Develop Context class

[ubdbra001]

closes #32 (eventually)

I'm happy to leave this open and just add to it as I approach the rest of the methods, but if you'd like to open a PR for each of the rest of the methods then I'm also happy to defer to you on that.

Here's my initial attempt at this:

• I've developed the low-hanging fruit for Context (path, entities, datatype, suffix, extension, modality, and size) and added stubs for the rest
• I've also added tests for the methods developed

One thing I wasn't sure about is where it would be beneficial to use cached_property over property for this class (and I suppose more generally). Any advice?

My next step will be to develop the subjects method along with the Sessions class. I think I'll start by creating test for these (so you can make sure I understand how these are meant to work) and then go from there.

[codecov]

Codecov Report

❌ Patch coverage is 88.60759% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.37%. Comparing base (0a62540) to head (72dbbeb).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/bids_validator/context.py	86.15%	9 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #34      +/-   ##
==========================================
+ Coverage   86.21%   86.37%   +0.15%     
==========================================
  Files          12       12              
  Lines         624      697      +73     
  Branches      103      104       +1     
==========================================
+ Hits          538      602      +64     
- Misses         65       73       +8     
- Partials       21       22       +1     

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[effigies]

Cool. A couple quick notes.

[ubdbra001]

I just added the tests for the subject method and Sessions class. Do they make sense? Am I missing anything?

[effigies]

Makes sense to me. I would just skip sessions.phenotype. That's been removed in the latest version of BIDS, since it was never used.

[ubdbra001]

Started playing around with this and I'm using the walk_back function to work backwards from the specific file in Context to get the tree for the subject entity.

1. Does this make sense?
2. If yes, the walk_back / _walk_back function throws an error because FileParts now expects schema to be passed (Line 249). Shall I just update this so that schema is passed to walk_back? Or do you have a better suggestion?

[effigies]

I would actually probably create subject once when entering a subject directory, and then pass Context(dataset, subject, file) on each file inside it.

def walk(directory, dataset, subject=None):
    if subject is None and is_subject_dir(directory):
        subject = Subject(directory, dataset)

    for child in directory.children:
        yield Context(child, dataset, subject)
        if child.is_dir():
            yield from walk(child, dataset, subject)

tree = FileTree.read_from_filesystem(root)
dataset = Dataset(root, schema)
for context in walk(tree, dataset):
    ...

[ubdbra001]

Right, that does make sense. This should be in __main__.py where we're starting walking through the FileTree from the root directory?
Is this the only part of the context that would benefit from earlier creation it earlier in the walk and then passing it to the Context object?
Looking at the list in #32 I don't think so, but I thought it would be worth double checking.

[ubdbra001]

Also, am I right in thinking that we'll still be using the walk_back functions for the sidecar? And if so we'll still need to fix up those functions to pass schema on?

[effigies]

This should be in __main__.py where we're starting walking through the FileTree from the root directory?

Yes, or wherever we do the walk.

Is this the only part of the context that would benefit from earlier creation it earlier in the walk and then passing it to the Context object?

Yes, Dataset and Subject are the only two.

Also, am I right in thinking that we'll still be using the walk_back functions for the sidecar?

Yes.

And if so we'll still need to fix up those functions to pass schema on?

Seems excessive. What do you think about making schema optional and just leaving datatype as None if schema is not passed?