feat: enhance logging for sample intersection to assist debugging "No gene exist." errors

[KaishinShaw]

Description

This PR improves the observability of the data preprocessing pipeline.

Currently, if a user encounters a "No gene exist." error, it is difficult to pinpoint whether the issue stems from:

1. Sample ID mismatch during intersection.
2. Mismatched Gene IDs in the provided gene list.
3. Overly aggressive expression filtering.

Changes

• Added logging.info statements to report gene and sample counts after key steps:
  • Raw phenotype loading.
  • User-provided gene list loading.
  • create_readydata (intersection of genotype, phenotype, and covariates).
  • Zero-expression filtering.
  • Final gene list and expression threshold filtering.
• Added a logging.warning if the dataset becomes empty immediately after intersection.
• Added a logging.error if the final gene count is zero.

[zixuanzhang]

Thank you for bringing this to our attention and make the edits accordingly! We are working on improving the software and will merge this changes in the future release!

[quattro]

Wow thank you so much. As @zixuanzhang mentioned, we have an updated version on another branch we're hoping to release soon, that also includes the features you developed here.

Hoping to get them out before the holidays.