Merge branch 'develop' into feature/libsundials

Author: syclik

Jenkinsfile

@@ -57,6 +57,10 @@ pipeline {
         OPENCL_PLATFORM_ID_CPU = 0
         OPENCL_PLATFORM_ID_GPU = 0
         PARALLEL = 4
+        GIT_AUTHOR_NAME = 'Stan Jenkins'
+        GIT_AUTHOR_EMAIL = '[email protected]'
+        GIT_COMMITTER_NAME = 'Stan Jenkins'
+        GIT_COMMITTER_EMAIL = '[email protected]'
     }
     stages {
 
@@ -85,14 +89,12 @@ pipeline {
                     usernameVariable: 'GIT_USERNAME', passwordVariable: 'GIT_PASSWORD')]) {
                     sh """#!/bin/bash
                         set -x
-                        git config user.email "[email protected]"
-                        git config user.name "Stan Jenkins"
                         git checkout -b ${branchName()}
                         clang-format --version
                         find stan test -name '*.hpp' -o -name '*.cpp' | xargs -n20 -P${PARALLEL} clang-format -i
                         if [[ `git diff` != "" ]]; then
                             git add stan test
-                            git commit --author='Stan BuildBot <[email protected]>' -m "[Jenkins] auto-formatting by `clang-format --version`"
+                            git commit -m "[Jenkins] auto-formatting by `clang-format --version`"
                             git push https://${GIT_USERNAME}:${GIT_PASSWORD}@github.com/${fork()}/math.git ${branchName()}
                             echo "Exiting build because clang-format found changes."
                             echo "Those changes are now found on stan-dev/math under branch ${branchName()}"
@@ -177,25 +179,62 @@ pipeline {
             }
         }
 
-        stage('Headers check') {
-            agent {
-                docker {
-                    image 'stanorg/ci:gpu-cpp17'
-                    label 'linux'
-                }
-            }
+        stage('Quick tests') {
             when {
                 expression {
                     !skipRemainingStages
                 }
             }
-            steps {
-                unstash 'MathSetup'
-                sh "echo CXX=${CLANG_CXX} -Werror > make/local"
-                sh "echo O=0 >> make/local"
-                sh "make -j${PARALLEL} test-headers"
+            failFast true
+            parallel {
+                stage('Headers check') {
+                    when {
+                        expression {
+                            !skipRemainingStages
+                        }
+                    }
+                    agent {
+                        docker {
+                            image 'stanorg/ci:gpu-cpp17'
+                            label 'linux'
+                        }
+                    }
+
+                    steps {
+                        unstash 'MathSetup'
+                        sh "echo CXX=${CLANG_CXX} -Werror > make/local"
+                        sh "make -j${PARALLEL} test-headers"
+                    }
+                    post { always { deleteDir() } }
+                }
+                stage('Run changed unit tests') {
+                    agent {
+                        docker {
+                            image 'stanorg/ci:gpu-cpp17'
+                            label 'linux'
+                            args '--cap-add SYS_PTRACE'
+                        }
+                    }
+                    when {
+                        allOf {
+                            expression {
+                                env.BRANCH_NAME ==~ /PR-\d+/
+                            }
+                            expression {
+                                !skipRemainingStages
+                            }
+                        }
+                    }
+                    steps {
+                        retry(3) { checkout scm }
+
+                        sh "echo CXXFLAGS += -fsanitize=address >> make/local"
+                        sh "./runTests.py -j${PARALLEL} --changed --debug"
+
+                    }
+                    post { always { retry(3) { deleteDir() } } }
+                }
             }
-            post { always { deleteDir() } }
         }
 
         stage('Full Unit Tests') {

runTests.py

@@ -87,13 +87,13 @@ def processCLIArgs():
         default=-1,
         help="number of files to split expressions tests in",
     )
-    tests_help_msg = "The path(s) to the test case(s) to run.\n"
-    tests_help_msg += "Example: 'test/unit', 'test/prob', and/or\n"
-    tests_help_msg += "         'test/unit/math/prim/fun/abs_test.cpp'"
-    parser.add_argument("tests", nargs="+", type=str, help=tests_help_msg)
     f_help_msg = "Only tests with file names matching these will be executed.\n"
     f_help_msg += "Example: '-f chol', '-f opencl', '-f prim'"
     parser.add_argument("-f", type=str, default=[], action="append", help=f_help_msg)
+    changed_help = (
+        "Use git to determine which tests may have changed, and run only those"
+    )
+    parser.add_argument("--changed", action="store_true", help=changed_help)
     parser.add_argument(
         "-d",
         "--debug",
@@ -127,6 +127,11 @@ def processCLIArgs():
         action="store_true",
         help="Build/run jumbo tests.",
     )
+
+    tests_help_msg = "The path(s) to the test case(s) to run.\n"
+    tests_help_msg += "Example: 'test/unit', 'test/prob', and/or\n"
+    tests_help_msg += "         'test/unit/math/prim/fun/abs_test.cpp'"
+    parser.add_argument("tests", nargs="*", type=str, help=tests_help_msg)
     # And parse the command line against those rules
     return parser.parse_args()
 
@@ -146,6 +151,8 @@ def isWin():
 
 batchSize = 20 if isWin() else 200
 jumboSize = 5 if isWin() else 12
+maxChangedTests = 20
+
 
 def mungeName(name):
     """Set up the makefile target name"""
@@ -306,6 +313,38 @@ def findTests(base_path, filter_names, do_jumbo=False):
     return tests
 
 
+def findChangedTests(debug):
+    import subprocess
+
+    changed_files = subprocess.run(
+        ["git", "diff", "--name-only", "origin/develop...HEAD"], text=True, capture_output=True
+    ).stdout.splitlines()
+    if debug:
+        print("Changed files:", changed_files)
+
+    # changes in prim should also test other non-prim signatures
+    test_deps = {"prim/": ["prim/", "rev/", "mix/", "fwd/"], "rev/": ["rev/", "mix/"], "fwd/": ["fwd/", "mix/"]}
+
+    changed_tests = set()
+    for f in changed_files:
+        if 'stan/' in f and f.endswith('.hpp') and 'opencl' not in f: # changed fn
+            maybe_test = f.replace('stan/', 'test/unit/').replace('.hpp', testsfx)
+            for (path, replacements) in test_deps.items():
+                if path in maybe_test:
+                    for rep in replacements:
+                        maybe_test = maybe_test.replace(path, rep)
+                        if os.path.exists(maybe_test):
+                            changed_tests.add(maybe_test)
+
+        if f.endswith(testsfx) and 'opencl' not in f:
+            changed_tests.add(f)
+
+    if len(changed_tests) > maxChangedTests:
+        stopErr("Number of changed tests excluded maximum, not running priority tests", 0)
+
+    return list(map(mungeName, changed_tests))
+
+
 def batched(tests):
     return [tests[i : i + batchSize] for i in range(0, len(tests), batchSize)]
 
@@ -357,30 +396,37 @@ def main():
             stan_mpi = "STAN_MPI" in f.read()
     except IOError:
         stan_mpi = False
-    # pass 0: generate all auto-generated tests
-    if any("test/prob" in arg for arg in inputs.tests):
-        generateTests(inputs.j)
-    tests = inputs.tests
 
     jumboFiles = []
-    if inputs.do_jumbo:
-        jumboFiles = generateJumboTests(tests, debug=inputs.debug)
-    try:
+
+    if inputs.changed:
+        tests = findChangedTests(inputs.debug)
+    else:
+        # pass 0: generate all auto-generated tests
+        if any("test/prob" in arg for arg in inputs.tests):
+            generateTests(inputs.j)
+
+        if inputs.do_jumbo:
+            jumboFiles = generateJumboTests(inputs.tests)
         if inputs.e == -1:
             if inputs.j == 1:
                 num_expr_test_files = 1
             else:
                 num_expr_test_files = inputs.j * 4
         else:
             num_expr_test_files = inputs.e
-        handleExpressionTests(tests, inputs.only_functions, num_expr_test_files)
+        handleExpressionTests(inputs.tests, inputs.only_functions, num_expr_test_files)
 
         tests = findTests(inputs.tests, inputs.f, inputs.do_jumbo)
 
-        if not tests:
-            stopErr("No matching tests found.", -1)
-        if inputs.debug:
-            print("Collected the following tests:\n", tests)
+    if not tests:
+        if inputs.changed:
+            stopErr("No changed tests were found!", 0)
+        stopErr(
+            "No matching tests found. Check the path passed on the command line", -1
+        )
+
+    try:
         # pass 1: make test executables
         for batch in batched(tests):
             if inputs.debug:
@@ -399,5 +445,6 @@ def main():
         cleanupJumboTests(jumboFiles)
         pass
 
+
 if __name__ == "__main__":
     main()

stan/math/prim/fun/asinh.hpp

@@ -65,7 +65,6 @@ inline std::complex<V> complex_asinh(const std::complex<V>& z) {
   return copysign(y, y_d);
 }
 }  // namespace internal
-
 }  // namespace math
 }  // namespace stan
 

test/unit/math/mix/fun/abs_test.cpp

@@ -14,6 +14,7 @@ TEST(mixFun, absBasics) {
   x << 1, 2, 3, 4, 5, 6;
   Eigen::Matrix<double, -1, -1> y = abs(x);
 
+  // test int -> int vectorization
   std::vector<int> u{1, 2, 3, 4};
   std::vector<int> v = abs(u);
 }