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The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.

Home Page: www.pecanproject.org

License: Other

R 48.45% Shell 6.26% Fortran 28.89% Makefile 0.09% CSS 0.18% Python 1.20% C++ 0.88% C 0.04% PHP 3.43% JavaScript 0.02% HTML 10.32% TeX 0.23% MATLAB 0.01%

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For reference, the main competitor to Zapier is IFTT (if this then that). Might also be a good place to look. https://ifttt.com/discover

Made an issue out of a slack comment

@kooper yeah, I knew that'd expired but didn't realize it was killing the sync. I think this may be part of IT

Made an issue out of a slack comment

's effort to get us off that machine and onto the new server

Made an issue out of a slack comment

Make sure you have PEcAn.ED installed on the HPC machine. If you used any modules to compile ED you will need to have those listed as well. In <host><job.sh> anything here will be put in the job.sh which is executed on the HPC machine. If you do any downloading of data from a met server you will need to install PEcAn.data.atmosphere as well.

Made an issue out of a slack comment

Oh, OK, sorry for messing up with your schedule, will let you know asap

Made an issue out of a slack comment

Registration changes with BETYdb changes

line 34-35: revisit registration when betydb has some of the things we hardcoded

outputtype
inputtype

register <- read.register(register.xml, con)

:worried: …sorry, I’m replying to the wrong thread here.

Made an issue out of a slack comment

yeah, there is a lot of output

Made an issue out of a slack comment

looks like any message posted in pecan becomes an issue.

Made an issue out of a slack comment

If we don’t like any of those and want to self-host, https://slackapi.github.io/hubot-slack/ seems to be the ~most popular of the open-source projects

Made an issue out of a slack comment

Or for those who want to stay in R: https://github.com/hrbrmstr/slackr

Made an issue out of a slack comment

Input IDs for different stages

line 27-32: what if the input is something other than met$id?
input id for latest step - how do we determine what it is and where to start the workflow? With naming?

  #get met source and potentially determine where to start in the process
  met <- ifelse(is.null(input_met$source), logger.error("Must specify met source"),input_met$source)

Aha: https://docs.travis-ci.com/user/caching/#Pull-request-builds-and-caches says “If a pull request is using a cache but you don’t want it to, you need to clear both the pull request cache and the cache of the target branch.”

Made an issue out of a slack comment

This is just of the top of my head.

Made an issue out of a slack comment

Ok, thanks! That's what I do right now.

Made an issue out of a slack comment

Thanks for the clarification! So the best is just to manually edit the pft part of the code in my pecan.xml?

Made an issue out of a slack comment

Since I'm the one who wrote the part to start at 1, here is the history. The goal was to allow PEcAn to use multiple PFTs with ED. Realizing that a PFT could only be used once, as well as the fact that we don't have a good mapping (I believe) from PFT to ED PFT number I decided to start at 1. The goal was always to have a table that maps the PFT to all the variables needed for an ED run, and override all the values for a PFT in the config.xml file.

Made an issue out of a slack comment

@black11 finally found the magic flag for postgresql `psql -o /dev/null -q < import.` this will still show errors, but the setval commands are considered outputs from sql and will thus be written to /dev/null.

Made an issue out of a slack comment

The post-signup redirect is very clear. When reading the docs I do instinctively click on the first link (http://pecanproject.slack.compecanproject.slack.com>) instead of the “request an invitation” link, but that’s not a problem for me on the second read or those who read before clicking on their first.

Made an issue out of a slack comment

@black11 @emcowdery Can you link to some issues created this way? Just curious to see what they look like.

Made an issue out of a slack comment

@felicien.meunier I think this issue has a bit of a history that I can't fully recall, but I believe you need to manually edit the part below in your pecan.xml for now, otherwise it automatically starts numbering PFTs from 1 ``` <pfts> <pft> <name>temperate.Early_Hardwood</name> <constants> <num>9</num> </constants> </pft> <pft> <name>temperate.Late_Conifer</name> <constants> <num>8</num> </constants> </pft> </pfts> ```

Made an issue out of a slack comment

@all bu people. I will be moving the bety postgres database on Monday 11am eastern time. This will take about 1 hour (probably less). At that point I will disable access to BETY and to the database. Once I'm done with this you will need to modify your config.php to point to the new database server `$db_bety_hostname="128.197.168.114";` @dietze will ask to change the DNS name, until that is done you will need to use the ip address.

Made an issue out of a slack comment

Zapier might be a good way to create an unofficial slack archive as well. We should scroll through all the existing slack-githup zaps

Made an issue out of a slack comment

@dietze syncs are failing with BU due to expired SSL certificate.

Made an issue out of a slack comment

Now if only Safari would stop melting down every time I ask it to display the Travis output, but I don’t think that’s our fault.

Made an issue out of a slack comment

@kooper there is no reason to think that this might go wrong, right? I am in the middle of some production runs that won't finish until Wednesday or so, but I would be fine with not having DB access for couple of hours on Monday. Just checking if it will be back up quickly

Made an issue out of a slack comment

Aha, “new mention”. This looks promising

Made an issue out of a slack comment

Yup it's excessive

Made an issue out of a slack comment

I’m trying out the issue maker zap

Made an issue out of a slack comment

I’m stuck on how to specify both a keyword and a channel, but @emcowdery it sounds like you’re ahead of me.

Made an issue out of a slack comment

Do we necessarily want both a keyword and a channel? It might be nice to be able to create new issues from a keyword in any channel.

Made an issue out of a slack comment

Let me know when you are done and I'll do it then. Don't want to mess anything up.

Made an issue out of a slack comment

Reconcile Ameriflux formats records

We currently have three format records for the same Ameriflux files.
The discrepancies are due to the fact that query.formats.vars and met2CF.CSV are parsing and converting dates differently.
See:
https://github.com/bcow/pecan/blob/master/db/R/query.format.vars.R#L89
vs.
https://github.com/bcow/pecan/blob/master/modules/data.atmosphere/R/met2CF.csv.R#L148

I can't properly add assignees right now so: @ankurdesai

https://github.com/bcow/pecan/issues

Made an issue out of a slack comment

yeah, but that can be done from the webinterface as well, by clicking edit pecan.xml.

Made an issue out of a slack comment

It’s dinnertime over here, so I’m out for a while. If there’s not already an issue bot running when I get back, I’ll take another stab :slightly_smiling_face:

Made an issue out of a slack comment

If anyone is interested, the NEON/LTER/CZO meeting on data integration that I'm going to next week will have a live stream: We will be live streaming the meeting on Days 1 and 3 (2/13 and 2/15). Feel free to let your colleagues know in case they might be interested to watch the talks and/or our synthesis and next steps discussions. Link to join on the meeting webpage: http://www.neonscience.org/obs-networks-earth-system-understanding-2018.

Made an issue out of a slack comment

that is my plan for monday

Made an issue out of a slack comment

Can you do the manual dump and move to the new server or is that something I'm going to have to find time to do?

Made an issue out of a slack comment

@kooper Nice find!

Made an issue out of a slack comment

I’ve sucessfully made one that posts for every message to #github, but I don’t see how to limit it beyond that.

Made an issue out of a slack comment

question is who will make the first :mike: emoji

Made an issue out of a slack comment

the pecan invite url, now sends you to the following page: https://pecanproject.github.io/pecan-documentation/develop/about-the-pecan-book.html#slackreturn let me know if that is clearer.

Made an issue out of a slack comment

Printing checks

Do we actually want to print out the checks at each step?

start CHECK
dataframe
end CHECK

@ashiklom NL

Made an issue out of a slack comment

Every time someone comments on this thread it makes an issue

Made an issue out of a slack comment

Awesome, thanks!

Made an issue out of a slack comment

Where are you that it's currently dinnertime?

Made an issue out of a slack comment

NA Strings field in formats record

Add a text field to BETY formats that stores NA strings separated by commas.

Starting from this website, I would create a Zap that takes a slack keyword mention (maybe `create_issue`, or something that's intuitive but unlikely to be typed accidentally) and uses that to create a GitHub issue. https://zapier.com/apps/slack/integrations/github

Made an issue out of a slack comment

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