Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-06-25

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All times shown according to UTC.

Time Nick Message
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13:01 kcranstn jar286 - you joining the nescent meeting?
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14:47 travis-ci OpenTreeOfLife/phylesystem-api#796 (opentree-issue-641 - e9b1104 : Mark T. Holder): The build passed.
14:47 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/commit/e9b1104bc418
14:47 travis-ci Build details : https://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/68325225
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18:05 kcranstn I am back (short appointment)
18:05 kcranstn can review PRs any time
18:05 jimallman i’m here too. it looks like mtholder has been busy, some PRs worth reviewing
18:06 jimallman i have more progress on stats, but not yet fully baked
18:10 jar286 now I’m here too
18:10 jar286 https://github.com/pulls?user=OpenTreeOfLife
18:11 jar286 I assume skip stats, tree collections ?
18:11 kcranstn why not the ones from mtholder?
18:11 jimallman yes, neither is ready for prime time. mtholder’s are more promising
18:11 kcranstn https://github.com/OpenTreeOfLife/peyotl/pull/124
18:11 kcranstn (we can talk abotu the other two at the end)
18:12 jimallman i’m trying to reproduce the failure (and test the fix) in #151… looks like this has not been merged to development yet
18:12 * jimallman is reading #124 now
18:13 jar286 I always go from oldest to newest, that’s why I asked about stats & collections
18:14 kcranstn whoops, misread your post about skipping
18:15 jimallman i wish the changes in #124 removed the dead code, instead of commenting it out.
18:15 jimallman from the surrounding discussion it sounds like this service will never again make sense
18:16 jar286 there is a small argument in favor of versioning decoupling among components
18:16 kcranstn but we might re-implement that service at some point (ideally)
18:17 jar286 e.g. we might revive an old version of treemachine to look at an old graphdb… handwave… pretty tenuous
18:17 kcranstn assuming that mtholder leaving that code commented for future changes?
18:17 kcranstn no, we might have a service that returns the tree that supports a node
18:17 jar286 we should have the service in the API, but in the future it won’t be serviced by treemachine, I presume
18:17 kcranstn yes
18:18 jar286 #124 looks pretty good to me
18:18 kcranstn ok, merging
18:18 jar286 https://github.com/OpenTreeOfLife/phylesystem-api/pull/151
18:19 kcranstn should there be a link to the feedback page?
18:19 kcranstn or issue tracker?
18:19 jimallman this looks straightforward, and presumably mtholder has tested it, but it doesn’t seem to be on dev
18:20 jar286 hmm. thinking about link.  yes, that would be nice
18:20 jar286 link could be put either in the PR or in the issue (since github backlinks)
18:21 jar286 it’s https://github.com/OpenTreeOfLife/feedback/issues/61, or https://github.com/OpenTreeOfLife/peyotl/pull/123
18:22 kcranstn ?
18:22 jimallman i’m lost, are we talking about putting a link in the 500 (error) respose text?
18:22 kcranstn does that make sense? is that text displayed in the UI?
18:22 jar286 I’m probably confused
18:22 kcranstn yes, jimallman
18:23 jimallman yes, i believe it will appear in the pinkish footer, when the import fails
18:23 jar286 I guess 62 is something different.
18:23 kcranstn maybe that is overkill
18:23 jar286 this seems properly linked, to opentree #641
18:23 jar286 s/62/61/
18:24 kcranstn jar286 - I was asking about putting a link where the 500 error code says “Please report this bug"
18:24 jimallman so we should be able to add a hyperlink in “Please [report this bug] to the OpenTree…”
18:24 jar286 oh.
18:24 jar286 I haven’t looked at the context but I would expect that for all 500 responses
18:24 jar286 it should be in whatever the web api framework is
18:25 jimallman hm, i see your point
18:25 kcranstn ok, let’s leave this one as is, then
18:25 jar286 I don’t think it should be a special case here, since there are dozens of such exceptions leading to 500s
18:26 jar286 could raise an issue… maybe in germinator repo since it’s systemwide…
18:26 jimallman i’ll make an issue with the suggestion to add [report this bug] to all error messages in footer, and self-assign
18:26 jimallman i think the general feedback repo makes sense
18:27 jar286 we can merge #151 I think
18:27 kcranstn +1
18:28 jar286 you’re doing the merges...
18:28 kcranstn one
18:28 kcranstn done
18:28 jimallman here’s the new issue (should be quick to add, will need to test with anonymous users, etc) https://github.com/OpenTreeOfLife/opentree/issues/662
18:29 jar286 almost done: https://github.com/OpenTreeOfLife/peyotl/pull/125
18:30 jar286 travis build is in progress…
18:30 jar286 we already merged 124 as directed…
18:31 jar286 all nexson consumers need to be robust in presence of edgeless trees
18:32 kcranstn should I wait for travis?
18:33 jimallman it looks like the caller of convert_tree properly skips a tree with a None result:  https://github.com/OpenTreeOfLife/peyotl/blob/opentree-issue-641/peyotl/nexson_syntax/direct2optimal_nexson.py#L139-L141
18:33 jar286 I don’t know. wonder why it’s taking so long.
18:34 jar286 I would rather not say: “you can depend on there being no edgeless trees in a nexson” - because this isn’t true of NeXML and the whole point of nexson is to reduce conversion and documentation load
18:34 jar286 the PR is fine, but I wish it wasn’t necessary
18:35 jimallman do you suppose we need the same fix in optimal2direct_nexson.py?
18:36 jar286 No comment at top of file saying what it’s about.
18:36 jar286 oh, I see class comment now
18:37 jar286 I hope not (as I said)
18:37 kcranstn I am bored waiting for travis. What else can we discuss
18:38 jar286 I’m going to add a comment to the PR
18:45 jar286 #641 travis finished.  I say merge
18:45 kcranstn you mean #125?
18:46 jar286 yes #125 (= opentree 641)
18:47 jimallman so, merge under protest? or merge with known issues? or wait to discuss with mtholder?
18:47 jimallman (referring more to jar286’s reservations than my own question about optimal2direct_nexson)
18:50 jar286 merge without reservation.  my comment has been made (and it says ‘the PR is fine’)
18:50 * jimallman nods
18:50 kcranstn https://github.com/OpenTreeOfLife/phylografter/pull/127
18:51 jimallman i don’t recall why this old PR is stalled… i see that pmidford assigned it to rhr (Rick), perhaps it needs more love?
18:52 jimallman maybe it’s still “awaiting feedback on edge formatting”?
18:55 kcranstn I don’t see that
18:57 jimallman it’s in the commit message for f07ced2
18:57 jar286 That repo is not being maintained. Last commit was June 2014.
18:57 kcranstn does that mean we can’t merge this?
18:58 jar286 I would say let’s merge it, even though that will have no effect
18:58 jimallman i’m tempted to run it by Rick, since he’s the current assignee
18:58 jar286 other than getting it off of our list, which would be salutory
18:58 kcranstn I can ping rick in a comment
18:59 jimallman “have no effect”? has this been superceded by another phylografter repo?
19:00 jar286 what I mean by “have no effect” is “have no effect on the world”… the change will go into the repo, but Rick probably won’t pick it up, and he’s the only one running code related to this
19:00 jimallman gotcha
19:01 jar286 no idea whether there’s any study curation using phylografter at all, and if it were it would likely not find its way back into phylesystem
19:03 jar286 I’ll update the servers at 3:30 or so
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20:04 travis-ci OpenTreeOfLife/phylesystem-api#798 (master - e44ae15 : Karen Cranston): The build passed.
20:04 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/08a77e3f49a1...e44ae1565238
20:04 travis-ci Build details : https://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/68365261
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21:13 jar286 updating api.opentreeoflife.org now
21:15 jar286 smoke tests pass, all done
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