Fixes for FreeBSD

src/bout++.cxx

@@ -67,11 +67,10 @@ const char DEFAULT_DIR[] = "data";
 
 #include <csignal>
 #include <ctime>
+#include <filesystem>
 #include <string>
 #include <vector>
 
-#include <sys/stat.h>
-
 // Value passed at compile time
 // Used for MD5SUM, BOUT_LOCALE_PATH, and REVISION
 #define BUILDFLAG1_(x) #x
@@ -81,12 +80,6 @@ const char DEFAULT_DIR[] = "data";
 #define INDIRECT0_BOUTMAIN(...) INDIRECT1_BOUTMAIN(#__VA_ARGS__)
 #define STRINGIFY(a) INDIRECT0_BOUTMAIN(a)
 
-// Define S_ISDIR if not defined by system headers (that is, MSVC)
-// Taken from https://github.com/curl/curl/blob/e59540139a398dc70fde6aec487b19c5085105af/lib/curl_setup.h#L748-L751
-#if !defined(S_ISDIR) && defined(S_IFMT) && defined(S_IFDIR)
-#define S_ISDIR(m) (((m) & S_IFMT) == S_IFDIR)
-#endif
-
 #ifdef _MSC_VER
 #include <windows.h>
 inline auto getpid() -> int { return GetCurrentProcessId(); }
@@ -506,9 +499,8 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
 }
 
 void checkDataDirectoryIsAccessible(const std::string& data_dir) {
-  struct stat test;
-  if (stat(data_dir.c_str(), &test) == 0) {
-    if (!S_ISDIR(test.st_mode)) {
+  if (std::filesystem::exists(data_dir)) {
+    if (!std::filesystem::is_directory(data_dir)) {
       throw BoutException(_("DataDir \"{:s}\" is not a directory\n"), data_dir);
     }
   } else {

tests/integrated/test-backtrace/CMakeLists.txt

@@ -1,5 +1,6 @@
 bout_add_integrated_test(test-backtrace
   SOURCES boutexcept.cxx
   REQUIRES BOUT_USE_BACKTRACE
+  CONFLICTS CMAKE_SYSTEM_NAME MATCHES "FreeBSD"
   USE_RUNTEST
   )

tests/integrated/test-bout-override-default-option/runtest

@@ -1,3 +1,3 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 make && ./test-bout-override-default-option

tests/integrated/test-code-style/runtest

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #requires not make
 

tests/integrated/test-command-args/runtest

@@ -5,18 +5,22 @@ import os
 import re
 import shutil
 import unittest
+import platform
+
+
+OUTPUT_FILE = "stdout.log" if platform.system() == "FreeBSD" else "stderr.log"
 
 
 class TestCommandLineArgs(unittest.TestCase):
-    command = "./command-args 2>stderr.log"
+    command = "./command-args >stdout.log 2>stderr.log"
 
     def makeDirAndCopyInput(self, path):
         os.mkdir(path)
         shutil.copy("BOUT.inp", path)
 
     def setUp(self):
         try:
-            os.remove("stderr.log")
+            os.remove(OUTPUT_FILE)
         except OSError:
             pass
         shutil.rmtree("./data", ignore_errors=True)
@@ -29,7 +33,7 @@ class TestCommandLineArgs(unittest.TestCase):
     def testNoArgumentsNoDirectory(self):
         with self.assertRaises(RuntimeError):
             launch_safe(self.command, pipe=True, nproc=1, mthread=1)
-        with open("stderr.log") as f:
+        with open(OUTPUT_FILE) as f:
             contents = f.read()
             self.assertIn(
                 '"data" does not exist',
@@ -97,7 +101,7 @@ class TestCommandLineArgs(unittest.TestCase):
             launch_safe(
                 self.command + " -d non_existent", pipe=True, nproc=1, mthread=1
             )
-        with open("stderr.log") as f:
+        with open(OUTPUT_FILE) as f:
             contents = f.read()
             self.assertIn(
                 '"non_existent" does not exist',
@@ -108,7 +112,7 @@ class TestCommandLineArgs(unittest.TestCase):
     def testDirectoryArgumentNonDirectory(self):
         with self.assertRaises(RuntimeError):
             launch_safe(self.command + " -d runtest", pipe=True, nproc=1, mthread=1)
-        with open("stderr.log") as f:
+        with open(OUTPUT_FILE) as f:
             contents = f.read()
             self.assertIn(
                 '"runtest" is not a directory',
@@ -175,21 +179,24 @@ class TestCommandLineArgs(unittest.TestCase):
             "--foo_flag",
             "some:option=value",
         ]
-        _, out = launch_safe(
+        launch_safe(
             self.command + " " + " ".join(extra_options), pipe=True, nproc=1, mthread=1
         )
 
-        command_line_options = None
-        for line in out.splitlines():
-            if line.lstrip().startswith("Command line"):
-                command_line_options = line
+        with open("stdout.log") as f:
+            contents = f.read()
 
-        for option in extra_options:
-            self.assertIn(
-                option,
-                command_line_options,
-                msg="FAIL: option {} not printed out".format(option),
-            )
+            command_line_options = None
+            for line in contents.splitlines():
+                if line.lstrip().startswith("Command line"):
+                    command_line_options = line
+
+            for option in extra_options:
+                self.assertIn(
+                    option,
+                    command_line_options,
+                    msg="FAIL: option {} not printed out".format(option),
+                )
 
 
 if __name__ == "__main__":

tests/integrated/test-compile-examples-petsc/runtest

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #requires: all_tests
 #requires: not make

tests/integrated/test-compile-examples/runtest

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #requires: all_tests
 #requires: not make

tests/integrated/test-coordinates-initialization/runtest

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # Cores: 3
 

tests/integrated/test-drift-instability/qsubcase.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # Create a set of runs and submit to a queueing system e.g. Sun Grid Engine
 #

tests/integrated/test-include/runtest

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #requires: all_tests
 #Requires: not make

tests/integrated/test-interchange-instability/qsubcase.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 QSUB=mpich2sub # Common values are qsub, mpisub  
 NP=4

tests/integrated/test-stopCheck/runtest

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 make || exit
 

tests/unit/src/test_bout++.cxx

@@ -70,7 +70,7 @@ class SignalHandlerTest : public ::testing::Test {
 
 using SignalHandlerTestDeathTest = SignalHandlerTest;
 
-#if !defined(__NVCC__)
+#if !defined(__NVCC__) and !defined(__FreeBSD__)
 TEST_F(SignalHandlerTestDeathTest, SegFault) {
   bout::experimental::setupSignalHandler(bout::experimental::defaultSignalHandler);
   // This test is *incredibly* expensive, maybe as much as 1s, so only test the one signal

tests/unit/sys/test_timer.cxx

@@ -271,7 +271,7 @@ TEST(TimerTest, ListAllInfo) {
 
   using namespace ::testing;
   EXPECT_THAT(cout_capture.str(), HasSubstr("Timer name         |"));
-  EXPECT_THAT(cout_capture.str(), ContainsRegex("one *| 0\\.\\d+ | 1    | 0\\.\\d+"));
-  EXPECT_THAT(cout_capture.str(), ContainsRegex("two *| 0 * | 2    | 0\\.\\d+"));
+  EXPECT_THAT(cout_capture.str(), ContainsRegex("one *| 0\\.[0-9]+ | 1    | 0\\.[0-9]+"));
+  EXPECT_THAT(cout_capture.str(), ContainsRegex("two *| 0 * | 2    | 0\\.[0-9]+"));
 }
 #endif