Re: packaging python-cyvcf2

[Alexis Simon]

On 22/03/2024 08:25, Simon Tournier wrote:
> Hi,
>
> On jeu., 21 mars 2024 at 18:03, Alexis Simon via Guix-Science 
> <guix-science@gnu.org> wrote:
>
> > The build is failing with this error:
> > running build_ext
> > # cyvcf2: htslib mode is BUILTIN
> > # cyvcf2: htslib configure options is None
> > error: [Errno 2] No such file or directory: './configure'
> > error: in phase 'build': uncaught exception:
> > %exception #<&invoke-error program: "python" arguments: ("./setup.py"
> > "build") exit-status: 1 term-signal: #f stop-signal: #f>
> >
> > What is very disturbing is that it builds fine in a debugging
> > environment following the documentation [2]
>
> Indeed!  Well, another undocumented trick. ;-)
>
>          guix build -L . python-cyvcf2 \
>               --with-source=python-cyvcf2=/tmp/cyvcf2-0.30.28
>
> where /tmp/cyvcf2-0.30.28 is the uncompressed output of “guix build -S”
> that I tweak.  Adding this:
>
> --8<---------------cut here---------------start------------->8---
> diff -u /tmp/guix-build-python-cyvcf2-0.30.28.drv-0/cyvcf2-0.30.28/setup.py 
> /tmp/cyvcf2-0.30.28/setup.py
> --- /tmp/guix-build-python-cyvcf2-0.30.28.drv-0/cyvcf2-0.30.28/setup.py 
> 2024-01-30 17:46:32.000000000 +0100
> +++ /tmp/cyvcf2-0.30.28/setup.py        2024-03-22 16:15:28.124301350 +0100
> @@ -83,7 +83,13 @@
>           if htslib_configure_options:
>               configure_args.extend(htslib_configure_options.split())
>   
> -        subprocess.run(configure_args, check=True)
> +        print(configure_args,
> +              "File exists?", os.path.exists(configure_args[0]),
> +              flush=True)
> +        try:
> +            subprocess.run(configure_args, check=True)
> +        except:
> +            print("BANG!")
>       subprocess.run(["make"], check=True)
>   
>       os.chdir(current_directory)
> --8<---------------cut here---------------end--------------->8---
>
> It leads to this output:
>
> --8<---------------cut here---------------start------------->8---
> running build_ext
> # cyvcf2: htslib mode is BUILTIN
> # cyvcf2: htslib configure options is None
> ['./configure', 'CFLAGS=-fPIC'] File exists? True
> echo '# Default htscodecs.mk generated by Makefile' > htscodecs.mk
> echo 'include $(HTSPREFIX)htscodecs_bundled.mk' >> htscodecs.mk
> ./hts_probe_cc.sh 'gcc' '-g -Wall -O2 -fvisibility=hidden ' '-fvisibility=hidden' 
> >> htscodecs.mk
> /gnu/store/rib9g2ig1xf3kclyl076w28parmncg4k-bash-minimal-5.1.16/bin/sh: line 1: 
> ./hts_probe_cc.sh: No such file or directory
> Makefile:141: htscodecs.mk: No such file or directory
> make: *** [Makefile:124: htscodecs.mk] Error 127
> BANG!
> Traceback (most recent call last):
> [...]
> --8<---------------cut here---------------end--------------->8---
>
> Arf, then I have not investigated further.
>
> I think it does not come from ’./configure’ as wrongly reported but from
> something triggered by it.
>
> Let me know your progress.  Maybe I could give a closer look next week.

Thanks a lot for the trick, I was able to finish compiling it, but going 
another route (i.e. unbundling htslib).

I've abandoned running the tests though, I'm hitting a module not found 
error. pytest doesn't manage to load the just built module, probably an 
issue with the paths.

I'm attaching the new version for reference.

Cheers,
Alexis

> Cheers,
> simon

cyvcf2.scm
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