fix: add missing stacklevel=2 to 14 warnings.warn() calls (Fixes #1164)

[rtmalikian]

Fixes #1164

Summary

Add stacklevel=2 to 14 warnings.warn() calls across 8 files that were missing it. Without stacklevel=2, warnings point to library internals instead of the user's code, making them confusing and hard to act on.

Changes

File	Calls Fixed	Warning Context
pyhealth/data/__init__.py	1	Visit class deprecation
pyhealth/datasets/__init__.py	4	BaseEHRDataset, BaseSignalDataset, SampleEHRDataset, SampleSignalDataset deprecations
pyhealth/datasets/mimic3.py	1	Prescriptions table date-only timestamps
pyhealth/datasets/mimic4.py	2	Discharge/discharge_detail table date-only timestamps
pyhealth/models/concare.py	1	Nested sequence vocab_size warning
pyhealth/models/stagenet.py	2	Missing time intervals and mask warnings
pyhealth/models/stagenet_mha.py	2	Missing time intervals and mask warnings
pyhealth/models/text_embedding.py	1	Text chunk truncation warning

Verification

# Syntax check all modified files
python3 -c "import ast, os; [ast.parse(open(os.path.join(r,f)).read()) for r,d,fs in os.walk('pyhealth') for f in fs if f.endswith('.py')]"

# Verify all warnings.warn() calls have stacklevel
python3 -c "
import ast, os
for r, d, fs in os.walk('pyhealth'):
    for f in fs:
        if f.endswith('.py'):
            tree = ast.parse(open(os.path.join(r,f)).read())
            for node in ast.walk(tree):
                if isinstance(node, ast.Call) and isinstance(node.func, ast.Attribute) and node.func.attr == 'warn':
                    assert any(kw.arg == 'stacklevel' for kw in node.keywords), f'{os.path.join(r,f)}:{node.lineno}'
print('All warnings.warn() calls have stacklevel')
"

Changelog

Date	Change	Author
2026-06-20	Add stacklevel=2 to 14 warnings.warn() calls across 8 files	rtmalikian

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About the Author: Raphael Malikian — Clinical AI Solutions Architect. I specialise in building and fixing AI/ML systems for healthcare, including vector databases, RAG pipelines, and clinical NLP. If you need help with your project or think I can add value to your organisation, feel free to reach out — I'd love to connect.

📧 rtmalikian@gmail.com
🔗 GitHub: https://github.com/rtmalikian
🔗 LinkedIn: http://www.linkedin.com/in/raphael-t-malikian-mbbs-bsc-hons-71075436a

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Disclosure: This code was developed with assistance from mimo-v2.5-pro (Xiaomi) via Hermes Agent (Nous Research). All changes were reviewed, tested against the actual codebase, and verified for correctness.