pip install error python3.8

[alshai]

Hello,

I'm having trouble installing cyvcf2 on my linux machine:

• arch linux kernel version 5.5.4-arch1-1

• python version 3.8.1

• GCC version 9.2.0

• output when I run pip install --user cyvcf2: err.txt

specifically, this kind of error shows up:

  cyvcf2/cyvcf2.c:318:11: error: too many arguments to function ‘PyCode_New’
    318 |           PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
        |           ^~~~~~~~~~
  cyvcf2/cyvcf2.c:61959:34: note: in expansion of macro ‘__Pyx_PyCode_New’
  61959 |   __pyx_codeobj__80 = (PyObject*)__Pyx_PyCode_New(6, 0, 14, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_cyvcf2_cyvcf2_pyx, __pyx_n_s_par_relatedness_2, 34, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__80)) __PYX_ERR(0, 34, __pyx_L1_error)
        |                                  ^~~~~~~~~~~~~~~~
  In file included from /usr/include/python3.8/compile.h:5,
                   from /usr/include/python3.8/Python.h:138,
                   from cyvcf2/cyvcf2.c:4:
  /usr/include/python3.8/code.h:122:28: note: declared here
    122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
        |                            ^~~~~~~~~~

[alshai]

I was able to successfully install from source using the instructions on the README, though the above should still be addressed for those facing similar issues with pip.

[CholoTook]

I added a couple of docker containers to help make such reports more concrete... I don't know the exact versions of python 3.8 and gcc, but these are at least working.

https://github.com/brentp/cyvcf2/pull/283

Can you submit a docker container that reproduces your exact versions?

Thanks