slightly better error messages for missing arguments and files

[Elendol]

• make sage fail earlier than later when parameters are not set in the JSON file and are not command line arguments (it made the program panic once the computation started)
• use anyhow's context for errors when reading files, now the problematic file is displayed

Error: Failed to read parameters from `missing_file.json`

Caused by:
    IO error: No such file or directory (os error 2)

[Elendol]

you may want to squash my commits

[lazear]

Definitely going to squash!

[Elendol]

as of now we get this error message with problematic mzML files

; cargo run -- tests/config.json tests/LQSRPAAPPAPGPGQLTLR.mzML tests/aa.mzML tests/bb.mzML s3://beep
    Finished dev [unoptimized + debuginfo] target(s) in 0.11s
     Running `target/debug/sage tests/config.json tests/LQSRPAAPPAPGPGQLTLR.mzML tests/aa.mzML tests/bb.mzML 's3://beep'`
[2023-05-09T21:48:24Z INFO  sage] generated 1845 fragments in 6ms
[2023-05-09T21:48:24Z INFO  sage] processing files 0 .. 4 
Error: Failed to process mzML files

Caused by:
    Processing chunk 0 failed
        Failed to process `tests/aa.mzML`: IO error - No such file or directory (os error 2)
        Failed to process `tests/bb.mzML`: IO error - No such file or directory (os error 2)
        Failed to process `s3://beep`: S3 error - failed to construct request - key was missing: cannot be empty or unset

[lazear]

Awesome, thanks!

Sorry to flip flop... but I realized yesterday I have a couple of workflows that actually depend on sage not failing if files are missing (incremental searching of datasets as they come off MS...). I'll try to keep the most recent commit in the git history in case we want to use it in the future. I will try to squash and merge everything today

[Elendol]

cool, no problem, you might want to work on a proper refactor to different checks and errors, not just something a bit hacky about the files being present.

[lazear]

Ok, I squashed your branch and merged it in - I'm closing this one without merging.

Thanks again!