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pfmc-assessments / pfmc_assessment_handbook

PFMC Groundfish Assessment Best Practices Handbook
https://pfmc-assessments.github.io/pfmc_assessment_handbook/
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consider appendix showing running compilation of support software to load #1

Open aaronmberger-nwfsc opened 2 years ago

aaronmberger-nwfsc commented 2 years ago

One thing that is very time consuming is moving your assessment workflow structure (program, dependencies, etc.) from one computer to another. And now that the NWFSC has a four-year base laptop refresh schedule, we will be doing these transformations more often.

A group software list would be beneficial to have for quick reference as it pertains to doing assessments, building documents, and perhaps other standard software needs.

At one point Hastie asked me and I mentioned the following that pertain to assessments and other things, but clearly there are more to add, including R packages and dependencies.

Adobe acrobat pro, R, ADMB-IDE, Emacs, Microsoft office suite or similar, Winmerge, Mendeley, RStudio, GitShell, GitHub Desktop, Google Earth, GIMP, GoToMeeting, Sublime Text, JAVA, MiKTeX, VLC (or other) media player

Do others think this is a good idea? And is this a good place for this ever-evolving list? Clearly, there will be individual preferences to consider.

kellijohnson-NOAA commented 2 years ago

Installing tinytex via R is much easier than doing the full install of MiKTeX.

okenk commented 2 years ago

I think this is a great idea @aaronmberger-nwfsc if you want to add it somewhere. Maybe 05-other.qmd since that already has notes on software?

I would also add stan and Rtools to the list. (Or at least IT installed Stan for me and it worked, and I have found it to be a big fussy headache to install yourself, so I would recommend that route.) I use Zotero instead of Mendeley so maybe a generic "reference management software."

I think there are ways to export a list of installed R packages, because you ideally should update R more often than your computer. That might only work for packages on CRAN though.

John-R-Wallace-NOAA commented 2 years ago

A clean install of R and Rtools 4.2 (and perhaps beyond) will break TMB's gdbsource() if Rtools 3.5 is not also installed to supply the gnu debugger GDB. This is part of my submission to Google's TMB Users forum "Improving gdbsource() under Windows with Sys.which(), 'quit' in gdb, and Rtools 3.5": https://groups.google.com/g/tmb-users/c/2WmMsL3faYw

The submission points here: https://github.com/John-R-Wallace-NOAA/Improving_TMB_gdbsource_under_Windows/blob/main/README.md

If you want avoid Rtools entirely and use Ubuntu on WSL (Windows Subsystem for Linux) which would provide a single folder (with all your software loaded) to then backup, move to your new machine, copy for test changes, and/or share with colleagues, see: https://github.com/John-R-Wallace-NOAA/TMB_on_Windows_Subsystem_for_Linux

Multiple instances of WSL can be run simultaneously by opening a new PowerShell in Windows. Each instance of WSL can, in turn, run multiple R sessions in the background.

WSL can also be used as a platform to test your R code/functions/packages in Linux.

iantaylor-NOAA commented 1 year ago

I was looking at issues in this repository and was reminded of this unfinished discussion about software which I think would be useful to continue. I've attempted to compile the comments in this thread into the list below. Please edit this comment (via the option available when clicking the three dots on the upper right of the comment) to fill in the question marks or add or move stuff around as you wish.

Stuff that everyone should have

Other stuff (purpose; who uses it)

Stuff that we shouldn't use any more