Merge pull request #3226 from stan-dev/release/v2.33.0

Merge release v2.33.0 into master

.github/ISSUE_TEMPLATE.md

@@ -24,4 +24,4 @@ Describe what you expect the output to be. Knowing the correct behavior is also
 Provide any additional information here.
 
 #### Current Version:
-v2.32.2
+v2.33.0

Jenkinsfile

@@ -3,6 +3,7 @@ import org.stan.Utils
 
 def utils = new org.stan.Utils()
 def skipRemainingStages = false
+def skipOpenCL = false
 
 def setupCXX(failOnError = true, CXX = CXX, String stanc3_bin_url = "nightly") {
     errorStr = failOnError ? "-Werror " : ""
@@ -105,6 +106,11 @@ pipeline {
         GIT_AUTHOR_EMAIL = '[email protected]'
         GIT_COMMITTER_NAME = 'Stan Jenkins'
         GIT_COMMITTER_EMAIL = '[email protected]'
+        OPENCL_DEVICE_ID_CPU = 0
+        OPENCL_DEVICE_ID_GPU = 0
+        OPENCL_PLATFORM_ID = 1
+        OPENCL_PLATFORM_ID_CPU = 0
+        OPENCL_PLATFORM_ID_GPU = 0
     }
     stages {
 
@@ -236,6 +242,9 @@ pipeline {
                     ].join(" ")
 
                     skipRemainingStages = utils.verifyChanges(paths)
+
+                    def openCLPaths = ['src/stan/model/indexing'].join(" ")
+                    skipOpenCL = utils.verifyChanges(openCLPaths)
                 }
             }
             post {
@@ -255,9 +264,6 @@ pipeline {
                     agent { label 'windows' }
                     when {
                         expression {
-                            ( env.BRANCH_NAME == "develop" ||
-                            env.BRANCH_NAME == "master" ||
-                            params.run_tests_all_os ) &&
                             !skipRemainingStages
                         }
                     }
@@ -284,13 +290,20 @@ pipeline {
                         docker {
                             image 'stanorg/ci:gpu'
                             label 'linux'
-                            args '--pull always'
+                            args '--pull always --gpus 1'
                         }
                     }
                     steps {
                         unstash 'StanSetup'
                         setupCXX(true, LINUX_CXX, stanc3_bin_url())
-                        sh "make -j${PARALLEL} test-headers"
+                        sh """
+                            echo STAN_OPENCL=true > make/local
+                            echo OPENCL_PLATFORM_ID=${OPENCL_PLATFORM_ID_GPU} >> make/local
+                            echo OPENCL_DEVICE_ID=${OPENCL_DEVICE_ID_GPU} >> make/local
+                        """
+                        sh """
+                            make -j${PARALLEL} test-headers
+                        """
                         runTests("src/test/unit")
                     }
                     post { always { deleteDir() } }
@@ -425,9 +438,6 @@ pipeline {
                     agent { label 'windows' }
                     when {
                         expression {
-                            ( env.BRANCH_NAME == "develop" ||
-                            env.BRANCH_NAME == "master" ||
-                            params.run_tests_all_os ) &&
                             !skipRemainingStages
                         }
                     }
@@ -504,7 +514,7 @@ pipeline {
                 enabledForFailure: true,
                 aggregatingResults : false,
                 filters: [
-                    excludeFile('/lib/.*')
+                    excludeFile('lib/.*')
                 ],
                 tools: [
                     gcc4(id: "pipeline_gcc4", name: "GNU C Compiler"),

RELEASE-NOTES.txt

@@ -5,6 +5,21 @@ Note: these are the release notes for the stan-dev/stan repository.
 Further changes may arise at the interface level (stan-dev/{rstan,
 pystan, cmdstan}) and math library level (stan-dev/math).
 
+v2.33.0 (5 September 2023)
+======================================================================
+
+- Added Pathfinder and Multi-pathfinder to the service APIs. (#3123, #3205)
+- Added the `unconstrain_array` method to the model base class as the inverse of `write_array`. (#3179, #3211)
+- Support Tuple indices in Stan CSV Header Reader. (#3190)
+- Add callback writer to output JSON data for diagnostics. (#3191, #3202)
+- Replace use of `boost::lexical_cast` with `std::strol`, etc, and remove spurious header includes. (#3206)
+- Fixed several typos in documentation. (#3210)
+- Added multi chain service functions for hmc nuts for adapatation and nonadaption for the unit e, diag, and dense metrics. (#3212)
+- Made the service functions consistently catch exceptions and favor return codes. (#3214)
+- Added a hard copy of the event vector for OpenCL before making a copy to go from a tbb concurrent vector to a standard vector. (#3217)
+- Added missing size checks to vectors of Eigen types. (#3218)
+- Remove deprecated syntax from remaining tests. (#3220)
+
 v2.32.2 (15 May 2023)
 ======================================================================
 

make/tests

@@ -173,23 +173,22 @@ test/integration/libmtu_%.so : test/integration/mtu/%_1.o test/integration/mtu/%
 
 test/integration/multiple_translation_units_test$(EXE) : test/integration/libmtu_model.so test/integration/libmtu_mcmc.so
 
-
 ############################################################
 ##
 # Use the stanc compiler to generate C++ from Stan programs
 ##
 TEST_MODELS = $(call findfiles,src/test/test-models,*.stan)
 $(patsubst src/%.stan,%.hpp,$(TEST_MODELS)) : test/test-models/%.hpp : src/test/test-models/%.stan bin/stanc$(EXE)
 	@mkdir -p $(dir $@)
-	$(WINE) bin/stanc$(EXE) $< --o=$@
+	$(WINE) bin/stanc$(EXE) $(STANCFLAGS) $< --o=$@
 
 ##
 # Generate C++ from Stan standalone functions
 ##
 TEST_FUNCTIONS = $(call findfiles,src/test/test-models,*.stanfuncs)
 $(patsubst src/%.stanfuncs,%.hpp,$(TEST_FUNCTIONS)) : test/test-models/%.hpp : src/test/test-models/%.stanfuncs bin/stanc$(EXE)
 	@mkdir -p $(dir $@)
-	$(WINE) bin/stanc$(EXE) --standalone-functions $< --o=$@
+	$(WINE) bin/stanc$(EXE) $(STANCFLAGS) --standalone-functions $< --o=$@
 
 ##
 # Compile models depends on every model within

src/doxygen/doxygen-footer.html

@@ -1,5 +1,5 @@
 <hr/>
-<div class="conents" style="font-size:80%;">
+<div class="contents" style="font-size:80%;">
   <span style="float:left; margin=0 1em 0 1em;">
   &nbsp;&nbsp;&nbsp;&nbsp;
   [ <a href="http://mc-stan.org/">Stan Home Page</a> ]

src/doxygen/doxygen.cfg

@@ -38,7 +38,7 @@ PROJECT_NAME           = "Stan"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.32.2
+PROJECT_NUMBER         = 2.33.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -1076,7 +1076,7 @@ HTML_STYLESHEET        =
 # cascading style sheets that are included after the standard style sheets
 # created by doxygen. Using this option one can overrule certain style aspects.
 # This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefor more robust against future updates.
+# standard style sheet and is therefore more robust against future updates.
 # Doxygen will copy the style sheet files to the output directory.
 # Note: The order of the extra stylesheet files is of importance (e.g. the last
 # stylesheet in the list overrules the setting of the previous ones in the
@@ -1619,8 +1619,8 @@ EXTRA_PACKAGES         = amsmath
 # Note: Only use a user-defined header if you know what you are doing! The
 # following commands have a special meaning inside the header: $title,
 # $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
-# for the replacement values of the other commands the user is refered to
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty string,
+# for the replacement values of the other commands the user is referred to
 # HTML_HEADER.
 # This tag requires that the tag GENERATE_LATEX is set to YES.