Merge remote-tracking branch 'origin/develop' into fix/sparse-vari-impl

Author: SteveBronder

.github/ISSUE_TEMPLATE.md

@@ -25,4 +25,4 @@ If this is a **feature request**, show what you expect to happen if the feature
 
 
 #### Current Version:
-v4.7.0
+v4.8.1

.github/workflows/header_checks.yml

@@ -27,7 +27,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 

.github/workflows/main.yml

@@ -25,7 +25,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
@@ -35,21 +35,12 @@ jobs:
     - name: Set path for Rtools40
       if: runner.os == 'Windows'
       run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
-    - name: Install mingw32-make and check toolchain path
-      if: runner.os == 'Windows'
-      run: |
-        pacman -Syu mingw-w64-x86_64-make --noconfirm
-        g++ --version
-        Get-Command g++ | Select-Object -ExpandProperty Definition
-        mingw32-make --version
-        Get-Command mingw32-make | Select-Object -ExpandProperty Definition
-      shell: powershell
 
     - name: Build Math libs
       shell: powershell
       run: |
         Add-Content make\local "O=1`n"
-        mingw32-make -f make/standalone math-libs -j2
+        make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -63,7 +54,7 @@ jobs:
         python.exe runTests.py -j2 test/unit/math/memory
 
     - name: Upload gtest_output xml
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: gtest_outputs_xml
@@ -75,7 +66,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
@@ -85,21 +76,12 @@ jobs:
     - name: Set path for Rtools40
       if: runner.os == 'Windows'
       run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
-    - name: Install mingw32-make and check toolchain path
-      if: runner.os == 'Windows'
-      run: |
-        pacman -Syu mingw-w64-x86_64-make --noconfirm
-        g++ --version
-        Get-Command g++ | Select-Object -ExpandProperty Definition
-        mingw32-make --version
-        Get-Command mingw32-make | Select-Object -ExpandProperty Definition
-      shell: powershell
 
     - name: Build Math libs
       shell: powershell
       run: |
         Add-Content make\local "O=1`n"
-        mingw32-make -f make/standalone math-libs -j2
+        make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -117,7 +99,7 @@ jobs:
         python.exe runTests.py test/unit/math/mix/*_test.cpp -j2
 
     - name: Upload gtest_output xml
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: gtest_outputs_xml
@@ -129,7 +111,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
@@ -139,21 +121,12 @@ jobs:
     - name: Set path for Rtools40
       if: runner.os == 'Windows'
       run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
-    - name: Install mingw32-make and check toolchain path
-      if: runner.os == 'Windows'
-      run: |
-        pacman -Syu mingw-w64-x86_64-make --noconfirm
-        g++ --version
-        Get-Command g++ | Select-Object -ExpandProperty Definition
-        mingw32-make --version
-        Get-Command mingw32-make | Select-Object -ExpandProperty Definition
-      shell: powershell
 
     - name: Build Math libs
       shell: powershell
       run: |
         Add-Content make\local "O=1`n"
-        mingw32-make -f make/standalone math-libs -j2
+        make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -166,19 +139,19 @@ jobs:
         python.exe runTests.py $MixFunTests[0..$HalfNumberTests]
 
     - name: Upload gtest_output xml
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: gtest_outputs_xml
         path: '**/*_test.xml'
-        
+
   mix-fun-2:
     name: mix/fun tests 2
     runs-on: windows-latest
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
@@ -188,21 +161,12 @@ jobs:
     - name: Set path for Rtools40
       if: runner.os == 'Windows'
       run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
-    - name: Install mingw32-make and check toolchain path
-      if: runner.os == 'Windows'
-      run: |
-        pacman -Syu mingw-w64-x86_64-make --noconfirm
-        g++ --version
-        Get-Command g++ | Select-Object -ExpandProperty Definition
-        mingw32-make --version
-        Get-Command mingw32-make | Select-Object -ExpandProperty Definition
-      shell: powershell
 
     - name: Build Math libs
       shell: powershell
       run: |
         Add-Content make\local "O=1`n"
-        mingw32-make -f make/standalone math-libs -j2
+        make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -215,7 +179,7 @@ jobs:
         python.exe runTests.py $MixFunTests[($HalfNumberTests + 1)..($NumberTests - 1)]
 
     - name: Upload gtest_output xml
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: gtest_outputs_xml

Jenkinsfile

@@ -4,6 +4,7 @@ import org.stan.Utils
 
 def runTests(String testPath, boolean jumbo = false) {
     try {
+        sh "cat make/local"
         if (jumbo && !params.disableJumbo) {
             sh "python3 runTests.py -j${env.PARALLEL} ${testPath} --jumbo --debug"
         } else {
@@ -141,11 +142,11 @@ pipeline {
             }
             post {
                 always {
-                    recordIssues enabledForFailure: true, tools:
-                        [cppLint(),
-                         groovyScript(parserId: 'mathDependencies', pattern: '**/dependencies.log')]
+                    recordIssues( 
+                        enabledForFailure: true, 
+                        tools: [cppLint(),groovyScript(parserId: 'mathDependencies', pattern: '**/dependencies.log')]
+                    )
                     deleteDir()
-
                 }
             }
         }
@@ -193,9 +194,11 @@ pipeline {
                     }
 
                     steps {
-                        unstash 'MathSetup'
-                        sh "echo CXX=${CLANG_CXX} -Werror > make/local"
-                        sh "make -j${PARALLEL} test-headers"
+                        retry(1){
+                            unstash 'MathSetup'
+                            sh "echo CXX=${CLANG_CXX} -Werror > make/local"
+                            sh "make -j${PARALLEL} test-headers"
+                        }
                     }
                     post { always { deleteDir() } }
                 }
@@ -342,6 +345,7 @@ pipeline {
                             runTests("test/unit/multiple_translation_units_test.cpp")
                         }
                     }
+                    post { always { retry(3) { deleteDir() } } }
                 }
             }
         }
@@ -391,13 +395,15 @@ pipeline {
                             sh "python ./test/varmat_compatibility_test.py"
                             withEnv(['PATH+TBB=./lib/tbb']) {
                                 sh "python ./test/expressions/test_expression_testing_framework.py"
+                                sh "cat make/local"
                                 try { sh "./runTests.py -j${PARALLEL} test/expressions" }
                                 finally { junit 'test/**/*.xml' }
                             }
                             sh "make clean-all"
                             sh "echo STAN_THREADS=true >> make/local"
                             withEnv(['PATH+TBB=./lib/tbb']) {
                                 try {
+                                    sh "cat make/local"
                                     sh "./runTests.py -j${PARALLEL} test/expressions --only-functions reduce_sum map_rect"
 				                }
                                 finally { junit 'test/**/*.xml' }
@@ -416,19 +422,21 @@ pipeline {
                     }
                     steps {
                         script {
-                            unstash 'MathSetup'
-                            sh "echo CXX=${CLANG_CXX} -Werror > make/local"
-                            sh "echo STAN_THREADS=true >> make/local"
-                            sh "export STAN_NUM_THREADS=4"
-                            if (isBranch('develop') || isBranch('master')) {
-                                runTests("test/unit")
-                                sh "find . -name *_test.xml | xargs rm"
-                            } else {
-                                runTests("test/unit -f thread")
-                                sh "find . -name *_test.xml | xargs rm"
-                                runTests("test/unit -f map_rect")
-                                sh "find . -name *_test.xml | xargs rm"
-                                runTests("test/unit -f reduce_sum")
+                            retry(1){
+                                unstash 'MathSetup'
+                                sh "echo CXX=${CLANG_CXX} -Werror > make/local"
+                                sh "echo STAN_THREADS=true >> make/local"
+                                sh "export STAN_NUM_THREADS=4"
+                                if (isBranch('develop') || isBranch('master')) {
+                                    runTests("test/unit")
+                                    sh "find . -name *_test.xml | xargs rm"
+                                } else {
+                                    runTests("test/unit -f thread")
+                                    sh "find . -name *_test.xml | xargs rm"
+                                    runTests("test/unit -f map_rect")
+                                    sh "find . -name *_test.xml | xargs rm"
+                                    runTests("test/unit -f reduce_sum")
+                                }
                             }
                         }
                     }
@@ -494,6 +502,7 @@ pipeline {
                                             sh "echo CXXFLAGS+=-DSTAN_PROB_TEST_ALL >> make/local"
                                         }
                                     }
+                                    sh "cat make/local"
                                     sh "./runTests.py -j${PARALLEL} ${names}"
                                 }
                                 deleteDir()
@@ -565,7 +574,10 @@ pipeline {
     post {
         always {
             node("linux") {
-                recordIssues enabledForFailure: false, tool: clang()
+                recordIssues(
+                    enabledForFailure: false, 
+                    tool: clang()
+                )
             }
         }
         success {

RELEASE-NOTES.txt

@@ -1,5 +1,41 @@
 Stan Math Library Release Notes
 
+======================================================================
+v4.8.1 (23 January 2024)
+======================================================================
+
+- The distributions defined over cholesky factors now check that their arguments are in support (#3007)
+- Fixed an issue with the `inv_wishart_cholesky_rng` function (#3007)
+
+======================================================================
+v4.8.0 (16 January 2024)
+======================================================================
+
+ - Updated Boost headers to v1.81 (#2955)
+ - Added the Dirichlet-Multinomial distribution to the Stan Math library (dirichlet_multinomial_lpmf, dirichlet_multinomial_log, and dirichlet_multinomial_rng). (#2979)
+ - `binomial_logit_glm_lpmf` distribution added (#2946)
+ - Improved numerical stability of Bernoulli CDF functions (#2784)
+ - Replaced the `std::vector`s  for read/write events in `matrix_cl` with `tbb::concurrent_vectors` (#2905)
+ - Added framework for generic higher-order autodiff support through finite-differences. (#2929)
+ - Minor cleanup of numerical stability, constants, compound functions in OpenCL kernels (#2934)
+ - Fixes aliasing issue in adjoint acccumulation for OpenCL (#2943)
+ - Improve numerical stability of `binomial_logit` distribution (#2945)
+ - Automatically detect UCRT toolchain use on Windows (#2948)
+ - Update multiple functions to delegate to the compound functions (`log1p_exp`, etc.) where possible (#2950)
+ - Fixed the RPATH to the TBB library being passed twice on the command line (#2952)
+ - Split `eigendecompose` mix tests to fix CI memory issues (#2953)
+ - Fix distribution test failures with row-vector integer inputs to bernoulli CDF functions (#2954)
+ - Simplified usage of ref-type deduction (#2958)
+ - Added OpenCL support for the `binomial_logit_glm` distribution (#2960)
+ - Fixed a build configuration issue where the optional tbbmalloc and tbbmalloc_proxy libraries were built unconditionally. (#2969)
+ - Remove unused meta requires (#2976)
+ - Bugfix for uninitialized `var_value<Matrix>` types and assignment when the rhs of the assignment is an expression (#2978)
+ - Invert the input matrix in-place which reduces the memory requirement for this function. (#2981)
+ - Fixes the rng function for the Inverse Wishart Cholesky distribution. (#2984)
+ - Fixed a compilation issue with the `check_symmetric` function on complex-valued inputs under LLVM 17 (#2991)
+ - Fixed missing include guard for OpenCL rev headers (#2996)
+ - Add helpful context to the failure message for the ad testing framework (#2997)
+
 ======================================================================
 v4.7.0 (5 September 2023)
 ======================================================================

benchmarks/benchmark.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 from __future__ import print_function
 
 import itertools

doxygen/doxygen.cfg

@@ -48,7 +48,7 @@ PROJECT_NAME           = "Stan Math Library"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.7.0
+PROJECT_NUMBER         = 4.8.1
 
 # 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