Add cli commands

[Leahh02]

This PR adds cli commands for the curl requests for the ci demonstrator. I implemented it very similarly to the way the requests are implemented in the ci demonstrator, but I can change it to use the requests library, for instance.

[kchilleri]

Tested these commands through Gitlab CI pipeline and they all work as expected. I'm going to think of possible unit tests now and look at the actual code.

@pagrubel do we want this remote stuff to be a part of our documentation?

[Leahh02]

I added some simple documentation to rest_api.rst, we will discuss the location and content.

I realized I didn't add any error handling into remote_client.py, I will consider adding this.

[Leahh02]

I learned about modules to test fastapi apps: https://fastapi.tiangolo.com/tutorial/testing/ and a module to test typer apps: https://typer.tiangolo.com/tutorial/testing/

[arhall0]

This command is making the directory locally. But also, the directory should exist on remote if remote was setup properly.

This errors for me because I can't make the folder locally because of permissions issues. If I comment this out, it works as expected.

[arhall0]

After the most recent commits I can run a workflow end-to-end from local on remote. For cat-grep-tar these are the commands:

beeflow remote droppoint $SSH_TARGET
beeflow package $BEE_PATH/examples/cat-grep-tar .
beeflow remote copy $USER $SSH_TARGET cat-grep-tar.tgz
mkdir cat-grep-tar-workdir
cp $BEE_PATH/examples/cat-grep-tar/lorem.txt cat-grep-tar-workdir
beeflow remote copy $USER $SSH_TARGET cat-grep-tar-workdir
beeflow remote submit $SSH_TARGET test_remote cat-grep-tar.tgz workflow.cwl input.yml

I think that this works well. It's maybe a bit verbose so maybe there are things we could do in the future to improve the workflow.

Another improvement for the future would be a way to check the status of your job & pull down the results to local. Automating these things to as few as commands as possible would improve their utility over just using things like rsync and scp.

[arhall0]

In general test coverage is good. For remote_client.py, test coverage is missing mostly for lines which are checking for errors or exceptions:

--------- coverage: platform darwin, python 3.10.13-final-0 ----------
Name                                                  Stmts   Miss  Cover   Missing
-----------------------------------------------------------------------------------
beeflow/client/remote_client.py                          80     60    25%   22, 27, 36-48, 54-71, 79-102, 112-141, 147-159

This is probably not a big deal.

I also noticed the droppoint folder is created when you run tests. This also probably doesn't matter too much.

[kchilleri]

I still need to test these new changes on the Gitlab CI work, please don't merge yet!

[kchilleri]

Besides the requested changes for adding a bit more error checking everything else looks good to me!

[kchilleri]

When reviewing this command, I forgot to run the beeflow remote droppoint command that creates the droppoint.env file. This gave me a "FileNotFoundError" error. I think it would be helpful to add an exception, something like:
except FileNotFoundError:
warn("Error: File droppoint.env not found. Did you run 'beeflow remote droppoint $ssh_target' to create this file?")