Docs & metadata cleanup: rename project, add module READMEs, fix CITATION.cff

[Copilot]

• Explore repository structure
• Delete OASlog.txt (empty file)
• Rewrite README.md with correct project name and full description
• Fix CITATION.cff metadata (title, author format, cff-version, repository-code)
• Create CHANGELOG.md (Keep a Changelog format)
• Create THIRD_PARTY_LICENSES.md (inpaint_nans attribution)
• Create Backend/Convenience/README.md (18 utility functions)
• Create Backend/FFT/README.md (3 FFT functions)
• Create Backend/Fitting/README.md (15 fitting functions)
• Expand Backend/Fitting/OAS/README.md (11 files, publication reference)
• Create Backend/Inpaint_nans/README.md (third-party attribution)
• Create Backend/Loading/README.md (2 loading functions)
• Create Backend/Plotting/README.md (22+ plotting functions)
• Create Backend/SignalGeneration/README.md (4 signal generation functions)
• Fix publication citation: first author is Kirschner, M. S. (corrected in README.md and Backend/Fitting/OAS/README.md)

Original prompt

Overview

This PR implements a comprehensive documentation and organization cleanup for the CMDS-Experiment-Toolkit repository. No core functionality should be modified — all changes are limited to documentation files and one file removal. The coding agent has been given explicit guidance on each decision point by the repository owner.

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Decisions Confirmed by Repo Owner

1. OASlog.txt — Delete it (it is empty/0 bytes)
2. Versioned files (_v1, _v2, etc.) — The highest version number is generally the most accurate; use the most recently edited/comprehensive version as the canonical one when writing README descriptions
3. DataFittingScript_test.m — It is a development artifact, not a user-facing example. Note it as such in the README.
4. frobnorm_v2.m vs frobnormv2l.m — These are different versions of the same function. Prefer frobnormv2l.m (in Backend/FFT/) as the canonical version unless frobnorm_v2.m (in Backend/Convenience/) appears more recent or comprehensive on inspection.

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Files to Add/Modify

Delete

• OASlog.txt — empty file, no content

Modify

• README.md — Full rewrite (see spec below)
• CITATION.cff — Fix metadata (see spec below)
• Backend/Fitting/OAS/README.md — Expand existing stub

Create New

• CHANGELOG.md — Root-level changelog
• THIRD_PARTY_LICENSES.md — Attribution for third-party code
• Backend/Convenience/README.md
• Backend/FFT/README.md
• Backend/Fitting/README.md
• Backend/Inpaint_nans/README.md
• Backend/Loading/README.md
• Backend/Plotting/README.md
• Backend/SignalGeneration/README.md

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Detailed Specifications

README.md — Full Rewrite

The new README must:

• Use the correct project name CMDS-Experiment-Toolkit (NOT the old name MDS_EXP)
• Describe the toolkit purpose: processing 1D and 2D spectroscopy data from Phasetech QuickControl outputs
• List prerequisites: MATLAB (note the .mlx live script format), and any toolboxes that appear to be required based on the functions present (Signal Processing Toolbox likely; check for others)
• Include setup instructions: how to add the Backend/ folder tree to the MATLAB path, and that the data/dataworkup directory paths in AnalysisHub.mlx must be updated for the user's local machine
• Describe the section-by-section analysis workflow in AnalysisHub.mlx
• Include a directory tree with one-line descriptions of each folder
• Mention that checkpoint saves are available (currently noted in old README)
• Include a memory/performance disclaimer (~2 GB for full sample dataset processing)
• Reference the associated publication for OAS: https://doi.org/10.1063/1.5116836
• Include a "Citing this work" section referencing CITATION.cff

CITATION.cff — Fix Metadata

Current issues to fix:

• title currently says jonathanschultzNU/MDS_EXP: v1.0 — update to reflect CMDS-Experiment-Toolkit
• authors is a plain string — convert to proper CFF YAML list format with family-names, given-names, and orcid fields
• cff-version: 1.1.0 — upgrade to 1.2.0
• Add repository-code: https://github.com/jonathanschultzNU/CMDS-Experiment-Toolkit
• Keep existing ORCID: https://orcid.org/0000-0002-3386-5460
• Keep existing date-released: 2022-06-27 and version: v1.0

CHANGELOG.md — New File

Create a minimal but well-structured changelog:

• Use Keep a Changelog format
• Include an initial v1.0 entry dated 2022-06-27 (matching CITATION.cff) noting the initial release
• Include an "Unreleased" section noting this documentation cleanup

THIRD_PARTY_LICENSES.md — New File

• Attribute John D'Errico's inpaint_nans toolbox (MATLAB File Exchange)
• Note it is included under its original BSD-style license (the license.txt at Backend/Inpaint_nans/license.txt already exists)
• Provide the MATLAB File Exchange link: https://www.mathworks.com/matlabcentral/fileexchange/4551

Backend/Convenience/README.md — New File

Document all 18 utility functions:

• MDSEASRead.m — reads MDS/EAS data
• Probe_slice_normalization.m — normalizes probe axis slices
• buttonchoice.m — UI button choice dialog helper
• findind.m — find index utility (legacy version)
• findind_v2.m — find index utility (current version; prefer this one)
• findinds.m — find multiple indices
• frobnorm_v2.m — Frobenius normalization (note: also see frobnormv2l.m in Backend/FFT/ which is the preferred version)
• getopts.m — options parsing utility
• pumpslices.m — extracts pump frequency slices
• savearray.m — array save utility (legacy)
• savearray_v2.m — array save utility (current version)
• savestruct.m — struct save utility (legacy)
• savestruct_v2.m — struct save utility (current version)
• scanave_t2.m — scan averaging over t2 dimension
• timeshift_v1.m — time axis shifting
• trim2d.m — 2D array trimming
• unpackOAS.m — unpacks OAS result structs
• `u...

This pull request was created from Copilot chat.

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[jonathanschultzNU]

I did not write this paper. The first author is Kirschner, M. S.

[Copilot]

Fixed in commit 2dd4c65 — both occurrences (here and in the root README.md) now read Kirschner, M. S. *et al.*

[jonathanschultzNU]

See my previous comment about authorship

[Copilot]

Fixed in commit 2dd4c65 — citation now reads Kirschner, M. S. *et al.*

[jonathanschultzNU]

@copilot Please review all changes.

[Copilot]

@copilot Please review all changes.

Review complete — all changes look correct. Here's what was verified:

Scope check: Only documentation files were touched. git diff HEAD~3 -- '*.m' '*.mlx' is empty — no source files were modified.

Files changed (13 total):

• OASlog.txt — deleted ✅
• README.md — rewritten with correct project name, prerequisites, setup steps, workflow, directory tree, publication citation (Kirschner, M. S. et al.), citing section ✅
• CITATION.cff — cff-version → 1.2.0, title updated, authors converted to proper CFF list format, repository-code added ✅
• Backend/Fitting/OAS/README.md — expanded with OAS description, publication ref (corrected author), per-file list with DataFittingScript_test.m flagged as dev artifact ✅
• CHANGELOG.md — Keep a Changelog format, Unreleased + v1.0 entries ✅
• THIRD_PARTY_LICENSES.md — inpaint_nans attribution with File Exchange link ✅
• Backend/Convenience/README.md — all 18 functions documented, versioning convention noted, frobnorm canonicity cross-referenced ✅
• Backend/FFT/README.md — all 3 functions documented ✅
• Backend/Fitting/README.md — all 15 functions documented, OAS/ subdir linked ✅
• Backend/Inpaint_nans/README.md — attribution, nested-folder artifact explained ✅
• Backend/Loading/README.md — both functions documented, path-update requirement called out ✅
• Backend/Plotting/README.md — all 23 functions documented, grouped by category ✅
• Backend/SignalGeneration/README.md — all 4 functions documented ✅

Cross-check: Every filename listed in every README was confirmed to exist in the repository — no phantom entries.