Skip to content

v2.0.0

Choose a tag to compare

View all tags
@NCCU-Schultz-Lab NCCU-Schultz-Lab released this 22 Mar 17:35
· 124 commits to main since this release
v2.0.0
f3bf358

[2.0.0] - 2026-03-17

Added

Statistical Testing Suite (modules/math.py)

  • 12 new hypothesis-testing functions: one-sample/two-sample/paired t-tests, Mann-Whitney U,
    Wilcoxon signed-rank, Kruskal-Wallis, one-way ANOVA, Tukey HSD, Bonferroni correction,
    Pearson/Spearman correlation, chi-square independence
  • Two-way ANOVA (anova_twoway) via optional statsmodels dependency
  • Effect size display (Cohen's d with Small/Medium/Large interpretation) in the GUI

Signal Processing (modules/signal.py — new module)

  • 16 functions: moving-average/Savitzky-Golay/Gaussian smoothing; Butterworth low/high/band/band-stop
    filters (zero-phase sosfiltfilt); FFT + inverse FFT + power spectrum; 1st/2nd derivative;
    polynomial/rolling-ball/asymmetric-least-squares baseline correction; cubic/linear/nearest interpolation
  • "Signal Processing" tab (6 sub-tabs) added to Analysis Tools page

Peak Analysis (modules/peaks.py — new module)

  • 5 functions: find_peaks, integrate_peaks, compute_fwhm, fit_peak, fit_multipeak
  • Gaussian/Lorentzian/Voigt/pseudo-Voigt peak models; multi-peak simultaneous fitting
  • "Peak Analysis" tab (2 sub-tabs: Find & Measure, Fit Peaks) in Analysis Tools page

Extended Plot Types (modules/plotting.py)

  • 13 new plot types: bar chart (simple/grouped/stacked), waterfall plot, dual y-axis, z-colored
    scatter, bubble chart, polar plot, pair plot, 2D histogram/hexbin, interactive 3D scatter,
    scatter with regression, residual plot, interactive ternary, broken axis, inset plot
  • Error bar support (yerr/xerr) added to scatter_plot and line_plot
  • COLORBLIND_PALETTE (Okabe-Ito 8 colors) added; get_color_palette('colorblind', n) works
  • Total plot types: 26 (was 13 at v1.0.0)

Data Manipulation Layer (modules/data_tools.py — new module)

  • 12 non-destructive functions: formula columns (safe eval), normalization, transpose,
    pivot/melt, row filter, sort, merge/join, fill/drop NaN, resample, rolling transforms
  • Page 9 — Data Tools: dedicated Streamlit page with 10 operation tabs

Figure Layout & Annotation (modules/annotations.py — new module)

  • 7 overlay types: hline, vline, hspan, vspan, text, rectangle, ellipse
  • Annotation panel added to Quick Plot (add/delete/clear overlays; persists across re-renders)
  • Multi-Plot Dashboard expanded: 10 grid layouts up to 4×4; axis sharing; combined PNG/PDF export

Instrument File Import (modules/io.py)

  • 5 new loaders: JCAMP-DX (.jdx/.dx), HDF5 (.h5/.hdf5), NetCDF (.nc/.cdf),
    SPC (.spc), generic ASC/text (.asc)
  • mzML/mzXML loader (load_mzml) via optional pymzml dependency

Spectroscopy & Molecular Analysis (modules/spectroscopy.py, modules/molecular/ — new)

  • 18 spectroscopy functions covering IR/Raman, UV-Vis/Beer-Lambert/FRET, NMR, and mass spec
  • modules/molecular/ package: CPK atom data, Gaussian/ORCA/Molden vibrational parsers,
    Plotly 3D molecule + displacement-arrow figure builder (no RDKit dependency)
  • Page 10 — Spectroscopy; Page 11 — Molecular Viz (vibrational mode animation)
  • NIST WebBook integration (modules/nist.py): fetch IR JCAMP spectra by CAS number

Batch GUI & Automation (modules/batch.py — new module)

  • 5 functions: scan_directory, batch_load_files, batch_statistics, batch_curve_fit,
    batch_peak_analysis
  • Page 12 — Batch Analysis: Statistics/Curve Fit/Peak Analysis across multiple datasets + CSV export
  • Workflow presets: save/load/delete named analysis pipeline configs persisted to config.json
  • Batch folder import expander added to Data Upload page

PDF Report Generation (modules/report.py — new module)

  • generate_pdf_report() using matplotlib.backends.backend_pdf.PdfPages (no new dependencies)
  • Report section added to Export Results page (title, author, DPI slider, one-click download)

Plugin System (modules/plugin_loader.py — new module)

  • Auto-discovers plugin_*.py files from the plugins/ directory via importlib.util
  • discover_plugins, get_plugin_plot_types, get_plugin_analysis_tools, list_plugins
  • plugins/plugin_example.py starter template; plugin status shown in Settings page

Performance Utilities (modules/io.py)

  • downsample_for_preview(df, max_rows=10_000, method='systematic') — fast preview for large data
  • load_large_csv(filepath, max_rows=500_000, chunksize=50_000) — chunked CSV loading
  • Large-file warning (> 50 MB or > 10k rows) with auto-downsampled preview in Data Upload

New GUI Pages (7 total added)

  • Page 7 — Export Results (plots, datasets, analysis JSON, session save/load, PDF report)
  • Page 8 — Gallery (pre-generated example figures for all 26 plot types; "Load this config" button)
  • Page 9 — Data Tools
  • Page 10 — Spectroscopy
  • Page 11 — Molecular Viz
  • Page 12 — Batch Analysis
  • Page 13 — Help (Getting Started, Plot Types, Analysis Tools, File Formats, Tips & Tricks)
  • Page 14 — Settings (moved to bottom of sidebar)
  • Home page redesigned: Dashboard tab (metric cards, smart CTA) + Help tab (Quick Start, formats, tips)

UX & Visual Polish

  • Nunito Google Font applied globally via CSS injection
  • Style presets: save/load/delete named Quick Plot configurations persisted to config.json
  • "Convert to Plotly (zoom/pan)" toggle on every matplotlib figure in Quick Plot
  • PNG bytes stored in session state (fixes MediaFileHandler: Missing file Streamlit bug)
  • Equal-height CSS for Gallery cards; compact Data Upload (3-tab layout)

Testing

  • Test suite expanded from 258 to ~900+ tests across 17 test files
  • 12 new test modules: test_signal, test_peaks, test_data_tools, test_annotations,
    test_spectroscopy, test_molecular_parsers, test_batch, test_report,
    test_plugin_loader, test_nist, plus expansions to test_plotting, test_math, test_io

Code Quality

  • Switched formatter from black to ruff-format
  • Line length bumped to 100; E501 enforced
  • .pre-commit-config.yaml: ruff, ruff-format, trailing-whitespace, end-of-file-fixer,
    check-merge-conflict

Changed

  • GUI entry point renamed from modules/gui.py to modules/Home.py
  • Settings page renumbered from 6_Settings.py to 14_Settings.py (sidebar ordering)
  • use_container_width= fully replaced with width='stretch' / width='content' (all pages)
  • black replaced by ruff-format in CI lint job and pyproject.toml dev dependencies
  • ruff check now covers all new modules in CI

Fixed

  • NIST WebBook IR fetch: corrected URL format to ?JCAMP=C{cas}&Index={idx}&Type=IR-SPEC
    (was returning HTTP 404 with old ?ID=cas&JCAMP=1 format)
  • mpl_to_plotly conversion now re-applies style config after conversion so font sizes
    and colors persist when toggling "Convert to Plotly"
  • generate_gallery.py: fixed 7 bugs (column name mismatches, dpi leaking into plot kwargs,
    duplicate kwargs, unsupported annotate kwarg for heatmap, broken figsize handling)
Assets 2
Loading