Improve Colab launch behavior and README landing documentation

[kbhalajiyadav]

Pull Request

Summary

This pull request improves the public launch and documentation experience for the Peel Trace Evaluation for Soft Substrates repository. It adds Colab-safe notebook bootstrap behavior, revises the README landing/quick-start sections, adds a representative README QC plot, updates documentation indexing, and corrects notebook text-encoding artifacts.

The manuscript-baseline analysis method is unchanged.

Type of change

Select all that apply.

• Documentation update
• Bug fix
• New analysis feature
• Workflow or notebook update
• Dependency/environment update
• Figure/table/output update
• Repository maintenance
• Other

What changed?

• Updated README.md with a clearer landing section, badges, manuscript-baseline release line, and separated Binder/Colab/local quick-start instructions.
• Added Google Colab launch guidance and documented that Step 0 automatically clones the repository when the backend file is missing.
• Updated Peel_Trace_Evaluation_for_Soft_Substrates.ipynb Step 0 with Colab-safe bootstrap logic.
• Avoided force-installing the full requirements.txt stack inside Colab to prevent NumPy/SciPy runtime mismatch errors.
• Added a representative QC plot at docs/example_outputs/scotch_tape_qc_trace.png.
• Added an Example outputs section to the README.
• Updated the README repository tree to include docs/example_outputs/.
• Updated docs/README.md to document the new visual asset.
• Updated CHANGELOG.md with a sorted Unreleased section separating post-v1.4.0-rc15 changes from the archived v1.4.0-rc15 release state.
• Cleaned notebook text-encoding artifacts in displayed markdown/UI text, including corrupted dash, multiplication, inequality, registered-trademark, bullet, and stick–slip symbols.

Why is this change needed?

Colab often opens only the notebook file rather than the full GitHub repository, which can cause the backend module import to fail. The updated Step 0 logic makes Colab behave more like Binder by automatically cloning the repository when needed.

The README updates improve first-screen clarity for new users while preserving the repository’s reproducibility framing. The example QC plot gives visitors a direct visual sense of what the workflow exports. The changelog update also separates already archived v1.4.0-rc15 release contents from newer post-release repository improvements.

Reproducibility impact

Does this pull request affect any of the following?

• Input data
• Data preprocessing
• Analysis settings
• Metric definitions
• Output files
• Figures or tables
• Dependency versions
• Release or DOI documentation
• No reproducibility impact

If any item is checked, briefly explain the impact.

The checked items are documentation-facing only. A representative QC plot was added as a README display asset, and the changelog/release-history documentation was reorganized to separate post-v1.4.0-rc15 changes from the archived release section.

This PR does not change input data, preprocessing, metric definitions, analysis settings, validation thresholds, backend calculations, dependency versions, or manuscript-baseline outputs.

Testing / verification

For notebook changes, complete the relevant checks below:

• Notebook JSON opens correctly and is not corrupted.
• All edited cells run without syntax or indentation errors.
• Step 1 Scotch Tape reference validation still passes.
• Step 2 file upload/manual-path workflow displays correctly.
• Step 3 mapping confirmation still works.
• Step 4 manuscript-baseline profile can still be activated.
• Step 5 analysis can run on the reference/example dataset.
• No manuscript-baseline parameters were changed unless intentionally documented.
• No metric definitions were changed unless intentionally documented.
• No generated output folders, temporary files, or large raw datasets were accidentally committed.

Additional notes:

Step 0 was tested in a clean Google Colab runtime. The notebook successfully cloned the repository automatically and imported fabric_peel_guided_core_v1_4_0_rc15.py without running pip install -r requirements.txt inside Colab.

Step 1 Scotch Tape reference validation should be run before merge if it has not already been run after the final notebook save.

Manuscript or public-release relevance

For manuscript-linked repositories, state whether this change affects submitted, published, or archived results.

• Affects manuscript/public-release results
• Does not affect manuscript/public-release results
• Not applicable

Explanation:

This PR does not change the manuscript-baseline method, backend calculations, metric definitions, analysis thresholds, validation thresholds, input data, or generated manuscript-baseline outputs. It improves README presentation, Colab launch behavior, documentation organization, and notebook text readability.

The existing v1.4.0-rc15 release/archive remains historically unchanged. New post-release changes are documented under Unreleased in CHANGELOG.md.

Checklist

• The change is focused and described clearly.
• README or documentation was updated if needed.
• CHANGELOG was updated if appropriate.
• Dependency files were updated if needed.
• Generated or temporary files were not accidentally committed.
• Large or sensitive data were not committed without approval.