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* packaging python-cyvcf2
@ 2024-03-22  1:03 Alexis Simon
  2024-03-22  1:03 ` Alexis Simon via Guix-Science
  2024-03-22 15:25 ` Simon Tournier
  0 siblings, 2 replies; 6+ messages in thread
From: Alexis Simon @ 2024-03-22  1:03 UTC (permalink / raw)
  To: help-guix, guix-science

[-- Attachment #1: Type: text/plain, Size: 1007 bytes --]

Hi, I've spent nearly the day on this and it's driving me crazy.

I am trying to package this cyvcf2 [1]
I am attaching the packaging I've tried.

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]

The .configure file is present in the failed build, so there must be 
something going on with the setup.py not managing to change directory to 
htslib in the build_htslib function.

If anyone has any guidelines to debug this further it would be much 
appreciated.

Thanks,
Alexis

[1] https://github.com/brentp/cyvcf2/
[2] https://guix.gnu.org/manual/en/guix.html#Debugging-Build-Failures

[-- Attachment #2: cyvcf2.scm --]
[-- Type: text/x-scheme, Size: 2158 bytes --]

(define-module (cyvcf2)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages tls)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system python)
  #:use-module (guix build-system cargo)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system pyproject))

(define-public python-cyvcf2
  (package
    (name "python-cyvcf2")
    (version "0.30.28")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cyvcf2" version))
       (sha256
        (base32 "03ycp7php5nzvhgj89k8js8z2xm3i8d1f76jlsfdy472f0apgryx"))))
    (build-system python-build-system)
    (arguments
     `(#:use-setuptools? #f
       #:phases
        (modify-phases %standard-phases
          (add-before 'build 'setenv
             (lambda _
                     (setenv "CYVCF2_HTSLIB_MODE" "BUILTIN")))))) ; unnecessary
    (propagated-inputs (list python-click
                             python-coloredlogs
                             python-numpy))
    (native-inputs (list zlib
                         libdeflate
                         curl
                         openssl
                         autoconf
                         automake
                         ; htslib
                         python-cython))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "fast vcf parsing with cython + htslib")
    (description "fast vcf parsing with cython + htslib")
    (license license:expat)))


^ permalink raw reply	[flat|nested] 6+ messages in thread

* packaging python-cyvcf2
  2024-03-22  1:03 packaging python-cyvcf2 Alexis Simon
@ 2024-03-22  1:03 ` Alexis Simon via Guix-Science
  2024-03-22 15:25 ` Simon Tournier
  1 sibling, 0 replies; 6+ messages in thread
From: Alexis Simon via Guix-Science @ 2024-03-22  1:03 UTC (permalink / raw)
  To: help-guix, guix-science

[-- Attachment #1: Type: text/plain, Size: 1007 bytes --]

Hi, I've spent nearly the day on this and it's driving me crazy.

I am trying to package this cyvcf2 [1]
I am attaching the packaging I've tried.

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]

The .configure file is present in the failed build, so there must be 
something going on with the setup.py not managing to change directory to 
htslib in the build_htslib function.

If anyone has any guidelines to debug this further it would be much 
appreciated.

Thanks,
Alexis

[1] https://github.com/brentp/cyvcf2/
[2] https://guix.gnu.org/manual/en/guix.html#Debugging-Build-Failures

[-- Attachment #2: cyvcf2.scm --]
[-- Type: text/x-scheme, Size: 2158 bytes --]

(define-module (cyvcf2)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages tls)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system python)
  #:use-module (guix build-system cargo)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system pyproject))

(define-public python-cyvcf2
  (package
    (name "python-cyvcf2")
    (version "0.30.28")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cyvcf2" version))
       (sha256
        (base32 "03ycp7php5nzvhgj89k8js8z2xm3i8d1f76jlsfdy472f0apgryx"))))
    (build-system python-build-system)
    (arguments
     `(#:use-setuptools? #f
       #:phases
        (modify-phases %standard-phases
          (add-before 'build 'setenv
             (lambda _
                     (setenv "CYVCF2_HTSLIB_MODE" "BUILTIN")))))) ; unnecessary
    (propagated-inputs (list python-click
                             python-coloredlogs
                             python-numpy))
    (native-inputs (list zlib
                         libdeflate
                         curl
                         openssl
                         autoconf
                         automake
                         ; htslib
                         python-cython))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "fast vcf parsing with cython + htslib")
    (description "fast vcf parsing with cython + htslib")
    (license license:expat)))


^ permalink raw reply	[flat|nested] 6+ messages in thread

* Re: packaging python-cyvcf2
  2024-03-22  1:03 packaging python-cyvcf2 Alexis Simon
  2024-03-22  1:03 ` Alexis Simon via Guix-Science
@ 2024-03-22 15:25 ` Simon Tournier
  2024-03-22 19:38   ` Alexis Simon
  1 sibling, 1 reply; 6+ messages in thread
From: Simon Tournier @ 2024-03-22 15:25 UTC (permalink / raw)
  To: Alexis Simon, help-guix, guix-science

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.

Cheers,
simon



^ permalink raw reply	[flat|nested] 6+ messages in thread

* Re: packaging python-cyvcf2
  2024-03-22 15:25 ` Simon Tournier
@ 2024-03-22 19:38   ` Alexis Simon
  2024-03-22 19:38     ` Alexis Simon via Guix-Science
  2024-03-26 15:47     ` Simon Tournier
  0 siblings, 2 replies; 6+ messages in thread
From: Alexis Simon @ 2024-03-22 19:38 UTC (permalink / raw)
  To: Simon Tournier, help-guix, guix-science

[-- Attachment #1: Type: text/plain, Size: 3332 bytes --]


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
> 

[-- Attachment #2: cyvcf2.scm --]
[-- Type: text/x-scheme, Size: 3137 bytes --]

(define-module (cyvcf2)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages tls)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build-system python)
  #:use-module (guix build-system cargo)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system pyproject))

(define-public python-cyvcf2
  (package
    (name "python-cyvcf2")
    (version "0.30.28")
    (source
     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/brentp/cyvcf2")
              (commit (string-append "v" version))))
        (sha256
          (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            (delete-file-recursively "htslib")))))
    (build-system pyproject-build-system)
    (arguments
     `(#:tests? #f
       #:phases
        (modify-phases %standard-phases
          ; (add-before 'check 'rm-folder
          ;   (lambda _
          ;           (copy-recursively "cyvcf2/tests" "./tests")
          ;           (delete-file-recursively "cyvcf2")
          ;           (mkdir-p "cyvcf2")
          ;           (copy-recursively "tests" "cyvcf2/tests")))
          (add-after 'unpack 'fix-setup
             (lambda* (#:key inputs #:allow-other-keys)
                     (substitute* "setup.py"
                                  ((" or not check_libhts\\(\\)") "")
                                  (("library_dirs=htslib_library_dirs")
                                   (string-append "library_dirs=[\"" (assoc-ref inputs "htslib") "/lib\"]"))
                                  (("\\+ htslib_include_dirs")
                                   (string-append "+ [\"" (assoc-ref inputs "htslib") "/include\"]")))))
          (add-before 'build 'setenv
             (lambda _
                     (setenv "CYTHONIZE" "1")
                     (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL"))))))
    (inputs (list htslib zlib libdeflate curl openssl python-cython))
    (native-inputs (list python-pytest))
    (propagated-inputs (list python-click
                             python-coloredlogs
                             python-numpy))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "fast vcf parsing with cython + htslib")
    (description "fast vcf parsing with cython + htslib")
    (license license:expat)))


^ permalink raw reply	[flat|nested] 6+ messages in thread

* Re: packaging python-cyvcf2
  2024-03-22 19:38   ` Alexis Simon
@ 2024-03-22 19:38     ` Alexis Simon via Guix-Science
  2024-03-26 15:47     ` Simon Tournier
  1 sibling, 0 replies; 6+ messages in thread
From: Alexis Simon via Guix-Science @ 2024-03-22 19:38 UTC (permalink / raw)
  To: Simon Tournier, help-guix, guix-science

[-- Attachment #1: Type: text/plain, Size: 3332 bytes --]


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
> 

[-- Attachment #2: cyvcf2.scm --]
[-- Type: text/x-scheme, Size: 3137 bytes --]

(define-module (cyvcf2)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages tls)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build-system python)
  #:use-module (guix build-system cargo)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system pyproject))

(define-public python-cyvcf2
  (package
    (name "python-cyvcf2")
    (version "0.30.28")
    (source
     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/brentp/cyvcf2")
              (commit (string-append "v" version))))
        (sha256
          (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            (delete-file-recursively "htslib")))))
    (build-system pyproject-build-system)
    (arguments
     `(#:tests? #f
       #:phases
        (modify-phases %standard-phases
          ; (add-before 'check 'rm-folder
          ;   (lambda _
          ;           (copy-recursively "cyvcf2/tests" "./tests")
          ;           (delete-file-recursively "cyvcf2")
          ;           (mkdir-p "cyvcf2")
          ;           (copy-recursively "tests" "cyvcf2/tests")))
          (add-after 'unpack 'fix-setup
             (lambda* (#:key inputs #:allow-other-keys)
                     (substitute* "setup.py"
                                  ((" or not check_libhts\\(\\)") "")
                                  (("library_dirs=htslib_library_dirs")
                                   (string-append "library_dirs=[\"" (assoc-ref inputs "htslib") "/lib\"]"))
                                  (("\\+ htslib_include_dirs")
                                   (string-append "+ [\"" (assoc-ref inputs "htslib") "/include\"]")))))
          (add-before 'build 'setenv
             (lambda _
                     (setenv "CYTHONIZE" "1")
                     (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL"))))))
    (inputs (list htslib zlib libdeflate curl openssl python-cython))
    (native-inputs (list python-pytest))
    (propagated-inputs (list python-click
                             python-coloredlogs
                             python-numpy))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "fast vcf parsing with cython + htslib")
    (description "fast vcf parsing with cython + htslib")
    (license license:expat)))


^ permalink raw reply	[flat|nested] 6+ messages in thread

* Re: packaging python-cyvcf2
  2024-03-22 19:38   ` Alexis Simon
  2024-03-22 19:38     ` Alexis Simon via Guix-Science
@ 2024-03-26 15:47     ` Simon Tournier
  1 sibling, 0 replies; 6+ messages in thread
From: Simon Tournier @ 2024-03-26 15:47 UTC (permalink / raw)
  To: Alexis Simon, help-guix, guix-science

Hi Alexis,

On ven., 22 mars 2024 at 12:38, Alexis Simon <alexis.simon@runbox.com> wrote:

> I'm attaching the new version for reference.

Cool!  Well, maybe this package could be part of Guix Science channel or
another.  WDYT?

Cheers,
simon


^ permalink raw reply	[flat|nested] 6+ messages in thread

end of thread, other threads:[~2024-03-26 21:16 UTC | newest]

Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2024-03-22  1:03 packaging python-cyvcf2 Alexis Simon
2024-03-22  1:03 ` Alexis Simon via Guix-Science
2024-03-22 15:25 ` Simon Tournier
2024-03-22 19:38   ` Alexis Simon
2024-03-22 19:38     ` Alexis Simon via Guix-Science
2024-03-26 15:47     ` Simon Tournier

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