Re: Please use our scripts to save time and enhance quality [Was: [Git][med-team/igdiscover][master] 2 commits: Adjusting build dependencies]
Hi Andreas,
Thank you for fixing this and for caring in the first place.
igdiscover is already with us for a llooooonngggg time, just parked in
the new queue, for so long that I just yesterday updated it to remain
compatible with newer versions of cutadapt when I rebuilt it for the
"Debian Med Crash Space" :) - med.functional.domains for those who have
not followed that thread. So I don't feel too bad about IgDiscover. But
I do feel bad for https://salsa.debian.org/med-team/python-alignlib
which I added just a few days ago - would you mind to have a pointer to
that script right on top of https://salsa.debian.org/med-team where the
"New project" button is? I must admit that I used even used the script
once but have not really grasped / ignored the nitty-gritty technical
infrastructure behind it and there was this overhead on getting the
authentication done.
I am busy with other things, which is also why I just do what is under
my fingertips and don't reeducate me on scripts / not even think about
them. It all needs to become simpler. Just like allowing me to be
sufficiently functional when my mind is not. After all, we do this
Debian bits too often only after the working day has already ended. So,
I propose to start with a more visible pointer to that script right on
top of everything. And then there will more and more patches against
that script to help adopting that in some interactive fashion. A first
patch I would then look into is how to add hooks to projects that are
already on salsa with the same script.
Best,
Steffen
On 02.08.19 06:58, Andreas Tille wrote:
> Hi,
>
> since I have realised the upload of igdiscover to new and no according
> commit message in our commit mailing list I added the commit hooks
> manually. There would be no need for manual intervention if everybody
> who creates a new repository would use
>
> https://salsa.debian.org/med-team/community/helper-scripts/blob/master/inject-into-salsa-git
>
> This script should be called from a new local git repository and will
> create the remote one on salsa.d.o and sets all the hooks we want. I
> would be happy if everybody would prefer this over manual creation of
> repositories since usually this will not include all settings we want
> to have.
>
> Hope this helps
>
> Andreas.
>
>
> ----- Forwarded message from Andreas Tille <gitlab@salsa.debian.org> -----
>
> Date: Fri, 02 Aug 2019 03:28:05 +0000
> From: Andreas Tille <gitlab@salsa.debian.org>
> To: debian-med-commit@lists.alioth.debian.org
> Subject: [Git][med-team/igdiscover][master] 2 commits: Adjusting build dependencies
>
>
>
> Andreas Tille pushed to branch master at Debian Med / igdiscover
>
>
> Commits:
> 1cc07041 by Steffen Möller at 2019-02-12T09:25:15Z
> Adjusting build dependencies
>
> - - - - -
> df76dec7 by Steffen Möller at 2019-08-01T23:06:59Z
> Fixed FTBFS with new cutadapt (>= 2.3)
>
> - - - - -
>
>
> 4 changed files:
>
> - debian/changelog
> - debian/control
> - + debian/patches/minoverlap.patch
> - + debian/patches/series
>
>
> Changes:
>
> =====================================
> debian/changelog
> =====================================
> @@ -1,4 +1,11 @@
> -igdiscover (0.11-1) UNRELEASED; urgency=medium
> +igdiscover (0.11-2) unstable; urgency=medium
> +
> + * Introduced patch for compatibility with later versions
> + of cutadapt - upstream has it already in their master branch.
> +
> + -- Steffen Moeller <moeller@debian.org> Fri, 02 Aug 2019 00:55:02 +0200
> +
> +igdiscover (0.11-1) unstable; urgency=medium
>
> * Initial release (Closes: #919718)
>
>
>
> =====================================
> debian/control
> =====================================
> @@ -38,9 +38,8 @@ Depends: ${python3:Depends},
> python3-cutadapt,
> python3-scipy (>=0.16.1),
> python3-xopen (>=0.3.2),
> + python3-seaborn (>=0.9),
> python3-ruamel.yaml
> -Recommends: python3-seaborn (>=0.8.1),
> - python3-matplotlib
> Suggests: snakemake,
> igdiscover-doc
> Description: analyzes antibody repertoires to find new V genes
>
>
> =====================================
> debian/patches/minoverlap.patch
> =====================================
> @@ -0,0 +1,14 @@
> +Index: igdiscover/igdiscover/utils.py
> +===================================================================
> +--- igdiscover.orig/igdiscover/utils.py
> ++++ igdiscover/igdiscover/utils.py
> +@@ -330,8 +330,7 @@ def find_overlap(s, t, min_overlap=1):
> + >>> find_overlap('ABC', 'X') is None
> + True
> + """
> +- aligner = Aligner(s, max_error_rate=0)
> +- aligner.min_overlap = min_overlap
> ++ aligner = Aligner(s, max_error_rate=0, min_overlap=min_overlap)
> + result = aligner.locate(t)
> + if result is None:
> + return None
>
>
> =====================================
> debian/patches/series
> =====================================
> @@ -0,0 +1 @@
> +minoverlap.patch
>
>
>
> View it on GitLab: https://salsa.debian.org/med-team/igdiscover/compare/dc8ee7231d33b6e526845fcb32a407ead20cb1a1...df76dec71814551cc3d7914005f4a2e15635b7be
>
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