Add a folder of outputs to acro

[mahaalbashir]

Create a function that:

1. Takes a folder from the user and adds each file in that folder to an acro object as a custom output.
2. Rename the outputs from numbers (output_0, output_1,..) to the name of the files.
3. Call "finalise" to create the SDC files (config.json, checksums, results.json).

[codecov]

Codecov Report

Merging #130 (8e86986) into main (9f3ec7e) will increase coverage by 0.05%.
Report is 3 commits behind head on main.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #130      +/-   ##
==========================================
+ Coverage   97.14%   97.20%   +0.05%     
==========================================
  Files           6        6              
  Lines         666      680      +14     
==========================================
+ Hits          647      661      +14     
  Misses         19       19              

Files Changed	Coverage Δ
acro/acro.py	99.02% <100.00%> (+0.04%)	⬆️
acro/record.py	98.51% <100.00%> (+0.03%)	⬆️

[mahaalbashir]

@rpreen I would like your advice on something, please.
The case:
If the user calls the add_to_acro function twice. For example: if the user calls it first then adds other files and calls it again.

The problem:
When the user first calls the function, the SDC files config.json, checksums, and results.json are created. Then if the user calls it again the function will assume that the SDC files are part of the user's files and will add them to the results.json and to the checksum folder.

The solution (now):
Before the function add the files to the acro object, it checks if the SDC files exist and deletes them if they are.

if "results.json" in os.listdir(path):  # pragma: no cover
         os.remove(f"{path}/results.json")
if "config.json" in os.listdir(path):  # pragma: no cover
        os.remove(f"{path}/config.json")
if "checksums" in os.listdir(path):  # pragma: no cover
        shutil.rmtree(f"{path}/checksums")

Do you think there is a better solution?

[rpreen]

Maybe have the user specify both src and dest paths; and don't worry about what happens in the dest in this PR?

In another PR, we need to prompt to ask the user if they are ok with overwriting or changing the dest for finalise() anyway, so that will then cover this use case?

[rpreen]

This wont work if (a) If the file doesn't exist (b) the file is in a folder in a parent directory (c) what if there are multiple subdirectories which have the same filename - it'll just use the first one found? There is also no warning if any of these things happen, it just doesn't make it to the destination folder.

Actually, I think if the file doesn't exist the current custom_output() will just pretend to add the file without actually checking whether it exists so we should fix that here too...

[rpreen]

I think the message should be more explicit:

logger.info("WARNING: Unable to add %s because the file does not exist", filename)

Part of me thinks this should be using warnings.warn() but then I think it will print the source line in record.py which is probably too much info for the researcher here