Atomic molc.cpp uses deprecated Python 3.9 calls

[Tom Goddard]

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.

[Tom Goddard]

The molc.cpp code is using

PyEval_CallObject()
PyUnicode_GET_DATA_SIZE()
PyUnicode_AS_DATA()

The first PyEval_CallObject() is not a documented API and this Python issue ​https://bugs.python.org/issue29548 says to use PyObject_Call(). The second two calls were deprecated in Python 3.3.

Eric added all these for insertion code and idatm methods so he can fix them.

[pett]

Well, PyEval_CallObject was certainly documented when I used it. It's not like I go looking for internal Python APIs to use! Nonetheless, I will fix it.

[goddard@…]

Not sure PyEval_CallObject was ever documented, but it does appear in programming examples.

[pett]

I want to replace PyEval_CallObject() with PyObject_CallNoArgs(), which isn't available until 3.9 -- so when we go to 3.9 I will apply the attached patch.