TAVIA 1.0.0 Beta 1

Release status: TAVIA 1.0.0 Beta 1, package version 1.0.0b1.

Current repository revisions may include unreleased documentation and behavior listed in CHANGELOG.md under Unreleased. The package version remains 1.0.0b1 until the release metadata and version tests are intentionally updated together.

TAVIA is a PySide6 desktop application for editable data tables, statistical analyses, scientific graphs, reports, and saved projects.

Installation

Python 3.11 or newer is required.

• Windows: run INSTALL-WINDOWS.bat
• Linux: run ./install-linux.sh
• macOS: run ./install-macos.command

The installer can install the current SourceForge Mercurial default branch or the bundled source. The checked-out revision must match SourceForge's HTTPS code browser. Repository candidates are downloaded into a disposable checkout, validated, built, installed, and started before they become active. A local repository cache that fails cloning, pulling, checkout, validation, or revision verification is bypassed with a clean remote clone. The validated repository cache is refreshed after activation. If cache refresh fails, the installed application remains active and the previous cache is retained. On Windows, the private Mercurial environment is driven through its Python interpreter rather than pip's generated hg.exe launcher.

install.py can also be distributed by itself as a small online installer:

python install.py download

That command downloads the current validated SourceForge source and installs it for the current user. The bundled command requires the complete extracted source archive beside install.py; a lone uploaded install.py cannot provide an offline bundled install.

Direct commands:

python install.py current
python install.py download
python install.py bundled
python install.py update
python install.py repair
python install.py diagnose
python install.py uninstall

Research toolkit and command line

The statistical engine is also available without the desktop interface. This makes TAVIA usable from scripts, notebooks, automated pipelines, and reviewer verification workflows. Results include source-file hashes, analysis options, package and dependency versions, and JSON-compatible numerical output.

tavia-analyze list-analyses
tavia-analyze validate
tavia-analyze run data.csv --analysis summary \
  --options '{"columns":["A","B"]}' --output result.json

The public Python entry points are tavia.toolkit.load_table, tavia.toolkit.analyze_table, tavia.toolkit.analyze_file, and tavia.toolkit.write_json. See docs/PROGRAMMATIC-API.md and the executable examples/reference-analysis workflow.

Only one installer process may modify a per-user installation at a time. Installer locks are atomically published, validate process identity, and recover malformed or stale local lock files.

Analyses

Supported saved analyses are:

• descriptive summaries
• distribution diagnostics
• paired t-test and Wilcoxon signed-rank comparison
• Student t-test, Welch t-test, and Mann-Whitney U comparison
• ordinary one-way ANOVA, Welch one-way ANOVA, and Kruskal-Wallis comparison
• linear, quadratic, cubic, logarithmic, exponential, and power regression
• four-parameter logistic dose-response fitting

XY regression and dose-response analyses can fit multiple response columns against one shared X or dose column. Result tables keep observed values, residuals, fitted curves, and confidence bands separated by response.

Unsupported saved analysis identifiers are rejected.

Graphs and interface

Graph mean intervals use Student t critical values. Percentile bootstrap intervals retain asymmetric lower and upper bounds, and one-observation groups remain renderable without an interval. Linked scatter and line graphs add and refresh regression or dose-response curves with confidence bands when a matching linked analysis exists.

Pairwise and paired statistical overlays render as comparison brackets on category graphs, including bar means, box plots, violin plots, raincloud plots, beeswarm plots, and paired plots. Overlays that do not match graph categories remain readable callouts instead of being forced into misleading brackets. Distribution-diagnostic overlays keep separate p-value labels for each measured column.

Graph styles include publication neutral, publication, presentation, color-vision-safe, and black/gray/white. Selecting a style updates figure and series controls immediately. Graph, analysis, import, replicate, export, and plugin dialogs are resizable and expose maximize controls. Dropdown controls expand within their layouts and size their item views to show long entries without elision.

User manual

The complete illustrated manual is in manual/TAVIA-1.0.0-Beta-1-User-Manual.pdf. Its maintainable LaTeX source, figures, and build instructions are in the same manual/ directory.

Development

python -m venv .venv
.venv/bin/python -m pip install -e .
.venv/bin/python -m pytest -q
.venv/bin/python -m tavia.cli validate
.venv/bin/python examples/reference-analysis/run_reference.py
.venv/bin/python -m tavia

On Windows, use .venv\Scripts\python.exe.

Qt tests are skipped when PySide6 is unavailable. For headless Linux Qt tests, set QT_QPA_PLATFORM=offscreen.

Spreadsheet imports read raw rows before applying one shared header-detection policy, so numeric headerless workbooks keep their first data row. TAVIA CSV and TSV exports carry a UTF-8 header marker for deterministic re-import, including all-text tables. Unmarked third-party all-text files remain inherently ambiguous and should be checked after import.

Plugins

The source tree includes examples/tavia-tutorial-plugin. Tools > Plugin Manager can create the same complete tutorial plugin, load reviewed manifest-based plugins, display embedded Markdown tutorials, and run declared non-destructive self-tests. Plugin manifests use API version 1 and may expose analysis, import, export, report, and graph hooks. Loaded hooks remain disabled until explicitly enabled, and host code can call an enabled hook through PluginRegistry.call_hook.

Security

Input limits, project encryption, repository trust, plugin permissions, and export behavior are documented in SECURITY.md.

Contributing and support

See CONTRIBUTING.md for issue reports, support requests, proposed changes, and verification requirements. Project changes are recorded in CHANGELOG.md.

License

GPL-3.0-only. See LICENSE.