April 2013 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] release notes
by Nomi Harris 22 Apr '13

22 Apr '13

Well, we had a (somewhat arbitrary) convention that release notes are put in a file called RELEASE_NOTES.txt in the main directory of the git repo. We introduced the idea of release notes at the November build but didn't end up enforcing them because release notes are not very useful for an initial release. They are, however, very useful for subsequent releases, like this one. I don't have a strong opinion about where the release notes should go or what they should be called, or whether they should all be concatenated in one big file or be separate files for each release. Maybe Mike has opinions? However, I do think the release notes should be compiled by the developers, not by the build teams. Only the developers know exactly what they've changed. Nomi On Apr 22, 2013, at 12:54 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > If we had them, where is the right place to document and communicate them? > At times we have used the spreadsheet for this. > > Miriam > > On 4/22/13 3:52 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: > >> Yes--I didn't get a chance to discuss this during today's meeting but I >> would like to see release notes for the services that are included in >> this minor release. This would be useful both internally (for testing, as >> Miriam notes) and externally (so users know what has changed). >> Nomi >> >> On Apr 22, 2013, at 12:47 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >> >>> All, >>> >>> Do we have anything like release notes for this build? For testing >>> purposes, it would be nice to have a list of things to specifically test >>> for. >>> >>> Miriam

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Re: [Release-team] release notes
by Land, Miriam L. 22 Apr '13

22 Apr '13

If we had them, where is the right place to document and communicate them? At times we have used the spreadsheet for this. Miriam On 4/22/13 3:52 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >Yes--I didn't get a chance to discuss this during today's meeting but I >would like to see release notes for the services that are included in >this minor release. This would be useful both internally (for testing, as >Miriam notes) and externally (so users know what has changed). > Nomi > >On Apr 22, 2013, at 12:47 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > >> All, >> >> Do we have anything like release notes for this build? For testing >>purposes, it would be nice to have a list of things to specifically test >>for. >> >> Miriam >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >

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Re: [Release-team] release notes
by Nomi Harris 22 Apr '13

22 Apr '13

Yes--I didn't get a chance to discuss this during today's meeting but I would like to see release notes for the services that are included in this minor release. This would be useful both internally (for testing, as Miriam notes) and externally (so users know what has changed). Nomi On Apr 22, 2013, at 12:47 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > All, > > Do we have anything like release notes for this build? For testing purposes, it would be nice to have a list of things to specifically test for. > > Miriam > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] of special interest to test
by Land, Miriam L. 22 Apr '13

22 Apr '13

Are they all called by 'make test'? Miriam On 4/22/13 12:34 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >Hi Miriam, > >Here is the list of files that I modified in the genome_annotation module >this morning. They should be tested more rigorously than just ensuring >that the script returns 0. > >Chris, I'm including you because these are related to your bootcamps. The >change could be in production by the end of this week. > >Tom > ># modified: recompile_typespec ># modified: scripts/annotate_genome.pl ># modified: scripts/assign_functions_to_CDSs.pl ># modified: scripts/call_CDSs.pl ># modified: scripts/call_CDSs_by_glimmer.pl ># modified: scripts/call_CDSs_by_projection.pl ># modified: scripts/call_RNAs.pl ># modified: scripts/call_pyrrolysoproteins.pl ># modified: scripts/call_selenoproteins.pl ># modified: scripts/cs_to_genome.pl ># modified: scripts/fasta_to_genome.pl ># modified: scripts/genomeTO_strep_pneumo_repeats.pl ># modified: scripts/genomeTO_strep_suis_repeats.pl ># modified: scripts/genomeTO_to_coding_regions.pl ># modified: scripts/genomeTO_to_feature_data.pl ># modified: scripts/genomeTO_to_reconstructionTO.pl ># modified: scripts/merge_features.pl ># modified: scripts/reconstructionTO_to_roles.pl ># modified: scripts/reconstructionTO_to_subsystems.pl

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release notes
by Land, Miriam L. 22 Apr '13

22 Apr '13

All, Do we have anything like release notes for this build? For testing purposes, it would be nice to have a list of things to specifically test for. Miriam

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Re: [Release-team] genome_annotation module
by Dan Olson 22 Apr '13

22 Apr '13

There is a good cert for kbase.us now. ----- Original Message ----- > From: "Robert Olson" <olson(a)mcs.anl.gov> > To: "Thomas Brettin" <brettin(a)mcs.anl.gov> > Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)lists.kbase.us > Sent: Monday, April 22, 2013 11:28:46 AM > Subject: Re: genome_annotation module > > excellent, thanks tom > > have we tested out all the services against the https target? I'm > wondering if the perl client stuff is doing the right thing in the > face of SSL endpoints that do not have known host certs (or do we > have a good cert on there now?) > > > On Apr 22, 2013, at 11:27 AM, Thomas Brettin wrote: > > > I just pushed the changes to git.kbase.us master. > > > > In short, changed references to bio-data to kbase.us > > > > Changed the protocol from http to https. > > > > In a couple scripts, the url of the id server changed to point at > > https://kbase.us/.… > > > > > > t > >

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of special interest to test
by Thomas Brettin 22 Apr '13

22 Apr '13

Hi Miriam, Here is the list of files that I modified in the genome_annotation module this morning. They should be tested more rigorously than just ensuring that the script returns 0. Chris, I'm including you because these are related to your bootcamps. The change could be in production by the end of this week. Tom # modified: recompile_typespec # modified: scripts/annotate_genome.pl # modified: scripts/assign_functions_to_CDSs.pl # modified: scripts/call_CDSs.pl # modified: scripts/call_CDSs_by_glimmer.pl # modified: scripts/call_CDSs_by_projection.pl # modified: scripts/call_RNAs.pl # modified: scripts/call_pyrrolysoproteins.pl # modified: scripts/call_selenoproteins.pl # modified: scripts/cs_to_genome.pl # modified: scripts/fasta_to_genome.pl # modified: scripts/genomeTO_strep_pneumo_repeats.pl # modified: scripts/genomeTO_strep_suis_repeats.pl # modified: scripts/genomeTO_to_coding_regions.pl # modified: scripts/genomeTO_to_feature_data.pl # modified: scripts/genomeTO_to_reconstructionTO.pl # modified: scripts/merge_features.pl # modified: scripts/reconstructionTO_to_roles.pl # modified: scripts/reconstructionTO_to_subsystems.pl

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Re: [Release-team] genome_annotation module
by Thomas Brettin 22 Apr '13

22 Apr '13

good question for Dan. I'm just going a statement from Dan that we are ready to cut over to https. Guess we'll find out soon :-) (Miriam) t On Apr 22, 2013, at 11:28 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > excellent, thanks tom > > have we tested out all the services against the https target? I'm wondering if the perl client stuff is doing the right thing in the face of SSL endpoints that do not have known host certs (or do we have a good cert on there now?) > > > On Apr 22, 2013, at 11:27 AM, Thomas Brettin wrote: > >> I just pushed the changes to git.kbase.us master. >> >> In short, changed references to bio-data to kbase.us >> >> Changed the protocol from http to https. >> >> In a couple scripts, the url of the id server changed to point at https://kbase.us/.… >> >> >> t >

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Re: [Release-team] genome_annotation module
by Robert Olson 22 Apr '13

22 Apr '13

excellent, thanks tom have we tested out all the services against the https target? I'm wondering if the perl client stuff is doing the right thing in the face of SSL endpoints that do not have known host certs (or do we have a good cert on there now?) On Apr 22, 2013, at 11:27 AM, Thomas Brettin wrote: > I just pushed the changes to git.kbase.us master. > > In short, changed references to bio-data to kbase.us > > Changed the protocol from http to https. > > In a couple scripts, the url of the id server changed to point at https://kbase.us/.… > > > t

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genome_annotation module
by Thomas Brettin 22 Apr '13

22 Apr '13

I just pushed the changes to git.kbase.us master. In short, changed references to bio-data to kbase.us Changed the protocol from http to https. In a couple scripts, the url of the id server changed to point at https://kbase.us/.… t

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