 8053855.511928 7928562.733122 6749727.324782 4941106.844677 4889320.054517 3336544.795077 3493357.306140 2355406.162758 1779128.275752 1300672.379941 1198476.736746 980764.381908 643239.058128 515444.775398 457978.302818 439721.435000 376711.683920 259084.881637 182721.348452 227777.924571
+female 23167525.677952 17119886.400306 12242622.246416 8068024.469335 7956758.658503 6781102.637607 4962888.348235 4905658.956549 3341723.524037 3489619.923448 2345841.922178 1766374.298895 1288034.814954 1184537.685702 967696.690930 633562.496514 506901.070366 449994.305438 431965.153151 369853.603272 254210.882764 179043.707839 219482.129038
 *end
 
 *partition[state2]
 year: 2018
 time_step: Sep_Nov
 values {dataframe_with_row_labels}
 category 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
-male 0.000000 21264232.075721 15853262.559736 11423775.390763 7574310.324411 7504610.336059 6425618.562182 4728023.235244 4699912.905346 3220390.057577 3373404.255732 2268005.334002 1707799.486642 1244342.393761 1142423.364470 931241.592146 608185.377069 485140.389102 428940.410135 409665.713712 348964.318631 238528.087676 375426.623466
-female 0.000000 21266967.315510 15858066.780743 11432164.381390 7588304.216292 7531527.632099 6454809.556973 4747444.305218 4713452.896950 3223694.723539 3368064.094734 2257759.560659 1694910.095465 1231892.713954 1128916.258401 918747.082356 599040.365094 477149.898752 421547.938000 402557.209341 342739.841802 234146.024195 364664.159977
+male 0.000000 21264232.075721 15853262.559736 11423775.390764 7574310.324412 7504610.336059 6425618.562182 4728023.235244 4699912.905346 3220390.057577 3373404.255732 2268005.334002 1707799.486642 1244342.393761 1142423.364470 931241.592146 608185.377069 485140.389102 428940.410135 409665.713712 348964.318631 238528.087676 375426.623466
+female 0.000000 21266967.315511 15858066.780743 11432164.381390 7588304.216292 7531527.632099 6454809.556973 4747444.305218 4713452.896950 3223694.723538 3368064.094734 2257759.560659 1694910.095465 1231892.713954 1128916.258401 918747.082356 599040.365094 477149.898752 421547.938000 402557.209341 342739.841802 234146.024195 364664.159977
 *end
 
 *estimate_value[estimated_values]
@@ -5374,8 +5372,6 @@ Values {vector}
 
 *info[messages_encountered]
 Values {string}
-Setting the random number seed to 20
-Estimable parameters were set from the input configuration files
 Creating default report for catchability summerTANq
 Creating default report for catchability autumnTANq
 Creating default report for derived quantity SSB