Reproducibility fixes and data documentation

Post-publication updates to make the repository reproducible and self-documenting.
No published figures or data are changed by this release — the committed base
figures and the shipped processed.zip are the same as at publication. The only
behavior change (medfilt 3 → 5) is in code that regenerates calibration data,
not in the shipped processed spectra.

Reproduction fixes

• Documented the required data-unpacking step (unzip data/raw.zip and
  data/processed.zip, or make data); previously undocumented, so CSV loading failed.
• Removed a hardcoded absolute path in generate_figures.ipynb (now relative).
• Added the missing figures/fig2/ directory so the figure notebook doesn't error on save.
• Switched generate_figures.ipynb to %matplotlib inline so it runs headlessly.

Documentation

• README now covers: the data unpacking step and extracted directory tree, the filename
  convention, and a dictionary of the CSV columns and calibration/performance file types.
• Added the pub DOI, a note that arcadia-pycolor 0.5.1 (pinned in envs/dev.yml) is
  required, a generate_figures step in the workflow, and a note that processed.zip
  lets you skip calibration and reproduce figures directly.
• generate_figures.ipynb intro now lists the required data and acquisition dates it uses.

Housekeeping

• Standardized the medfilt kernel to 5 across the calibration notebook and apply_calibration.py.
• Tk().deiconify() → Tk().withdraw() in the calibration notebook.
• Added make data / make figures / make reproduce targets.
• Re-zipped the data archives without __MACOSX/.DS_Store junk.
• Removed the leftover TODO placeholder in the PR template.

2025-diyraman-bio v1.0

This release is associated with the pub titled, "DIY Raman spectroscopy for biological research."