Discussion:
[MoM] Fwd: Outreachy project (CI for all biological applications inside Debian)
(too old to reply)
merlettaia
2016-03-21 05:26:17 UTC
Permalink
Hi, All!
My name is Tatiana Malygina, I'm another girl from Russia, who wants to
help with writing tests for biological applications in Debian =)

For Andreas: me and Ann were in the same study group in university, and
actually we are friends. But out experience in bioinformatics and our
primary research areas differ - that's why I want something structural
bioinformatics-related as starting packaging project.
For example, project from this list would be great: dssp, Concavity,
bio3d, ncols, norsnet, visualization (PyMol, garlic, ...) or
docking-related (autodock, autodock-vina, racoon, etc.). If I'm not a
perfect candidate for outreachy internship, I would like to help with
packaging for these tools as a volunteer - with some of them (I mean
docking software) I had no prior experience, and for me it is a great
chance to obtain it (and a motivation to finally read docking-related
articles).

I've created account on alioth (username - latticetower-guest), I also like
git.

Tanya.

---------- Forwarded message ----------
From: Andreas Tille <***@debian.org>
Date: 2016-03-17 10:51 GMT+03:00
Subject: Re: Outreachy project (CI for all biological applications inside
Debian)
To: merlettaia <***@gmail.com>


Hi Tanya,

thanks for your interest in the GSoC project of the Debian Med team. I
admit I'm impressed that so many students have contacted me since I had
considered the strong focus to bioinformatics a constraint but it is
obviously not. Your CV looks impressive and you seem to be a very good
candidate.

Since the discussion has started in public on the Debian Med mailing list
I'd recommend you simply start reading the thread beginning here:

https://lists.debian.org/debian-med/2016/02/msg00116.html

I prefer open discussion anyway so it would be really great if you could
subscribe this mailing list, give a short introduction there and we sort
out any questions there. Another candidate (as well a woman from Russia
- I wonder whether this is by chance or whether Russia is good in
educating in this field ... I'm originated from the former GDR so I have
some connection to Russia) has shown interest in writing a test suite for
bwa and I also suggested prodigal out of random since I recently touched
this package. Another random pick would be the package murasaki which
I uploaded yesterday.

If you do not have any idea about Debian packaging that's no problem at
all - we can teach you on the list in a MoM project[1]. Your main
qualification is your bioinformatics background. Feel free to ask any
question you might have on the list.

Looking forward to work together with you

Andreas.

[1] https://wiki.debian.org/DebianMed/MoM
Hi!
My name is Tatiana Malygina (github page: https://github.com/latticetower,
my current CV is attached).
I'm interested in bioinformatics-related project, can you tell me what
starting contribution I can make?
Regards,
Tanya.
--
http://fam-tille.de



--
Andreas Tille
2016-03-21 07:27:03 UTC
Permalink
Hi Tanya,
Post by merlettaia
My name is Tatiana Malygina, I'm another girl from Russia, who wants to
help with writing tests for biological applications in Debian =)
I admit I'm really happy to get several competent students for this
project since when I was registering it I was afraid that nobody would
sign on.
Post by merlettaia
For Andreas: me and Ann were in the same study group in university, and
actually we are friends. But out experience in bioinformatics and our
primary research areas differ - that's why I want something structural
bioinformatics-related as starting packaging project.
For example, project from this list would be great: dssp, Concavity,
bio3d, ncols, norsnet, visualization (PyMol, garlic, ...) or
Regarding PyMol: We also need to get the new upstream version of PyMol
(1.8) build for Debian. I remember there were some issues in building
it.
Post by merlettaia
docking-related (autodock, autodock-vina, racoon, etc.). If I'm not a
perfect candidate for outreachy internship, I would like to help with
packaging for these tools as a volunteer - with some of them (I mean
docking software) I had no prior experience, and for me it is a great
chance to obtain it (and a motivation to finally read docking-related
articles).
I have the hope that we might get even two students since there is
outreachy program and Google summer of code. No idea whether this works
- but from my perspective we have tasks even for two students. ;-)

For sure any volunteer is welcome as well and the Mentoring of Month
project is open for anybody. So getting some packaging training should
be granted.
Post by merlettaia
I've created account on alioth (username - latticetower-guest), I also like
git.
latticetower-guest is now member of the Debian Med team and has commit
permissions. I'm also busy to migrate those packages from SVN to Git
which I consider sensible candidates for creating a test suite (recently
I moved stacks and exonerate - feel free to ask me for moving others).

If you are interested in Garlic I noticed that the packaging is in a
quite old fashioned state. We could negotiate with DebiChem team what
might be the best way to enhance the packaging (either you will get
commit permission to their VCS and we move it into their Git or we take
it over into Debian Med team. Its also lacking a test suite. Just let
us know where you would like to start.

Kind regards

Andreas.
--
http://fam-tille.de
merlettaia
2016-03-21 16:31:13 UTC
Permalink
Hi Andreas,
I've decided to start with Concavity.
Is there a sample of a well-test-covered package?

Tanya
Post by merlettaia
Hi Tanya,
Post by merlettaia
My name is Tatiana Malygina, I'm another girl from Russia, who wants to
help with writing tests for biological applications in Debian =)
I admit I'm really happy to get several competent students for this
project since when I was registering it I was afraid that nobody would
sign on.
Post by merlettaia
For Andreas: me and Ann were in the same study group in university, and
actually we are friends. But out experience in bioinformatics and our
primary research areas differ - that's why I want something structural
bioinformatics-related as starting packaging project.
For example, project from this list would be great: dssp, Concavity,
bio3d, ncols, norsnet, visualization (PyMol, garlic, ...) or
Regarding PyMol: We also need to get the new upstream version of PyMol
(1.8) build for Debian. I remember there were some issues in building
it.
Post by merlettaia
docking-related (autodock, autodock-vina, racoon, etc.). If I'm not a
perfect candidate for outreachy internship, I would like to help with
packaging for these tools as a volunteer - with some of them (I mean
docking software) I had no prior experience, and for me it is a great
chance to obtain it (and a motivation to finally read docking-related
articles).
I have the hope that we might get even two students since there is
outreachy program and Google summer of code. No idea whether this works
- but from my perspective we have tasks even for two students. ;-)
For sure any volunteer is welcome as well and the Mentoring of Month
project is open for anybody. So getting some packaging training should
be granted.
Post by merlettaia
I've created account on alioth (username - latticetower-guest), I also
like
Post by merlettaia
git.
latticetower-guest is now member of the Debian Med team and has commit
permissions. I'm also busy to migrate those packages from SVN to Git
which I consider sensible candidates for creating a test suite (recently
I moved stacks and exonerate - feel free to ask me for moving others).
If you are interested in Garlic I noticed that the packaging is in a
quite old fashioned state. We could negotiate with DebiChem team what
might be the best way to enhance the packaging (either you will get
commit permission to their VCS and we move it into their Git or we take
it over into Debian Med team. Its also lacking a test suite. Just let
us know where you would like to start.
Kind regards
Andreas.
--
http://fam-tille.de
Andreas Tille
2016-03-21 18:03:56 UTC
Permalink
Hi Tanya,
Post by merlettaia
I've decided to start with Concavity.
Fine.
Post by merlettaia
Is there a sample of a well-test-covered package?
I'm not sure about what is a recommended example, but here are several
packages that have tests inside packaging git if I call the following in
the dir where I keep my Debian Med Git repositories:

find . -type d -name tests | grep debian/tests | sort
./aegean/debian/tests
./artfastqgenerator/debian/tests
./art-nextgen-simulation-tools/debian/tests
./axe-demultiplexer/debian/tests
./bcftools/debian/tests
./beast2-mcmc/debian/tests
./beast-mcmc/debian/tests
./bedtools/debian/tests
./bowtie2/debian/tests
./eigensoft/debian/tests
./falconkit/debian/tests
./fast5/debian/tests
./fastaq/debian/tests
./genometools/debian/tests
./gwama/debian/tests
./jellyfish/debian/tests
./khmer/debian/tests
./kmc/debian/tests
./libcereal/debian/tests
./libtabixpp/debian/tests
./microbiomeutil/debian/tests
./miniasm/debian/tests
./minimap/debian/tests
./nanopolish/debian/tests
./partitionfinder/debian/tests
./pbbarcode/debian/tests
./pbgenomicconsensus/debian/tests
./pbsim/debian/tests
./permute/debian/tests
./pipasic/debian/tests
./plast/debian/tests
./plink1.9/debian/tests
./plink2/debian/tests
./proteinortho/debian/tests
./python-biom-format/debian/tests
./python-biopython/debian/tests
./python-cobra/debian/tests
./python-csb/debian/tests
./python-pbcommand/debian/tests
./python-pbcore/debian/tests
./python-pbh5tools/debian/tests
./python-pysam/debian/tests
./python-ruffus/debian/tests
./python-screed/debian/tests
./python-skbio/debian/tests
./r-bioc-biobase/debian/tests
./r-bioc-biocgenerics/debian/tests
./r-bioc-cummerbund/debian/tests
./r-bioc-ebseq/debian/tests
./r-bioc-edger/debian/tests
./r-bioc-limma/debian/tests
./r-cran-ggplot2/debian/tests
./r-cran-metamix/debian/tests
./r-cran-plyr/debian/tests
./r-cran-reshape2/debian/tests
./r-cran-rsqlite/debian/tests
./r-cran-scales/debian/tests
./r-cran-vegan/debian/tests
./reapr/debian/tests
./samtools/debian/tests
./snpomatic/debian/tests
./snp-sites/debian/tests
./spades/debian/tests
./spdlog/debian/tests
./subread/debian/tests
./tabix/debian/tests
./toppred/debian/tests
./transdecoder/debian/tests
./trinityrnaseq/debian/tests
./trnascan-se/debian/tests
./velvet/debian/tests
./vsearch/debian/tests


Feel free to ask for more details if this hint does not turn out has
very helpful (I'm a bit busy with real life things currently).

Hope this helps

Andreas.
--
http://fam-tille.de
Andreas Tille
2016-04-04 13:55:25 UTC
Permalink
Hi Tanya and Anna,

I have not heard from you both since some time. I wonder how your progress
to find some target package and try to reproduce package building might be
as a first step to add an autopkgtest.

Kind regards

Andreas.
Post by merlettaia
Hi Tanya,
Post by merlettaia
I've decided to start with Concavity.
Fine.
Post by merlettaia
Is there a sample of a well-test-covered package?
I'm not sure about what is a recommended example, but here are several
packages that have tests inside packaging git if I call the following in
find . -type d -name tests | grep debian/tests | sort
./aegean/debian/tests
./artfastqgenerator/debian/tests
./art-nextgen-simulation-tools/debian/tests
./axe-demultiplexer/debian/tests
./bcftools/debian/tests
./beast2-mcmc/debian/tests
./beast-mcmc/debian/tests
./bedtools/debian/tests
./bowtie2/debian/tests
./eigensoft/debian/tests
./falconkit/debian/tests
./fast5/debian/tests
./fastaq/debian/tests
./genometools/debian/tests
./gwama/debian/tests
./jellyfish/debian/tests
./khmer/debian/tests
./kmc/debian/tests
./libcereal/debian/tests
./libtabixpp/debian/tests
./microbiomeutil/debian/tests
./miniasm/debian/tests
./minimap/debian/tests
./nanopolish/debian/tests
./partitionfinder/debian/tests
./pbbarcode/debian/tests
./pbgenomicconsensus/debian/tests
./pbsim/debian/tests
./permute/debian/tests
./pipasic/debian/tests
./plast/debian/tests
./plink1.9/debian/tests
./plink2/debian/tests
./proteinortho/debian/tests
./python-biom-format/debian/tests
./python-biopython/debian/tests
./python-cobra/debian/tests
./python-csb/debian/tests
./python-pbcommand/debian/tests
./python-pbcore/debian/tests
./python-pbh5tools/debian/tests
./python-pysam/debian/tests
./python-ruffus/debian/tests
./python-screed/debian/tests
./python-skbio/debian/tests
./r-bioc-biobase/debian/tests
./r-bioc-biocgenerics/debian/tests
./r-bioc-cummerbund/debian/tests
./r-bioc-ebseq/debian/tests
./r-bioc-edger/debian/tests
./r-bioc-limma/debian/tests
./r-cran-ggplot2/debian/tests
./r-cran-metamix/debian/tests
./r-cran-plyr/debian/tests
./r-cran-reshape2/debian/tests
./r-cran-rsqlite/debian/tests
./r-cran-scales/debian/tests
./r-cran-vegan/debian/tests
./reapr/debian/tests
./samtools/debian/tests
./snpomatic/debian/tests
./snp-sites/debian/tests
./spades/debian/tests
./spdlog/debian/tests
./subread/debian/tests
./tabix/debian/tests
./toppred/debian/tests
./transdecoder/debian/tests
./trinityrnaseq/debian/tests
./trnascan-se/debian/tests
./velvet/debian/tests
./vsearch/debian/tests
Feel free to ask for more details if this hint does not turn out has
very helpful (I'm a bit busy with real life things currently).
Hope this helps
Andreas.
--
http://fam-tille.de
--
http://fam-tille.de
Tatiana Malygina
2016-04-05 16:42:04 UTC
Permalink
Hi, Andreas!

I'm sorry for delay and not showing any response for some time, I was
unexpectedly busy :(

I've already installed VM with jessie64 distribution (Virtual
Box+vagrant-based), installed package and tried to write couple of tests
(thanks to Yaroslav, his advice was useful). I think I'll commit
something in next few days.
Tanya.
Anna Lioznova
2016-04-05 16:48:57 UTC
Permalink
Hi, Andreas!
Thank you for your letter.
I'm sorry for silence, I was busy with my studies. Also me and Tanya were
struggling to decide who should reply first :)

I'm done with package building and writing some tests, but my initial tests
are too simple to commit. I'll improve them in the nearest time.

I'll be glad to have a chance to improve bio packages for Debian (actually
I can do it anyway), but I really want to recommend Tanya for this project
-- she is great!)

Regards,
Anya
Post by Tatiana Malygina
Hi, Andreas!
I'm sorry for delay and not showing any response for some time, I was
unexpectedly busy :(
I've already installed VM with jessie64 distribution (Virtual
Box+vagrant-based), installed package and tried to write couple of tests
(thanks to Yaroslav, his advice was useful). I think I'll commit something
in next few days.
Tanya.
Andreas Tille
2016-04-05 20:16:02 UTC
Permalink
Hi Tanya and Anna,
Post by Tatiana Malygina
Hi, Andreas!
Thank you for your letter.
I'm sorry for silence, I was busy with my studies. Also me and Tanya were
struggling to decide who should reply first :)
:-)
Post by Tatiana Malygina
I'm done with package building and writing some tests, but my initial tests
are too simple to commit. I'll improve them in the nearest time.
Just a general remark: I do not consider even a minimal test as to
simple. It could be a reasonable proof of concept. So you can both
feel free to commit even trivial things.
Post by Tatiana Malygina
I'll be glad to have a chance to improve bio packages for Debian (actually
I can do it anyway), but I really want to recommend Tanya for this project
-- she is great!)
Nice to see true friends!

Kind regards

Andreas.
--
http://fam-tille.de
Andreas Tille
2016-04-18 07:23:24 UTC
Permalink
Hi Tatiana,
Post by Tatiana Malygina
I'm sorry for delay and not showing any response for some time, I was
unexpectedly busy :(
Seem you found some time since I've seen your commit. Thanks a lot for
your contribution. I added some additional commits. Please check these
out and read the log. Please ask if something remains unclear.

Kind regards

Andreas.
--
http://fam-tille.de
Yaroslav Halchenko
2016-03-22 07:04:54 UTC
Permalink
Fwiw, for all packages I maintain, wherever upstream provides tests, I am executing them at build time (scikit-learn, stats models, pymvpa2 are few random ones for eg). For many, I (or contributors) also started to enable autopkgtests, see eg pandas. Depending on where to draw the line for bio, those might be good examples.
Post by merlettaia
Hi Andreas,
I've decided to start with Concavity.
Is there a sample of a well-test-covered package?
Tanya
Post by merlettaia
Hi Tanya,
Post by merlettaia
My name is Tatiana Malygina, I'm another girl from Russia, who
wants to
Post by merlettaia
Post by merlettaia
help with writing tests for biological applications in Debian =)
I admit I'm really happy to get several competent students for this
project since when I was registering it I was afraid that nobody
would
Post by merlettaia
sign on.
Post by merlettaia
For Andreas: me and Ann were in the same study group in university,
and
Post by merlettaia
Post by merlettaia
actually we are friends. But out experience in bioinformatics and
our
Post by merlettaia
Post by merlettaia
primary research areas differ - that's why I want something
structural
Post by merlettaia
Post by merlettaia
bioinformatics-related as starting packaging project.
For example, project from this list would be great: dssp,
Concavity,
Post by merlettaia
Post by merlettaia
bio3d, ncols, norsnet, visualization (PyMol, garlic, ...) or
Regarding PyMol: We also need to get the new upstream version of
PyMol
Post by merlettaia
(1.8) build for Debian. I remember there were some issues in
building
Post by merlettaia
it.
Post by merlettaia
docking-related (autodock, autodock-vina, racoon, etc.). If I'm not
a
Post by merlettaia
Post by merlettaia
perfect candidate for outreachy internship, I would like to help
with
Post by merlettaia
Post by merlettaia
packaging for these tools as a volunteer - with some of them (I
mean
Post by merlettaia
Post by merlettaia
docking software) I had no prior experience, and for me it is a
great
Post by merlettaia
Post by merlettaia
chance to obtain it (and a motivation to finally read
docking-related
Post by merlettaia
Post by merlettaia
articles).
I have the hope that we might get even two students since there is
outreachy program and Google summer of code. No idea whether this
works
Post by merlettaia
- but from my perspective we have tasks even for two students. ;-)
For sure any volunteer is welcome as well and the Mentoring of Month
project is open for anybody. So getting some packaging training
should
Post by merlettaia
be granted.
Post by merlettaia
I've created account on alioth (username - latticetower-guest), I
also
Post by merlettaia
like
Post by merlettaia
git.
latticetower-guest is now member of the Debian Med team and has
commit
Post by merlettaia
permissions. I'm also busy to migrate those packages from SVN to Git
which I consider sensible candidates for creating a test suite
(recently
Post by merlettaia
I moved stacks and exonerate - feel free to ask me for moving
others).
Post by merlettaia
If you are interested in Garlic I noticed that the packaging is in a
quite old fashioned state. We could negotiate with DebiChem team
what
Post by merlettaia
might be the best way to enhance the packaging (either you will get
commit permission to their VCS and we move it into their Git or we
take
Post by merlettaia
it over into Debian Med team. Its also lacking a test suite. Just
let
Post by merlettaia
us know where you would like to start.
Kind regards
Andreas.
--
http://fam-tille.de
--
Sent from a phone which beats iPhone.
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