use github actions to compile SS

[k-doering-NOAA]

The goal here would be to build windows, linux, and mac versions of ss automatically. Jenkins can only build the linux version for now.

Started to put this together (24c3b78)

The steps I see toward doing this are:

• [x] compile ss safe on Linux to get familiar with github actions. Linux uses less github action min than windows or mac
• [x] compile ss safe on mac. Probably can expand the same script.
• [x] compile ss safe on windows to expand capabilities. May need a separate script as using a different shell and the commands are probably somewhat different?
• [x] Expand to compile all versions of ss.

[k-doering-NOAA]

I am stuck on this. I've been working on a workflow in: https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/setup-gh-actions/.github/workflows/build.yml

The issue is I can't figure out how to add ADMB to the PATH; the admb command is therefore not recognized. I've tried many different ways, including the recommended way and methods I've used on Jenkins, but I haven't gotten anything to work so that ADMB is found.

I will try reaching out to people who have used github actions before to see if they have any idea what I'm doing wrong.

[kellijohnson-NOAA]

Try @ChristineStawitz-NOAA

[k-doering-NOAA]

Sara Ogaz figured it out in 10 min! EDIT: the issues was I had to add admb-12.2/bin to the path instead of admb-12.2 or admb-12.2/bin/admb

[k-doering-NOAA]

Making good progress on this. Some notes:

• If we wanted to distribute the linux exe, we would prob. want to use docker and redhat instead of ubuntu. For some reason, SS compiled on ubuntu doesn't work on redhat, but SS compiled on redhat seems to work fine on ubuntu and redhat.
• I checked that the ss mac version could run on the mac mini; it ran, but in the process of copying over, it seems to not have the right permissions for anyone to execute it. I'm not sure why this is, as it has the correct permissions after it is compiled (checked by adding ls -l to the script. Maybe in the process of archiving or copying? I will look into this more, as we want the binary we post on vlab to have the correct permissions.

[k-doering-NOAA]

Successfully was able to setup workflows to compile all mac and windows SS binaries! Remaining issues to clean up:

• [ ] File permissions for mac artifacts (the ss binaries). According to the readme for the upload artifacts github action, this can only be done by compressing the files into .tar format. However, I'm still having issues figuring out how to extract the .tar on windows and still maintain the permissions. Either we will have to figure out how to expand .tar or make a conscious effort to change the file permissions before uploading to vlab. This is only a problem for linux and mac
• [x] Finish creating a linux version that uses centos for the OS instead of Ubuntu. This means a docker image needs to be used. This is necessary b/c it seems that compiling on Ubuntu creates a version of SS that Centos can't run, but for some reason the Centos version runs fine on Ubuntu (anecdotally from SS users).
• [x] Document how to run these jobs, in the SS compile notes google doc

[k-doering-NOAA]

After talking a bit with @iantaylor-NOAA about file permissions and reading a little more online, I'm not sure if the permissions for linux and mac binaries were created correctly even before github actions. I'm not sure if there was any way to guarantee this aside from distributing the executables some other way (for example, in the .tar format, which supposedly ships files with their permissions?) I think the simplest solution for now would be not to worry about permissions and instead document this potential problem so that users know they can run chmod a+x to make SS executable. I would expect linux users know this, but mac users may not (as someone who used mac for many years and never thought about file permissions).

If anyone has other thoughts about how to deal with this issue, please let me know!

[kellijohnson-NOAA]

I pinged a few people that are Mac users and they said that this has been an issue for them, especially when teaching a class where they are trying to distribute the executable. Their workaround was to use "chmod 755 ss" to get it to work and manually copy the executable (or at least the path to the executable) to each directory they used.

[k-doering-NOAA]

Thanks for confirming my suspicion, @kellijohnson-NOAA! Given this, I think just adding to the SS website/documentation that you may have to change permissions on your machine using chmod may be the best path forward for now.

I'm going to close this issue, but we can reopen it or create a new issue if we get another lead about a way to fix distribution permissions problems.

[kellijohnson-NOAA]

Lee Qi confirmed that chmod +x ss didn't work for some people, but chmod 755 did.

[k-doering-NOAA]

Thanks, I just assumed chmod a+x alone would work, but maybe the write and read privileges are important, too. The a+x is easier for me to remember, which is why I use it, but I will stick to the numbers from now on to be more specific! Theses are the specific permissions 755 gives, in case it is helpful: https://chmodcommand.com/chmod-755/