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meeting_saved_chat.txt
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08:58:13 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Welcome everyone!!
08:58:28 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://github.com/agu-ossi/2020-agu-oss
09:01:53 From Serge Sambolian : Is the workshop recorded and will it be available later ? (need to assist as a panelist in another session)
09:01:54 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Welcome everyone from snowy Colorado!!
09:02:10 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : For those just joining — this s the GitHub repo we w ill use - https://github.com/agu-ossi/2020-agu-oss
09:02:16 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : the workshop will be recorded by agues!
09:02:21 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Oops **AGU
09:02:27 From Serge Sambolian : Thank you :D
09:02:48 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : of course!!
09:04:50 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : For those who just joined — https://github.com/agu-ossi/2020-agu-oss
09:11:43 From Mousumi Ghosh : Will the slides of this presentation be made available to us?
09:11:49 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : yes!
09:12:26 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : All links are h ere in the readme - https://github.com/agu-ossi/2020-agu-oss
09:12:51 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : and h ere is the link tot he slides in case ou want to follow along now - https://docs.google.com/presentation/d/1dvtxWFthZA6S1ZGs2OetkesyIB_hPEAjFn7pyo2iz6o/edit#slide=id.p
09:14:32 From Sanjukta : Can we download the presentation from that link?
09:14:38 From Mousumi Ghosh : Thankyou
09:14:55 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Yup - go to file —> download
09:14:59 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : in the google slides interface
09:15:07 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : @mousumi you’re welcome!
09:16:11 From Sanjukta : Thanks :)
09:16:24 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : @Sanjukta of course!
09:17:34 From Lindsey Heagy : If you are interested in contributing to shared notes, we have a document for everyone here: https://docs.google.com/document/d/1KrBm1FEnd7gcnscCXyWP_-NEKIDcvgsy3Gfo56pLPpE/edit#heading=h.rqb5s4drunt3
09:27:22 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : for t hose who just joined — this is the repo we are using — https://github.com/agu-ossi/2020-agu-oss all links to slides and notes and such are located in the readme file! Welcome!
09:35:23 From Rene Gassmoeller : https://github.com/agu-ossi/2020-agu-oss
09:39:09 From Sanjukta : Are you running the code in the hub? or just the code body?
09:39:29 From Bane Sullivan (Kitware) : The notebook on GitHub is just a preview
09:40:06 From Bane Sullivan (Kitware) : We can run the notebook interactivity here: https://mybinder.org/v2/gh/agu-ossi/2020-agu-oss/main
09:45:48 From Cécile Coulon : is there a risk to overwrite files when making the modifications?
09:46:21 From Ed Santilli : You don't step on each other's toes while working.
09:46:58 From Rene Gassmoeller : github = cloud backup
09:47:02 From Sophie Goliber (she/her) : Backups
09:47:18 From Bane Sullivan (Kitware) : The risk is greatly minimized with a version control system like Git as the state of all files is tracked throughout time. Even if you delete a file, it still exists in the history.
09:47:37 From Jacob Schaperow : Are there file limits? Do we worry about these?
09:48:04 From Ed Santilli : What are the practical differences between forking and cloning?
09:48:16 From Rene Gassmoeller : I think there is a limit of 50 MB per file, and a total repository size of ~1 GB or so (not sure). This is meant for source code, not large data
09:48:19 From Bane Sullivan (Kitware) : There are general file size limits: 50MB typically. Though there is such a thing as Git Large File Storage. But there is no limit to the number of files you can have
09:49:18 From Bane Sullivan (Kitware) : Cloning is making a local copy on your computer. Forking is adding a copy (remote) to your GitHub account
09:49:52 From Ed Santilli : Thank you, Bane.
09:50:22 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://github.com/lwasser/2020-agu-oss/blob/main/agu_oss/clean_data.py
09:50:30 From Ed Santilli : We always clone to collaborate. But now that I think of it, I guess forking prevents the need to give everyone write access. Correct?
09:50:48 From Bane Sullivan (Kitware) : That is exactly correct.
09:50:50 From Ed Santilli : *write access to the main repo
09:50:56 From Ed Santilli : great. Thanks
09:58:05 From Ed Santilli : Does the testing only work on interpreted languages?
09:58:28 From Bane Sullivan (Kitware) : FYI, the slides are here: https://docs.google.com/presentation/d/1dvtxWFthZA6S1ZGs2OetkesyIB_hPEAjFn7pyo2iz6o/edit?usp=sharing
09:58:38 From Cécile Coulon : Can the main owner of the repository see the modifications you made on your forked repository? Or can he only see if you do a pull request?
09:59:14 From Sanjukta : Thanks Leah. Thanks for introducing to git :)
09:59:21 From Bane Sullivan (Kitware) : Typically those changes are only visible once you make a pull request
09:59:40 From Bane Sullivan (Kitware) : Testing can work for any language, not just interpreted languages like Python
10:00:28 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : @cecile bane is exactly correct! But if the main owner follows your repo they could see when you make changes and also if your repo is public they could go to your repo to see what you are doing
10:00:31 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Given this is all open!
10:02:02 From Ed Santilli : Bane, even a project with C++/Fortran? Does it need to have a makefile? I have a lot of questions here. Is there somewhere I can read about this?
10:02:47 From Cécile Coulon : Thank you for your answers!
10:02:48 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : of course @sanjukta !!
10:03:27 From Bane Sullivan (Kitware) : Ed, yes. You’ll have to do a bit more work to get that running for C++ than Python but it is absolutely possible! It is incredibly common to have tests for software regardless of language. I will see if I can find a resource for you shortly….
10:04:54 From Rene Gassmoeller : Ed, we will also have a dedicated part about testing in the next block. Also I am developing a C++ code including tests. We use a tool called ctest (part of the cmake software) combined with the same github actions we are using in this tututorial
10:05:44 From Ed Santilli : Great. Thank you everyone.
10:05:52 From Malambo : No sound?
10:06:19 From Ed Santilli : I have kids running around, etc. So I may be in and out. But I will rewatch the recording tonight to catch what I miss.
10:06:21 From Ed Santilli : Thank you
10:06:35 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : No worries Ed! We understand!
10:18:32 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : @malambo are you having audio issues or can you hear things ok? I do hear the audio so I wanted to ensure you can too
10:36:25 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : feel free to add comments to the chat if you can’t unmute!
10:38:13 From Rene Gassmoeller : if you want to follow along: https://mybinder.org/v2/gh/agu-ossi/2020-agu-oss/main
10:38:27 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Some of you did an excellent job of breaking things!! Go team!
10:56:50 From Vinícius Chagas : When testing, should we worry about optimizing the code? Or only if it's running correctly? When should we care about optimization?
10:57:58 From Roberto Ortega : In a test, is there a difference when the code breaks (e.g. stack overflow…) and when it actually does not pass??…
10:58:03 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Huh that’s an interesting question - might be good to pose it to the group but they are separate and related
10:58:09 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : testing — make sure the code runs as expected
10:58:28 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Optimization make sure the code is efficient. Often tests use data subsets to minimize run time
10:59:13 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : I’ll unmute in a minute to ask Lindsey to chat about this too!
10:59:59 From Rene Gassmoeller : @Roberto: Both will break the test, but in a good test framework you will see if it crashed or gave the wrong answer
10:59:59 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Roberto I’m trying to follow your question. A test could fail for different reasons - sometimes it fails because the code has broken
11:00:24 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : Ahh thanks Rene :)
11:00:56 From Rene Gassmoeller : I think Bane will talk about test frameworks next (at the example of github actions)
11:11:45 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : This is a great example. So here you add a build in test to raise and error in your code - and if you want you can then write an actual external test to check that when a function is given something t hat isn’t a list or a tray, that it fails gracefully with a useful message - great for usability
11:13:40 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : sorry my typing is terrible today :)
11:17:36 From Vinícius Chagas : Thank you!
11:19:36 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://docs.google.com/presentation/d/1dvtxWFthZA6S1ZGs2OetkesyIB_hPEAjFn7pyo2iz6o/edit#slide=id.g75d8cb0173_2_90
11:19:41 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : ^^^ slides!
11:20:10 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : We are here now - https://docs.google.com/presentation/d/1dvtxWFthZA6S1ZGs2OetkesyIB_hPEAjFn7pyo2iz6o/edit#slide=id.g7a995a9710_0_73
11:24:11 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : here is where bane is working - https://github.com/agu-ossi/2020-agu-oss/tree/main/.github/workflows
11:25:12 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : <note - you could automate this workflow to grab any and all notebooks - I manually coded this> you could also add additional python versions and OS’s to this build easily so it’s running your notebook on many different operating systems and python versions
11:30:06 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://github.com/marketplace/actions/lintly-flake8
11:31:58 From Cécile Coulon : There is a GitHub repository I’ve forked to make several small modifications. My modifications may be useful to others, but my level of coding is a lot less elegant than the main owners, so I’m hesitant to do a pull request. In these cases do you think it’s still ok to do a pull request?
11:33:13 From Rene Gassmoeller : This is a great question. Lets discuss it in the whole group later. In short: If they have a contributing policy that states they are happy about contributions this is absolutely ok.
11:34:10 From Allison Chartrand : yes, very interested in documentation!
11:38:17 From Cécile Coulon : thanks!
11:39:47 From Ed Santilli : Does it support Latex?
11:41:54 From Cécile Coulon : How do you get your README.md to show on the ‘home page’ of agu-ossi/2020-agu-oss? Is it done automatically?
11:42:15 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://www.sphinx-doc.org/en/master/latex.html
11:42:29 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : There are many modules that extend th e functionality of sphinx
11:42:38 From Ed Santilli : Great!
11:42:40 From Ed Santilli : ty
11:42:41 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : but that may be built in!
11:43:01 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : @Cecile that is an automatic function o f GitHub
11:43:12 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : If you have a README.md file it will render on the home page
11:45:05 From Aatish Anshuman : Does sphinx creates a website for example in readthedocs or somewhere?
11:45:12 From Cécile Coulon : thank you @Leah!
11:45:18 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : of course Cecile
11:45:35 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : You have many options when using sphinx - you can setup an auto build using readthedocs
11:45:52 From Bane Sullivan (Kitware) : Sphinx creates a rich HTML documentation site that you can publish anywhere. In our example we use Github Pages to publish it
11:46:09 From Bane Sullivan (Kitware) : But ReadTheDocs is another service you can publish to
11:46:48 From Aatish Anshuman : Thanks. what is GitHub.io ? Is it website hosting service ?
11:46:58 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : ^^ yes what bane said - if your environment is complex, making sure it runs can be tricky on read the docs so running it via actions is nice
11:47:19 From Bane Sullivan (Kitware) : GitHub.io is a domain for publishing static websites like documentation from GitHub repositories for free
11:47:44 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : there’s a new discussion feature too!
11:48:06 From Aatish Anshuman : Great! Thanks!
11:48:25 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : I just turned on discussions ON in our repo!
11:52:53 From Aatish Anshuman : Just found it :)
11:55:28 From Bane Sullivan (Kitware) : https://github.com/agu-ossi/2020-agu-oss/discussions
11:57:14 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://github.com/agu-ossi/2020-agu-oss/pull/26
11:59:10 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : https://docs.google.com/forms/d/e/1FAIpQLSeaO0QIwBquK_wYur5-ko0UgrhCwu4SBsofwEzo_4rGzcqVXA/viewform
11:59:24 From Leah Wasser (she/her) Earth Lab / earthdatascience.org / pyOpenSci : ^^^ the survey if you have a minute to take it!
11:59:46 From Biljana Music : Thank you.
11:59:49 From Kelly Kapsar (she/her) : Thank you! This was extremely helpful!
11:59:51 From Peter Makus : Thanks!
11:59:53 From Cécile Coulon : thank you!
11:59:56 From Facu Sapienza : Thank you!
11:59:56 From Ed Santilli : Thank you!
11:59:57 From Xin Zhou : Thank you!