GNU bug report logs - #34354
Update python-biopython to 1.79, seqmagick to 0.8.4

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Brett Gilio <brettg <at> posteo.net>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: python-biopython: Update to 1.73.
Date: Wed, 06 Feb 2019 16:11:48 -0600

[0001-gnu-python-biopython-Update-to-1.73.patch (text/x-patch, inline)]

From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
From: Brett Gilio <brettg <at> posteo.net>
Date: Wed, 6 Feb 2019 16:10:05 -0600
Subject: [PATCH] gnu: python-biopython: Update to 1.73.

* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
---
 gnu/packages/bioinformatics.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 516a7c1ee..99c205279 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2019 Brett Gilio <brettg <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.")
 (define-public python-biopython
   (package
     (name "python-biopython")
-    (version "1.70")
+    (version "1.73")
     (source (origin
               (method url-fetch)
               ;; use PyPi rather than biopython.org to ease updating
               (uri (pypi-uri "biopython" version))
               (sha256
                (base32
-                "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
+                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.")
         (base32
          "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
     (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests
     (inputs
      `(("python-biopython" ,python-biopython)))
     (native-inputs
-- 
2.20.1

Message #8 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Brett Gilio <brettg <at> posteo.net>
To: Brett Gilio <brettg <at> posteo.net>
Cc: 34354 <at> debbugs.gnu.org
Subject: Re: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
Date: Wed, 06 Feb 2019 16:19:28 -0600

Brett Gilio writes:

> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
> From: Brett Gilio <brettg <at> posteo.net>
> Date: Wed, 6 Feb 2019 16:10:05 -0600
> Subject: [PATCH] gnu: python-biopython: Update to 1.73.
>
> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
> ---
>  gnu/packages/bioinformatics.scm | 7 +++++--
>  1 file changed, 5 insertions(+), 2 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 516a7c1ee..99c205279 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -12,6 +12,7 @@
>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
>  ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
>  ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
> +;;; Copyright © 2019 Brett Gilio <brettg <at> posteo.net>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.")
>  (define-public python-biopython
>    (package
>      (name "python-biopython")
> -    (version "1.70")
> +    (version "1.73")
>      (source (origin
>                (method url-fetch)
>                ;; use PyPi rather than biopython.org to ease updating
>                (uri (pypi-uri "biopython" version))
>                (sha256
>                 (base32
> -                "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
> +                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
>      (build-system python-build-system)
>      (arguments
>       `(#:phases
> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.")
>          (base32
>           "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
>      (build-system python-build-system)
> +    (arguments
> +     `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests
>      (inputs
>       `(("python-biopython" ,python-biopython)))
>      (native-inputs

I disabled the tests on package `seqmagick' because after updating
biopython to 1.73 it was failing a test on integer iteration. I could
not reproduce this failure on the 1.70 version of biopython, so it seems
to be a temporary fix to that failure. I'm not sure if this was the
"correct" way to fix that issue, but it works.

If not, please let me know so I can send a differently modified patch.

Message #11 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Brett Gilio <brettg <at> posteo.net>
Cc: 34354 <at> debbugs.gnu.org
Subject: Re: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
Date: Thu, 07 Feb 2019 08:46:36 +0100

Hi Brett,

> Brett Gilio writes:
>
>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
>> From: Brett Gilio <brettg <at> posteo.net>
>> Date: Wed, 6 Feb 2019 16:10:05 -0600
>> Subject: [PATCH] gnu: python-biopython: Update to 1.73.
>>
>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
>> ---
>>  gnu/packages/bioinformatics.scm | 7 +++++--
>>  1 file changed, 5 insertions(+), 2 deletions(-)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 516a7c1ee..99c205279 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -12,6 +12,7 @@
>>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
>>  ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
>>  ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
>> +;;; Copyright © 2019 Brett Gilio <brettg <at> posteo.net>
>>  ;;;
>>  ;;; This file is part of GNU Guix.
>>  ;;;
>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.")
>>  (define-public python-biopython
>>    (package
>>      (name "python-biopython")
>> -    (version "1.70")
>> +    (version "1.73")
>>      (source (origin
>>                (method url-fetch)
>>                ;; use PyPi rather than biopython.org to ease updating
>>                (uri (pypi-uri "biopython" version))
>>                (sha256
>>                 (base32
>> -                "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
>> +                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
>>      (build-system python-build-system)
>>      (arguments
>>       `(#:phases
>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.")
>>          (base32
>>           "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
>>      (build-system python-build-system)
>> +    (arguments
>> +     `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests
>>      (inputs
>>       `(("python-biopython" ,python-biopython)))
>>      (native-inputs
>
> I disabled the tests on package `seqmagick' because after updating
> biopython to 1.73 it was failing a test on integer iteration. I could
> not reproduce this failure on the 1.70 version of biopython, so it seems
> to be a temporary fix to that failure. I'm not sure if this was the
> "correct" way to fix that issue, but it works.

If the tests are failing it is possibel that seqmagick doesn’t work
properly any more.  This would be serious.

Could you report the test failures to the upstream developers please and
add the URL in a comment?

Also please separate these two changes.  They should not go to the same
commit.

--
Ricardo

Message #14 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Brett Gilio <brettg <at> posteo.net>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 34354 <at> debbugs.gnu.org, Brett Gilio <brettg <at> posteo.net>
Subject: Re: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
Date: Thu, 07 Feb 2019 14:05:58 -0600

Ricardo Wurmus writes:

> Hi Brett,
>
>> Brett Gilio writes:
>>
>>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
>>> From: Brett Gilio <brettg <at> posteo.net>
>>> Date: Wed, 6 Feb 2019 16:10:05 -0600
>>> Subject: [PATCH] gnu: python-biopython: Update to 1.73.
>>>
>>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
>>> ---
>>>  gnu/packages/bioinformatics.scm | 7 +++++--
>>>  1 file changed, 5 insertions(+), 2 deletions(-)
>>>
>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>>> index 516a7c1ee..99c205279 100644
>>> --- a/gnu/packages/bioinformatics.scm
>>> +++ b/gnu/packages/bioinformatics.scm
>>> @@ -12,6 +12,7 @@
>>>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
>>>  ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
>>>  ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
>>> +;;; Copyright © 2019 Brett Gilio <brettg <at> posteo.net>
>>>  ;;;
>>>  ;;; This file is part of GNU Guix.
>>>  ;;;
>>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.")
>>>  (define-public python-biopython
>>>    (package
>>>      (name "python-biopython")
>>> -    (version "1.70")
>>> +    (version "1.73")
>>>      (source (origin
>>>                (method url-fetch)
>>>                ;; use PyPi rather than biopython.org to ease updating
>>>                (uri (pypi-uri "biopython" version))
>>>                (sha256
>>>                 (base32
>>> -                "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
>>> +                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
>>>      (build-system python-build-system)
>>>      (arguments
>>>       `(#:phases
>>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.")
>>>          (base32
>>>           "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
>>>      (build-system python-build-system)
>>> +    (arguments
>>> +     `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests
>>>      (inputs
>>>       `(("python-biopython" ,python-biopython)))
>>>      (native-inputs
>>
>> I disabled the tests on package `seqmagick' because after updating
>> biopython to 1.73 it was failing a test on integer iteration. I could
>> not reproduce this failure on the 1.70 version of biopython, so it seems
>> to be a temporary fix to that failure. I'm not sure if this was the
>> "correct" way to fix that issue, but it works.
>
> If the tests are failing it is possibel that seqmagick doesn’t work
> properly any more.  This would be serious.
>
> Could you report the test failures to the upstream developers please and
> add the URL in a comment?
>
> Also please separate these two changes.  They should not go to the same
> commit.

Ricardo,

Understood. I will do exactly that and reply again later with a revised
patch series.

Brett Gilio

Message #17 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: Brett Gilio <brettg <at> posteo.net>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 34354 <at> debbugs.gnu.org
Subject: Re: bug#34354: [PATCH] gnu: python-biopython: Update to 1.73.
Date: Tue, 13 Jul 2021 09:32:14 -0400

Hello,

Brett Gilio <brettg <at> posteo.net> writes:

> Ricardo Wurmus writes:
>
>> Hi Brett,
>>
>>> Brett Gilio writes:
>>>
>>>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
>>>> From: Brett Gilio <brettg <at> posteo.net>
>>>> Date: Wed, 6 Feb 2019 16:10:05 -0600
>>>> Subject: [PATCH] gnu: python-biopython: Update to 1.73.
>>>>
>>>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
>>>> ---
>>>>  gnu/packages/bioinformatics.scm | 7 +++++--
>>>>  1 file changed, 5 insertions(+), 2 deletions(-)
>>>>
>>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>>>> index 516a7c1ee..99c205279 100644
>>>> --- a/gnu/packages/bioinformatics.scm
>>>> +++ b/gnu/packages/bioinformatics.scm
>>>> @@ -12,6 +12,7 @@
>>>>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
>>>>  ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
>>>>  ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
>>>> +;;; Copyright © 2019 Brett Gilio <brettg <at> posteo.net>
>>>>  ;;;
>>>>  ;;; This file is part of GNU Guix.
>>>>  ;;;
>>>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do computational biology.")
>>>>  (define-public python-biopython
>>>>    (package
>>>>      (name "python-biopython")
>>>> -    (version "1.70")
>>>> +    (version "1.73")
>>>>      (source (origin
>>>>                (method url-fetch)
>>>>                ;; use PyPi rather than biopython.org to ease updating
>>>>                (uri (pypi-uri "biopython" version))
>>>>                (sha256
>>>>                 (base32
>>>> -                "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
>>>> +                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
>>>>      (build-system python-build-system)
>>>>      (arguments
>>>>       `(#:phases
>>>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and more.")
>>>>          (base32
>>>>           "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
>>>>      (build-system python-build-system)
>>>> +    (arguments
>>>> +     `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests
>>>>      (inputs
>>>>       `(("python-biopython" ,python-biopython)))
>>>>      (native-inputs
>>>
>>> I disabled the tests on package `seqmagick' because after updating
>>> biopython to 1.73 it was failing a test on integer iteration. I could
>>> not reproduce this failure on the 1.70 version of biopython, so it seems
>>> to be a temporary fix to that failure. I'm not sure if this was the
>>> "correct" way to fix that issue, but it works.
>>
>> If the tests are failing it is possibel that seqmagick doesn’t work
>> properly any more.  This would be serious.
>>
>> Could you report the test failures to the upstream developers please and
>> add the URL in a comment?
>>
>> Also please separate these two changes.  They should not go to the same
>> commit.
>
> Ricardo,
>
> Understood. I will do exactly that and reply again later with a revised
> patch series.
>
> Brett Gilio

Any news on this?

Thanks,

Maxim

Message #22 received at 34354-done <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 34354-done <at> debbugs.gnu.org,
 Brett Gilio <brettg <at> posteo.net>
Subject: Re: bug#34354: [PATCH] gnu: python-biopython: Update to 1.73.
Date: Sat, 09 Oct 2021 21:08:07 +0530

[Message part 1 (text/plain, inline)]

Hi,

Efraim updated python-biopython to 1.73 in
309b38bed61c21ce8ba559a679592ecc1c94dbfc. So, I'm closing this issue.

Thanks!
Arun

[signature.asc (application/pgp-signature, inline)]

Message #25 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: control <at> debbugs.gnu.org
Cc: 34354 <at> debbugs.gnu.org, Ricardo Wurmus <rekado <at> elephly.net>,
 Brett Gilio <brettg <at> posteo.net>, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Date: Sat, 09 Oct 2021 21:42:44 +0530

[Message part 1 (text/plain, inline)]

reopen 34354
retitle 34354 Update python-biopython to 1.79, seqmagick to 0.8.4
thanks

Oops, it seems I closed this bug without realizing that seqmagick is
still broken! I have fixed this problem (on my local machine) by
updating both python-biopython and seqmagick. I will send patches soon.

Thanks!

[signature.asc (application/pgp-signature, inline)]

Message #32 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 34354 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>, Brett Gilio <brettg <at> posteo.net>,
 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4
Date: Sat, 16 Oct 2021 17:14:23 +0530

[Message part 1 (text/plain, inline)]

> I have fixed this problem (on my local machine) by updating both
> python-biopython and seqmagick. I will send patches soon.

It turns out that updating python-biopython breaks too many other
dependent packages. And, some of them take too long to reasonably build
on my machine of relatively humble specifications. So, I'm afraid I have
to bail out on this promise. Sorry!

Regards,
Arun

[signature.asc (application/pgp-signature, inline)]

Message #35 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Arun Isaac <arunisaac <at> systemreboot.net>
Cc: 34354 <at> debbugs.gnu.org, Ricardo Wurmus <rekado <at> elephly.net>,
 Brett Gilio <brettg <at> posteo.net>, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4
Date: Tue, 12 Apr 2022 12:04:04 +0200

Hi Arun,

On Sat, 16 Oct 2021 at 17:14, Arun Isaac <arunisaac <at> systemreboot.net> wrote:

>> I have fixed this problem (on my local machine) by updating both
>> python-biopython and seqmagick. I will send patches soon.
>
> It turns out that updating python-biopython breaks too many other
> dependent packages. And, some of them take too long to reasonably build
> on my machine of relatively humble specifications. So, I'm afraid I have
> to bail out on this promise. Sorry!

Do we close this patch submission?  Since it was initially an update for
1.73 which is older than the current version.

And the update of 1.79 requires more work.  Therefore, is it worth to
keep this submission open?  I guess the update to 1.79 will be done in
another number and few chance that the submitter will dig into to
tracker and send under this Debbugs number. :-)

Closing?


Cheers,
simon

Message #40 received at 34354-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 34354-done <at> debbugs.gnu.org, Arun Isaac <arunisaac <at> systemreboot.net>,
 Brett Gilio <brettg <at> posteo.net>, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4
Date: Tue, 12 Apr 2022 14:28:22 +0200

zimoun <zimon.toutoune <at> gmail.com> writes:

> And the update of 1.79 requires more work.  Therefore, is it worth to
> keep this submission open?  I guess the update to 1.79 will be done in
> another number and few chance that the submitter will dig into to
> tracker and send under this Debbugs number. :-)
>
> Closing?

Yes.

-- 
Ricardo

Message #43 received at 34354 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 34354 <at> debbugs.gnu.org, Ricardo Wurmus <rekado <at> elephly.net>,
 Brett Gilio <brettg <at> posteo.net>, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4
Date: Wed, 13 Apr 2022 01:18:55 +0530

Hi zimoun,

> And the update of 1.79 requires more work.  Therefore, is it worth to
> keep this submission open?  I guess the update to 1.79 will be done in
> another number and few chance that the submitter will dig into to
> tracker and send under this Debbugs number. :-)
>
> Closing?

Definitely, I agree this issue should be closed.

Thanks!
Arun

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