Update master to Release/v2.35.0 (#3292)

.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:
-v2.34.1
+v2.35.0

Jenkinsfile

@@ -96,7 +96,7 @@ pipeline {
         preserveStashes(buildCount: 7)
         parallelsAlwaysFailFast()
         buildDiscarder(logRotator(numToKeepStr: '20', daysToKeepStr: '30'))
-        disableConcurrentBuilds(abortPrevious: env.BRANCH_NAME != "downstream_tests" || env.BRANCH_NAME != "downstream_hotfix")
+        disableConcurrentBuilds(abortPrevious: env.BRANCH_NAME != "downstream_tests" && env.BRANCH_NAME != "downstream_hotfix")
     }
     environment {
         GCC = 'g++'
@@ -192,19 +192,17 @@ pipeline {
             }
             post {
                 always {
-
-                    recordIssues id: "lint_doc_checks",
-                    name: "Linting & Doc checks",
-                    enabledForFailure: true,
-                    aggregatingResults : true,
-                    tools: [
-                        cppLint(id: "cpplint", name: "Linting & Doc checks@CPPLINT")
-                    ],
-                    blameDisabled: false,
-                    qualityGates: [[threshold: 1, type: 'TOTAL', unstable: true]],
-                    healthy: 10, unhealthy: 100, minimumSeverity: 'HIGH',
-                    referenceJobName: env.BRANCH_NAME
-
+                    recordIssues(
+                        id: "lint_doc_checks",
+                        name: "Linting & Doc checks",
+                        enabledForFailure: true,
+                        aggregatingResults : true,
+                        tools: [
+                            cppLint(id: "cpplint", name: "Linting & Doc checks@CPPLINT")
+                        ],
+                        qualityGates: [[threshold: 1, type: 'TOTAL', unstable: true]],
+                        healthy: 10, unhealthy: 100, minimumSeverity: 'HIGH'
+                    )
                     deleteDir()
                 }
             }
@@ -266,8 +264,8 @@ pipeline {
                                 SET \"PATH=C:\\PROGRA~1\\R\\R-4.1.2\\bin;%PATH%\"
                                 SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
                                 SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
-                                mingw32-make.exe -f lib/stan_math/make/standalone math-libs
-                                mingw32-make.exe -j${PARALLEL} test-headers
+                                make.exe -f lib/stan_math/make/standalone math-libs
+                                make.exe -j${PARALLEL} test-headers
                             """
                             setupCXX(false, WIN_CXX, stanc3_bin_url())
                             runTestsWin("src/test/unit")
@@ -450,7 +448,7 @@ pipeline {
                                 SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
                                 SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
                                 cd performance-tests-cmdstan/cmdstan
-                                mingw32-make.exe -j${PARALLEL} build
+                                make.exe -j${PARALLEL} build
                                 cd ..
                                 python ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 stanc3/test/integration/good
                                 python ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 example-models
@@ -498,21 +496,21 @@ pipeline {
     post {
         always {
             node("linux") {
-                recordIssues id: "pipeline",
-                name: "Entire pipeline results",
-                enabledForFailure: true,
-                aggregatingResults : false,
-                filters: [
-                    excludeFile('lib/.*')
-                ],
-                tools: [
-                    gcc4(id: "pipeline_gcc4", name: "GNU C Compiler"),
-                    clang(id: "pipeline_clang", name: "LLVM/Clang")
-                ],
-                blameDisabled: false,
-                qualityGates: [[threshold: 30, type: 'TOTAL', unstable: true]],
-                healthy: 10, unhealthy: 100, minimumSeverity: 'HIGH',
-                referenceJobName: env.BRANCH_NAME
+                recordIssues(
+                    id: "pipeline",
+                    name: "Entire pipeline results",
+                    enabledForFailure: true,
+                    aggregatingResults : false,
+                    filters: [
+                        excludeFile('lib/.*')
+                    ],
+                    tools: [
+                        gcc4(id: "pipeline_gcc4", name: "GNU C Compiler"),
+                        clang(id: "pipeline_clang", name: "LLVM/Clang")
+                    ],
+                    qualityGates: [[threshold: 30, type: 'TOTAL', unstable: true]],
+                    healthy: 10, unhealthy: 100, minimumSeverity: 'HIGH'
+                )
             }
         }
         success {

RELEASE-NOTES.txt

@@ -5,6 +5,17 @@ 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).
 
+v2.35.0 (3 June 2024)
+======================================================================
+
+ - The algorithms no longer catch `std::exception` unconditionally. The Math library uses `std::domain_error` for recoverable errors, and these are the ones which are caught. (#3259)
+ - Allow laplace sampling without evaluating `log_prob` for each draw. (#3261)
+ - Allow laplace sampling to save the Hessian as a diagnostic output. (#3261)
+ - Stan's RNG usages now uses a type definition `stan::rng_t` rather than hard coding a specific Boost RNG. (#3263)
+ - Switched the pRNG used by default in the services and tests to be `boost::mixmax`. Note that this means seeds from previous versions will lead to different numerical results in this version. (#3264)
+ - Add a new ranked R-hat diagnostic from [Vehtari](https://arxiv.org/abs/1903.08008). (#3266)
+ - Fixed an issue where Pathfinder would sometimes return more draws than requested. (#3279)
+
 v2.34.1 (23 January 2024)
 ======================================================================
 

make/tests

@@ -85,12 +85,15 @@ HEADER_TESTS := $(addsuffix -test,$(call findfiles,src/stan,*.hpp))
 
 ifeq ($(OS),Windows_NT)
   DEV_NULL = nul
+  ifeq ($(IS_UCRT),true)
+    UCRT_NULL_FLAG = -S
+  endif
 else
   DEV_NULL = /dev/null
 endif
 
 %.hpp-test : %.hpp test/dummy.cpp
-	$(COMPILE.cpp) -O0 -include $^ -o $(DEV_NULL)
+	$(COMPILE.cpp) -O0 -include $^ $(UCRT_NULL_FLAG) -o $(DEV_NULL)
 
 test/dummy.cpp:
 	@mkdir -p test

runTests.py

@@ -80,8 +80,6 @@ def doCommand(command, exit_on_failure=True):
     """Run command as a shell command and report/exit on errors."""
     print("------------------------------------------------------------")
     print("%s" % command)
-    if isWin() and command.startswith("make "):
-        command = command.replace("make ", "mingw32-make ")
     p1 = subprocess.Popen(command, shell=True)
     p1.wait()
     if exit_on_failure and (not (p1.returncode is None) and not (p1.returncode == 0)):

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         = 2.34.1
+PROJECT_NUMBER         = 2.35.0
 
 # 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