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Changelog

All notable changes to this repository are documented here.

This changelog is for software, notebook-interface, documentation, and repository-structure changes. The manuscript-baseline method profile should not be changed without explicit versioning and disclosure.

Unreleased

Method status

  • Manuscript-baseline calculations are unchanged.
  • No metric definitions, preprocessing settings, analysis thresholds, validation thresholds, or backend calculations were changed.
  • This update improves repository usability, Colab launch behavior, README first-screen clarity, README visual documentation, and notebook text readability only.

Added

  • Added a Google Colab badge to the README.
  • Added Google Colab quick-start instructions explaining that Step 0 automatically clones the repository when the backend file is missing.
  • Added Colab-safe Step 0 bootstrap logic to the notebook so Colab can load the backend module without requiring manual repository setup.
  • Added a representative QC plot under docs/example_outputs/scotch_tape_qc_trace.png.
  • Added an Example outputs section to the README showing a processed peel trace, selected analysis window, Top5/Bot5 extraction points, force descriptors, and QC diagnostics.
  • Documented the new README visual asset in docs/README.md.

Changed

  • Simplified the README title by moving v1.4.0-rc15 from the main heading into a separate manuscript-baseline release line.
  • Revised the README opening description to frame the repository as a multi-criteria peel-trace analysis workflow for soft substrates.
  • Updated the README Quick start section to separate Binder, Colab, and local execution paths.
  • Updated the README repository layout tree to include docs/example_outputs/.
  • Cleaned notebook text-encoding artifacts in displayed markdown and UI labels, including corrupted dash, multiplication, inequality, registered-trademark, bullet, and stick–slip symbols.

Notes

  • In Colab, the notebook intentionally does not force-install the full requirements.txt file because replacing NumPy/SciPy inside an active Colab runtime can cause package mismatch errors.
  • Binder and local installations continue to use the repository environment and requirements.txt.
  • The new example QC image is a README display asset and does not change the analysis workflow or generated manuscript-baseline outputs.

v1.4.0-rc15

Method status

  • Manuscript-baseline calculations are unchanged.
  • The locked manuscript_baseline_v1 profile remains read-only.
  • Recovery or sensitivity runs remain labeled as NON_MANUSCRIPT_MODIFIED.
  • Built-in Scotch Tape validation remains separate from user-run diagnostics.
  • User benchmarks remain separate from bundled reference-validation files.

Added

  • Step 3 mapping review with live-count filters.
  • Step 3 batch editing for included/excluded sheets, geometry, labels, notes, and common units.
  • Step 4 sheet-aware window-feasibility cautions for user-created profiles.
  • Step 4 visible Save and activate user profile action in create/edit mode.
  • Step 5 duplicate-run blocking for unchanged file, mapping, profile, and backend version.
  • Step 6 duplicate-run blocking for unchanged non-manuscript modified recovery/sensitivity runs.
  • Step 6 recovery-profile controls and user-profile reuse.
  • Compact notebook display for audit/output tables, with full tables exported to CSV/Excel.
  • Improved QC-plot layout with figure-level legend, status title, metric boxes, and tighter save padding.
  • Closable help widgets for major mapping, profile, analysis, recovery, benchmark, and output-guide controls.
  • Concise README quick-start instructions for Binder and local Jupyter use.
  • Detailed workflow documentation in docs/WORKFLOW.md.
  • Detailed output documentation in docs/OUTPUT_GUIDE.md.
  • Troubleshooting documentation in docs/TROUBLESHOOTING.md.
  • Method-profile documentation in docs/METHOD_PROFILE.md.
  • Documentation index in docs/README.md.
  • Release checklist in docs/RELEASE_CHECKLIST.md.
  • Contributor guidance in CONTRIBUTING.md.
  • Pull request template in .github/pull_request_template.md for documenting analysis-sensitive changes before merging.
  • CODEOWNERS file in .github/CODEOWNERS for review ownership of reproducibility-sensitive files.
  • Issue templates in .github/ISSUE_TEMPLATE/ for bug reports and documentation updates.
  • Dependabot configuration in .github/dependabot.yml for dependency-maintenance guidance.
  • Security reporting guidance in SECURITY.md.
  • Project governance guidance in docs/GOVERNANCE.md.
  • Maintainer information in docs/MAINTAINERS.md.
  • Repository formatting support through .editorconfig.
  • Git attributes configuration through .gitattributes.
  • .gitignore rules for local environments, notebook checkpoints, and generated analysis outputs.
  • Workflow overview figure in docs/peel_trace_workflow_overview.png and documentation index entry in docs/README.md.
  • Added a GitHub Actions workflow for automated Scotch Tape reference validation using the bundled validation workbook.
  • Added attribution, repository, and reproducibility notes to generated HTML and Markdown run reports.

Changed

  • Confirmed file, mapping, and profile panels collapse after confirmation to reduce visual clutter.
  • Step 3 automatically switches from Needs review (0) to All sheets when no mapping items need review.
  • Step 3 displays a problem-focused banner before mapping confirmation.
  • Step 4 user-profile guidance is shown on demand so the activation button and acknowledgments are easier to find.
  • Detailed audit tables are closed by default in the notebook view.
  • The final reproducibility manager handles user benchmarks without overwriting bundled Scotch reference files.
  • Moved long release-candidate history out of README.md and into CHANGELOG.md.
  • Updated the README to keep public-facing instructions concise while linking to detailed documentation files.
  • Removed the duplicate notebook copy from the notebooks/ folder; the root notebook remains the public Binder/Colab entry point.
  • Updated requirements.txt with compatible version ranges for reproducible Binder/local setup.
  • Updated README.md and docs/README.md to include repository governance and maintenance documentation links.
  • Release checklist in docs/RELEASE_CHECKLIST.md.
  • Updated Peel-specific release checklist in docs/RELEASE_CHECKLIST.md.
  • Removed the UTF-8 byte-order mark from Peel_Trace_Evaluation_for_Soft_Substrates.ipynb to prevent Binder/Jupyter NotJSONError loading failures.
  • Updated the Binder badge to use the urlpath=tree/... notebook-opening route.
  • Replaced the corrupted or incorrectly named Scotch Tape validation workbook with the corrected ScotchTapeTpeel.xlsx file at the repository root and in validation_data/.
  • Improved notebook upload guidance and marked code cells hidden by default for public usability.

Safeguards

  • Step 1 built-in reference validation must pass before downstream user-data analysis.
  • Step 3 blocks normal mapping confirmation when included sheets still need review unless the user explicitly acknowledges the remaining issues.
  • Step 4 and Step 6 require explicit acknowledgment for advanced short-window or infeasible-window profiles.
  • Output-consistency failures indicate that exported CSV/Excel outputs should not be used until rerunning or debugging.

Notes

  • The root notebook is kept at the repository root for Binder, Colab, and local Jupyter compatibility.
  • The backend Python file is imported by the notebook and should not be run directly by most users.
  • Release-specific interface notes are documented here instead of in the main README.
  • The bundled Scotch Tape validation workbook is named ScotchTapeTpeel.xlsx and is included at the repository root and in validation_data/ for notebook and validation compatibility.