Merge branch 'release-1.0.12'

.gitignore

@@ -9,3 +9,4 @@ dist/
 Tests/FunctionalTests/Jobs
 /.gitignore
 /MANIFEST
+.settings

.gitlab-ci.yml

@@ -77,7 +77,7 @@ build:osx:
     - build
     expire_in: 1 day
   tags:
-    - mac
+    - macmini2
 
 test:osx:
   stage: test
@@ -95,7 +95,7 @@ test:osx:
   dependencies:
     - build:osx
   tags:
-    - mac
+    - macmini2
 
 deploy:osx:
   stage: deploy
@@ -110,7 +110,7 @@ deploy:osx:
     paths:
      - BuildServer/Darwin/Build/*.dmg
   tags:
-    - mac
+    - macmini2
 
 # # windows 7 pipeline
 

BuildServer/Darwin/Scripts/build.py

@@ -17,7 +17,7 @@ if sys.platform.startswith('darwin'):
         u'LSApplicationCategoryType': u'public.app-category.science'
     }
     OPTIONS = {
-        'argv_emulation': True,
+        'argv_emulation': False,# has to be False otherwise triggers problems zith wxPython which lose some events that are captured by OS
         'iconfile': u'../../../MDANSE/GUI/Icons/mdanse.icns',
         'excludes': 'PyQt4',
 		'matplotlib_backends': '-',
@@ -26,14 +26,15 @@ if sys.platform.startswith('darwin'):
         'bdist_base': '../Build/build',
         'dist_dir': '../Build/dist',
         'graph': False,
-        'xref': False
+        'xref': False,
+        'packages' : ["MDANSE","MMTK","Scientific"]
     }
 
     setup(
-        name="MDANSE",
+        name='MDANSE',
         app=APP,
         options={'py2app': OPTIONS},
         setup_requires=['py2app']
     )
 else:
-   print 'No build_app implementation for your system.'
+    print 'No build_app implementation for your system.'

BuildServer/Darwin/Scripts/change_dylib_path.sh

+#!/bin/bash
+
+files=`ls ./dist/MDANSE.app/Contents/Frameworks/libwx*.dylib`
+
+libs="osx_cocoau_xrc osx_cocoau_webview osx_cocoau_html osx_cocoau_qa osx_cocoau_adv osx_cocoau_core baseu_xml baseu_net baseu"
+
+for f in $files
+do
+    chmod 777 $f
+    for l in $libs
+    do
+        install_name_tool -change /usr/local/lib/libwx_$l-3.0.dylib @executable_path/../Frameworks/libwx_$l-3.0.dylib $f
+    done
+done
+

BuildServer/Darwin/Scripts/run_build.sh

@@ -11,7 +11,7 @@ ROUGE="\\033[1;31m"
 BLEU="\\033[1;34m"
 
 ##Select the build target
-BUILD_TARGET=darwin
+
 
 # take the latest version of nmoldyn available on the forge
 echo -e "$BLEU""Getting last MDANSE revision" "$NORMAL"
@@ -31,10 +31,10 @@ rm -rf build
 rm -rf dist
 
 # Remove previous install of MDANSE
-rm /usr/local/bin/mdanse*
-rm /usr/local/lib/python2.7/site-packages/MDANSE*.egg-info
-rm -rf /usr/local/lib/python2.7/site-packages/MDANSE
+rm /Library/Frameworks/Python.framework/Versions/2.7/bin/mdanse*
+rm /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MDANSE*.egg-info
+rm -rf /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MDANSE
 
 # Build and install MDANSE to the homebrewed python
-/usr/local/bin/python setup.py build >> BuildServer/Darwin/Scripts/build_log.txt 2>&1
-/usr/local/bin/python setup.py install >> BuildServer/Darwin/Scripts/build_log.txt 2>&1
+/Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py build >> BuildServer/Darwin/Scripts/build_log.txt 2>&1
+/Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install >> BuildServer/Darwin/Scripts/build_log.txt 2>&1

BuildServer/Darwin/Scripts/run_deploy.sh

@@ -36,7 +36,7 @@ export DISTUTILS_DEBUG=0
 
 cd BuildServer/Darwin/Scripts
 
-/usr/local/bin/python build.py py2app >> build_log.txt 2>&1
+/usr/local/bin/python build.py py2app
 
 rc=$?
 if [[ $rc != 0 ]]; then
@@ -63,6 +63,25 @@ hdiutil unmount /Volumes/MDANSE -force -quiet
 
 sleep 5
 
+# When launching the bundle, the executable target (i.e. MDANSE) modify the python that is shipped with the bundle (si.e. package path, dylib dependencies ...)
+# see http://joaoventura.net/blog/2016/embeddable-python-osx/ for technical details
+# In our case we also want the user to be able to start directly python without launching the bundle executable (e.g. to run scripts in command line) which is the reason
+# why we have to modify the python executable appropriately with the following commands
+cp -r /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ ./dist/MDANSE.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7
+rm -rf ./dist/MDANSE.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/*
+cp /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python ./dist/MDANSE.app/Contents/MacOS/python
+cp /Library/Frameworks/Python.framework/Versions/2.7/Python ./dist/MDANSE.app/Contents/Frameworks/Python.framework/Versions/2.7/libpython2.7.dylib
+install_name_tool -change /Library/Frameworks/Python.framework/Versions/2.7/Python @executable_path/../Frameworks/Python.framework/Versions/2.7/libpython2.7.dylib ./dist/MDANSE.app/Contents/MacOS/python
+chmod 777 ./dist/MDANSE.app/Contents/Frameworks/Python.framework/Versions/2.7/libpython2.7.dylib
+install_name_tool -id @executable_path/../Frameworks/Python.framework/Versions/2.7/libpython2.7.dylib ./dist/MDANSE.app/Contents/Frameworks/Python.framework/Versions/2.7/libpython2.7.dylib
+
+# In order that the modified python in the bundle import the zipped sitepackages located in Contents/Resources we provide a modified site.py that will
+# update the sys.path accordingly
+cp ../Scripts/site.py ./dist/MDANSE.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/.
+
+chmod 777 ../Scripts/change_dylib_path.sh
+../Scripts/change_dylib_path.sh
+
 ../Tools/create-dmg/create-dmg --background "../Resources/background.jpg" --volname "MDANSE" --window-pos 200 120 --window-size 800 400 --icon MDANSE.app 200 190 --hide-extension MDANSE.app --app-drop-link 600 185 "${MDANSE_DMG}" ./dist
 
 exit

BuildServer/Darwin/Scripts/run_tests.sh

@@ -4,7 +4,7 @@ ROUGE="\\033[1;31m"
 
 # Performs the unit tests
 cd Tests/UnitTests
-nosetests --verbosity=3 -P .
+/Library/Frameworks/Python.framework/Versions/2.7/bin/nosetests --verbosity=3 -P .
 # Exit now if unable to run tests
 if [ $? -ne 0 ]; then
 	status = $?
@@ -14,8 +14,8 @@ fi
 cd ../..
 
 cd Tests/FunctionalTests/Jobs
-python BuildJobTests.py
-nosetests --verbosity=3 --exe -P .
+/Library/Frameworks/Python.framework/Versions/2.7/bin/python BuildJobTests.py
+/Library/Frameworks/Python.framework/Versions/2.7/bin/nosetests --verbosity=3 --exe -P .
 if [ $? -ne 0 ]; then
 	status=$?
 	echo -e "$ROUGE""One or several functional tests failed"

BuildServer/Darwin/Scripts/site.py

+"""Append module search paths for third-party packages to sys.path.
+
+****************************************************************
+* This module is automatically imported during initialization. *
+****************************************************************
+
+In earlier versions of Python (up to 1.5a3), scripts or modules that
+needed to use site-specific modules would place ``import site''
+somewhere near the top of their code.  Because of the automatic
+import, this is no longer necessary (but code that does it still
+works).
+
+This will append site-specific paths to the module search path.  On
+Unix (including Mac OSX), it starts with sys.prefix and
+sys.exec_prefix (if different) and appends
+lib/python<version>/site-packages as well as lib/site-python.
+On other platforms (such as Windows), it tries each of the
+prefixes directly, as well as with lib/site-packages appended.  The
+resulting directories, if they exist, are appended to sys.path, and
+also inspected for path configuration files.
+
+A path configuration file is a file whose name has the form
+<package>.pth; its contents are additional directories (one per line)
+to be added to sys.path.  Non-existing directories (or
+non-directories) are never added to sys.path; no directory is added to
+sys.path more than once.  Blank lines and lines beginning with
+'#' are skipped. Lines starting with 'import' are executed.
+
+For example, suppose sys.prefix and sys.exec_prefix are set to
+/usr/local and there is a directory /usr/local/lib/python2.5/site-packages
+with three subdirectories, foo, bar and spam, and two path
+configuration files, foo.pth and bar.pth.  Assume foo.pth contains the
+following:
+
+  # foo package configuration
+  foo
+  bar
+  bletch
+
+and bar.pth contains:
+
+  # bar package configuration
+  bar
+
+Then the following directories are added to sys.path, in this order:
+
+  /usr/local/lib/python2.5/site-packages/bar
+  /usr/local/lib/python2.5/site-packages/foo
+
+Note that bletch is omitted because it doesn't exist; bar precedes foo
+because bar.pth comes alphabetically before foo.pth; and spam is
+omitted because it is not mentioned in either path configuration file.
+
+After these path manipulations, an attempt is made to import a module
+named sitecustomize, which can perform arbitrary additional
+site-specific customizations.  If this import fails with an
+ImportError exception, it is silently ignored.
+
+"""
+
+import sys
+import os
+import __builtin__
+import traceback
+
+# Prefixes for site-packages; add additional prefixes like /usr/local here
+PREFIXES = [sys.prefix, sys.exec_prefix]
+# Enable per user site-packages directory
+# set it to False to disable the feature or True to force the feature
+ENABLE_USER_SITE = None
+
+# for distutils.commands.install
+# These values are initialized by the getuserbase() and getusersitepackages()
+# functions, through the main() function when Python starts.
+USER_SITE = None
+USER_BASE = None
+
+
+def makepath(*paths):
+    dir = os.path.join(*paths)
+    try:
+        dir = os.path.abspath(dir)
+    except OSError:
+        pass
+    return dir, os.path.normcase(dir)
+
+
+def abs__file__():
+    """Set all module' __file__ attribute to an absolute path"""
+    for m in sys.modules.values():
+        if hasattr(m, '__loader__'):
+            continue   # don't mess with a PEP 302-supplied __file__
+        try:
+            m.__file__ = os.path.abspath(m.__file__)
+        except (AttributeError, OSError):
+            pass
+
+
+def removeduppaths():
+    """ Remove duplicate entries from sys.path along with making them
+    absolute"""
+    # This ensures that the initial path provided by the interpreter contains
+    # only absolute pathnames, even if we're running from the build directory.
+    L = []
+    known_paths = set()
+    for dir in sys.path:
+        # Filter out duplicate paths (on case-insensitive file systems also
+        # if they only differ in case); turn relative paths into absolute
+        # paths.
+        dir, dircase = makepath(dir)
+        if not dircase in known_paths:
+            L.append(dir)
+            known_paths.add(dircase)
+    sys.path[:] = L
+    return known_paths
+
+
+def _init_pathinfo():
+    """Return a set containing all existing directory entries from sys.path"""
+    d = set()
+    for dir in sys.path:
+        try:
+            if os.path.isdir(dir):
+                dir, dircase = makepath(dir)
+                d.add(dircase)
+        except TypeError:
+            continue
+    return d
+
+
+def addpackage(sitedir, name, known_paths):
+    """Process a .pth file within the site-packages directory:
+       For each line in the file, either combine it with sitedir to a path
+       and add that to known_paths, or execute it if it starts with 'import '.
+    """
+    if known_paths is None:
+        _init_pathinfo()
+        reset = 1
+    else:
+        reset = 0
+    fullname = os.path.join(sitedir, name)
+    try:
+        f = open(fullname, "rU")
+    except IOError:
+        return
+    with f:
+        for n, line in enumerate(f):
+            if line.startswith("#"):
+                continue
+            try:
+                if line.startswith(("import ", "import\t")):
+                    exec line
+                    continue
+                line = line.rstrip()
+                dir, dircase = makepath(sitedir, line)
+                if not dircase in known_paths and os.path.exists(dir):
+                    sys.path.append(dir)
+                    known_paths.add(dircase)
+            except Exception as err:
+                print >>sys.stderr, "Error processing line {:d} of {}:\n".format(
+                    n+1, fullname)
+                for record in traceback.format_exception(*sys.exc_info()):
+                    for line in record.splitlines():
+                        print >>sys.stderr, '  '+line
+                print >>sys.stderr, "\nRemainder of file ignored"
+                break
+    if reset:
+        known_paths = None
+    return known_paths
+
+
+def addsitedir(sitedir, known_paths=None):
+    """Add 'sitedir' argument to sys.path if missing and handle .pth files in
+    'sitedir'"""
+    if known_paths is None:
+        known_paths = _init_pathinfo()
+        reset = 1
+    else:
+        reset = 0
+    sitedir, sitedircase = makepath(sitedir)
+    if not sitedircase in known_paths:
+        sys.path.append(sitedir)        # Add path component
+    try:
+        names = os.listdir(sitedir)
+    except os.error:
+        return
+    dotpth = os.extsep + "pth"
+    names = [name for name in names if name.endswith(dotpth)]
+    for name in sorted(names):
+        addpackage(sitedir, name, known_paths)
+    if reset:
+        known_paths = None
+    return known_paths
+
+
+def check_enableusersite():
+    """Check if user site directory is safe for inclusion
+
+    The function tests for the command line flag (including environment var),
+    process uid/gid equal to effective uid/gid.
+
+    None: Disabled for security reasons
+    False: Disabled by user (command line option)
+    True: Safe and enabled
+    """
+    if sys.flags.no_user_site:
+        return False
+
+    if hasattr(os, "getuid") and hasattr(os, "geteuid"):
+        # check process uid == effective uid
+        if os.geteuid() != os.getuid():
+            return None
+    if hasattr(os, "getgid") and hasattr(os, "getegid"):
+        # check process gid == effective gid
+        if os.getegid() != os.getgid():
+            return None
+
+    return True
+
+def getuserbase():
+    """Returns the `user base` directory path.
+
+    The `user base` directory can be used to store data. If the global
+    variable ``USER_BASE`` is not initialized yet, this function will also set
+    it.
+    """
+    global USER_BASE
+    if USER_BASE is not None:
+        return USER_BASE
+    from sysconfig import get_config_var
+    USER_BASE = get_config_var('userbase')
+    return USER_BASE
+
+def getusersitepackages():
+    """Returns the user-specific site-packages directory path.
+
+    If the global variable ``USER_SITE`` is not initialized yet, this
+    function will also set it.
+    """
+    global USER_SITE
+    user_base = getuserbase() # this will also set USER_BASE
+
+    if USER_SITE is not None:
+        return USER_SITE
+
+    from sysconfig import get_path
+    import os
+
+    if sys.platform == 'darwin':
+        from sysconfig import get_config_var
+        if get_config_var('PYTHONFRAMEWORK'):
+            USER_SITE = get_path('purelib', 'osx_framework_user')
+            return USER_SITE
+
+    USER_SITE = get_path('purelib', '%s_user' % os.name)
+    return USER_SITE
+
+def addusersitepackages(known_paths):
+    """Add a per user site-package to sys.path
+
+    Each user has its own python directory with site-packages in the
+    home directory.
+    """
+    # get the per user site-package path
+    # this call will also make sure USER_BASE and USER_SITE are set
+    user_site = getusersitepackages()
+
+    if ENABLE_USER_SITE and os.path.isdir(user_site):
+        addsitedir(user_site, known_paths)
+    return known_paths
+
+def getsitepackages():
+    """Returns a list containing all global site-packages directories
+    (and possibly site-python).
+
+    For each directory present in the global ``PREFIXES``, this function
+    will find its `site-packages` subdirectory depending on the system
+    environment, and will return a list of full paths.
+    """
+    sitepackages = []
+    seen = set()
+
+    for prefix in PREFIXES:
+        if not prefix or prefix in seen:
+            continue
+        seen.add(prefix)
+
+        if sys.platform in ('os2emx', 'riscos'):
+            sitepackages.append(os.path.join(prefix, "Lib", "site-packages"))
+        elif os.sep == '/':
+            sitepackages.append(os.path.join(prefix, "lib",
+                                        "python" + sys.version[:3],
+                                        "site-packages"))
+            sitepackages.append(os.path.join(prefix, "lib", "site-python"))
+        else:
+            sitepackages.append(prefix)
+            sitepackages.append(os.path.join(prefix, "lib", "site-packages"))
+    return sitepackages
+
+def addsitepackages(known_paths):
+    """Add site-packages (and possibly site-python) to sys.path"""
+    for sitedir in getsitepackages():
+        if os.path.isdir(sitedir):
+            addsitedir(sitedir, known_paths)
+
+    return known_paths
+
+def setBEGINLIBPATH():
+    """The OS/2 EMX port has optional extension modules that do double duty
+    as DLLs (and must use the .DLL file extension) for other extensions.
+    The library search path needs to be amended so these will be found
+    during module import.  Use BEGINLIBPATH so that these are at the start
+    of the library search path.
+
+    """
+    dllpath = os.path.join(sys.prefix, "Lib", "lib-dynload")
+    libpath = os.environ['BEGINLIBPATH'].split(';')
+    if libpath[-1]:
+        libpath.append(dllpath)
+    else:
+        libpath[-1] = dllpath
+    os.environ['BEGINLIBPATH'] = ';'.join(libpath)
+
+
+def setquit():
+    """Define new builtins 'quit' and 'exit'.
+
+    These are objects which make the interpreter exit when called.
+    The repr of each object contains a hint at how it works.
+
+    """
+    if os.sep == ':':
+        eof = 'Cmd-Q'
+    elif os.sep == '\\':
+        eof = 'Ctrl-Z plus Return'
+    else:
+        eof = 'Ctrl-D (i.e. EOF)'
+
+    class Quitter(object):
+        def __init__(self, name):
+            self.name = name
+        def __repr__(self):
+            return 'Use %s() or %s to exit' % (self.name, eof)
+        def __call__(self, code=None):
+            # Shells like IDLE catch the SystemExit, but listen when their
+            # stdin wrapper is closed.
+            try:
+                sys.stdin.close()
+            except:
+                pass
+            raise SystemExit(code)
+    __builtin__.quit = Quitter('quit')
+    __builtin__.exit = Quitter('exit')
+
+
+class _Printer(object):
+    """interactive prompt objects for printing the license text, a list of
+    contributors and the copyright notice."""
+
+    MAXLINES = 23
+
+    def __init__(self, name, data, files=(), dirs=()):
+        self.__name = name
+        self.__data = data
+        self.__files = files
+        self.__dirs = dirs
+        self.__lines = None
+
+    def __setup(self):
+        if self.__lines:
+            return
+        data = None
+        for dir in self.__dirs:
+            for filename in self.__files:
+                filename = os.path.join(dir, filename)
+                try:
+                    fp = file(filename, "rU")
+                    data = fp.read()
+                    fp.close()
+                    break
+                except IOError:
+                    pass
+            if data:
+                break
+        if not data:
+            data = self.__data
+        self.__lines = data.split('\n')
+        self.__linecnt = len(self.__lines)
+
+    def __repr__(self):
+        self.__setup()
+        if len(self.__lines) <= self.MAXLINES:
+            return "\n".join(self.__lines)
+        else:
+            return "Type %s() to see the full %s text" % ((self.__name,)*2)
+
+    def __call__(self):
+        self.__setup()
+        prompt = 'Hit Return for more, or q (and Return) to quit: '
+        lineno = 0
+        while 1:
+            try:
+                for i in range(lineno, lineno + self.MAXLINES):
+                    print self.__lines[i]
+            except IndexError:
+                break
+            else:
+                lineno += self.MAXLINES
+                key = None
+                while key is None:
+                    key = raw_input(prompt)
+                    if key not in ('', 'q'):
+                        key = None
+                if key == 'q':
+                    break
+
+def setcopyright():
+    """Set 'copyright' and 'credits' in __builtin__"""
+    __builtin__.copyright = _Printer("copyright", sys.copyright)
+    if sys.platform[:4] == 'java':
+        __builtin__.credits = _Printer(
+            "credits",
+            "Jython is maintained by the Jython developers (www.jython.org).")
+    else:
+        __builtin__.credits = _Printer("credits", """\
+    Thanks to CWI, CNRI, BeOpen.com, Zope Corporation and a cast of thousands
+    for supporting Python development.  See www.python.org for more information.""")
+    here = os.path.dirname(os.__file__)
+    __builtin__.license = _Printer(
+        "license", "See https://www.python.org/psf/license/",
+        ["LICENSE.txt", "LICENSE"],
+        [os.path.join(here, os.pardir), here, os.curdir])
+
+
+class _Helper(object):
+    """Define the builtin 'help'.
+    This is a wrapper around pydoc.help (with a twist).
+
+    """
+
+    def __repr__(self):
+        return "Type help() for interactive help, " \
+               "or help(object) for help about object."
+    def __call__(self, *args, **kwds):
+        import pydoc
+        return pydoc.help(*args, **kwds)
+
+def sethelper():
+    __builtin__.help = _Helper()
+
+def aliasmbcs():
+    """On Windows, some default encodings are not provided by Python,
+    while they are always available as "mbcs" in each locale. Make
+    them usable by aliasing to "mbcs" in such a case."""
+    if sys.platform == 'win32':
+        import locale, codecs