Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-25

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06:43 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#624 (configurable-pref - a47985b : Mark T. Holder): The build passed.
06:43 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/4a0b3c00952e...a47985b3739c
06:43 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/36227221
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14:55 kcranstn hey mtholder… in comment on https://github.com/OpenTreeOfLife/peyotl/pull/30
14:55 kcranstn you mention “editor now shows me all of the pylint warnings/errors “
14:55 kcranstn what editor?
14:55 mtholder vim. I just added the syntastic plug-in
14:56 kcranstn cool
14:57 mtholder it is indeed. lots of formats/languages supported: https://github.com/scrooloose/syntastic/tree/master/syntax_checkers
14:58 mtholder I toned down the pylint warnings quite a bit, too. https://raw.githubusercontent.com/OpenTreeOfLife/peyotl/master/dev/pylintrc
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15:15 kcranstn jonathan and I were wondering about reviewing PRs at 2 pm EDT today (here, via irc)
15:17 towodo josephwb ^
15:24 josephwb reviewing PRs: that was for me?
15:24 kcranstn everyone
15:24 josephwb ok.
15:32 josephwb do you guys use linux?
15:32 kcranstn os x
15:32 kcranstn why?
15:33 josephwb my office (linux, synthesis!) computer died. since I will be reinstalling things, I am entertaining different flavours of linux.
15:33 josephwb was using Ubuntu
15:33 josephwb maybe Debian?
15:33 josephwb def more geek cred
15:33 kcranstn :)
15:48 towodo personally I prefer Debian. more conservative, less hype, less lard.
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17:11 kcranstn towodo - is the “you” in your email me?
17:11 towodo I doubt it
17:12 towodo I think I meant John & Chris
17:12 josephwb thanks for the linux advice towodo. i think i will try it.
17:12 towodo sorry
17:12 kcranstn I am not sure where the “untitled” tab is
17:12 kcranstn confused
17:13 kcranstn ah, I see it
17:13 kcranstn I also created an issue for a link to the blog from tree.opentreeoflife
17:13 towodo in which repo?
17:13 kcranstn opentree
17:15 kcranstn https://github.com/OpenTreeOfLife/opentree/issues/451
17:17 towodo I don’t get why they don’t feel a greater sense of ownership. Or maybe they think their site isn’t ready and don’t want the splash page out there yet?
17:19 kcranstn no idea
17:20 kcranstn I asked Karl to write up a description of the educational page for the blog
17:20 kcranstn want to wait for that before we make the changes
17:20 kcranstn just to give people an overview of the changes to the site structure
17:23 towodo the splash page is a static design. no attempt to make it mobile friendly…
17:30 kcranstn boo
17:31 kcranstn i can’t actually get it to load on my phone
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18:00 kcranstn hello!
18:01 towodo hello
18:01 kcranstn https://github.com/OpenTreeOfLife/opentree/pull/448
18:02 towodo I looked it over. it seems OK and if it’s wrong it will fail quickly and catastrophically, which is good.
18:02 towodo possible trouble with tabs
18:03 kcranstn isn’t there a commit that fixes that?
18:03 towodo although I think he said he was going to change all tabs to spaces
18:03 kcranstn https://github.com/OpenTreeOfLife/opentree/commit/75b88baf9c46de189683ca79bfe61e3fc372f60a
18:03 kcranstn ok to merge?
18:04 towodo yes
18:04 kcranstn done
18:05 towodo https://github.com/OpenTreeOfLife/opentree/pull/433
18:05 towodo there was an issue. would be nice if the issue & the PR were linked
18:05 kcranstn we can do that
18:06 kcranstn link to issue?
18:06 towodo looking for it. github doesn’t provide a way to search contents of issues
18:07 towodo search for getJSONFromNode turns up empty
18:07 towodo maybe I just told him in email or irc… I don’t know… I say move on. looking at diff
18:08 towodo very straightforward. merg
18:08 kcranstn peyotl or treemachine next?
18:09 towodo peyotl. mtholder, pmidford2, josephwb, wanna join the fun or just observing?
18:09 josephwb towodo: i think you can search for issue contents
18:09 pmidford2 Mostly observing, but if I can help
18:09 kcranstn https://github.com/OpenTreeOfLife/peyotl/issues
18:09 towodo how? is that ‘This repository Search’ at the top?
18:09 josephwb couldn't that tho...
18:09 josephwb no, on issues, next to Filters
18:09 kcranstn yes, that does search issues. But there is no issue that relates to PR 433
18:10 mtholder happy to help..
18:10 kcranstn moving on...
18:10 towodo https://github.com/OpenTreeOfLife/peyotl/issues/32
18:10 towodo oops not a pr
18:10 mtholder that is not fixed yet.
18:11 towodo https://github.com/OpenTreeOfLife/peyotl/pull/33 is a PR
18:11 kcranstn TravisCI failing
18:11 mtholder https://github.com/OpenTreeOfLife/peyotl/pull/22 is the first open one
18:12 kcranstn ok 22 then
18:12 towodo oh. right, start at the bottom of the list (earliest)
18:12 mtholder travis fails on 33 because that was branched off of master before I implemented any of the travis checking.
18:13 towodo how to test #22?
18:13 kcranstn there is an example script
18:14 mtholder note that  examples/list_supporting_files_for_nexson.py  is a client script for the functionality.  You have to install that PR and https://github.com/OpenTreeOfLife/phylesystem-api/pull/112
18:14 mtholder then the server has the file retrieval functionality
18:15 mtholder there is also a test in phylesystem-api/pull/112 in ws-tests/test_file_get.sh
18:17 towodo ws-tests?
18:18 mtholder https://github.com/OpenTreeOfLife/phylesystem-api/blob/master/TESTING.md
18:18 towodo hmm.  maybe the peyotl repo should have a TESTING.md with a link
18:18 mtholder ws-tests is a subdir of phylesystem-api that tests the web-services offered by that repo
18:18 mtholder "python setup.py test"
18:20 towodo and I would know about “python setup.py test” how?…
18:20 mtholder that is the standard trigger for unit tests in python.
18:20 mtholder or https://github.com/OpenTreeOfLife/peyotl/wiki/testing
18:20 mtholder I can add a TESTING.md file
18:21 kcranstn all passes for me
18:21 towodo didn’t occur to me to look at that wiki.
18:21 towodo I think everything one would want to know about testing should be discoverable (either documented or linked) from TESTING.md
18:22 towodo some of us don’t know python very well
18:22 mtholder there is a link to the wiki in the README, FWIW
18:23 towodo hmm.
18:25 towodo this one looks fine to me. I will make a note to myself to give it a try in staging. merge?
18:25 kcranstn merge!
18:26 towodo https://github.com/OpenTreeOfLife/peyotl/pull/27
18:26 kcranstn reminder: g + p in github UI gets you back to the list of PRs
18:26 kcranstn g + i = list of issues
18:27 towodo clicking on the little ! and PR tabs on the right does it too
18:27 kcranstn clicking?!?!
18:28 towodo cool, there be lambdas
18:28 towodo so pylint has it in for import * ?
18:29 mtholder yeah. bit cryptic
18:29 towodo so what’s the history here, you just one day decided to see what happened when you ran pylint?
18:30 mtholder hold up. A better order is probably https://github.com/OpenTreeOfLife/peyotl/pull/28, https://github.com/OpenTreeOfLife/peyotl/pull/29 then https://github.com/OpenTreeOfLife/peyotl/pull/27
18:31 mtholder I originially had "cleanup" merging to master in PR26
18:31 mtholder but I thought it was confusing to have PR26 contain PR 22 (the one that karen just merged).
18:31 towodo you’re saying the merges will be cleaner in that order?
18:32 mtholder yes.
18:32 towodo ok. 27 looks good to me but let’s move to 28
18:32 mtholder Emily will be here next week, and we'd like to submit a note on peyotl. Hence the effort to get it cleaned up (pylint, etc).
18:33 kcranstn cool
18:33 towodo travis build failed
18:33 towodo no Rakefile found
18:33 mtholder no .travis.yml back then.
18:34 towodo ok
18:34 pmidford2 any way to poke travis into trying this again?
18:35 towodo travis will start with the same commit, and it will still have no yml file
18:36 towodo so restarting not enough… you’d have to arrange to add a yml file to this code… not worth the bother
18:36 pmidford2 got it
18:37 towodo #28 looks innocuous
18:37 mtholder 29 is wrappers for client code (not the core infrastructure parts of peyotl)
18:38 towodo the PR says “I'm about to deploy another branch for testing”, did you do that? or shall we just merge and forge ahead?
18:38 kcranstn merging 28?
18:38 mtholder with the oti exception noted in the comment
18:38 mtholder I deployed tested, and then later redeployed a different branch
18:39 towodo merge #28.
18:40 towodo https://github.com/OpenTreeOfLife/peyotl/pull/29
18:40 kcranstn https://github.com/OpenTreeOfLife/peyotl/commit/9f40b7e64491aa10b99193aa74e39bd4883e77d3
18:40 kcranstn :)
18:41 towodo ok, now I admit that the commit comment was appropriate.
18:41 towodo this is a huge commit.
18:41 mtholder #28 was set up to merge to supp-file (which has now been merged to master). I'm going to pull it to master
18:42 mtholder yes 29 is wrapping the v2 apis
18:42 mtholder w/o breaking the v1 apis
18:42 towodo thanks for noticing that.  I see #29 merges to cleanup…
18:43 mtholder yes. i wanted to make the sequential rather than overlapping. Not sure what the best practice is...
18:43 towodo can’t each PR request a merge to master?… oh I see the problem. the commits from the first would be listed under the second
18:44 mtholder Yes. They were all huge, then. note that a file in peyotl/api/... is a wrapper for third-party clients. There are some calls to oti in phylesystem, but otherwise that code is not used in our deployed services.
18:46 towodo goodness.  I would not have bothered to retain the option to use v1… would have waited until v2 was fully deployed, then just switched over
18:47 kcranstn mtholder is nice
18:47 towodo he’s a better person than I
18:47 josephwb mtholder ist schön
18:47 mtholder impressive Deutsch, there
18:48 pmidford2 er ist nett
18:50 kcranstn ok, PR 29 people
18:50 towodo I was running the tests
18:50 kcranstn *sound of whip cracking*
18:50 towodo ImportError: No module named peyotl.nexson_syntax
18:50 towodo Conversion of "data/nexson/otu/v1.0.json" to JSON failed
18:50 towodo "validate-nexml" was not found on the path. Validation against schema will be skipped.
18:51 towodo The PR said “You can test by running the test.sh in peyotl.” which I tried to do, and it failed.
18:52 kcranstn passed for me
18:53 towodo maybe the relevant failure for me is: integration-tests.sh: nexml roundtrip test skipped due to lack of saxon-xslt
18:53 towodo ?
18:54 mtholder hmmm. those pass for me, but I should have said "python setup.py test" rather than test.sh
18:55 mtholder both should work, but test.sh requires more configuration.
18:55 kcranstn ah, that’s what I ran (lazy - simply grabbed the command from bash history)
18:55 towodo ImportError: No module named sh
18:56 mtholder pip install -r requirements.txt
18:56 towodo attempting pip install -r requirements.txt in a virtualenv
18:57 towodo I only figured out what to do by reading .travis.yml.  as a general to-do we should figure out how to make testing more transparent
18:58 towodo tests passed.  merge
18:59 towodo now #27
18:59 mtholder https://github.com/OpenTreeOfLife/peyotl/wiki/installation
19:00 towodo I think the algorithm for testing should be: for each repo, read TESTING.md and do what it says
19:00 towodo shouldn’t be a need to look at other files unless TESTING.md tells you to
19:01 mtholder so repeat the installation instructions in TESTING.md ?
19:01 towodo https://github.com/OpenTreeOfLife/peyotl/pull/27
19:02 towodo no, have instructions in TESTING.md that say to find installation instructions in README or wiki or wherever
19:02 towodo reference is fine, what I’m trying to get at is the “follow your nose” principle
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19:05 towodo travis build passed for #27 and I skimmed the diffs. I say merge
19:06 kcranstn me to
19:06 kcranstn o
19:07 towodo My only question here is where this should be documented so that someone can find the feature when they need it. I don’t know
19:08 towodo e.g. I would like to use the feature and don’t know where I would look to learn how.
19:08 towodo but that’s not a fatal flaw.
19:09 mtholder which feature?
19:10 towodo the study id custom-prefix feature (we’re looking at #33)
19:10 towodo https://github.com/OpenTreeOfLife/peyotl/pull/33
19:11 mtholder Ah. OK. I'll add it to the phylesystem-api README. that is the user-facing code for that feature.
19:14 towodo I would say allow prefixes of any length, but I can submit that as a separate issue
19:14 towodo I think I can figure out how to use it just by reading this diff
19:15 mtholder yeah. I seem to recall expecting 2-letters then _. I'm not sure if I coded that assumption in. I need to check. I agree that it is ridiculous to make that restriction.
19:15 towodo this looks straightforward. I assume it was tested, but it’s ok if it doesn’t work since the goal is to make sure that nothing that currently works breaks.
19:16 towodo if len(pre_content) != 3 or not valid_pat.match(pre_content):
19:16 towodo merge?
19:16 kcranstn ok
19:17 kcranstn that feels like enough for one day
19:17 kcranstn unless there is something urgent
19:17 towodo hmph.  I’m going to keep going as soon as asterales is up
19:18 kcranstn https://github.com/OpenTreeOfLife/phylesystem-api/pulls
19:45 towodo nothing to do for ot-base
19:46 towodo no taxomachine PRs… but it doesn’t build.
19:46 kcranstn nice
19:47 kcranstn I see passed on the readme
19:47 mtholder that's becaue the repo has 666 commits right now - no build for you!
19:48 towodo taxomachine/src/main/java/org/opentree/taxonomy/MainRunner.java:[4,16] cannot find symbol
19:48 towodo [ERROR] symbol  : class TreePrinter
19:48 towodo [ERROR] location: package jade.tree
19:48 towodo I just pulled & recompiled jade and ot-base
19:50 towodo no travis
19:51 mtholder i have the same err. removing ~/.m2
19:52 mtholder no dice.
19:53 towodo There really is no TreePrinter class in the jade repo. Cody must have forgotten to add it to the commit.
19:57 towodo wait, there are passing travis builds in the PR conversation. the last one, 9b620b4, passed. And that’s what’s on ot10.
19:57 towodo so the failure must be a product of the merge commit
19:58 towodo i.e. an interaction
19:59 towodo I see, the jade master branch is not up to date
20:00 towodo the correct commits were made to the new_branch branch and never pushed to master
20:01 towodo https://github.com/FePhyFoFum/jade/issues/4
20:02 towodo workaround: check out new_branch instead of master in jade repo.
20:03 towodo nope, that doesn’t work. it’s not on github!
20:04 mtholder hmm. I had not pulled taxomachine. It now works for me with master jade and ot-base. Recompiling to double-check...
20:07 towodo I don’t get it. TreePrinter is on github. I did git pull. No TreePrinter locally.
20:09 towodo Sure, I can delete my clone and re-clone, but this is disturbing.
20:09 josephwb towodo: it is on my machine
20:09 mtholder you're on jade commit 7919f7c0748751f738bf8478c6554fb1af065409
20:09 mtholder ?
20:09 mtholder and you have no uncommitted changes
20:09 mtholder ?
20:09 josephwb i mean, i pulled, and it is there
20:10 towodo I said ‘git pull’ and it’s on commit 8052 from April
20:10 towodo I see the problem…
20:10 mtholder hmm. perhaps you --set-upstream to an old branch
20:11 towodo for some reason my clone has upstream set to a fork
20:11 towodo never mind
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20:11 towodo I was faked out early by doing ‘git log’ on ot10 instead of locally
20:17 josephwb "Konversation terminated!" <- badass
21:03 towodo why is this so painful…
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