Thanks for the information! I've had to work on other project in the meantime,
but was able to get back to this again.
In an effort to wrap my head around the project's code, I realized that I did
not have a line like:
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
in it. So, I added the line, fixed the errors the resulted, and recompiled.
And immediately got segmentation faults.
Investigating, I discovered that the problem was that the pointers to my new
member variables change mysteriously to invalid values. The basic flow is:
1) I call PyArray_New with a pointer to my new NamedArrayObject subclass.
2) It does stuff
3) It calls the NamedArrayObject_alloc function we wrote, which creates the new
'rowNames' PyList.
4) It does more stuff
5) It calls the NamedArrayObject_Finalize function we wrote. The 'rowNames'
object now has a different, and incorrect, pointer, and at this point if I ever
call PyList_Size(self->rowNames), I get a segmentation fault.
If, however, I re-comment out the '#define NPY_NO_DEPRECATED_API
NPY_1_7_API_VERSION" line, everything works fine! Part 4 above doesn't change
the 'rowNames' pointer to anything, and it remains valid for the rest of the
program.
(If I change 1_7_ to 1_23_, I get identical behavior.)
Normally, I'd be happy to just say 'well, I guess I have to use the deprecated
API', but this issue combined with the fact that I'm getting the "C subclassed
NumPy array, void scalar, or allocated in a non-standard way" error message,
makes me think that something has changed in a fundamental way since the code
was first written in 2014, and that I should do things the new way. I just...
don't know what that new way might be ;-)
The upshot is that I have two questions:
1) Does this look like a bug I should file?
2) What areas should I start looking into to change this old code to work with
modern NumPy?
and possibly:
3) Is there a worked example of a C-extended NumPy array somewhere I could
steal?
The full code is at
https://github.com/sys-bio/roadrunner/blob/develop/wrappers/Python/roadrunner/PyUtils.cpp
if that helps anyone. The branch where I'm trying to change things is at
https://github.com/sys-bio/roadrunner/blob/update-numpy/wrappers/Python/roadrunner/PyUtils.cpp
which has a bunch of print statements added, since I was working without a
debugger on Windows. The relevant output for a simple Python script that calls
this was (for the broken #define version):
```
NA_N 0
Debug: PyObject* rr::NamedArrayObject_alloc(PyTypeObject*, Py_ssize_t)
rownames new ref 0x77362180
rownames added to object 0x7747e750
rownames size 0
rownames ref 0x77362180
rownames size 0
Debug: namedArrayObject allocated: 0x7747e750
Debug: namedArrayObject returned obj: 0x7747e750
Debug: Done
Debug: PyObject* rr::NamedArrayObject_Finalize(rr::NamedArrayObject*, PyObject*)
rownames ref 0x55f4f830
Debug: finalizing object self: 0x7747e750; args 0x55aca3e0
rownames ref 0x55f4f830
Debug: NamedArrayObject initialized from constructor. 'None' path taken
Debug: PyObject*
rr::NamedArrayObject_Finalize_FromConstructor(rr::NamedArrayObject*)
rownames ref 0x55f4f830
rownames ref 0x55f4f830
Debug: Done
```
and for the working non-#define version:
```
NA_N 0
Debug: PyObject* rr::NamedArrayObject_alloc(PyTypeObject*, Py_ssize_t)
rownames new ref 0x77362140
rownames added to object 0x7752e1e0
rownames size 0
rownames ref 0x77362140
rownames size 0
Debug: namedArrayObject allocated: 0x7752e1e0
Debug: namedArrayObject returned obj: 0x7752e1e0
Debug: Done
Debug: PyObject* rr::NamedArrayObject_Finalize(rr::NamedArrayObject*, PyObject*)
rownames ref 0x77362140
Debug: finalizing object self: 0x7752e1e0; args 0x55aca3e0
rownames ref 0x77362140
Debug: NamedArrayObject initialized from constructor. 'None' path taken
Debug: PyObject*
rr::NamedArrayObject_Finalize_FromConstructor(rr::NamedArrayObject*)
rownames ref 0x77362140
rownames ref 0x77362140
Debug: Done
```
Thanks for bearing with me though this long message! And particular thanks to
Sebastien for answering my initial question, which I hope to be able to
actually address again soon ;-)
-Lucian
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