id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4841	Atomic molc.cpp uses deprecated Python 3.9 calls	Tom Goddard	Eric Pettersen	"make install
../../../ChimeraX.app/Contents/bin/ChimeraX --nogui --safemode --exit --cmd ""devel install . user false exit true  ""
Executing: devel install . user false exit true  
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g

compile options: '-std=c++11 -stdlib=libc++ -DDYNAMIC_LIBRARY=1 -I/Users/goddard/ucsf/chimerax/src/bundles/atomic/../../../ChimeraX.app/Contents/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic_lib/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/arrays/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c'
gcc: atomic_cpp/molc.cpp
atomic_cpp/molc.cpp:832:37: warning: 'PyEval_CallObjectWithKeywords' is deprecated
      [-Wdeprecated-declarations]
            if (disable) Py_XDECREF(PyEval_CallObject(disable, NULL));
                                    ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/ceval.h:24:5: note: 
      expanded from macro 'PyEval_CallObject'
    PyEval_CallObjectWithKeywords(callable, arg, (PyObject *)NULL)
    ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/ceval.h:17:1: note: 
      'PyEval_CallObjectWithKeywords' has been explicitly marked deprecated here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: note: 
      expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
atomic_cpp/molc.cpp:851:36: warning: 'PyEval_CallObjectWithKeywords' is deprecated
      [-Wdeprecated-declarations]
            if (enable) Py_XDECREF(PyEval_CallObject(enable, NULL));
                                   ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/ceval.h:24:5: note: 
      expanded from macro 'PyEval_CallObject'
    PyEval_CallObjectWithKeywords(callable, arg, (PyObject *)NULL)
    ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/ceval.h:17:1: note: 
      'PyEval_CallObjectWithKeywords' has been explicitly marked deprecated here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: note: 
      expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
atomic_cpp/molc.cpp:2750:25: warning: '_PyUnicode_get_wstr_length' is deprecated
      [-Wdeprecated-declarations]
            auto size = PyUnicode_GET_DATA_SIZE(py_ic);
                        ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:268:6: note: 
      expanded from macro 'PyUnicode_GET_DATA_SIZE'
    (PyUnicode_GET_SIZE(op) * Py_UNICODE_SIZE)
     ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:261:7: note: 
      expanded from macro 'PyUnicode_GET_SIZE'
      PyUnicode_WSTR_LENGTH(op) :                    \
      ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: 
      expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: 
      '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: note: 
      expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
atomic_cpp/molc.cpp:2750:25: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
            auto size = PyUnicode_GET_DATA_SIZE(py_ic);
                        ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:268:6: note: 
      expanded from macro 'PyUnicode_GET_DATA_SIZE'
    (PyUnicode_GET_SIZE(op) * Py_UNICODE_SIZE)
     ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:262:14: note: 
      expanded from macro 'PyUnicode_GET_SIZE'
      ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
             ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:580:1: note: 
      'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: note: 
      expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
atomic_cpp/molc.cpp:2750:25: warning: '_PyUnicode_get_wstr_length' is deprecated
      [-Wdeprecated-declarations]
            auto size = PyUnicode_GET_DATA_SIZE(py_ic);
                        ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:268:6: note: 
      expanded from macro 'PyUnicode_GET_DATA_SIZE'
    (PyUnicode_GET_SIZE(op) * Py_UNICODE_SIZE)
     ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:264:8: note: 
      expanded from macro 'PyUnicode_GET_SIZE'
       PyUnicode_WSTR_LENGTH(op)))
       ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: 
      expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: 
      '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: note: 
      expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
atomic_cpp/molc.cpp:2757:23: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                val = PyUnicode_AS_DATA(py_ic)[0];
                      ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:283:21: note: 
      expanded from macro 'PyUnicode_AS_DATA'
    ((const char *)(PyUnicode_AS_UNICODE(op)))
                    ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:279:7: note: 
      expanded from macro 'PyUnicode_AS_UNICODE'
      PyUnicode_AsUnicode(_PyObject_CAST(op)))
      ^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:580:1: note: 
      'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: note: 
      expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
6 warnings generated.
"	defect	closed	moderate		Structure Analysis		fixed						all	ChimeraX