v0.1.1

🚀 IntelliCage Analysis Toolkit v0.1.1

This release improves the display controls for several functions and also corrects
a timeline creation bug introduced in v0.1.0 that affected phase-subset plots. We therefore recommend to upgrade to this release if you are using v0.1.0.

✨ Features

• Added additional display controls to .plot_NP_adaptation(): show_all_visits, show_all_groups_SEM, and single_group_display.
• The all-groups NPA adaptation plot can now hide total visits and show only drinking visits, or add shaded group spread bands.
• Single-group NPA adaptation plots can now switch between group mean plus spread and thin individual-mouse traces with a thicker group mean.
• Bottle-preference plots can now optionally show awake/sleep background indicators and calculate bin-wise group statistics with significance-star annotations.
• Added calc="all" to .plot_bottle_preference() for total liquid-consumption trajectories across both bottle sides.
• Added .plot_bottle_preference_day() for group violin endpoint comparisons of bottle preference or total liquid uptake on a selected experimental day.

🧩 Changes

• Updated the all-groups NPA adaptation line semantics: total visits are drawn as solid lines and drinking visits as dashed lines.
• Fixed the timeline handling in NPA, nose-poke-count, licking-count, general activity, and bottle-preference plots. All-phase plots now reuse the prepared shared experiment-time axis, true phase subsets remove omitted protocol phases, and phase-only views preserve the correct clock position of each event within the selected phase.
• Restricted bottle-preference phase-subset plots to the requested visible phase window while keeping the x-axis on elapsed experimental time.
• Moved the all-groups general-activity legend inside the plot area below the day/night indicator bar.
• Bottle-preference plots keep the day/night indicator disabled by default and draw it only when day_night_indicator is explicitly provided.
• Renamed the default output folder of .plot_phase_activity_summary() from plr_activity to visit_activity_summary.
• Moved .plot_phase_activity_summary() onto the general metric/plotting layer and updated its median/mean connector styling to use group colors with configurable line width and marker size.
• Phase-activity summary significance labels are now rendered in black at a shared y-position instead of being placed independently above each box.
• Phase-activity summary boxplot medians now use group colors and the same configurable line width as the connected phase-summary traces; outlier markers are scaled below the phase-summary marker size.
• Phase-subset views that start with the first protocol phase still preserve the visible initial cage-entry delay of late-starting cage runs.
• Updated the public synthetic dataset so the Group B run starts 12 days after Group A while its first phase-1 visits are delayed by 7.5 h, providing a stronger regression case for cage-run-independent phase analyses without shifting later protocol phases into the wrong mouse-day window.

📚 Documentation

• Updated the public documentation to describe the toolkit as a general IntelliCage analysis package with PL/PR as the first supported workflow.
• Documented the new object-oriented synthetic-data example and subject metadata pattern.
• Documented the cage-run/export-block input layout and clarified that export-block folders are technical raw-data pieces rather than biological phases.
• Expanded the PL/PR usage example with modular analysis sections, plot interpretation, and mathematical definitions for rates, ratios, error rates, threshold onsets, experience-learning onsets, and cumulative preference onsets.