added logging output and description

[enriquea]

PR Type

Enhancement, Documentation

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Description

• Added logging outputs for key operations in batch correction.

• Enhanced command-line interface with a short help description.

• Improved documentation for the correct_batches command.

• Logged metadata creation in AnnData object utility.

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Changes walkthrough 📝

Relevant files

Enhancement

correct_batches.py Added logging and improved CLI documentation                          ibaqpy/commands/correct_batches.py Introduced logging for loading data, batch correction, and exporting. Added a short help description to the correct-batches command. Enhanced docstring for the correct_batches command. Logged completion of batch correction process. +14/-1    file_utils.py Logged metadata creation in AnnData utility                            ibaqpy/ibaq/file_utils.py Added logging for AnnData object creation. Enhanced visibility into metadata creation process. +3/-0

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Summary by CodeRabbit

• New Features
  • Enhanced process tracking with improved logging, providing greater visibility into key batch correction and data export steps.
• Documentation
  • Updated command help texts and usage descriptions for clearer guidance on applying batch effect corrections.

[coderabbitai]

Walkthrough

The changes add logging capabilities to two modules. In the commands module, logging statements have been inserted within the batch correction routine to note key steps, and the command’s docstring and decorator have been enhanced with clearer descriptions and a short help. In the file utilities module, the logging module is imported and a log statement is added to record the creation of an AnnData object. The core logic and execution flow remain unchanged.

Changes

File(s)	Change Summary
ibaqpy/commands/correct_batches.py	Added logging statements in run_batch_correction; expanded the command’s docstring and updated the click decorator with a short help description.
ibaqpy/ibaq/file_utils.py	Introduced the logging module and added a log call in create_anndata to record the creation of the AnnData object.

Possibly related PRs

• Added cli option for batch correction #91: The changes in the main PR, which enhance logging and documentation for the correct_batches command, are directly related to the modifications in the retrieved PR that also involve the correct_batches command and its associated functions. Both PRs focus on the same command and its functionality.

Suggested labels

Review effort [1-5]: 4

Poem

I'm a rabbit with code so neat,
Logging each step with a rhythmic beat.
Batches corrected with gentle care,
Docstrings and decorators now clear and fair.
I nibble on carrots as the log entries flow,
Hopping through updates, watch our project grow!
🐇🥕

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between bdbe25c and 17215dd.

📒 Files selected for processing (2)

• ibaqpy/commands/correct_batches.py (5 hunks)
• ibaqpy/ibaq/file_utils.py (2 hunks)

🚧 Files skipped from review as they are similar to previous changes (2)

• ibaqpy/ibaq/file_utils.py
• ibaqpy/commands/correct_batches.py

⏰ Context from checks skipped due to timeout of 90000ms (2)

• GitHub Check: build
• GitHub Check: Codacy Static Code Analysis

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PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Error Handling The logging messages are added after the try blocks, so they won't be logged if an error occurs. Consider moving logging statements inside try blocks for better error tracking. logging.info(f"Loading iBAQ data from TSV files in folder '{folder}'") try: df_ibaq = combine_ibaq_tsv_files(folder, pattern=pattern, comment=comment, sep=sep) except Exception as e: raise ValueError(f"Failed to load input files: {str(e)}") Log Level All logging statements use info level. Consider using different log levels (debug, warning, error) for different types of messages to enable better log filtering. logging.info(f"Loading iBAQ data from TSV files in folder '{folder}'") try: df_ibaq = combine_ibaq_tsv_files(folder, pattern=pattern, comment=comment, sep=sep) except Exception as e: raise ValueError(f"Failed to load input files: {str(e)}") # Reshape the data to wide format df_wide = pivot_wider( df_ibaq, row_name=protein_id_column, col_name=sample_id_column, values=ibaq_raw_column, fillna=True, ) # Validate the sample IDs if not is_valid_sample_id(df_wide.columns, SAMPLE_ID_REGEX): raise ValueError("Invalid sample IDs found in the data.") # Get the batch IDs batch_ids = get_batch_id_from_sample_names(df_wide.columns) # Run batch correction logging.info("Applying batch correction to iBAQ values") df_corrected = apply_batch_correction(df_wide, list(batch_ids), kwargs={}) # Convert the data back to long format df_corrected = df_corrected.reset_index() df_corrected_long = pivot_longer( df_corrected, row_name=protein_id_column, col_name=sample_id_column, values=ibaq_corrected_column, ) # Add the corrected ibaq values to the original dataframe. # Use sample/protein ID keys to merge the dataframes. df_ibaq = df_ibaq.merge( df_corrected_long, how="left", on=[sample_id_column, protein_id_column] ) # Save the corrected iBAQ values to a file if output: try: df_ibaq.to_csv(output, sep=sep, index=False) except Exception as e: raise ValueError(f"Failed to save output file: {str(e)}") # Export the raw and corrected iBAQ values to an AnnData object if export_anndata: logging.info("Exporting raw and corrected iBAQ values to an AnnData object") output_path = Path(output) if not output_path.exists(): raise FileNotFoundError(f"Output file {output} does not exist!") adata = create_anndata( df_ibaq, obs_col=sample_id_column, var_col=protein_id_column, value_col=ibaq_raw_column, layer_cols=[ibaq_corrected_column], ) adata_filename = output_path.with_suffix('.h5ad') try: adata.write(adata_filename) except Exception as e: raise ValueError(f"Failed to write AnnData object: {e}") logging.info("Batch correction completed...")

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	Improve logging severity levels Add log level to the logging messages to better indicate severity. Use logging.debug() for detailed progress info and logging.warning()/error() for issues. ibaqpy/commands/correct_batches.py [109-113] -logging.info(f"Loading iBAQ data from TSV files in folder '{folder}'") +logging.debug(f"Loading iBAQ data from TSV files in folder '{folder}'") try: df_ibaq = combine_ibaq_tsv_files(folder, pattern=pattern, comment=comment, sep=sep) except Exception as e: + logging.error(f"Failed to load input files: {str(e)}") raise ValueError(f"Failed to load input files: {str(e)}") Apply this suggestion Suggestion importance[1-10]: 7 __ Why: The suggestion improves logging practices by using appropriate severity levels and adds error logging before raising exceptions, which enhances debugging capabilities and log completeness.	Medium
	Add data size to logs The AnnData object logging should include size information to help track memory usage and data scale. ibaqpy/ibaq/file_utils.py [108] -logging.info(f"Created AnnData object:\n {adata}") +logging.info(f"Created AnnData object with shape {adata.shape} and {len(adata.layers)} layers") Apply this suggestion Suggestion importance[1-10]: 6 __ Why: The suggestion enhances logging by including specific size information about the AnnData object, which is valuable for monitoring memory usage and understanding data scale in production environments.	Low

[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (2)

ibaqpy/ibaq/file_utils.py (1)

108-109: Consider adjusting the logging level and format.

1. For large AnnData objects, logging at INFO level might be too verbose. Consider using DEBUG level instead.
2. The newline character in the format string might affect log parsing.

Apply this diff to improve the logging:

-    logging.info(f"Created AnnData object:\n {adata}")
+    logging.debug(f"Created AnnData object: {adata}")

ibaqpy/commands/correct_batches.py (1)

109-109: Enhance logging messages with more context.

The logging statements could provide more detailed information about the process:

1. Include the pattern when logging file loading
2. Include the batch correction parameters
3. Include the output path when logging AnnData export
4. Include summary statistics in the completion message

Apply this diff to improve the logging messages:

-    logging.info(f"Loading iBAQ data from TSV files in folder '{folder}'")
+    logging.info(f"Loading iBAQ data from TSV files in folder '{folder}' with pattern '{pattern}'")

-    logging.info("Applying batch correction to iBAQ values")
+    logging.info(f"Applying batch correction to iBAQ values for {len(batch_ids)} batches")

-    logging.info("Exporting raw and corrected iBAQ values to an AnnData object")
+    logging.info(f"Exporting raw and corrected iBAQ values to AnnData object at {adata_filename}")

-    logging.info("Batch correction completed...")
+    logging.info(f"Batch correction completed. Processed {len(df_ibaq)} samples across {len(batch_ids)} batches")

Also applies to: 132-132, 159-159, 176-176

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 5ced41d and bdbe25c.

📒 Files selected for processing (2)

• ibaqpy/commands/correct_batches.py (6 hunks)
• ibaqpy/ibaq/file_utils.py (2 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (2)

• GitHub Check: Codacy Static Code Analysis
• GitHub Check: build

🔇 Additional comments (4)

ibaqpy/ibaq/file_utils.py (2)

2-2: LGTM!

The logging module import is correctly placed with other standard library imports.

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1-110: Verify logging configuration.

Ensure that logging is properly configured at the application level to handle these log messages effectively.

Run this script to check for logging configuration:

🧰 Tools

🪛 Ruff (0.8.2)

78-78: No explicit stacklevel keyword argument found

(B028)

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99-99: No explicit stacklevel keyword argument found

(B028)

ibaqpy/commands/correct_batches.py (2)

1-1: LGTM!

The logging module import is correctly placed at the top with other standard library imports.

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181-181: LGTM!

The command decorator and docstring improvements enhance clarity and usability:

1. Short help description is concise and informative
2. Docstring clearly explains the command's functionality

Also applies to: 254-260