Merge pull request #66 from lbl-srg/issue64_headlessLinux

Issue64 headless linux
lbl-srg · Sep 6, 2023 · 14b485f · 14b485f
2 parents 5ea4ef9 + 342efde
commit 14b485f
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diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -12,19 +12,23 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-18.04, ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['2.7', '3.8']
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.8', '3.9']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - name: Enable Developer Command Prompt
+        uses: ilammy/[email protected]
+        if: startsWith(matrix.os, 'windows')
 
       - name: Setup cmake
-        uses: jwlawson/actions-setup-cmake@v1.8
+        uses: jwlawson/actions-setup-cmake@v1.13
         with:
-          cmake-version: '3.19.x'
+          cmake-version: '3.22.x'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -62,11 +66,12 @@ jobs:
         run: ctest -C $BUILD_TYPE --verbose
 
       - name: Push changes to remote
-        if: contains(matrix.os, 'latest') && contains(matrix.python-version, '3.8')
+        if: contains(matrix.os, 'latest') && contains(matrix.python-version, '3.9')
         run: |
           git config --global user.name $GH_USERNAME
           git config --global user.email [email protected]
+          git config --global pull.rebase false
           git add ${{ github.workspace }}/pyfunnel/lib
-          git commit -m "Add binaries" --allow-empty
+          git commit -m "Add ${{ matrix.os }} binaries" --allow-empty
           git pull
           git push
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,7 +14,7 @@
 #
 
 cmake_policy(SET CMP0048 NEW)
-cmake_minimum_required(VERSION 3.11...3.19)
+cmake_minimum_required(VERSION 3.22)
 file(READ "${CMAKE_SOURCE_DIR}/pyfunnel/VERSION" VERSION)
 project(funnel VERSION ${VERSION} LANGUAGES C)
 enable_testing()
@@ -34,17 +34,15 @@ else()
 endif()
 
 # Set compiling and linking options.
-set(UNIX_COMPILE_FLAGS "-Wall -Wextra -Werror -Wfloat-equal -Wpedantic -o3 -fPIC")
-set(WIN_COMPILE_FLAGS "/Wall /O2")
-set(UNIX_LINK_FLAGS "-fPIC")
-
-if(LINUX OR MACOSX)  # CMake 3.13.*: support for add_compile_options and add_link_options
-    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${UNIX_COMPILE_FLAGS}")
-    SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${UNIX_LINK_FLAGS}")
+if(LINUX OR MACOSX)
+    set(CMAKE_C_FLAGS "-fPIC -Wall -Wextra -Werror -Wfloat-equal -Wpedantic -O3")
+    set(CMAKE_SHARED_LINKER_FLAGS "-fPIC")
 else()
-    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${WIN_COMPILE_FLAGS}")
+    set(CMAKE_C_FLAGS "/Wall /O2")
 endif()
 
+message("CMAKE_C_FLAGS=${CMAKE_C_FLAGS}")
+
 # Set target directories.
 # NOTE: always add quotes to protect spaces in path when setting new variables.
 if (WINDOWS)
@@ -81,7 +79,8 @@ add_subdirectory(tests)
 ############################################################
 
 # Manage tests.
-include(FindPythonInterp)
+find_package (Python)
+message("Python interpreter used for testing: ${Python_EXECUTABLE}")
 set(CTEST_OUTPUT_ON_FAILURE ON)  # verbose if failed test
 set(CMAKE_TEST_DIR "${CMAKE_SOURCE_DIR}/tests")
 
@@ -102,22 +101,22 @@ add_test(
 set(TEST_ARGS_0 --reference trended.csv --test simulated.csv --atolx 0.002 --atoly 0.002 --output results)
 add_test(
     NAME test_py_0
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_0}
+    COMMAND ${Python_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_0}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 ### Wrong arguments
 set(TEST_ARGS_1 --reference wrong.csv --test simulated.csv --atolx 0.002 --atoly 0.002 --output results)
 add_test(
     NAME test_py_1
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_1}
+    COMMAND ${Python_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_1}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 set_tests_properties(test_py_1 PROPERTIES PASS_REGULAR_EXPRESSION "No such file")
 ### Wrong arguments
 set(TEST_ARGS_2 --reference trended.csv --test simulated.csv --atolx 0.002 --atoly 0.002)
 add_test(
     NAME test_py_2
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_2}
+    COMMAND ${Python_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_2}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 set_tests_properties(test_py_2 PROPERTIES PASS_REGULAR_EXPRESSION "Output directory not specified")
@@ -142,7 +141,7 @@ foreach(t RANGE ${len_tests})
     )
     add_test(
         NAME ${test_name}
-        COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_TEST_DIR}/test_numerics.py" ${test_name} ${test_dir} ${tmp_dir}
+        COMMAND ${Python_EXECUTABLE} "${CMAKE_TEST_DIR}/test_numerics.py" ${test_name} ${test_dir} ${tmp_dir}
         WORKING_DIRECTORY ${tmp_dir}
     )
     if (${test_case} MATCHES "fail4")  # WILL_FAIL shall not be used simultaneously with PASS_REGULAR_EXPRESSION!
@@ -156,15 +155,15 @@ endforeach()
 ## Plot function testing.
 add_test(
     NAME test_plot
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_TEST_DIR}/test_plot.py" "${CMAKE_TEST_DIR}/fail1/results"
+    COMMAND ${Python_EXECUTABLE} "${CMAKE_TEST_DIR}/test_plot.py" "${CMAKE_TEST_DIR}/fail1/results"
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 set_tests_properties(test_plot PROPERTIES FAIL_REGULAR_EXPRESSION "Exception;Error;Traceback")
 
 ## Configure pre/post test.
 set(summary_path "${CMAKE_TEST_DIR}/test_summary.py")
 set(CTEST_CUSTOM_POST_TEST
-    "${PYTHON_EXECUTABLE} ${summary_path} ${CMAKE_TEST_DIR}"
+    "${Python_EXECUTABLE} ${summary_path} ${CMAKE_TEST_DIR}"
 )
 set(content "# Numerics testing configuration file
     set(CTEST_CUSTOM_PRE_TEST

diff --git a/README.md b/README.md
@@ -69,7 +69,7 @@ The software is tested on the following platforms.
   * Windows x64
   * macOS
 
-A Python binding is available to access the library. It is compatible with Python 2 and 3.
+A Python binding is available to access the library. It is supported on Python versions 3.8 through 3.9.
 
 ### Installing
 
@@ -140,7 +140,7 @@ $ python ../../pyfunnel/pyfunnel.py --reference trended.csv --test simulated.csv
 
 ### System Requirements
 
-The cross-platform build system relies on CMake (version between `3.11.*` and `3.19.*`).
+The cross-platform build system relies on CMake (version `3.22`).
 
 The distributed binaries are built with Microsoft Visual Studio C/C++ compiler
 (Windows), Clang (macOS) and GCC (Linux).

diff --git a/pyfunnel/core.py b/pyfunnel/core.py
@@ -42,11 +42,13 @@
     BROWSER=None,
 )
 
-# Get the real browser name in case webbrowser.get(browser).name returns 'xdg-open' on Ubuntu.
+# Get the real browser name in case webbrowser.get(browser).name returns 'xdg-open' on Linux.
+# This is only for guarding against Chromium bug (excess logging on /var/log/syslog).
+# The browser name retrieved in LINUX_DEFAULT is not compatible with browser names from the webbrowser module.
 LINUX_DEFAULT = None
 if platform.system() == 'Linux':
     try:
-        LINUX_DEFAULT = str(subprocess.check_output('xdg-settings get default-web-browser', shell=True))
+        LINUX_DEFAULT = str(subprocess.check_output('xdg-settings get default-web-browser 2>/dev/null', shell=True))
     except BaseException:
         pass
 
@@ -359,10 +361,10 @@ def server_close(self):
             print('Could not close logger: {}'.format(e))
 
     def browse(self, *args, **kwargs):
-        """Launch server and web browser.
+        """Launch server, and web browser if available.
 
         kwargs:
-            browser (str): name of browser, see https://docs.python.org/3.8/library/webbrowser.html
+            browser (str): name of browser, see https://docs.python.org/3/library/webbrowser.html
             timeout (float): maximum time (s) before server shutdown
         """
         global CONFIG
@@ -373,44 +375,68 @@ def browse(self, *args, **kwargs):
         cmd = 'import webbrowser; webbrowser.get().open("http://localhost:{}/funnel")'.format(
             self.server_port
         )
+        launch_browser = True
         if browser is None:
             # This assignment cannot be done with browser = kwargs.pop('browser', CONFIG['BROWSER'])
             # as another module can call browse(browser=None).
+            # browser may still be None after this assignment, which means "use default browser".
             browser = CONFIG['BROWSER']
+        # We now test for the existence of a GUI browser.
+        try:
+            browser_ctrl = webbrowser.get(browser)
+            if 'BackgroundBrowser' in str(browser_ctrl.__class__):
+                launch_browser = False
+        except webbrowser.Error:
+            launch_browser = False
+
+        # Create command to launch browser in subprocess.
+        cmd = 'import webbrowser; webbrowser.get().open("http://localhost:{}/funnel")'.format(
+            self.server_port
+        )
+        # Add browser name within quotes but only if not None.
         if browser is not None:
-            webbrowser.get(browser)  # Throw exception in case of missing browser.
-            # Pass browser name within quotes.
             cmd = re.sub(r'get\(\)', 'get("{}")'.format(browser), cmd)
         webbrowser_cmd = [sys.executable, '-c', cmd]
         # Move to directory with *.csv before launching local server.
         cur_dir = os.getcwd()
         os.chdir(self._BROWSE_DIR)
+
         try:
             self.server_launch()
             # Launch browser as a subprocess command to avoid web browser error into terminal.
-            with open(os.devnull, 'w') as pipe:
-                proc = subprocess.Popen(webbrowser_cmd, stdout=pipe, stderr=pipe)
+            if launch_browser:
+                with open(os.devnull, 'w') as pipe:
+                    proc = subprocess.Popen(webbrowser_cmd, stdout=pipe, stderr=pipe)
             # Watch syslog for error.
             chrome_error = False
             if platform.system() == 'Linux':
-                if (browser is None and 'chrome' in LINUX_DEFAULT) or (
-                        browser is not None and 'chrome' in browser):
-                    with open('/var/log/syslog') as f:
-                        for l in follow(f, 2):
-                            if 'ERROR:gles2_cmd_decoder' in l:
-                                chrome_error = True
-                                break
+                if (browser is None and LINUX_DEFAULT is not None and 'chrome' in LINUX_DEFAULT) or (
+                    browser is not None and 'chrome' in browser):
+                    log_path = '/var/log/syslog'  # Ubuntu
+                    if not os.path.exists(log_path):
+                        log_path = '/var/log/messages'  # RHEL/CentOS
+                    if not os.path.exists(log_path):
+                        log_path = None
+                    if log_path is not None:
+                        with open(log_path) as f:
+                            for l in follow(f, 2):
+                                if 'ERROR:gles2_cmd_decoder' in l:
+                                    chrome_error = True
+                                    break
             if chrome_error:
                 proc.terminate()  # Terminating the process does not stop Chrome in background.
                 subprocess.check_call(['pkill', 'chrome'])  # This does.
                 inp = 'y'
                 while True:  # Prompt user to retry.
                     inp = input(
-                        ('Launching browser yields syslog errors, '
-                         'probably because Chrome is used and the display entered screensaver mode.\n'
-                         'All related processes have been killed by precaution.\n'
-                         'If you have Firefox installed and want to use it persistently, enter p\n'
-                         'Otherwise, do you simply want to retry ([y]/n/p)? '))
+                        (
+                            'Launching browser yields syslog errors, '
+                            'probably because Chrome is used and the display entered screensaver mode.\n'
+                            'All related processes have been killed by precaution.\n'
+                            'If you have Firefox installed and want to use it persistently, enter p\n'
+                            'Otherwise, do you simply want to retry ([y]/n/p)? '
+                        )
+                    )
                     if inp not in ['y', 'n', 'p']:
                         continue
                     else:
@@ -419,7 +445,7 @@ def browse(self, *args, **kwargs):
                     # Current module for future calls to the function.
                     CONFIG['BROWSER'] = 'firefox'
                     save_config()  # Configuration file for future imports.
-                    browser = 'firefox'  # Current function for immediate retry.
+                    browser = 'firefox'  # Use firefox browser for immediate retry.
                     cmd = re.sub(r'get\(.*?\)', 'get("{}")'.format(browser), cmd)
                     webbrowser_cmd = [sys.executable, '-c', cmd]
                 if inp == 'y' or inp == 'p':
@@ -429,13 +455,12 @@ def browse(self, *args, **kwargs):
                         proc = subprocess.Popen(webbrowser_cmd, stdout=pipe, stderr=pipe)
                 else:
                     raise KeyboardInterrupt
-            if timeout > 10:  # Do not pollute terminal if HTML page is served only for a short time.
-                print('Server will run for {} (s) or until KeyboardInterrupt.'.format(timeout))
+
+            print('Server will run for {} s (or until KeyboardInterrupt) at:\n'.format(timeout) + \
+                  'http://localhost:{}/funnel'.format(self.server_port))
             wait_until(exit_test, timeout, 0.1, self.logger, *args)
         except KeyboardInterrupt:
             print('KeyboardInterrupt')
-        except Exception as e:
-            print(e)
         finally:
             os.chdir(cur_dir)
             try:  # Objects may not be defined in case of exception.

diff --git a/pyfunnel/lib/darwin64/libfunnel.dylib b/pyfunnel/lib/darwin64/libfunnel.dylib
diff --git a/pyfunnel/lib/linux64/libfunnel.so b/pyfunnel/lib/linux64/libfunnel.so
diff --git a/pyfunnel/lib/win64/funnel.dll b/pyfunnel/lib/win64/funnel.dll
diff --git a/pyfunnel/lib/win64/funnel.lib b/pyfunnel/lib/win64/funnel.lib
diff --git a/requirements.txt b/requirements.txt
@@ -2,8 +2,6 @@
 six==1.14.0
 
 # Test and documentation
-pandas==1.2.4; python_version>='3.6'
-pandas==0.24.2; python_version~='2.7'
-setuptools==46.0.0; python_version>='3.6'
-setuptools==44.0.0; python_version~='2.7'
+pandas==1.2.4; python_version>='3.8'
+setuptools==46.0.0; python_version>='3.8'
 wheel
diff --git a/setup.py b/setup.py
@@ -31,16 +31,15 @@
     long_description=README,
     long_description_content_type='text/markdown',
     license="3-clause BSD",
-    python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*',
+    python_requires='>=3.8',
     install_requires=['six>=1.11'],
     packages=[MAIN_PACKAGE],
     include_package_data=True,
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
         'License :: OSI Approved :: BSD License',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.8',
         'Programming Language :: C',
         'Intended Audience :: End Users/Desktop',
         'Intended Audience :: Science/Research',

diff --git a/src/algorithmRectangle.c b/src/algorithmRectangle.c
@@ -48,7 +48,7 @@
  * --------------------
  *   creates new linked list node
  */
-node_t * createNode() {
+node_t * createNode(void) {
   node_t* temp;
   temp = malloc(sizeof(node_t));
   if (temp == NULL){

diff --git a/src/algorithmRectangle.h b/src/algorithmRectangle.h
@@ -13,7 +13,7 @@ typedef struct node {
   struct node * next;
 } node_t;
 
-node_t * createNode();
+node_t * createNode(void);
 
 node_t * addNode(node_t* head, double newVal);
 

diff --git a/src/compare.c b/src/compare.c
@@ -5,6 +5,13 @@
 #define equ(a,b) (fabs((a)-(b)) < 1e-10 ? true : false)  /* (b) required by Win32 compiler for <0 values */
 #endif
 
+/*
+*   Descriptor of the file used for logging the numerical processing errors
+*   (all other errors like memory, file access, bad argument...
+*   are still output to stderr.)
+*/
+FILE *log_file;
+
 /*
  * Function: buildPath
  * -----------------------

diff --git a/src/compare.h b/src/compare.h
@@ -15,13 +15,6 @@
 
 #define MAX 100
 
-/*
-*   Descriptor of the file used for logging the numerical processing errors
-*   (all other errors like memory, file access, bad argument...
-*   are still output to stderr.)
-*/
-FILE *log_file;
-
 /*
  * Function: compareAndReport
  * -----------------------