pySEQTarget 0.13.5

This adds the two most recent additions to the R package:

• Add risk_times option

• Ensure stable factor encoding for categorical time-varying covariates in the outcome model

And

• Reduce the height and padding of the piccolo_theme top navigation bar in the readthedocs site

pySEQTarget 0.13.4

• Add warm starts for bootstrap GLM fits
• Print dataset summary information during the run when new SEQopts() verbose=True

pySEQTarget 0.13.3

• Pre-compute spline knots from full dataset to ensure consistency across bootstrap replications
• Replace squared spline term with the spline basis itself
• Add followup_spline_df parameter to control spline degrees of freedom
• Add Modelling Followup with a Natural Cubic Spline section to docs/vignettes/more_advanced_models.md

pySEQTarget 0.13.2

• Add expand_only option to SEQopts to return expanded dataset without running full analysis.

pySEQTarget 0.13.1

• Add Tom to maintainers

pySEQTarget 0.13.0

• Preserve eligible_col during expansion when referenced by weight_eligible_colnames
• Validate weight_eligible_colnames entries exist in data upfront
• Skip bootstrap replicates that fail with singular Hessian
• Silence non-interactive backend plt.show warnings in test suite
• Bump astral-sh/setup-uv to v8.1.0

pySEQTarget 0.12.9

• Fix expansion bug where subjects experiencing outcome early were carried forward with post-outcome rows

pySEQTarget 0.12.8

Hopefully remove <factory> from rendered docs and some optimizations and speed ups.

pySEQTarget 0.12.7

• In the bootstrapping use paired per-iteration estimates and monitor both risk difference and log risk ratio - there's no need for the delta-method.
• Document list field defaults in SEQopts docstrings to fix <factory> display on readthedocs site https://pyseqtarget.readthedocs.io/en/latest/sequential/seqopts.html
• Fixes the incorrect display of ncores=1 on the seqopts readthedocs site
• Fixes the display of summary and retrieve_data on https://pyseqtarget.readthedocs.io/en/latest/sequential/seqoutput.html
• Fixes the default of weight_preexpansion in the advanced models vignette

pySEQTarget 0.12.6

• Fixes SEQoutput.plot() to display figure by calling plt.show() instead of printing repr
• Fixes SEQuential.plot() to display figure by calling plt.show()
• Re-enables Python 3.10 as I think the lifelines package works under this once more
• Adds some more of the validation checks in the R package
• Amends the default values of weight_preexpansion, plot_type, and ncores to match those in SEQTaRget