Fix date range without times

[amc-corey-cox]

As shown in #160 , we don't properly assign the date range when a field doesn't include time. This should fix that and add a test to ensure it is properly assigned.

[amc-corey-cox]

Fixes #160

[Copilot]

Pull Request Overview

This PR fixes the issue of improperly assigning date ranges without times and improves schema slot range normalization. Key changes include updating tests for date and datetime inference, adding duplicate slot warnings and normalization in the RDF import engine, and adjusting dependency and GitHub Action configurations.

• Updated test expectations in the RDFS importer and CSV data generalizer tests.
• Enhanced type annotations and slot range normalization in the RDF import engine.
• Upgraded configuration in pyproject.toml and GitHub workflows.

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_importers/test_rdfs_importer.py	Updated expected slot count and added assertions for new slot names.
tests/test_generalizers/test_csv_data_generalizer.py	Added new test cases for date and datetime inference.
schema_automator/importers/rdfs_import_engine.py	Refactored type annotations, added warnings for duplicate slots, and introduced slot range normalization.
schema_automator/generalizers/csv_data_generalizer.py	Extended range inference with a check for dates without times.
pyproject.toml	Changed development dependency grouping.
.github/workflows/check-pull-request.yaml	Upgraded the caching action version from v2 to v3.

[amc-corey-cox]

Okay, I finally have the workflows all working and everything passing. I'm going to set this for merge and review. I had to disable windows-latest from the current workflow because it is having a jasonobj issue likely due to a stale dependency stack. I'll address the stale dependencies in #164 and #163 .

Fixes #162

[dalito]

The windows issue is related to linkml-runtime. The problem is in .venv\Lib\site-packages\linkml_runtime\utils\context_utils.py. I have a fix but need to find out how to add a proper test.

I believe it is the same problem as here https://github.com/linkml/linkml/pull/2675/files/eed9908418173ab084ac6963c68ea4e4c65d85ad#r2089780280

[dalito]

Here is a fix for windows: linkml/linkml-runtime#391

With the proposed change this PR passes all tests on Windows (I tested on a local machine). This was still with the old linkml and linkml-runtime from poetry.lock.

After updating all dependencies which brings linkml to 1.9.1 and linkml-runtime to 1.9.2, I had to fix the import of re in schema_automator\annotators\schema_annotator.py. Then I see only one other error:

FAILED tests/test_importers/test_jsonschema_importer.py::TestJsonSchemaImporter::test_import_hca_project -
FileNotFoundError: [Errno 2] No such file or directory: C:\\Users\\david\\MyProg\\gh-dalito\\schema-automator\\tests\\outputs\\hca\\type\\protocol\\sequencing\\module\\process\\sequencing\\S10x.yaml'

[ptgolden]

@dalito I fixed that one in 617433b. We'll move to that PR once this one is merged.

[ptgolden]

I made a couple suggestions about making the check for dates a little clearer.

[amc-corey-cox]

@ptgolden Does that look like it deals with the date parsing a little more sensibly?

[ptgolden]

This looks good! I think it's good to go.

Nitpickily, I would say that is_date_or_datetime is named like a function that returns a boolean, rather than False | "date" | "datetime".

(Also, is it necessary to include the fuzzy arg if it's not used?)