New features

[sanjaysgk]

Summary by Sourcery

Improve peptigram plotting to handle empty groups as empty rows, accept explicit group lists, standardize console logging, and refresh the README example image.

Enhancements:

• Render empty peptide groups as consistent empty rows instead of hiding axes
• Allow passing an explicit groups parameter to plot_peptigram for custom grouping
• Replace console.print with console.log when reporting protein list usage

Documentation:

• Update example visualization image link in the README to a new protein ID

Chores:

• Remove commented debug prints and unused code in viz.py
• Add a placeholder comment for console log saving in logger.py

[sourcery-ai]

Reviewer's Guide

This PR refactors the peptide plotting routine to handle empty groups with consistent axes rather than hiding them, adds debugging scaffolding for group extraction, updates the runner to use structured logging and pass explicit group context, introduces console log persistence hooks in the logger, and synchronizes the README’s example image with the latest identifier.

Sequence diagram for peptide group plotting with empty group handling

sequenceDiagram
    participant User
    participant Runner as run_pipeline
    participant Viz as plot_peptigram
    participant Matplotlib as ax
    User->>Runner: run_pipeline()
    Runner->>Viz: plot_peptigram(proteins, groups, ...)
    Viz->>Viz: For each group
    alt Group has peptides
        Viz->>Matplotlib: Plot peptides with color and layout
    else Group is empty
        Viz->>Matplotlib: Set xlim, ylim for empty plot
    end
    Viz->>Runner: Return figure
    Runner->>User: Output visualization

Loading

Class diagram for logging and plotting changes

classDiagram
    class Logger {
        +configure_logging(level, log_to_file)
        +save_console_log(output_dir, file_name)
    }
    class Runner {
        +run_pipeline(...)
    }
    class Viz {
        +plot_peptigram(...)
        -_calculate_plot_height(...)
    }
    Logger <.. Runner : uses
    Runner <.. Viz : uses

Loading

File-Level Changes

Change	Details	Files
Refactored empty-group handling in plot_peptigram to display consistent empty plots rather than hiding axes	Replace ax.set_visible(False)/continue with explicit empty‐plot setup (xlim, ylim, max_height) Enclose main peptide‐plot loop under an else branch for non‐empty groups	ProtPeptigram/viz.py
Added commented debug scaffolding for group determination in plot_peptigram	Insert alternative flattening expression as comment Add commented print statements for groups and proteins to plot	ProtPeptigram/viz.py
Updated runner script to improve logging and pass group context	Replace console.print with console.log for messages Include unique_samples as the groups argument when calling plot_peptigram	ProtPeptigram/runner.py
Introduced console logging capability in logger module	Add comment marker for console logging in save_console_log function	ProtPeptigram/logger.py
Updated README example image reference	Change image URL/filename in README.md to match updated example	README.md

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[sourcery-ai]

Hey @sanjaysgk - I've reviewed your changes and they look great!

Prompt for AI Agents

Please address the comments from this code review:
## Individual Comments

### Comment 1
<location> `ProtPeptigram/viz.py:573` </location>
<code_context>
-                    space_start = max(0, start - xlim[0])
-                    space_end = min(end - xlim[0], xlim[1] - xlim[0])
-
-                    if space_start >= spaces.shape[1] or space_end >= spaces.shape[1]:
-                        continue
-
-                    space_needed = spaces[height, space_start:space_end+1]
</code_context>

<issue_to_address>
Skipping peptides with out-of-bounds indices may silently drop data.

Currently, peptides outside the plotting range are skipped without notification, which can hinder debugging. Please add a warning or indicator when peptides are omitted for this reason.

Suggested implementation:

```python
+                    space_start = max(0, start - xlim[0])
+                    space_end = min(end - xlim[0], xlim[1] - xlim[0])
+
+                    if space_start >= spaces.shape[1] or space_end >= spaces.shape[1]:
+                        import warnings
+                        warnings.warn(
+                            f"Peptide ({start}, {end}) at height {height} is out of plotting range ({xlim[0]}, {xlim[1]}) and will be skipped.",
+                            UserWarning
+                        )
+                        continue

```

If the `warnings` module is already imported at the top of the file, you can remove the inline `import warnings` and use the existing import. Otherwise, for best practice, add `import warnings` at the top of the file.
</issue_to_address>

### Comment 2
<location> `README.md:12` </location>
<code_context>
 ProtPeptigram provides a comprehensive visualization platform for mapping immunopeptides to their source proteins across different biological samples. This tool can enables to identify peptide coverage patterns, analyze density distributions, and compare peptide presentations between experimental conditions.

 <p align="center">
</code_context>

<issue_to_address>
Grammatical error: 'can enables to identify' should be corrected.

Consider revising to 'can enable identification of', 'enables identification of', or 'can enable users to identify' for clarity and correctness.
</issue_to_address>

<suggested_fix>
<<<<<<< SEARCH
ProtPeptigram provides a comprehensive visualization platform for mapping immunopeptides to their source proteins across different biological samples. This tool can enables to identify peptide coverage patterns, analyze density distributions, and compare peptide presentations between experimental conditions.
=======
ProtPeptigram provides a comprehensive visualization platform for mapping immunopeptides to their source proteins across different biological samples. This tool enables identification of peptide coverage patterns, analysis of density distributions, and comparison of peptide presentations between experimental conditions.
>>>>>>> REPLACE

</suggested_fix>

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[sourcery-ai]

suggestion (bug_risk): Skipping peptides with out-of-bounds indices may silently drop data.

Currently, peptides outside the plotting range are skipped without notification, which can hinder debugging. Please add a warning or indicator when peptides are omitted for this reason.

Suggested implementation:

+                    space_start = max(0, start - xlim[0])
+                    space_end = min(end - xlim[0], xlim[1] - xlim[0])
+
+                    if space_start >= spaces.shape[1] or space_end >= spaces.shape[1]:
+                        import warnings
+                        warnings.warn(
+                            f"Peptide ({start}, {end}) at height {height} is out of plotting range ({xlim[0]}, {xlim[1]}) and will be skipped.",
+                            UserWarning
+                        )
+                        continue

If the warnings module is already imported at the top of the file, you can remove the inline import warnings and use the existing import. Otherwise, for best practice, add import warnings at the top of the file.

[sourcery-ai]

issue (typo): Grammatical error: 'can enables to identify' should be corrected.

Consider revising to 'can enable identification of', 'enables identification of', or 'can enable users to identify' for clarity and correctness.

Suggested change

	ProtPeptigram provides a comprehensive visualization platform for mapping immunopeptides to their source proteins across different biological samples. This tool can enables to identify peptide coverage patterns, analyze density distributions, and compare peptide presentations between experimental conditions.
	ProtPeptigram provides a comprehensive visualization platform for mapping immunopeptides to their source proteins across different biological samples. This tool enables identification of peptide coverage patterns, analysis of density distributions, and comparison of peptide presentations between experimental conditions.