[bug #61811] jinja2, extension-helpers, pybind11 not found, even though installed; pyyaml error

[Boud Roukema]

Update of bug #61811 (project reproduce):

                 Summary: jinja2, extension-helpers, pybind11 not found, even
though installed => jinja2, extension-helpers, pybind11 not found, even though
installed; pyyaml error

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Follow-up Comment #7:

DESCRIPTION: Running commit 4318670 of core maneage, with the addition of
_pyyaml_ as a target:

--- a/reproduce/software/config/TARGETS.conf
+++ b/reproduce/software/config/TARGETS.conf
@@ -39,7 +39,7 @@
 top-level-programs = gnuastro
 
 # Python libraries/modules.
-top-level-python =
+top-level-python = pyyaml

leads to compilation errors of the C source code of _pyyaml_. Independently,
in a research project package, the compilation error does not appear to block
a full configure of python packages, with _matplotlib_ selected in
_TARGETS.conf_. Thus, this is a bug in principle, though not (so far) an
obvious problem in practice. Nevertheless, it should be fixed, and seems to be
included in bug #61811 [0], which is why I'm adding it here.

LOG EXCERPT:

187806  /BUILD/software/installed/include/yaml.h:636:55: note: expected 'const
yaml_char_t *' {aka '
const unsigned char *'} but argument is of type 'char *'
187807    636 |         const yaml_char_t *anchor, const yaml_char_t *tag, int
implicit,
187808        |                                    ~~~~~~~~~~~~~~~~~~~^~~
187809  config.status: executing libtool commands
187810  ext/_yaml.c: In function '__pyx_tp_dealloc_5_yaml_CParser':
187811  ext/_yaml.c:23870:5: error: lvalue required as increment operand
187812  23870 |     ++Py_REFCNT(o);
187813        |     ^~
187814  ext/_yaml.c:23872:5: error: lvalue required as decrement operand
187815  23872 |     --Py_REFCNT(o);
187816        |     ^~
187817  ext/_yaml.c: In function '__pyx_tp_dealloc_5_yaml_CEmitter':
187818  ext/_yaml.c:24040:5: error: lvalue required as increment operand
187819  24040 |     ++Py_REFCNT(o);
187820        |     ^~
187821  ext/_yaml.c:24042:5: error: lvalue required as decrement operand
187822  24042 |     --Py_REFCNT(o);
187823        |     ^~
187824  ext/_yaml.c: In function '__Pyx_modinit_type_init_code':
187825  ext/_yaml.c:24844:25: error: 'PyTypeObject' {aka 'struct _typeobject'}
has no member named 'tp_print'
187826  24844 |   __pyx_type_5_yaml_Mark.tp_print = 0;
187827        |                         ^
187828  ext/_yaml.c:24864:28: error: 'PyTypeObject' {aka 'struct _typeobject'}
has no member named 'tp_print'
187829  24864 |   __pyx_type_5_yaml_CParser.tp_print = 0;
187830        |                            ^


HINTS:
It might be necessary to shift from our default python build rules to rules
that use 'wheel', per the discussion at [1]. Bug [2] appears to be related,
but it's not immediately clear what the bug is and whether there is a generic,
rather than OS-specific, fix.

Some descriptions of 'wheel' are at [3][4].

A related guess is in [5][6] - it could be that the 'wheel' files with the
'sdist' option are not correctly built in the upstream 'pyyaml' (or 'jinja2'
and so on) distributions.

Debugging this might require understanding the relation of cython to python,
pyyaml and the other packages, and understanding the various updates and bugs
in cython, and errors that people make when preparing python packages in
relation to cython. Disclaimer: I'm just guessing here.


WHAT DID NOT WORK:

I tried

--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -581,7 +581,8 @@ $(ipydir)/pythran-$(pythran-version): \
 
 $(ipydir)/pyyaml-$(pyyaml-version): \
                  $(ibidir)/yaml-$(yaml-version) \
-                 $(ipydir)/cython-$(cython-version)
+                 $(ipydir)/cython-$(cython-version) \
+                 $(ipydir)/wheel-$(wheel-version)
        tarball=pyyaml-$(pyyaml-version).tar.gz
        $(call import-source, $(pyyaml-url), $(pyyaml-checksum))
        $(call pybuild, tar -xf, PyYAML-$(pyyaml-version), , \

but the same error occurred.

URLs:

[0] https://savannah.nongnu.org/bugs/?61811
[1] https://github.com/PyWavelets/pywt/issues/602
[2] https://github.com/yaml/pyyaml/issues/416
[3] https://realpython.com/python-wheels
[4] https://pythonwheels.com
[5] https://github.com/yaml/pyyaml/issues/179
[6] https://github.com/yaml/pyyaml/pull/188



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