Re: where to begin - covid biohackathon

2020-04-07 Thread Olek Wojnar
Hi Dan! On Tue, Apr 7, 2020 at 3:24 PM wrote: > To debian-mentors list, > > I'm not a professional, my level at C / Unix is at Kerningham's Unix > Programming Environment (and I know a little CS from math courses)... it's > really a dream for me to contribute... Can anyone tell me where to begi

Re: [covid-19] Lots of JS dependencies [Was: Missing dependancies for streamlit]

2020-04-07 Thread Andreas Tille
Hi Andrius, On Wed, Apr 08, 2020 at 07:19:10AM +0300, mer...@debian.org wrote: > On 2020-04-07 22:49, Andreas Tille wrote: > > Aaaargh. Could we include Debian JS team into our sprint? I think we'd > > definitely need help here? Any volunteer to help us fighting Covid-19? > > I have some exper

Re: [covid-19] Lots of JS dependencies [Was: Missing dependancies for streamlit]

2020-04-07 Thread merkys
Hi Andreas, On 2020-04-07 22:49, Andreas Tille wrote: > Aaaargh. Could we include Debian JS team into our sprint? I think we'd > definitely need help here? Any volunteer to help us fighting Covid-19? I have some experience in packaging JS, and I would be willing to help. However, this is a lot

Re: Missing dependancies for streamlit

2020-04-07 Thread Mo Zhou
On Tue, Apr 07, 2020 at 11:49:07AM +0200, Andreas Tille wrote: > On Tue, Apr 07, 2020 at 08:56:45AM +0100, Rebecca N. Palmer wrote: > > tensorflow 1.10 was packaged in experimental, but with reduced performance, > > and was removed because this was considered not worth it: > > https://bugs.debian.o

Re: Missing dependancies for streamlit

2020-04-07 Thread Mo Zhou
On Tue, Apr 07, 2020 at 11:36:08AM +0200, Andreas Tille wrote: > with the last commit of Mo saying "I'm dropping this burden." in the log. > I know Mo as an expert in deep learning who is highly competent in > Debian packaging. I would not say that we should not tackle this - but > lets sort out m

[covid-19] Lots of JS dependencies [Was: Missing dependancies for streamlit]

2020-04-07 Thread Andreas Tille
Hi Rebecca, thanks a lot for your research! On Tue, Apr 07, 2020 at 06:40:14PM +0100, Rebecca N. Palmer wrote: > However, streamlit also has a Javascript component (the frontend directory), > with ~100 dependencies Debian doesn't have (plus a few that Debian has in > too old a version): Aaaargh.

Re: Missing dependancies for streamlit

2020-04-07 Thread Rebecca N. Palmer
However, streamlit also has a Javascript component (the frontend directory), with ~100 dependencies Debian doesn't have (plus a few that Debian has in too old a version): $ npm2deb depends /home/rnpalmer/Debian/builds/stackbuild/package.json Dependencies: NPM

Re: Missing dependancies for streamlit

2020-04-07 Thread Rebecca N. Palmer
From searching the source, it appears that only 2 tests (plus some examples) need tensorflow: hashing_test.py:HashTest.test_tensorflow_non_hashable and keras_test.py:KerasTest. Hence, skipping these tests may be a reasonable option after all.

Please support COVID-19 BioHackathon and choose a free license for parts of your code to build blat

2020-04-07 Thread Andreas Tille
Hi Kent, I've just opened https://github.com/ucscGenomeBrowser/kent/issues/32 Since we had also some past mail exchange which went also to our mailing list I'm copying the content here: Hi, we had some past discussion about the licensing of the complete code of this repository. I've unders

Re: Missing dependancies for streamlit

2020-04-07 Thread Andreas Tille
Cool, thanks a lot to all who clarified this Andreas. On Tue, Apr 07, 2020 at 01:05:03PM +0100, Rebecca N. Palmer wrote: > From #954150, it appears there _is_ a code vs data distinction: tests are > allowed to use the network but not to download and run code. > > https://ftp-master.debian.

Re: Missing dependancies for streamlit

2020-04-07 Thread Rebecca N. Palmer
From #954150, it appears there _is_ a code vs data distinction: tests are allowed to use the network but not to download and run code. https://ftp-master.debian.org/REJECT-FAQ.html Non-Main II I intend to post a patch to autopkgtest to document this. Manually running the tests in question befo

Re: Missing dependancies for streamlit

2020-04-07 Thread Rebecca N. Palmer
Internet-using tests are discouraged because they can fail for external reasons, but preferred to leaving online features untested: https://sources.debian.org/src/autopkgtest/5.12.1/doc/README.package-tests.rst/#L431 (Not sure if there are any rules about downloading code vs data) There is a pr

Re: Missing dependancies for streamlit

2020-04-07 Thread Graham Inggs
On Tue, 7 Apr 2020 at 12:46, Andreas Tille wrote: > > On Tue, Apr 07, 2020 at 11:15:17AM +0100, Rebecca N. Palmer wrote: > > A potential workaround for testing: while package builds (including > > build-time tests) are not allowed to use the network, autopkgtests *are* > > allowed to => skip the t

Re: Missing dependancies for streamlit

2020-04-07 Thread Michael Crusoe
https://salsa.debian.org/ci-team/autopkgtest/raw/master/doc/README.package-tests.rst In general, tests are also allowed to access the internet. As this > usually makes tests less reliable, this should be kept to a minimum; but > for many packages their main purpose is to interact with remote web >

Re: Missing dependancies for streamlit

2020-04-07 Thread Andreas Tille
On Tue, Apr 07, 2020 at 11:15:17AM +0100, Rebecca N. Palmer wrote: > A potential workaround for testing: while package builds (including > build-time tests) are not allowed to use the network, autopkgtests *are* > allowed to => skip the tensorflow-needing tests in build, but run them (with > tensor

Re: Missing dependancies for streamlit

2020-04-07 Thread Rebecca N. Palmer
A potential workaround for testing: while package builds (including build-time tests) are not allowed to use the network, autopkgtests *are* allowed to => skip the tensorflow-needing tests in build, but run them (with tensorflow from PyPI) in autopkgtest?

Re: Missing dependancies for streamlit

2020-04-07 Thread Andreas Tille
Hi Rebecca, On Tue, Apr 07, 2020 at 08:56:45AM +0100, Rebecca N. Palmer wrote: > tensorflow 1.10 was packaged in experimental, but with reduced performance, > and was removed because this was considered not worth it: > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=935769 Ah I simply forgot th

Re: Bug#950311: FastQC users attention: Please comment on the remaining failures! (Was: Bug#950311: fastqc: autopkgtest regression: debhelper bump moved files to different location)

2020-04-07 Thread Andreas Tille
Hi Tony, On Mon, Apr 06, 2020 at 04:22:03PM -0700, tony mancill wrote: > > This sounds all pretty convincing. Feel free to do a team upload > > implementing your suggestion. > > I went ahead and implemented this as a comparison of the summary output > with the "known good" output and pushed as a

Re: Missing dependancies for streamlit

2020-04-07 Thread Andreas Tille
On Tue, Apr 07, 2020 at 09:44:48AM +0200, Michael Crusoe wrote: > > On Tue, Apr 7, 2020, 03:27 timsn_thtree_net wrote: > > > Not certain what distro/config streamlit was made in, but the Makefile > > assumes that pip = pip3, and it looks like they really want python 3.8, > > but things seem to m

Re: Missing dependancies for streamlit

2020-04-07 Thread Rebecca N. Palmer
tensorflow 1.10 was packaged in experimental, but with reduced performance, and was removed because this was considered not worth it: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=935769 streamlit requires tensorflow only for testing: https://github.com/streamlit/streamlit/blob/develop/lib/P

Re: Missing dependancies for streamlit

2020-04-07 Thread Michael Crusoe
-- Michael R. Crusoe On Tue, Apr 7, 2020, 03:27 timsn_thtree_net wrote: > Hi Andreas, > > Not certain what distro/config streamlit was made in, but the Makefile > assumes that pip = pip3, and it looks like they really want python 3.8, > but things seem to move ahead with the 3.7.3 version instal