Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-05-12

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All times shown according to UTC.

Time Nick Message
00:09 jar286 anyone want to review my commit? https://github.com/OpenTreeOfLife/oti/commit/b3c961b7c35d2d2fb4290e999ea358bcb87c35ab
00:11 codiferous why did you define a function called main instead of using "if __name__ == '__main__'"?
00:12 jar286 I like for the more important code to be toward the top of the file, with utilities lower down.  so I always define a main() and it’s often at the top.
00:12 jar286 I don’t have the if __main__ idiom memorized, so I leave it out if it’s not going to be needed
00:13 jar286 the ot-base PR is compatible, I assume… I’m going to merge it to master
00:14 codiferous well, no matter, it is just a style thing
00:15 jar286 yeah, that’s what I said to Hemingway
00:16 codiferous heh. well then, you should consider still adding the if __name__ == '__main__': conditional at the bottom and rename your 'main method named something pythonic :p
00:16 codiferous bleh, please excuse the poor wording, was correcting it when i hit return
00:17 jar286 what would be pythonic?  ‘main’ has a long tradition, going back to 1960 or before
00:17 jar286 oh, I see, if it’s a module you wouldn’t call it that
00:17 codiferous right
00:17 codiferous index_studies or something
00:18 jar286 in that case I’d want to introduce argparser...
00:18 codiferous typically yes
00:19 jar286 and put the arg parsing in main(), and the thing that does the real work in a descriptively named function...
00:19 codiferous well you typically don't define a method for the code that would typically go in a java main() method
00:20 jar286 can I leave it as it is and consider myself on warning?
00:21 jar286 there’s an awful lot of other cleanup that could be done to that file
00:21 codiferous heh, of course. minor style issues. doesn't make it difficult to follow the logic
00:21 codiferous just letting you know that is nonstandard python
00:21 jar286 ok
00:27 jar286 merge?  it’s been tested on devapi
00:31 codiferous i don't see why not
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01:13 jar286 codiferous, I think my rewrite of map-trees is ready for your review. lots of questions
01:20 jar286 the map-trees section of the supplment, that is
01:21 codiferous ok, i will take a look
01:40 jimallman sorry i missed the review, but glad we’re merging!
01:45 jimallman regarding idiomatic python and why it matters, this recent PyCon video is a great explanation. Raymond starts out kinda slow and fussy, but bear with it and he really delivers:  https://www.caktusgroup.com/blog/2015/05/05/pycon-2015-must-see-talk-beyond-pep-8-raymond-hettinger-26/
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16:05 josephwb hey mtholder
16:05 mtholder yes
16:05 josephwb do you have the numbers for "Step 4: Pruning the taxonomy to taxa required by phylogenetic inputs"?
16:05 josephwb in the supp.
16:06 josephwb you probably got an email?
16:06 mtholder not handy.
16:06 mtholder but I can calculate them
16:06 josephwb i don't know if i have these at all. i believe you enetered in those original values
16:07 josephwb they are logged somewhere during decomposition?
16:07 kcranstn can you please stay on the skype call?
16:33 jimallman a few links re: recovering deleted files on Google Drive
16:33 jimallman http://blog.backupify.com/2012/09/26/how-to-recover-lost-documents-and-data-in-google-drive/
16:33 jimallman https://support.google.com/drive/answer/2405957?hl=en
16:34 jimallman https://support.google.com/drive/answer/2375102?hl=en
16:35 jimallman kcranstn: ^
16:35 kcranstn yes, looking
16:36 kcranstn https://docs.google.com/document/d/1DxQRnHZSSK6NRlQaBkvaWSYvUm0Am0DMGVvUlm70X7A/edit
16:37 kcranstn I got it back through a link I emailed a few weeks ago. It was not in My Drive (but is now in the Open Tree of Life PNAS revision folder)
16:39 jimallman wow, i’ll have to remember that trick
16:43 jar286 amazing
16:43 josephwb would have appreciated a response to that issue; been depressed for days here.
17:00 jimallman sorry josephwb, i’d been meaning to do a quick search..
17:01 kcranstn I’ve been backpacking and without internet or cell phone
17:01 kcranstn just got computer back this morning and catching up
17:07 jar286 codiferous, are you in process of splitting the doc into 2 docs?
17:17 codiferous no, so far we don't have a way to preserve comments so i think we are leaving it as is
17:18 codiferous with a high priority goal of getting it to a point where we can remove the entire cody's text section
17:22 jar286 another kind of inefficiency here is that I make a comment or question which leads to a change in the text, but I never get notification that the text has changed, so don’t know that there has been a response and don’t get a chance to check the text (except by stumbling on it later, by accident)
17:22 jar286 I think that simply responding to the comment before marking it ‘resolved’ would be sufficient
17:23 codiferous i try to do that in general, but will try to be more conscientious about it
17:23 jar286 or, let the original author of the comment be the one to mark it ‘resolved’
17:28 jar286 codiferous, I have four questions on map trees. they are in comments in the ‘old mapping description below here’ section
17:32 codiferous ok, looking now
17:33 codiferous the name 'imaging function' was used in a previous version of the text. it is obsolete
17:36 codiferous ok, i have replied to your comments there. please resolve them if you can
17:51 jar286 two out of four
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18:07 codiferous posted more replies
18:17 jar286 I’ve got another contradiction.
18:17 jar286 some text was added that disagrees with the text that was there, which I rewrote
18:18 jar286 codiferous, “For each tree, an independent traversal of this type is initialized at each taxon node within the given subproblem that contains all the taxa in the tree.”  is new and contradicts previous text
18:18 jar286 I’ll have to come back to this later
18:20 codiferous what previous text? that is correct
18:20 jar286 the definition of m in the base case
18:20 jar286 the new text is a complete surprise
18:20 codiferous where is that / what is the contradiction?
18:21 codiferous that new text is what we had talked about with mark the other day
18:21 jar286 later, I have to prepare for the 2:30 call
18:21 codiferous note, it is each taxon node that must contain all the taxa in the tree, not the subproblem that contains all the taxa
18:21 codiferous ok
18:22 codiferous reordered the sentence to clarify that, in case that was the problem
18:23 jar286 that was not the problem
18:24 codiferous i found the sentence fragment that i think describes the base case: "m(x) where x = root(t) is defined to be all taxonomy nodes v such that ingroup(x) ⊆ ingroup(v)."
18:28 codiferous ah, not a fragment. and it seems to be consistent with the first statement you quoted above. i don't see how those differ
18:30 jar286 who’s initiating this hangout?
18:30 kcranstn good question. I will do so
18:32 kcranstn https://plus.google.com/hangouts/_/gxb66mxvwsqdl6sx7d6bw4yy24a?hl=en
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