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

Getting the release out
by Nomi Harris 27 Jun '13

27 Jun '13

I would love to see the release go out this week if only because it can then be "the June release" rather than becoming "the July release" (to be followed quickly by the August release). Assuming we get no response about fixing the communities_api so it can be included in the dmg, are we ready to go ahead and put the new dmg and ubuntu image up and announce the release? Or do we need a new dmg to test? I think Miriam must be on vacation--I haven't seen any email from her in quite a while. And I know Tom is now away for at least a week. Should we wait until they're back? Nomi

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Fwd: [JIRA] (KBASE-147) MK_CONFIG rule in Makefile.common fails with no such file or directory error
by Nomi Harris 27 Jun '13

27 Jun '13

It sounds like Michael Mundy fixed an issue in Makefile.common, but he didn't commit his change, either because he doesn't have write access to dev_container or because he knows that Tom prefers not to have random people make changes to that file. Who is the right person to assign this to? Tom is on vacation, and I know Bob O. is overloaded. I could commit the change but can't easily test that it works. Thanks, Nomi Begin forwarded message: > From: "Michael Mundy (JIRA)" <help(a)kbase.us> > Subject: [JIRA] (KBASE-147) MK_CONFIG rule in Makefile.common fails with no such file or directory error > Date: June 27, 2013 7:15:25 AM PDT > To: nlharris(a)lbl.gov > > > > Michael Mundy created KBASE-147 > MK_CONFIG rule in Makefile.common fails with no such file or directory error > Issue Type: Bug > Assignee: Meghan Drake > Components: service > Created: 27/Jun/13 9:14 AM > Description: > Line 32 of tools/Makefile.common has this rule: > > MK_CONFIG = $(TOOL_DIR)/mkcfg > > but in the tools directory the name of the script is mkcfg.pl. When running "make deploy" in KBaseFBAModeling that gives this error: > > /home/mmundy/kb/runtime/bin/perl ../../tools//mkcfg > Can't open perl script "../../tools//mkcfg": No such file or directory > make: *** [deploy-cfg] Error 2 > > I updated Makefile.common with the correct name of the script and the rule worked. > > I didn't see a dev_container service in the list to assign this issue. > > Project: KBase > Priority: Minor > Reporter: Michael Mundy > This message is automatically generated by JIRA. > If you think it was sent incorrectly, please contact your JIRA administrators > For more information on JIRA, see: http://www.atlassian.com/software/jira

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communities_api and/or communities_qc missing from dmg [was Re: Finishing off the last release]
by Nomi Harris 26 Jun '13

26 Jun '13

I looked back in my email about this and found: Begin forwarded message: > From: Thomas Brettin <brettin(a)mcs.anl.gov> > Subject: Re: [Release-team] new VM to test > Date: June 11, 2013 12:56:10 PM PDT > To: Robert Olson <olson(a)mcs.anl.gov> > Cc: release-team(a)kbase.us > > guys, i sat with Andi and showed him how to clean it up by paired programming on the communities_qc makefile. If it's not done on the communities_api, and according to the git logs it was not, then let;'s not worry about it. It must not be that important. I'll talk to Andi when I get a chance, but we need to get the computer to Susan. > > Tom > > > On Jun 11, 2013, at 2:54 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> the problem is that they've hardcoded /kb/deployment which breaks on the mac dmg build. >> >> On Jun 11, 2013, at 2:53 PM, Dan Olson wrote: >> >>> I was able to make it with make deploy-all without issues. >>> >>> ----- Original Message ----- >>>> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>> Sent: Tuesday, June 11, 2013 2:52:56 PM >>>> Subject: Re: [Release-team] new VM to test >>>> >>>> I fixed communities_qc for them, but not communities_api. >>>> >>>> >>>> On Jun 11, 2013, at 10:22 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>>> >>>>> communities_api was missing from the dmg because of makefile >>>>> issues; I don't know that they've been resolved. Tom - you had >>>>> mentioned something about it, did you fix or are we still waiting >>>>> on Andreas to fix it? So it sounds from what Tom is saying that communities_qc should be in the dmg, but communities_api is missing. But Dan said yesterday (see below) that the dmg is missing communities_qc (he didn't comment on communities_api). How about if I create a JIRA ticket stating that communities_api (and/or qc) is missing from the dmg because of makefile issues, and that these must be resolved by [Friday?] or they will not be included in the dmg for this release? Should I assign to Andreas or is there someone else who might be able to work on this? Nomi On Jun 25, 2013, at 3:40 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > No, as far as I know the communities code has not been fixed (no reply from the mail to andreas about it). > > ----- Original Message ----- >> We really need to get the last release posted to the website. >> >> My notes state: >> >> DMG - missing communities_qc >> >> VM - double gzipped, uuid needed changing >> >> >> I can fix up the VM, has the DMG been fixed? >> >> ---- >> Daniel Murphy-Olson >> Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055

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Re: [Release-team] Finishing off the last release
by Dan Olson 26 Jun '13

26 Jun '13

Strike this -"No new services have been added since the February 2013 release, but" ----- Original Message ----- > From: "Nomi Harris" <nlharris(a)lbl.gov> > To: release-team(a)kbase.us > Cc: "Nomi Harris" <nlharris(a)lbl.gov> > Sent: Wednesday, June 26, 2013 12:22:58 PM > Subject: Re: [Release-team] Finishing off the last release > > Tom asked me to write a release announcement for this release. > There's not much I can say, since we don't have release notes for > most of the services. How does this sound? > > We are pleased to announce a new release of KBase. No new services > have been added since the February 2013 release, but many of the > services have been improved. > > There are several ways to try out the KBase software: > • The Downloads [/developer-zone/downloads] page offers a Mac disk > image (DMG), which you can install and launch as an application. It > provides a KBase programming and execution environment complete with > client libraries and command-line scripts. We also offer an Ubuntu > Linux disk image. > • Alternatively, IRIS [http://www.prototype.net/iris/] allows users > to run the KBase command-line scripts from a web-based interface > without downloading any software. > • We are actively developing graphical user interfaces that will make > KBase more accessible to non-programmers. Some of these are linked > from the KBase Labs [/labs/] page. > > Tutorials [/for-users/tutorials] on the KBase website explain how to > solve biological problems using KBase, either via IRIS or from the > DMG or Ubuntu image. > > KBase is in a phase of rapid development, and we are eager for > beta-testers to try our tools and APIs and give us feedback as we > continue to develop and expand our resources. To send us bug reports > or suggestions for improvement about specific KBase tools or > services, please email help(a)kbase.us. > > > > On Jun 25, 2013, at 9:09 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > > True, he very well might, but at least then we'd have documentation > > about what was wrong, when it was reported, whether it was > > resolved, and we wouldn't have to keep that information in our > > heads or hunt through old email looking for it. > > Nomi > > > > On Jun 25, 2013, at 8:33 PM, Robert Olson <olson(a)mcs.anl.gov> > > wrote: > > > >> Not sure why he'd not ignore the ticket just like he ignored the > >> email. > >> > >> ----- Original Message ----- > >>> I would make a JIRA ticket for this. This is exactly the sort of > >>> situation it's useful for--something's wrong, we need to see if > >>> it's > >>> been resolved before we do the release, without the release team > >>> having to remember exactly what the issue was and then try to > >>> figure > >>> out whether it ever got fixed. > >>> > >>> We can even set a due date on the ticket so that JIRA will nag > >>> the > >>> person the ticket's assigned to. (We have not, so far, used that > >>> feature.) > >>> > >>> Nomi > >>> > >>> On Jun 25, 2013, at 3:40 PM, Robert Olson <olson(a)mcs.anl.gov> > >>> wrote: > >>> > >>>> No, as far as I know the communities code has not been fixed (no > >>>> reply from the mail to andreas about it). > >>>> > >>>> ----- Original Message ----- > >>>>> We really need to get the last release posted to the website. > >>>>> > >>>>> My notes state: > >>>>> > >>>>> DMG - missing communities_qc > >>>>> > >>>>> VM - double gzipped, uuid needed changing > >>>>> > >>>>> > >>>>> I can fix up the VM, has the DMG been fixed? > >>>>> > >>>>> ---- > >>>>> Daniel Murphy-Olson > >>>>> Systems Administrator > >>>>> Mathematics & Computer Science Division > >>>>> Argonne National Laboratory > >>>>> 630-252-0055 > >>> > >>> > > > > _______________________________________________ > 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] Finishing off the last release
by Nomi Harris 26 Jun '13

26 Jun '13

Tom asked me to write a release announcement for this release. There's not much I can say, since we don't have release notes for most of the services. How does this sound? We are pleased to announce a new release of KBase. No new services have been added since the February 2013 release, but many of the services have been improved. There are several ways to try out the KBase software: • The Downloads [/developer-zone/downloads] page offers a Mac disk image (DMG), which you can install and launch as an application. It provides a KBase programming and execution environment complete with client libraries and command-line scripts. We also offer an Ubuntu Linux disk image. • Alternatively, IRIS [http://www.prototype.net/iris/] allows users to run the KBase command-line scripts from a web-based interface without downloading any software. • We are actively developing graphical user interfaces that will make KBase more accessible to non-programmers. Some of these are linked from the KBase Labs [/labs/] page. Tutorials [/for-users/tutorials] on the KBase website explain how to solve biological problems using KBase, either via IRIS or from the DMG or Ubuntu image. KBase is in a phase of rapid development, and we are eager for beta-testers to try our tools and APIs and give us feedback as we continue to develop and expand our resources. To send us bug reports or suggestions for improvement about specific KBase tools or services, please email help(a)kbase.us. On Jun 25, 2013, at 9:09 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > True, he very well might, but at least then we'd have documentation about what was wrong, when it was reported, whether it was resolved, and we wouldn't have to keep that information in our heads or hunt through old email looking for it. > Nomi > > On Jun 25, 2013, at 8:33 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> Not sure why he'd not ignore the ticket just like he ignored the email. >> >> ----- Original Message ----- >>> I would make a JIRA ticket for this. This is exactly the sort of >>> situation it's useful for--something's wrong, we need to see if it's >>> been resolved before we do the release, without the release team >>> having to remember exactly what the issue was and then try to figure >>> out whether it ever got fixed. >>> >>> We can even set a due date on the ticket so that JIRA will nag the >>> person the ticket's assigned to. (We have not, so far, used that >>> feature.) >>> >>> Nomi >>> >>> On Jun 25, 2013, at 3:40 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>> >>>> No, as far as I know the communities code has not been fixed (no >>>> reply from the mail to andreas about it). >>>> >>>> ----- Original Message ----- >>>>> We really need to get the last release posted to the website. >>>>> >>>>> My notes state: >>>>> >>>>> DMG - missing communities_qc >>>>> >>>>> VM - double gzipped, uuid needed changing >>>>> >>>>> >>>>> I can fix up the VM, has the DMG been fixed? >>>>> >>>>> ---- >>>>> Daniel Murphy-Olson >>>>> Systems Administrator >>>>> Mathematics & Computer Science Division >>>>> Argonne National Laboratory >>>>> 630-252-0055 >>> >>> >

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Re: [Release-team] Finishing off the last release
by Nomi Harris 25 Jun '13

25 Jun '13

True, he very well might, but at least then we'd have documentation about what was wrong, when it was reported, whether it was resolved, and we wouldn't have to keep that information in our heads or hunt through old email looking for it. Nomi On Jun 25, 2013, at 8:33 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > Not sure why he'd not ignore the ticket just like he ignored the email. > > ----- Original Message ----- >> I would make a JIRA ticket for this. This is exactly the sort of >> situation it's useful for--something's wrong, we need to see if it's >> been resolved before we do the release, without the release team >> having to remember exactly what the issue was and then try to figure >> out whether it ever got fixed. >> >> We can even set a due date on the ticket so that JIRA will nag the >> person the ticket's assigned to. (We have not, so far, used that >> feature.) >> >> Nomi >> >> On Jun 25, 2013, at 3:40 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >> >>> No, as far as I know the communities code has not been fixed (no >>> reply from the mail to andreas about it). >>> >>> ----- Original Message ----- >>>> We really need to get the last release posted to the website. >>>> >>>> My notes state: >>>> >>>> DMG - missing communities_qc >>>> >>>> VM - double gzipped, uuid needed changing >>>> >>>> >>>> I can fix up the VM, has the DMG been fixed? >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Systems Administrator >>>> Mathematics & Computer Science Division >>>> Argonne National Laboratory >>>> 630-252-0055 >> >>

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Re: [Release-team] Finishing off the last release
by Robert Olson 25 Jun '13

25 Jun '13

Not sure why he'd not ignore the ticket just like he ignored the email. ----- Original Message ----- > I would make a JIRA ticket for this. This is exactly the sort of > situation it's useful for--something's wrong, we need to see if it's > been resolved before we do the release, without the release team > having to remember exactly what the issue was and then try to figure > out whether it ever got fixed. > > We can even set a due date on the ticket so that JIRA will nag the > person the ticket's assigned to. (We have not, so far, used that > feature.) > > Nomi > > On Jun 25, 2013, at 3:40 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > > > No, as far as I know the communities code has not been fixed (no > > reply from the mail to andreas about it). > > > > ----- Original Message ----- > >> We really need to get the last release posted to the website. > >> > >> My notes state: > >> > >> DMG - missing communities_qc > >> > >> VM - double gzipped, uuid needed changing > >> > >> > >> I can fix up the VM, has the DMG been fixed? > >> > >> ---- > >> Daniel Murphy-Olson > >> Systems Administrator > >> Mathematics & Computer Science Division > >> Argonne National Laboratory > >> 630-252-0055 > >

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Re: [Release-team] Finishing off the last release
by Nomi Harris 25 Jun '13

25 Jun '13

I would make a JIRA ticket for this. This is exactly the sort of situation it's useful for--something's wrong, we need to see if it's been resolved before we do the release, without the release team having to remember exactly what the issue was and then try to figure out whether it ever got fixed. We can even set a due date on the ticket so that JIRA will nag the person the ticket's assigned to. (We have not, so far, used that feature.) Nomi On Jun 25, 2013, at 3:40 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > No, as far as I know the communities code has not been fixed (no reply from the mail to andreas about it). > > ----- Original Message ----- >> We really need to get the last release posted to the website. >> >> My notes state: >> >> DMG - missing communities_qc >> >> VM - double gzipped, uuid needed changing >> >> >> I can fix up the VM, has the DMG been fixed? >> >> ---- >> Daniel Murphy-Olson >> Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055

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Re: [Release-team] Finishing off the last release
by Robert Olson 25 Jun '13

25 Jun '13

No, as far as I know the communities code has not been fixed (no reply from the mail to andreas about it). ----- Original Message ----- > We really need to get the last release posted to the website. > > My notes state: > > DMG - missing communities_qc > > VM - double gzipped, uuid needed changing > > > I can fix up the VM, has the DMG been fixed? > > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

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Finishing off the last release
by Dan Olson 25 Jun '13

25 Jun '13

We really need to get the last release posted to the website. My notes state: DMG - missing communities_qc VM - double gzipped, uuid needed changing I can fix up the VM, has the DMG been fixed? ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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