Fix hidden windows failures

[dalito]

This fixes two Windows path-related issues that were undetected because of the gh-action.

See runs in #358 for the hidden failures that are fixed by this PR.

Closes linkml/linkml#2490

[sneakers-the-rat]

I think this is probably not the fix we want, if it works - I think we do want to preserve windows paths here rather than casting to as_posix, and the thing that's bugged is my hardcoded string paths in the tests:

linkml-runtime/tests/test_utils/test_schemaview.py

Lines 527 to 543 in c0d73b1

	assert closure == [
	'linkml:types',
	'../neighborhood_parent',
	'neighbor',
	'../parent',
	'../L1_0_1/L2_0_1_0/grandchild',
	'../../L0_1/L1_1_0/L2_1_0_0/apple',
	'../../L0_1/L1_1_0/L2_1_0_0/index',
	'../../L0_1/L1_1_0/L2_1_0_1/banana',
	'../../L0_1/L1_1_0/L2_1_0_1/index',
	'../../L0_1/L1_1_0/index',
	'../../L0_1/cousin',
	'../L1_0_1/dupe',
	'./L2_0_0_0/child',
	'./L2_0_0_1/child',
	'main'
	]

The current test doesn't test for e.g. forward slashes in windows filenames which would get confused with as_posix here, where the reason this seems to work is that it's later rescued into a windows path by hbreader.

I'm not a windows user so idrc but imo we should fix the hardcoded strings in test rather than introduce another layer of path manipulation to schemaview

[dalito]

Thanks for checking. It was not very clear for me that the test is asserting file paths. In this case we can change the test to use PurePaths instead of strings and revert the change in schemaview.py. Purepath adapts correctly to the platform. Ok?

[dalito]

If I change the test to use PurePaths, The test fails with the original code. The paths are not consistently converted, see test output:

(.venv) λ pytest --lf -vv
================================================= test session starts =================================================
platform win32 -- Python 3.12.8, pytest-8.0.1, pluggy-1.4.0 -- C:\Users\david\MyProg\gh-dalito\linkml-runtime\.venv\Scripts\python.exe
cachedir: .pytest_cache
rootdir: C:\Users\david\MyProg\gh-dalito\linkml-runtime
collected 1 item
run-last-failure: rerun previous 1 failure (skipped 55 files)

tests/test_utils/test_schemaview.py::test_imports_relative FAILED                                                [100%]

====================================================== FAILURES =======================================================
________________________________________________ test_imports_relative ________________________________________________

    def test_imports_relative():
        """Relative imports from relative imports should evaluate relative to the *importing* schema."""
        sv = SchemaView(SCHEMA_RELATIVE_IMPORT_TREE)
        closure = sv.imports_closure(imports=True)

        assert len(closure) == len(sv.schema_map.keys())
>       assert closure == [
            'linkml:types',
            str(PurePath('../neighborhood_parent')),
            'neighbor',
            str(PurePath('../parent')),
            str(PurePath('../L1_0_1/L2_0_1_0/grandchild')),
            str(PurePath('../../L0_1/L1_1_0/L2_1_0_0/apple')),
            str(PurePath('../../L0_1/L1_1_0/L2_1_0_0/index')),
            str(PurePath('../../L0_1/L1_1_0/L2_1_0_1/banana')),
            str(PurePath('../../L0_1/L1_1_0/L2_1_0_1/index')),
            str(PurePath('../../L0_1/L1_1_0/index')),
            str(PurePath('../../L0_1/cousin')),
            str(PurePath('../L1_0_1/dupe')),
            str(PurePath('./L2_0_0_0/child')),
            str(PurePath('./L2_0_0_1/child')),
            'main'
        ]
E       AssertionError: assert ['linkml:types', '../neighborhood_parent', 'neighbor', '..\\L1_0_1\\L2_0_1_0\\grandchild', '..\\parent', '../parent', '..\\..\\L0_1\\L1_1_0\\L2_1_0_0\\apple', '..\\..\\L0_1\\L1_1_0\\L2_1_0_0\\index', '..\\..\\L0_1\\L1_1_0\\L2_1_0_1\\banana', '..\\..\\L0_1\\L1_1_0\\L2_1_0_1\\index', '..\\..\\L0_1\\L1_1_0\\index', '../../L0_1/cousin', '..\\L1_0_1\\dupe', './L2_0_0_0/child', './L2_0_0_1/child', 'main'] == ['linkml:types', '..\\neighborhood_parent', 'neighbor', '..\\parent', '..\\L1_0_1\\L2_0_1_0\\grandchild', '..\\..\\L0_1\\L1_1_0\\L2_1_0_0\\apple', '..\\..\\L0_1\\L1_1_0\\L2_1_0_0\\index', '..\\..\\L0_1\\L1_1_0\\L2_1_0_1\\banana', '..\\..\\L0_1\\L1_1_0\\L2_1_0_1\\index', '..\\..\\L0_1\\L1_1_0\\index', '..\\..\\L0_1\\cousin', '..\\L1_0_1\\dupe', 'L2_0_0_0\\child', 'L2_0_0_1\\child', 'main']
E
E         At index 1 diff: '../neighborhood_parent' != '..\\neighborhood_parent'
E         Left contains one more item: 'main'
E
E         Full diff:
E           [
E               'linkml:types',
E         -     '..\\neighborhood_parent',
E         ?        ^^
E         +     '../neighborhood_parent',
E         ?        ^
E               'neighbor',
E         +     '..\\L1_0_1\\L2_0_1_0\\grandchild',
E               '..\\parent',
E         -     '..\\L1_0_1\\L2_0_1_0\\grandchild',
E         +     '../parent',
E               '..\\..\\L0_1\\L1_1_0\\L2_1_0_0\\apple',
E               '..\\..\\L0_1\\L1_1_0\\L2_1_0_0\\index',
E               '..\\..\\L0_1\\L1_1_0\\L2_1_0_1\\banana',
E               '..\\..\\L0_1\\L1_1_0\\L2_1_0_1\\index',
E               '..\\..\\L0_1\\L1_1_0\\index',
E         -     '..\\..\\L0_1\\cousin',
E         ?        ^^  ^^    ^^
E         +     '../../L0_1/cousin',
E         ?        ^  ^    ^
E               '..\\L1_0_1\\dupe',
E         -     'L2_0_0_0\\child',
E         ?              ^^
E         +     './L2_0_0_0/child',
E         ?      ++        ^
E         -     'L2_0_0_1\\child',
E         ?              ^^
E         +     './L2_0_0_1/child',
E         ?      ++        ^
E               'main',
E           ]

tests\test_utils\test_schemaview.py:527: AssertionError
-------------------------------------------------- Captured log call --------------------------------------------------
WARNING  rdflib.term:term.py:278 C:\Users\david\MyProg\gh-dalito\linkml-runtime\linkml_runtime\linkml_model\model\schema\types does not look like a valid URI, trying to serialize this will break.
================================================== warnings summary ===================================================
.venv\Lib\site-packages\pydantic\_internal\_config.py:272
  C:\Users\david\MyProg\gh-dalito\linkml-runtime\.venv\Lib\site-packages\pydantic\_internal\_config.py:272: PydanticDeprecatedSince20: Support for class-based `config` is deprecated, use ConfigDict instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.6/migration/
    warnings.warn(DEPRECATION_MESSAGE, DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=============================================== short test summary info ===============================================
FAILED tests/test_utils/test_schemaview.py::test_imports_relative - AssertionError: assert ['linkml:types', '../neighborhood_parent', 'neighbor', '..\\L1_0_1\\L2_0_1_0\\grandchild', '...
============================================ 1 failed, 1 warning in 1.23s =============================================

[dalito]

@sneakers-the-rat The method SchemaView.imports_closure relies on consistent path-symbol "/". So I think we should stick with the proposed fix. But I will limit it to windows.

[sneakers-the-rat]

ok that inconsistency does make me concerned about my implementation there though, something here is wrong and i think it's my fault, so i won't hold this up but i do want to remember to follow up on it because it shouldn't be the case that we sometimes get forward slashes and sometimes don't out of schemaview.

the only thing i would be concerned with is the as_posix part, where if idk there is some windows path that can't be roundtripped to posix for some reason, but i don't know enough about windows paths and in fact don't use windows at all so i am the wrong person to be thinking about that.

[dalito]

The conversion with as_posix is limited to some paths with if sn.startswith('.') and ':' not in i: and so it should not cause issues. I agree with respect to a hidden inconsistency in the implementation.

From my perspective this should be a good enough to merge.

@pkalita-lbl, you are also in the windows-wg. Do you have time for a review?