Changelog

[0.4.1] - 2025-10-04

  • Fix convergence of the layout algorithm for some Demes models. Optimising the horizontal positions of demes is a quadratic optimisation problem, subject to linear inequality constraints, and has a global optimum. To optimise our objective function, we use scipy, and we were letting scipy calculate the Hessian (matrix of second partial derivatives of our objective function) using a 2-point finite-difference approximation. This approximation wasn’t very accurate, but didn’t noticeably affect the layout positions. However, it did lead to very slow convergence in some circumstances (e.g. see #287). This fix calculates the Hessian analytically, which results in very fast convergence. The vast majority of users shouldn’t notice any change.

[0.4.0] - 2023-05-03

  • Documented the layout algorithm used in tubes plots.

  • Added scale_bar option to demesdraw.tubes(), and --scale-bar option to the demesdraw tubes CLI, to draw a scale bar that indicates the population size.

  • Removed dependency on cvxpy by going back to scipy for optimisation of the deme positions. The trust-constr method with linear constraints seems to work well.

[0.3.1] - 2022-09-19

  • Added mouseover annotation popups for interactive tubes plots.

  • Dropped support for Python 3.6.

  • Performance improvement when calculating tube positions.

  • Fix incompatibility with “legend” labels and matplotlib 3.6.0.

[0.3.0] - 2022-01-08

  • Improved the default positions of demes in demesdraw.tubes() for tree-like models and more elaborate models with many demes. The previously used optimisation procedure (scipy’s SLSQP) has been removed in favour of constrained convex optimisation using cvxpy.

  • Increased the default amount of space that separates demes in demesdraw.tubes(), and use more space when there are more contemporary demes (see demesdraw.utils.separation_heuristic()).

  • Filter numpy warnings about overflow when using a log scale. The overflow in question is harmless and these warnings only serve to confuse users.

Breaking change

  • Removed the optimisation_rounds parameter to demesdraw.tubes().

[0.2.0] - 2021-12-01

Breaking change

  • Updates for demes 0.2.0, which changes the syntax for pulses from using a single source and proportion to using a list of sources and a list of proportions.

[0.1.4] - 2021-07-28

  • Added max_time parameter to demesdraw.tubes().

  • Don’t draw ancestry lines for vertically stacked demes.

  • Pin demes < 0.2 in install_requires.

  • Made some demesdraw.utils functions public and cleaned up namespace.

  • Added CLI, with tubes and size_history subcommands.

[0.1.3] - 2021-06-22

  • Fixed problem with numpy 1.21.

[0.1.2] - 2021-06-10

  • Reinstate support for Python 3.6.

[0.1.1] - 2021-06-09

  • Fix plotting of arrowheads (avoids a matplotlib warning; no visible change).

  • Add ISC license file.

  • Require demes >= 0.1.2 in install_requires.

  • Add linear size function (@noscode, #23).

[0.1.0] - 2021-04-19

  • Initial release, including demes.tubes() and demes.size_history() functions.