Merge pull request #1 from CellProfiler/py3-leek

Fixes #54 - Python 3.x support
LeeKamentsky · Mar 10, 2016 · a7ed071 · a7ed071
2 parents c20f6dc + 5ae5fa2
commit a7ed071
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Showing 8 changed files with 74 additions and 57 deletions.
diff --git a/_javabridge.pyx b/_javabridge.pyx
@@ -1072,7 +1072,7 @@ cdef class JB_Env:
         free(<void *>values)
         return result
 
-    def get_field_id(self, JB_Class c, char *name, char *sig):
+    def get_field_id(self, JB_Class c, name, sig):
         '''Get a field ID for a class
         
         :param c: class (from :py:meth:`.find_class` or similar)
@@ -1083,7 +1083,10 @@ cdef class JB_Env:
             jfieldID id
             __JB_FieldID jbid
 
-        id = self.env[0].GetFieldID(self.env, c.c, name, sig)
+        utf8name = name.encode('utf-8')
+        utf8sig = sig.encode('utf-8')
+
+        id = self.env[0].GetFieldID(self.env, c.c, utf8name, utf8sig)
         if id == NULL:
             return None
         jbid = __JB_FieldID()

diff --git a/demo/demo_nogui.py b/demo/demo_nogui.py
@@ -11,12 +11,13 @@
 
 """
 
+from __future__ import print_function
 import os
 import javabridge
 
 javabridge.start_vm(run_headless=True)
 try:
-    print javabridge.run_script('java.lang.String.format("Hello, %s!", greetee);', 
-                                dict(greetee='world'))
+    print(javabridge.run_script('java.lang.String.format("Hello, %s!", greetee);', 
+                                dict(greetee='world')))
 finally:
     javabridge.kill_vm()
diff --git a/java/org_cellprofiler_javabridge_CPython.c b/java/org_cellprofiler_javabridge_CPython.c
@@ -158,7 +158,7 @@ static int attach_env(JNIEnv *pEnv){
     javabridge.jni_enter(env)
     */
 
-    pPyEnv = PyCObject_FromVoidPtr((void *)pEnv, NULL);
+    pPyEnv = PyCapsule_New((void *)pEnv, NULL, NULL);
     if (PyErr_Occurred()) {
         throwWrappedError(pEnv, __LINE__);
         return -1;
@@ -272,7 +272,7 @@ static PyObject *wrapJObject(JNIEnv *pEnv, jobject j) {
         Py_DECREF(pJavabridge);
         return NULL;
     }
-    pCapsule = PyCObject_FromVoidPtr((void *)j, NULL);
+    pCapsule = PyCapsule_New((void *)j, NULL, NULL);
     if (! pCapsule) {
         throwWrappedError(pEnv, __LINE__);
         Py_DECREF(pTheEnv);

diff --git a/javabridge/_javabridge.cpython-34m.so b/javabridge/_javabridge.cpython-34m.so
diff --git a/javabridge/locate.py b/javabridge/locate.py
@@ -19,7 +19,9 @@
 is_mac = sys.platform == 'darwin'
 is_win = sys.platform.startswith("win")
 is_win64 = (is_win and (os.environ["PROCESSOR_ARCHITECTURE"] == "AMD64"))
-is_msvc = (is_win and sys.version_info[0] >= 2 and sys.version_info[1] >= 6)
+is_msvc = (is_win and 
+           ((sys.version_info.major == 2 and sys.version_info.minor >= 6) or
+            (sys.version_info.major == 3)))
 is_mingw = (is_win and not is_msvc)
 
 logger = logging.getLogger(__name__)
@@ -74,20 +76,23 @@ def get_out(cmd):
         jdk_dir = os.path.abspath(jdk_dir)
         return jdk_dir
     elif is_win:
-        import _winreg
+        if sys.version_info.major == 2:
+            import _winreg as winreg
+        else:
+            import winreg
         java_key_path = 'SOFTWARE\\JavaSoft\\Java Runtime Environment'
         looking_for = java_key_path
         try:
-            kjava = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, java_key_path)
+            kjava = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, java_key_path)
             looking_for = java_key_path + "\\CurrentVersion"
-            kjava_values = dict([_winreg.EnumValue(kjava, i)[:2]
-                                 for i in range(_winreg.QueryInfoKey(kjava)[1])])
+            kjava_values = dict([winreg.EnumValue(kjava, i)[:2]
+                                 for i in range(winreg.QueryInfoKey(kjava)[1])])
             current_version = kjava_values['CurrentVersion']
             looking_for = java_key_path + '\\' + current_version
-            kjava_current = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE,
+            kjava_current = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE,
                                             looking_for)
-            kjava_current_values = dict([_winreg.EnumValue(kjava_current, i)[:2]
-                                         for i in range(_winreg.QueryInfoKey(kjava_current)[1])])
+            kjava_current_values = dict([winreg.EnumValue(kjava_current, i)[:2]
+                                         for i in range(winreg.QueryInfoKey(kjava_current)[1])])
             return kjava_current_values['JavaHome']
         except:
             logger.error("Failed to find registry entry: %s\n" %looking_for,
@@ -102,20 +107,23 @@ def find_jdk():
     if is_mac:
         return find_javahome()
     if is_win:
-        import _winreg
-        import exceptions
+        if sys.version_info.major == 2:
+            import _winreg as winreg
+            from exceptions import WindowsError
+        else:
+            import winreg
         try:
             jdk_key_path = 'SOFTWARE\\JavaSoft\\Java Development Kit'
-            kjdk = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, jdk_key_path)
-            kjdk_values = dict([_winreg.EnumValue(kjdk, i)[:2]
-                                 for i in range(_winreg.QueryInfoKey(kjdk)[1])])
+            kjdk = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, jdk_key_path)
+            kjdk_values = dict([winreg.EnumValue(kjdk, i)[:2]
+                                 for i in range(winreg.QueryInfoKey(kjdk)[1])])
             current_version = kjdk_values['CurrentVersion']
-            kjdk_current = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE,
+            kjdk_current = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE,
                                            jdk_key_path + '\\' + current_version)
-            kjdk_current_values = dict([_winreg.EnumValue(kjdk_current, i)[:2]
-                                        for i in range(_winreg.QueryInfoKey(kjdk_current)[1])])
+            kjdk_current_values = dict([winreg.EnumValue(kjdk_current, i)[:2]
+                                        for i in range(winreg.QueryInfoKey(kjdk_current)[1])])
             return kjdk_current_values['JavaHome']
-        except exceptions.WindowsError as e:
+        except WindowsError as e:
             if e.errno == 2:
                 raise RuntimeError(
                     "Failed to find the Java Development Kit. Please download and install the Oracle JDK 1.6 or later")

diff --git a/javabridge/tests/test_cpython.py b/javabridge/tests/test_cpython.py
@@ -35,7 +35,7 @@ def fn(numerator, denominator, answer):
         jlocals.put("code", code)
         jlocals.put("answer", jref.o)
         self.cpython.execute(code, jlocals.o, None)
-        self.assertEqual(javabridge.to_string(jref.get(0)), "3")
+        self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
 
     def test_01_03_globals(self):
         jglobals = javabridge.JClassWrapper('java.util.HashMap')()
@@ -51,7 +51,7 @@ def fn():
     javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
 fn()
 """, None, jglobals.o)
-        self.assertEqual(javabridge.to_string(jref.get(0)), "3")
+        self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
 
     def test_01_04_globals_equals_locals(self):
         jglobals = javabridge.JClassWrapper('java.util.HashMap')()
@@ -69,4 +69,4 @@ def fn():
     javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
 fn()
 """, jglobals.o, jglobals.o)
-        self.assertEqual(javabridge.to_string(jref.get(0)), "3")        
+        self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
diff --git a/javabridge/tests/test_javabridge.py b/javabridge/tests/test_javabridge.py
@@ -41,7 +41,7 @@ def test_01_03_00_new_string_utf(self):
     def test_01_03_01_new_string_unicode(self):
         s = u"Hola ni\u00F1os"
         jstring = self.env.new_string(s)
-        self.assertEqual(self.env.get_string_utf(jstring).decode("utf-8"), s)
+        self.assertEqual(self.env.get_string_utf(jstring), s)
 
     def test_01_03_02_new_string_string(self):
         s = "Hello, world"
@@ -331,13 +331,14 @@ def test_03_08_call_method_double(self):
         self.assertAlmostEqual(self.env.call_method(jdouble, method_id), -55.64)
 
     def test_03_09_call_method_array(self):
-        jstring = self.env.new_string_utf("Hello, world")
+        s = "Hello, world"
+        jstring = self.env.new_string_utf(s)
         klass = self.env.get_object_class(jstring)
         method_id = self.env.get_method_id(klass, 'getBytes', '()[B')
         result = self.env.call_method(jstring, method_id)
         self.assertTrue(isinstance(result, jb.JB_Object))
         a = self.env.get_byte_array_elements(result)
-        self.assertEqual("Hello, world", a.tostring())
+        self.assertEqual(np.array(s, "S%d" % len(s)).tostring(), a.tostring())
 
     def test_03_10_call_method_object(self):
         hello = self.env.new_string_utf("Hello, ")
@@ -445,7 +446,7 @@ def test_05_06_get_static_long_field(self):
         klass = self.env.find_class("java/security/Key")
         field_id = self.env.get_static_field_id(klass, "serialVersionUID", "J")
         result = self.env.get_static_long_field(klass, field_id)
-        self.assertEqual(result, 6603384152749567654l) # see http://java.sun.com/j2se/1.4.2/docs/api/constant-values.html#java.security.Key.serialVersionUID
+        self.assertEqual(result, 6603384152749567654)
 
     def test_05_07_get_static_float_field(self):
         klass = self.env.find_class("java/lang/Float")

diff --git a/setup.py b/setup.py
@@ -44,7 +44,7 @@ def in_cwd(basename):
 
 def build_cython():
     """Compile the pyx files if we have them.
-    
+
     The git repository has the .pyx files but not the .c files, and
     the source distributions that are uploaded to PyPI have the .c
     files and not the .pyx files. (The reason for the latter is that
@@ -76,17 +76,17 @@ def get_jvm_include_dirs():
     elif is_mac:
         where_jni_h_is_post_6 = os.path.join(java_home, 'include')
         if os.path.isfile(os.path.join(where_jni_h_is_post_6, "jni.h")):
-            
+
             include_dirs += [where_jni_h_is_post_6,
                              os.path.join(java_home, 'include', 'darwin')]
         else:
             include_dirs += ["/System/Library/Frameworks/JavaVM.Framework/Headers"]
     elif is_linux:
         include_dirs += [os.path.join(java_home,'include'),
                          os.path.join(java_home,'include','linux')]
-        
+
     return include_dirs
-    
+
 def ext_modules():
     extensions = []
     extra_link_args = None
@@ -108,7 +108,7 @@ def ext_modules():
             # Build libjvm from jvm.dll on Windows.
             # This assumes that we're using mingw32 for build
             #
-            cmd = ["dlltool", "--dllname", 
+            cmd = ["dlltool", "--dllname",
                    os.path.join(jdk_home,"jre\\bin\\client\\jvm.dll"),
                    "--output-lib","libjvm.a",
                    "--input-def","jvm.def",
@@ -148,7 +148,7 @@ def ext_modules():
 
 SO = ".dll" if sys.platform == 'win32' \
     else ".jnilib" if sys.platform == 'darwin'\
-    else sysconfig.get_config_var("SO")
+    else ".so"
 
 def needs_compilation(target, *sources):
     try:
@@ -198,18 +198,19 @@ def run(self, *args, **kwargs):
     def build_jar_from_sources(self, jar, sources):
         if sys.platform == 'win32':
             sources = [source.replace("/", os.path.sep) for source in sources]
-        jar = self.get_ext_fullpath(jar)
-        jar = os.path.splitext(jar)[0] + ".jar"
+        jar_filename = jar.rsplit(".", 1)[1] + ".jar"
+        jar_dir = os.path.dirname(self.get_ext_fullpath(jar))
+        jar = os.path.join(jar_dir, jar_filename)
         jar_command = [find_jar_cmd(), 'cf', package_path(jar)]
-        
+
         javac_loc = find_javac_cmd()
         dirty_jar = False
         javac_command = [javac_loc, "-source", "6", "-target", "6"]
         for source in sources:
             javac_command.append(package_path(source))
             if needs_compilation(jar, source):
                 dirty_jar = True
-                
+
         self.spawn(javac_command)
         if dirty_jar:
             if not os.path.exists(os.path.dirname(jar)):
@@ -219,11 +220,11 @@ def build_jar_from_sources(self, jar, sources):
                     java_klass_path = klass[klass.index(os.path.sep) + 1:].replace(os.path.sep, "/")
                     jar_command.extend(['-C', package_path('java'), java_klass_path])
             self.spawn(jar_command)
-            
+
     def build_java2cpython(self):
         sources = self.java2cpython_sources
         distutils.log.info("building java2cpython library")
-        
+
 
         # First, compile the source code to object files in the library
         # directory.  (This should probably change to putting object
@@ -233,13 +234,15 @@ def build_java2cpython(self):
             get_jvm_include_dirs()
         python_lib_dir, lib_name = self.get_java2cpython_libdest()
         library_dirs = [python_lib_dir]
-        output_dir = os.path.splitext(self.get_ext_fullpath("javabridge.jars"))[0]
-        export_symbols = ['Java_org_cellprofiler_javabridge_CPython_exec'] 
+        output_dir = os.path.join(os.path.dirname(
+            self.get_ext_fullpath("javabridge.jars")), "jars")
+        export_symbols = ['Java_org_cellprofiler_javabridge_CPython_exec']
         objects = self.compiler.compile(sources,
                                         output_dir=self.build_temp,
                                         include_dirs=include_dirs,
                                         debug=self.debug)
-        extra_postargs = ["/MANIFEST"] if sys.platform == 'win32' else None
+        needs_manifest = sys.platform == 'win32' and sys.version_info.major == 2
+        extra_postargs = ["/MANIFEST"] if needs_manifest else None
         self.compiler.link(
             CCompiler.SHARED_OBJECT,
             objects, lib_name,
@@ -248,7 +251,7 @@ def build_java2cpython(self):
             library_dirs=library_dirs,
             export_symbols=export_symbols,
             extra_postargs=extra_postargs)
-        if sys.platform == 'win32':
+        if needs_manifest:
             temp_dir = os.path.dirname(objects[0])
             manifest_name = lib_name +".manifest"
             lib_path = os.path.join(output_dir, lib_name)
@@ -258,7 +261,7 @@ def build_java2cpython(self):
             out_arg = '-outputresource:%s;2' % lib_path
             try:
                 self.compiler.spawn([
-                    'mt.exe', '-nologo', '-manifest', manifest_file, 
+                    'mt.exe', '-nologo', '-manifest', manifest_file,
                     out_arg])
             except DistutilsExecError as msg:
                 raise LinkError(msg)
@@ -273,34 +276,34 @@ def get_java2cpython_libdest(self):
             python_lib_dir = sysconfig.get_config_var('LIBDIR')
             lib_name = "libjava2cpython" + SO
         return python_lib_dir, lib_name
-        
+
 
     def build_jar_from_single_source(self, jar, source):
         self.build_jar_from_sources(jar, [source])
-        
+
     def build_runnablequeue(self):
         jar = 'javabridge.jars.runnablequeue'
         source = 'java/org/cellprofiler/runnablequeue/RunnableQueue.java'
         self.build_jar_from_single_source(jar, source)
-        
+
     def build_cpython(self):
         jar = 'javabridge.jars.cpython'
         sources = [
             'java/org/cellprofiler/javabridge/CPython.java',
             'java/org/cellprofiler/javabridge/CPythonInvocationHandler.java']
         self.build_jar_from_sources(jar, sources)
-    
+
     def build_test(self):
         jar = 'javabridge.jars.test'
         source = 'java/org/cellprofiler/javabridge/test/RealRect.java'
         self.build_jar_from_single_source(jar, source)
-    
+
     def build_java(self):
         self.build_runnablequeue()
         self.build_test()
         self.build_cpython()
 
-    
+
 def get_version():
     """Get version from git or file system.
 
@@ -314,19 +317,19 @@ def get_version():
     if os.path.exists(os.path.join(os.path.dirname(__file__), '.git')):
         import subprocess
         try:
-            git_version = subprocess.Popen(['git', 'describe'], 
+            git_version = subprocess.Popen(['git', 'describe'],
                                            stdout=subprocess.PIPE).communicate()[0].strip().decode('utf-8')
         except:
             pass
 
-    version_file = os.path.join(os.path.dirname(__file__), 'javabridge', 
+    version_file = os.path.join(os.path.dirname(__file__), 'javabridge',
                                 '_version.py')
     if os.path.exists(version_file):
         with open(version_file) as f:
             cached_version_line = f.read().strip()
         try:
             # From http://stackoverflow.com/a/3619714/17498
-            cached_version = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", 
+            cached_version = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                                        cached_version_line, re.M).group(1)
         except:
             raise RuntimeError("Unable to find version in %s" % version_file)
@@ -357,7 +360,8 @@ def get_version():
           classifiers=['Development Status :: 5 - Production/Stable',
                        'License :: OSI Approved :: BSD License',
                        'Programming Language :: Java',
-                       'Programming Language :: Python :: 2 :: Only'
+                       'Programming Language :: Python :: 2',
+                       'Programming Language :: Python :: 3'
                        ],
           license='BSD License',
           install_requires=['numpy'],