Re: PyEnsembl - how does that help us?

[Nilesh Patra]

On 5/20/21 8:38 PM, Steffen Möller wrote:

>>> datacache: https://salsa.debian.org/med-team/python-datacache

Regarding datacache, I suppose the copyright holder should be "Mount Sinai 
School of Medicine" instead of
"Alex Rubinsteyn " -- since the former is what is 
written in all the files.
If you agree, I'll change this and upload. Rest changes from my end for this 
package are done

Nilesh


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Re: PyEnsembl - how does that help us?

[Steffen Möller]

Am 20.05.21 um 20:01 schrieb Nilesh Patra:
>
> On 5/20/21 8:38 PM, Steffen Möller wrote:
>> Am 20.05.21 um 16:36 schrieb Nilesh Patra:
>>> Hi,
>>>
>>> On 5/20/21 4:09 PM, Steffen Möller wrote:
 Am 20.05.21 um 12:19 schrieb Nilesh Patra:
> On Thu, 20 May, 2021, 3:45 pm Steffen Möller,  > wrote:
>
>
> Am 20.05.21 um 11:42 schrieb Andreas Tille:
> > On Thu, May 20, 2021 at 11:00:59AM +0530, Nilesh Patra wrote:
> >> This can be uploaded to NEW right now, no?
> > +1
> My fear was that this would take energies away from finishing the
> release. But yes, happily so.
>
>
> I think release situation for the med team's end is good.
> Since you told me and Etienne in the last video conference that your keys 
> expired - do you need sponsoring?
>
> If so, mind linking the repos here?
 memoized_property: 
 https://salsa.debian.org/python-team/packages/python-memoized-property
 serializable: 
 https://salsa.debian.org/python-team/packages/python-serializable
 typechecks: https://salsa.debian.org/med-team/python-typechecks
 datacache: https://salsa.debian.org/med-team/python-datacache
 gftparse: https://salsa.debian.org/med-team/python-gtfparse
 pyensembl: https://salsa.debian.org/med-team/pyensembl
 xpore: https://salsa.debian.org/med-team/xpore
>>> Uploaded: memoized_property, serializable, typechecks, gftparse after some 
>>> changes, and enabled salsa CI (consider taking a look)
>>>
>>> For xpore: There is a "Suggests: python-xpore-doc" However, there is no 
>>> such -doc package. The docs look good and should be built. Did you forget 
>>> to push in any case?
>> I was just sloppy - please remove that suggestion.
> I added a -doc package since building the docs looks good here. However one 
> question: the package vendors two binaries: usr/bin/xpore-dataprep and 
> usr/bin/xpore-diffmod
> Is this a python application or a python library? Or both?
> If it is application, the package needs renaming to simply xpore.
> If it is both, the binaries should go into a different binary package -- 
> thoughts?

Application, after another look at
https://xpore.readthedocs.io/en/latest/quickstart.html .

Sorry and thanks!

Steffen

Re: PyEnsembl - how does that help us?

[Steffen Möller]

Am 21.05.21 um 14:15 schrieb Nilesh Patra:
> On 5/20/21 8:38 PM, Steffen Möller wrote:
>
 datacache: https://salsa.debian.org/med-team/python-datacache
> Regarding datacache, I suppose the copyright holder should be "Mount Sinai 
> School of Medicine" instead of
> "Alex Rubinsteyn " -- since the former is what is 
> written in all the files.
> If you agree, I'll change this and upload. Rest changes from my end for this 
> package are done

Agreed. Thank you!

Steffen

Re: PyEnsembl - how does that help us?

[Nilesh Patra]

Hi Steffen,

I believe I have uploaded all 7 packages after making lintian happy and doing a 
few QA checks. I haven't added autopkgtest to xpore yet.
It seems doable, will try doing it in the next upload (after it gets accepted)

Thanks a lot for all your work!

Nilesh



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Re: PyEnsembl - how does that help us?

[Steffen Möller]

Hi Nilesh,

Am 21.05.21 um 20:12 schrieb Nilesh Patra:
> Hi Steffen,
>
> I believe I have uploaded all 7 packages after making lintian happy and doing 
> a few QA checks. I haven't added autopkgtest to xpore yet.
> It seems doable, will try doing it in the next upload (after it gets accepted)
>
> Thanks a lot for all your work!

Well, thank _you_! This dragged in much more than I thought it would, I
must admit.

I am currently addressing flappie - the source tree in salsa misses
files that had to be checked out with git lfs (large file support).
Funnily enough, the tarball provided by github is not aware of that.  I
am compressing with xz and do not expect this to turn out to be too
large. We'll see.

On a sidenote - I am a bit of a mission for a tool that allows to grep
on sequences in paired fastq files and create a subset of these two
files, that are then still paired, if an entry in either file was a hit.
Somehow there are myriad of options for single files but I have not yet
found anything for working paired end fastq files. Ideas would be most
welcome.

If someone needs a stimulus to package something - cuteSV
(https://github.com/tjiangHIT/cuteSV), please.

Best,

Steffen