updated new

[sanjaysgk]

Summary by Sourcery

Update example notebook version references and introduce a new demonstration notebook with pipeline usage and sample outputs

New Features:

• Add New_test.ipynb to showcase run_pipeline usage with logging and generated PeptiGram figures
• Create processed_peptides_prot-peptigram.csv under test_outputAPI to record pipeline output data

Enhancements:

• Bump protpeptigram version reference to 1.1.1.dev0 and clean up dependency log entries in example.ipynb

[sourcery-ai]

Reviewer's Guide

This PR refines the example notebook by bumping the protpeptigram package version and cleaning up extraneous output lines, and adds a new end-to-end test notebook plus its generated CSV output to demonstrate and validate the full pipeline.

File-Level Changes

Change	Details	Files
Update version and clean output in example.ipynb	Bumped protpeptigram version from 1.0.0.dev0 to 1.1.1.dev0 Removed redundant pip notices and reordered dependency lines Inserted missing “six” dependency line under python-dateutil	example/example.ipynb
Add comprehensive pipeline test notebook	Created New_test.ipynb with code cells to install, import, run and display pipeline logs Included full DataProcessor and runner output captures Demonstrated loading, filtering, formatting, and visualization steps	example/New_test.ipynb
Include processed peptides CSV output	Added processed_peptides_prot-peptigram.csv as pipeline artifact Ensures test_outputAPI directory now contains expected CSV	test_outputAPI/processed_peptides_prot-peptigram.csv

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[sourcery-ai]

Hey @sanjaysgk - I've reviewed your changes - here's some feedback:

• Remove committed notebook outputs and generated files (e.g. images, test_outputAPI) from version control and provide only the cleaned notebook or script.
• Avoid embedding absolute local file paths and environment-specific logs in the example notebooks to keep them portable.
• Fix or remove the incomplete !pip install cell in the new notebook to ensure the install command is valid.

Prompt for AI Agents

Please address the comments from this code review:
## Overall Comments
- Remove committed notebook outputs and generated files (e.g. images, test_outputAPI) from version control and provide only the cleaned notebook or script.
- Avoid embedding absolute local file paths and environment-specific logs in the example notebooks to keep them portable.
- Fix or remove the incomplete `!pip install` cell in the new notebook to ensure the install command is valid.

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