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Amend SEQoutput.plot() and SEQuential.plot(), re-enable Python 3.10, add some more validation checks, and amend some defaults to match R package#38

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remlapmot merged 15 commits intomainfrom
devel-2026-03-20
Mar 22, 2026
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Amend SEQoutput.plot() and SEQuential.plot(), re-enable Python 3.10, add some more validation checks, and amend some defaults to match R package#38
remlapmot merged 15 commits intomainfrom
devel-2026-03-20

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@remlapmot remlapmot commented Mar 20, 2026 •
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This,

  • 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

remlapmot added 11 commits March 20, 2026 10:42
@remlapmot
Fix SEQoutput.plot() to display figure instead of printing repr
104862b
@remlapmot
Add plot tests
64aa91f 
- `test_sequential_plot_returns_figure` — `SEQuential.plot()` stores a real `Figure`, not just a repr
- `test_seqoutput_plot_shows_figure` — `SEQoutput.plot()` runs without error after `collect()`
- `test_seqoutput_plot_raises_without_km_graph` — graceful error when `km_curves=False`
- `test_sequential_plot_risk` — risk plot type
- `test_sequential_plot_survival` — survival plot type
- `test_sequential_plot_subgroups` — subgroup faceted plot
@remlapmot
Bump version
1906e3a
@remlapmot
Fix SEQuential.plot() to display figure by calling plt.show()
d80109b
@remlapmot
Add test verifying SEQuential.plot() calls plt.show()
06bcd33
@remlapmot
Re-enable Python 3.10
0d30329 
The lifelines package seems to allow Python 3.10 again.
@remlapmot
Tighten SEQopts range validation
fbbf400 
Fix bootstrap_sample and selection_sample lower bounds

Add weight_min/max and followup_min/max ordering checks
@remlapmot
Add validation that columns cannot appear in both time_varying_cols a…
1b06c15 
…nd fixed_cols
@remlapmot
Add validation that all treatment_level values exist in the treatment…
7136bca 
… colum
@remlapmot
Add binary (0/1) validation for eligible_col, outcome_col, cense_elig…
4117386 
…ible_colname, and weight_eligible_colnames
@remlapmot
Amend single-transition check error message to be generic
45a04c6
@remlapmot remlapmot requested a review from ryan-odea March 20, 2026 12:50
@remlapmot remlapmot changed the title Amend SEQoutput.plot() and SEQuential.plot(), re-enable Python 3.10, and add some more validation checks Amend SEQoutput.plot() and SEQuential.plot(), re-enable Python 3.10, add some more validation checks, and amend some defaults to match R package Mar 22, 2026
ryan-odea
ryan-odea approved these changes Mar 22, 2026
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Looks good Tom! Great work.

@remlapmot remlapmot merged commit fe9764a into main Mar 22, 2026
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@ryan-odea ryan-odea deleted the devel-2026-03-20 branch March 23, 2026 17:00
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@ryan-odea ryan-odea ryan-odea approved these changes

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