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

Re: [Release-team] new VM to test
by Thomas Brettin 11 Jun '13

11 Jun '13

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> >>> To: "Robert Olson" <olson(a)mcs.anl.gov> >>> Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)kbase.us >>> 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? >>>> >>>> On Jun 11, 2013, at 10:17 AM, Dan Olson wrote: >>>> >>>>> The communities_api module was not included in the last vm. >>>>> >>>>> Please test the VM here. The only update is the inclusion of the >>>>> communities_api module from master. >>>>> http://bioseed.mcs.anl.gov/~dolson/kbase_20130611.vmdk.gz >>>>> >>>>> I believe this may be missing from the latest DMG as well. >>>>> >>>>> ---- >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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] new VM to test
by Robert Olson 11 Jun '13

11 Jun '13

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> >> To: "Robert Olson" <olson(a)mcs.anl.gov> >> Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)kbase.us >> 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? >>> >>> On Jun 11, 2013, at 10:17 AM, Dan Olson wrote: >>> >>>> The communities_api module was not included in the last vm. >>>> >>>> Please test the VM here. The only update is the inclusion of the >>>> communities_api module from master. >>>> http://bioseed.mcs.anl.gov/~dolson/kbase_20130611.vmdk.gz >>>> >>>> I believe this may be missing from the latest DMG as well. >>>> >>>> ---- >>>> 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 >>> >>> _______________________________________________ >>> 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] new VM to test
by Dan Olson 11 Jun '13

11 Jun '13

I was able to make it with make deploy-all without issues. ----- Original Message ----- > From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > To: "Robert Olson" <olson(a)mcs.anl.gov> > Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)kbase.us > 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? > > > > On Jun 11, 2013, at 10:17 AM, Dan Olson wrote: > > > >> The communities_api module was not included in the last vm. > >> > >> Please test the VM here. The only update is the inclusion of the > >> communities_api module from master. > >> http://bioseed.mcs.anl.gov/~dolson/kbase_20130611.vmdk.gz > >> > >> I believe this may be missing from the latest DMG as well. > >> > >> ---- > >> 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 > > > > _______________________________________________ > > 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] new VM to test
by Thomas Brettin 11 Jun '13

11 Jun '13

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? > > On Jun 11, 2013, at 10:17 AM, Dan Olson wrote: > >> The communities_api module was not included in the last vm. >> >> Please test the VM here. The only update is the inclusion of the communities_api module from master. >> http://bioseed.mcs.anl.gov/~dolson/kbase_20130611.vmdk.gz >> >> I believe this may be missing from the latest DMG as well. >> >> ---- >> 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 > > _______________________________________________ > 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] new VM to test
by Robert Olson 11 Jun '13

11 Jun '13

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? On Jun 11, 2013, at 10:17 AM, Dan Olson wrote: > The communities_api module was not included in the last vm. > > Please test the VM here. The only update is the inclusion of the communities_api module from master. > http://bioseed.mcs.anl.gov/~dolson/kbase_20130611.vmdk.gz > > I believe this may be missing from the latest DMG as well. > > ---- > 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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new VM to test
by Dan Olson 11 Jun '13

11 Jun '13

The communities_api module was not included in the last vm. Please test the VM here. The only update is the inclusion of the communities_api module from master. http://bioseed.mcs.anl.gov/~dolson/kbase_20130611.vmdk.gz I believe this may be missing from the latest DMG as well. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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Re: [Release-team] meeting today?
by Land, Miriam L. 11 Jun '13

11 Jun '13

I think India's email was delayed and does not apply to today. The time stamp below says that she sent it last week (Jun 3), but it showed up in my inbox today (Jun 11). Miriam On 6/11/13 9:47 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >I don't see this on my calendar. Sorry about the mix up. I'm on another >call right now. > >Tom > > >On Jun 3, 2013, at 11:08 AM, India Gordon <igordon(a)cels.anl.gov> wrote: > >> I think Tom's calling in right now, Dan. >> >> His last call ran over a few minutes. >> >> On Jun 3, 2013, at 11:02 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >> >> Are we still meeting today? I think I'm the only one on the call. >> >> ---- >> 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 >> >> India S. Gordon >> Administrative Secretary >> Computing, Environment and Life Sciences >> Argonne National Laboratory >> 9700 S. Cass Avenue >> Argonne, IL 60439 >> Phone: 630-252-4336 >> >> >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team > >_______________________________________________ >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] meeting today?
by Thomas Brettin 11 Jun '13

11 Jun '13

I don't see this on my calendar. Sorry about the mix up. I'm on another call right now. Tom On Jun 3, 2013, at 11:08 AM, India Gordon <igordon(a)cels.anl.gov> wrote: > I think Tom's calling in right now, Dan. > > His last call ran over a few minutes. > > On Jun 3, 2013, at 11:02 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > Are we still meeting today? I think I'm the only one on the call. > > ---- > 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 > > India S. Gordon > Administrative Secretary > Computing, Environment and Life Sciences > Argonne National Laboratory > 9700 S. Cass Avenue > Argonne, IL 60439 > Phone: 630-252-4336 > > > > _______________________________________________ > 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] Many services not ready for release because they lack release notes
by Thomas Brettin 07 Jun '13

07 Jun '13

can we talk? On Jun 7, 2013, at 12:37 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > On Jun 7, 2013, at 6:36 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >> analysis_book - not in the release - it's the ipython notebook that Folker did and its a MGRast product. > > It's still unclear what the release process is for Labs, but ok, we won't worry about this one for this release. > >> aux_store, not in the release as far as I know because the public can't really touch it. > > Right, yes, I should have marked that as internal only. > >> registry - not in the release, it's an internal experimental module > > I put that one in parens for that reason. > >> search - has api docs, just not in standard form. just ask guru where the url is > > Is search a service as well as a Lab? In either case, it should deploy API docs to the standard location. We shouldn't have to ask the developers where they've put their API docs. (If it's just a Lab and not a service, then the standards are less clear.) > >> I would just do a foreach repo, show me the git logs, or number of commits, or something. Many haven't really changed significantly. Based on a 15-30 minutes of detective work, i'd formulate a plan forward. > > Wait, so, if they haven't really changed, what does it mean for them to be "in this release"? If we're releasing them, then that's because they've changed, right? So the developers should be able to tell us how they've changed, if they want their modules to be included in this release. can we talk? > > Nomi > > >> >> On Jun 6, 2013, at 11:17 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> A few of the services have up-to-date release notes (and appropriately deployed API docs): >>> auth >>> jnomics >>> protein_info_service >>> translation >>> trees (? -- release notes updated 4/4) >>> >>> However, many do not have updated release notes and thus are not ready to be included in this release. (Some also don't have API docs in the expected location.) >>> analysis_book >>> assembly >>> auth_service >>> aux_store >>> cluster_service >>> communities_api >>> communities_qc >>> (erdb_service--internal only, right?) >>> experiment >>> feature_selection (also missing api docs) >>> (file_type_service) >>> genotype_phenotype_api >>> kb_seed >>> KBaseFBAModeling (also missing api docs) >>> matR >>> networks >>> ontology_service >>> phispy >>> plant_expression_service >>> (registry) >>> search (also missing api docs) >>> workspace_service >>> >>> What's the best way to get the missing release notes so we can finish up this release? Do Mike and I need to phone the relevant developers? >>> >>> Nomi >>> _______________________________________________ >>> 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] Many services not ready for release because they lack release notes
by Nomi Harris 07 Jun '13

07 Jun '13

On Jun 7, 2013, at 6:36 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > > analysis_book - not in the release - it's the ipython notebook that Folker did and its a MGRast product. It's still unclear what the release process is for Labs, but ok, we won't worry about this one for this release. > aux_store, not in the release as far as I know because the public can't really touch it. Right, yes, I should have marked that as internal only. > registry - not in the release, it's an internal experimental module I put that one in parens for that reason. > search - has api docs, just not in standard form. just ask guru where the url is Is search a service as well as a Lab? In either case, it should deploy API docs to the standard location. We shouldn't have to ask the developers where they've put their API docs. (If it's just a Lab and not a service, then the standards are less clear.) > I would just do a foreach repo, show me the git logs, or number of commits, or something. Many haven't really changed significantly. Based on a 15-30 minutes of detective work, i'd formulate a plan forward. Wait, so, if they haven't really changed, what does it mean for them to be "in this release"? If we're releasing them, then that's because they've changed, right? So the developers should be able to tell us how they've changed, if they want their modules to be included in this release. Nomi > > On Jun 6, 2013, at 11:17 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> A few of the services have up-to-date release notes (and appropriately deployed API docs): >> auth >> jnomics >> protein_info_service >> translation >> trees (? -- release notes updated 4/4) >> >> However, many do not have updated release notes and thus are not ready to be included in this release. (Some also don't have API docs in the expected location.) >> analysis_book >> assembly >> auth_service >> aux_store >> cluster_service >> communities_api >> communities_qc >> (erdb_service--internal only, right?) >> experiment >> feature_selection (also missing api docs) >> (file_type_service) >> genotype_phenotype_api >> kb_seed >> KBaseFBAModeling (also missing api docs) >> matR >> networks >> ontology_service >> phispy >> plant_expression_service >> (registry) >> search (also missing api docs) >> workspace_service >> >> What's the best way to get the missing release notes so we can finish up this release? Do Mike and I need to phone the relevant developers? >> >> Nomi >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >

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