On 12/4/22 20:39, Étienne Mollier wrote:
[...]
In such configuration, assert would test whether $1 is true,
and print $2 if it is not. I believe you might have wanted to
conver to:
assert $1 == $2
Oh. I did a direct substitution of `eq_(*)` with `assert` thinking that
they do the sa
Hello team,
I just updated python-gftparse[1] to a new upstream version and added a
patch to make the switch from nose->pytest (Bug #1018506).
Can somebody review + sponsor an upload please ?
[1] - https://salsa.debian.org/med-team/python-gtfparse
Thanks
--
Mohammed Bilal
2D65 BC1E B966 5A6E
On 12/4/22 00:53, Étienne Mollier wrote:
I'm under the impression I'm missing the commit.
Oops, sorry ! I forgot to `git push`. Done that now.
Thanks :)
--
Mohammed Bilal
2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F
OpenPGP_signature
Description: OpenPGP digital signature
On 12/3/22 23:50, Étienne Mollier wrote:
[..]
test_ncbi needs to be skipped.
Done. Thanks for spotting this :)
Also can you take a look at python-biom-format[2]. I've pushed a fix for
#1018464. The fix was a simple one (remove depends on nose). Upstream
already uses pytest. Someone probabl
Hello team,
I just pushed a a fix for porting insilicoseq's test to pytest. I would
request someone from the team to take a look and sponsor my changes
[1] - https://salsa.debian.org/med-team/insilicoseq
Thanks :)
--
Mohammed Bilal
2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F
OpenPGP_s
&literal=0
--
Thanks & Regards
Mohd Bilal
OpenPGP_signature
Description: OpenPGP digital signature
Hello team \o/ ,
I'm Mohammed Bilal and I've been the GSoC intern working with the Debian
Med Team during 2022 and the one who've been bugging this mailing list
for the past few months.This is my final report for the GSoC project
"Quality Assurance and Continuous Integration for Applications i
Hello team,
I tried adding autopkgtest for kmerresistance[1] but I'm getting an
error when using the installed binary.
I'm not able to run the binary with example data[2] from the package
installed via apt
But I'm able to run the command as expected if I built the binary from
source
I've
Hello team,
I've added autopkgtest for tvc[1]. Requesting someone to review and
sponsor my changes.
[1] -https://salsa.debian.org/med-team/tvc
Thanks
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E B966 5A6E 97F9 730A
Hello team,
I've added autopkgtests for gatb-core[1]. For the reprotest failure, the
source includes some system level interfaces[2] that fetches system info
which is used in other parts of the code. I tried patching but one or
the other way it ends in a build failure. So it would be better if
On 31 August 2022 8:57:33 pm IST, Nilesh Patra wrote:
>Granted you DM access.
>Also, for the libbigwig upload you did yesterday, the autopkgtest
>is failing on some archs.
>
>Can you fix it? (Feel free to upload yourself)
>
Sure, I'll take a look
--
Sent from my Android device with K-9 Mail. P
Hello team,
I've added autopkgtest for libncl[1]. Requesting a review and sponsor
for my changes.
[1] - https://salsa.debian.org/med-team/libncl
Thanks
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E B966 5A6E 97F9 730
Hello team,
I've added autopkgtest for libbigwig[1] and also fixed the blhc failure.
Requesting a review and sponsor for my changes.
[1] - https://salsa.debian.org/med-team/libbigwig
Thanks
--
╭───╮
│ Mohammed Bilal
On 8/28/22 23:14, Nilesh Patra wrote:
Rather than printing the ast, it'd be better to `assert' it equal to expected
output.
Please make this change before you upload.
It'd be even better if you can play around with the ast dump and compare
relevant parts.
I have made the changes as suggeste
Hello team,
I've added autopkgtest for python-wdlparse[1]. Requesting someone to
review and sponsor my changes.
[1] - https://salsa.debian.org/med-team/python-wdlparse
Thanks
--
╭───╮
│ Mohammed Bilal│
│ 2D65
Hello team,
I've added autopkgtests for emperor[1]. Requesting someone to review and
sponsor my changes.
[1] - https://salsa.debian.org/med-team/emperor
Thanks
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E B966 5A6E
On 8/23/22 00:39, Nilesh Patra wrote:
- Is it possible to run build time tests also as autopkgtests along with your
sample test?
If so, please do so.
- The indentation is inconsistent across `concat' and `test_basic' function,
please fix this
also format it a bit better.
Made the suggeste
Hello team,
I've added autopkgtest for nipype[1] and also fixed the reprotest
failures.Requesting someone to review my changes and sponsor the same.
[1] - https://salsa.debian.org/med-team/nipype
Thanks
--
╭───╮
│ Mohammed Bilal
On 8/20/22 19:34, Mathieu Malaterre wrote:
Are you going to make dcmtk depends on python package ?
```
cp -a /usr/lib/python3/dist-packages/pydicom/data/test_files/CT_small.dcm
"${AUTOPKGTEST_TMP}"
```
I've included python3-pydicom as a test dependency for the testbed,
Regular users of dcm
Hello team,
I have added autopkgtests for dcmtk[1]. Requesting a review on my
changes and sponsor the upload if everything's good.
I have included the autopkgtest log as an attachment since salsa-ci
doesn't have an autopkgtest job for this package.
[1] -
https://salsa.debian.org/med-team/d
Hello team ,
I've updated delly[1] to the latest upstream version (1.3.1) . Also I've
added in autopkgtests,fixed blhc and made the builds reproducible. The
CI shows an autopkgtest failure as of now[2] which I think is related to
an issue with the CI infra. The autopkgtests works fine when run
On 8/9/22 19:44, Andreas Tille wrote:
No objections, Andreas.
Thanks , I've opened a request for removal[1] with the FTP Master Team.
[1] - https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016909
--
╭───╮
│ Mohammed Bilal
On 8/8/22 18:05, Nilesh Patra wrote:
On 8/8/22 5:50 PM, Mohd Bilal wrote:
Hello Team,
I took a look at this and it seems the upstream[1] is not active
anymore and Ubuntu already has a long standing bug report[2] regarding
the same issue which hasn't seen any progress yet.
I tried t
On Sat, 6 Aug 2022 15:45:55 +0200 Paul Gevers wrote:
Source: zalign
Version: 0.9.1-6
Severity: serious
User: debian...@lists.debian.org
Usertags: fails-always
Dear maintainer(s),
You recently added an autopkgtest to your package zalign, great.
However, it fails. Currently this failure is bloc
Hello team,
I've fixed the autopkgtest regressions for megadepth[1] and mothur[2].
For megadepth the upstream[3] currently doesn't support architectures
outside x86. So as a workaround we may have to skip the tests in s390 arch.
Requesting someone to review and sponsor these packages[4][5].
Hello team,
gdcm[1] had an autopkgtest regression on s390x[2] which was preventing
its migration to testing. This was possibly due to the test data being
encoded for little endian hardware based on my understanding. So I've
changed the test data and now the test passes on s390. Here's the outp
On 8/1/22 19:54, Nilesh Patra wrote:
Add in a "skip-not-installable" restriction as well before you upload.
Done and Uploaded :)
Thanks
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 852
Hello team,
I've added autopkgtest for plastimatch[1].Requesting someone to review
and sponsor the same.
[1] - https://salsa.debian.org/med-team/plastimatch
Regards,
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E B966
Hello team,
I've added autopkgtest for zaling[1]. Requesting someone to review and
sponsor/grant permissions for the same.
[1] - https://salsa.debian.org/med-team/zalign
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E
Hello team,
I tried fixing #1013364 and was unsuccessful in it. There's little much
documentation available about the program on other architectures. So as
a workaround I have disabled the autopkgtest for s390 and i386 archs.
Requesting someone to sponsor these changes[2].
[1] - https://bugs
Hello team,
I've added autopkgtests for emmax[1].Requesting someone to review and
sponsor my changes.
[1] - https://salsa.debian.org/med-team/emmax
Thanks
--
╭───╮
│ Mohammed Bilal│
│ 2D65 BC1E B966 5A6E 97F9
Hello team,
I've added autopkgtests for rockhopper[1]. The piuparts currently fails
due to an issue with the pipeline[2] and had no problems when tested
locally. Requesting someone to review and sponsor my changes.
[1] - https://salsa.debian.org/med-team/rockhopper/
[2] - https://salsa.debian
Hello team,
I have added autopkgtests for megadepth[1]. Requesting someone to review
and sponsor my changes.
[1] - https://salsa.debian.org/med-team/megadepth
--
╭╮
│ Mohammed Bilal │
│ 2D65 BC1E B966 5A6E
On 7/4/22 19:54, Nilesh Patra wrote:
Unfortunately that is not an autopkgtest, only a smoke test (which does
nothing more than an `import`)
Can you add in a proper test for it?
Sorry. I added the smoke test by looking at other biomaj packages. I've
checked the docs[5] seems like it needs a
Hello team,
I've added autopkgtest for biomaj3-cli[1] and gdcm[2]. Requesting
someone to review and sponsor these changes.
Also I'm trying to add autopkgtest for elastix but I'm blocked by a
build failure in the CI. It looks like a problem with CI to me.Can
anyone help in fixing this build f
Hello team,
I've added autopkgtests for nifti2dicom[1].Requesting someone to review
my changes
[1] - https://salsa.debian.org/med-team/nifti2dicom
Regards
--
╭╮
│ Mohammed Bilal │
│ 2D65 BC1E B966 5A6E 97F
Good Day Team,
The upstream responded[1] to my query regarding the license of busco
datasets. Looks like it uses a non-free license (CC-BY-ND-4.0).
So I think adding this test data would make the package non-free.
Seeking everyone's opinion on what should be done next :)
[1] - https://gitla
I compared the size of installed package (apt show busco) with the size of
test data. So thought of adding the test data outside the debian directory as
suggested in the debian med policy[4]
[4] - https://med-team.pages.debian.net/policy/#embedding-large-test-data
Hello team,
I have added an autopkgtest for busco[1] as mentioned in bug report[2].
The license for the test data needs to be added. I have opened an
issue[3] upstream asking for clarification. Requesting someone to review
my changes .
Thanks,
rmb
[1] - https://salsa.debian.org/med-team/bu
On 6/3/22 00:21, Nilesh Patra wrote:
Also, please fix the lintian warnings (you added copyr in a wrong order as it
seems)
| W: gifticlib source: globbing-patterns-out-of-order debian/tests/data/new.gii
debian/* debian/tests/data/new.gii [debian/copyright:16]
| W: gifticlib source: missing-lic
On 6/2/22 01:46, Étienne Mollier wrote:
Hi Mohd Bilal,
Mohd Bilal, on 2022-06-01:
I've added autopkgtests for gifticlib[1].However the reprotest fails
currently. The error log looks similar to that of nifticlib. So should I
disable reprotest as done in nifticlib ?
[1] -
Hello team,
I've added autopkgtests for gifticlib[1].However the reprotest fails
currently. The error log looks similar to that of nifticlib. So should I
disable reprotest as done in nifticlib ?
[1] - https://salsa.debian.org/med-team/gifticlib/
Regards
--
╭─
On 5/31/22 22:40, Nilesh Patra wrote:
On Tue, May 31, 2022 at 10:10:45PM +0530, Mohd Bilal wrote:
I've added autopkgtests for nifticlib[1]. Requesting someone to review
and sponsor my changes.
Permissions granted, please wait for the mail to arrive.
Also, disable reprotest in sal
Hello team,
I've added autopkgtests for nifticlib[1]. Requesting someone to review
and sponsor my changes.
[1] - https://salsa.debian.org/med-team/nifticlib
Regards
--
╭╮
│ Mohammed Bilal │
│ 2D65 BC1E B966
Hello team,
I've added autopkgtests for dicomnifti[1]. Requesting someone to review
and sponsor/grant permissions.
[1] - https://salsa.debian.org/med-team/dicomnifti
Regards
--
╭╮
│ Mohammed Bilal │
│ 2D65 B
Hello team,
I've added autopkgtests for minc-tools[1]. Requesting someone to review.
If ok you may grant me upload permissions and I'll upload the same :)
[1] - https://salsa.debian.org/med-team/minc-tools
Regards
--
╭╮
│ Mohammed Bilal
On 5/24/22 00:31, Nilesh Patra wrote:
[ CCing list again ]
On Tue, May 24, 2022 at 12:26:54AM +0530, Mohd Bilal wrote:
On 5/24/22 00:17, Nilesh Patra wrote:
On Tue, May 24, 2022 at 12:01:22AM +0530, Mohd Bilal wrote:
I've added autopkgtests for openslide[1]. Requesting someone to r
Hello team,
I've added autopkgtests for openslide[1]. Requesting someone to review
and sponsor my changes.
[1] - https://salsa.debian.org/med-team/openslide
Regards,
--
╭╮
│ Mohammed Bilal │
│ 2D65 BC1E B9
Hello team,
I've added autopkgtests for dcm2niix[1]. Requesting someone to review
and suggest necessary changes. If it is okay please sponsor or grant me
upload permissions for the same.
Also I've had a look at adding autopkgtests for dcmtk[2] but I'm unable
to run any binaries and facing [3
On 5/21/22 00:59, Nilesh Patra wrote:
Hi all,
I hereby welcome Mohammed Bilal for
the GSoC project
"Quality Assurance for Biological and Medical Applications inside Debian"
Congrats Bilal, I hope to have fun mentoring you on this project.
Feel free to ask any questions on the list.
Thank
Andreas Tille wrote:
>Hi,
>
>Am Mon, Apr 11, 2022 at 11:23:13AM - schrieb Mohd Bilal:
>> >1. There is no information given where you obtained the data in
>> > debian/tests/data from. It is good style to add some script that
>> > fetches the dat
Andreas Tille wrote:
>Hi Mohd,
>
>Am Sun, Apr 10, 2022 at 08:08:42PM - schrieb Mohd Bilal:
>> I've added autopkgtest for pplacer[1] . As suggested in the matrix
>room , I've used the test prescribed in the Makefile as well as included
>some of the comma
Hello team,
I've added autopkgtest for pplacer[1] . As suggested in the matrix room , I've
used the test prescribed in the Makefile as well as included some of the
commands from the pplacer tutorial[2] .
Requesting someone to review and sponsor my changes.
[1] - https://salsa.debian.org/med-te
Nilesh Patra wrote:
>On Thu, Apr 07, 2022 at 10:37:24PM +0200, Andreas Tille wrote:
>> Am Thu, Apr 07, 2022 at 06:52:47PM - schrieb Mohd Bilal:
>> > I've enabled salsa ci and added autopkgtest for
>python-bioblend[1] . Requesting someone to review and sponsor my
Hello team,
I've enabled salsa ci and added autopkgtest for python-bioblend[1] . Requesting
someone to review and sponsor my changes.
[1] - https://salsa.debian.org/med-team/python-bioblend
Regards,
rmb-BEGIN PGP MESSAGE-
owGbwMvMwMW4+euUoFbFefKMa+4lcRZnpucllpQWpSb5Gx3ySM3JyVcoSU3M1eHi
Andreas Tille wrote:
>Hi Mohd,
>
>Am Wed, Apr 06, 2022 at 04:07:10PM - schrieb Mohd Bilal:
>> Hello team,
>>
>> I've added autopkgtest for bmtk[1] and would like someone to review
>and sponsor my changes.
>
>Thanks a lot for your effort.
>
&
Hello team,
I've added autopkgtest for bmtk[1] and would like someone to review and sponsor
my changes.
However I've some concerns.
https://salsa.debian.org/med-team/bmtk/-/tree/master/bmtk/simulator/filternet/lgnmodel/cell_metrics
has some csv files.
But I cannot find these csv files in
/usr
Nilesh Patra wrote:
>On Mon, Apr 04, 2022 at 04:58:53PM -0000, Mohd Bilal wrote:
>> I would like to add autopkgtest for atropos[1] but I'm stuck with
>some .pyx files that the tests import from.
>> I guess the tests require these C extensions to be built before running
Hello team,
I would like to add autopkgtest for atropos[1] but I'm stuck with some .pyx
files that the tests import from. I guess the tests require these C extensions
to be built before running the test. I've tried building[2] the extensions
using `$py setup.py build_ext --inplace` but it didn'
Nilesh Patra wrote:
>On Sat, Apr 02, 2022 at 11:16:07PM +0000, Mohd Bilal wrote:
>> Hello team,
>>
>> I've added autopkgtest for the package intake[1]. I've opened an
>MR[2] and would like someone to review my changes. I would also require
>sponsoring fo
Hello team,
I've added autopkgtest for the package intake[1]. I've opened an MR[2] and
would like someone to review my changes. I would also require sponsoring for my
changes.
Thanks & Regards,
rmb
[1] - https://salsa.debian.org/med-team/intake
[2] - https://salsa.debian.org/med-team/intake/-
Hello team,
I'm interested in contributing towards the Debian Med Team and would like to be
a part of it.I've had beginner experiences packaging some ruby gems for the
Ruby Team.
I've tried adding autopkgtest for python-datacache[1],parallel-fastq-dump[2]
which are maintained by the Debian Med
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