rtmalikian · 2026-06-20T06:45:47Z

Fixes #512

Summary

Add stacklevel=2 to 58 warnings.warn() calls across 34 files that were missing it. Without stacklevel, warnings point to edsnlp internals instead of the user code that triggered them.

Use stacklevel=3 for deprecated_extension() in utils/deprecation.py since it is called through the deprecated_getter_factory wrapper class.

Problem

The default stacklevel=1 in warnings.warn() means the warning location shows the file and line inside edsnlp rather than the caller's code. This makes it impossible for users to identify which of their API calls triggered the warning.

Affected Files (34 files, 58 calls)

Core modules:

core/pipeline.py (4 calls) — deprecation warnings for batch_size, path loading
core/stream.py (2 calls) — stream processing warnings
processing/multiprocessing.py (4 calls) — fork/deadlock warnings
processing/deprecated_pipe.py (1 call) — deprecated pipe warnings

Training:

training/loggers.py (3 calls) — CSV tracker, TensorBoard, Aim warnings
training/optimizer.py (2 calls) — optimizer warnings
training/trainer.py (2 calls) — trainer warnings

Pipes (20 files):

pipes/base.py, pipes/core/sentences/sentences.py, pipes/core/contextual_matcher/contextual_matcher.py
pipes/misc/dates/dates.py (2 calls)
pipes/ner/scores/base_score.py, pipes/ner/umls/patterns.py, pipes/ner/tnm/model.py
pipes/qualifiers/base.py
pipes/trainable/ner_crf/ner_crf.py (4 calls), pipes/trainable/span_classifier/span_classifier.py (4 calls)
pipes/llm/llm_span_qualifier/llm_span_qualifier.py, pipes/llm/llm_markup_extractor/llm_markup_extractor.py
pipes/trainable/embeddings/transformer/transformer.py, pipes/trainable/embeddings/span_pooler/span_pooler.py
pipes/trainable/span_linker/span_linker.py

Data:

data/converters.py (2 calls), data/parquet.py (3 calls), data/conll.py, data/json.py (2 calls)

Utilities 8000 :

utils/deprecation.py (stacklevel=3), utils/batching.py, utils/spark_dtypes.py
package.py, extensions.py, tune.py, connectors/brat.py, metrics/span_attribute.py

Verification

All modified files pass ast.parse() syntax check. The stacklevel=2 additions are syntactically correct and follow the existing indentation pattern.

# Verify all files parse cleanly
import ast, os
for root, dirs, files in os.walk('edsnlp'):
    for f in files:
        if f.endswith('.py'):
            ast.parse(open(os.path.join(root, f)).read())

Changelog

Date	Change	Author
2026-06-20	Add missing stacklevel=2 to 58 warnings.warn() calls across 34 files	rtmalikian

Files Changed

35 files changed, 91 insertions, 37 deletions

Verification

All 34 modified Python files pass AST syntax validation
stacklevel=2 used for direct warnings.warn() calls
stacklevel=3 used for deprecated_extension() (called through wrapper)

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

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

Add stacklevel=2 to 58 warnings.warn() calls across 34 files that were missing it. Without stacklevel, warnings point to edsnlp internals instead of the user code that triggered them, making it impossible for users to identify which of their calls caused the warning. Use stacklevel=3 for deprecated_extension() in utils/deprecation.py since it is called through the deprecated_getter_factory wrapper class. Files changed: - core/pipeline.py, core/stream.py (core module warnings) - processing/multiprocessing.py, processing/deprecated_pipe.py - training/loggers.py, training/optimizer.py, training/trainer.py - pipes/ (20 files: base, sentences, contextual_matcher, dates, etc.) - data/converters.py, data/parquet.py, data/conll.py, data/json.py - utils/deprecation.py, utils/batching.py, utils/spark_dtypes.py - package.py, extensions.py, tune.py, connectors/brat.py - metrics/span_attribute.py Signed-off-by: rtmalikian <rtmalikian@gmail.com>

sonarqubecloud · 2026-06-20T06:46:35Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

rtmalikian · 2026-06-28T01:09:59Z

Friendly ping — this PR has been ready for review for 8 days. Happy to address any feedback!

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fix: add missing stacklevel=2 to warnings.warn() calls (Fixes #512) - #513