Re: Broadinstitute catch - elegant way to disable tests requiring online access?
On 28 July 2021 3:00:08 am IST, Nilesh Patra <nilesh@debian.org> wrote:
>Hi Steffen,
>
>On Tue, 27 Jul 2021 at 23:05, Steffen Möller <steffen_moeller@gmx.de>
>wrote:
>
>> Hi Nilesh,
>>
>> Thank you tons for thinking along.
>>
>> It took me a bit but. Too long. The answer is that git does not lose
>the
>> sensation of a file being a git lfs reference even when you download
>a
>> tar.gz. For some reason I had expected that all genomes were truly
>gzipped
>> fasta files, but no, they were still references. Maybe I had
>inadvertently
>> transformed a few to what they point to during a first build and that
>is
>> why I then did not find the issue a bit earlier.
>>
>> The import of pristine-tar has worked after removing .gitattributes,
>but
>> then the git lfs references were still in the tarball and the
>upstream
>> branch. pristine-tar could be pushed, but then the other branches
>would
>> trigger git lfs errors when pushed to salsa. Only after having all
>fasta.gz
>> lfs files removed, the upload went smoothly and you all now find this
>on
>> https://salsa.debian.org/med-team/broad-catch
>>
>Is that really intended?
>We would not be able to run tests in this case since you essentially
>ended
>up repacking it , since several tests seem to be using that data.
>
>BTW, I tried to do a little solution for the lfs thingy, for it to not
>store "references" and committed it to my personal repository[1]
>Can you have a look and let me know if it looks sensible?
>
>Also, you might as well want to have a look at pristine-lfs[2] which
>could
>be interesting to use. I've attempted to use this too, please consider
>taking a look
>I admit, I'm not very used to the lfs workflow, so something could be
>wrong
>for sure.
>
>Not sure why the CI fails though -- probably it does not work fine with
>lfs, but just thinking of it as a ground for more ideas here :)
>I can clone it locally in a different space and re-produce the tarball,
>and
>I fixed a few tests (not all) -- please consider trying once and let me
>know
Edit: all tests pass now on a clean chroot for me
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
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