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Change History

tact 0.7.0

  • TACT has migrated to using a pure-Python optimizer (pyprima, #379). This removes the dependency on SciPy and should make it much easier to use TACT when the Docker installation method is not available. Our benchmarking shows that the speed and accuracy is comparable to the existing L-BFGS-B and simulated annealing optimizers.
  • Homebrew is no longer a supported installation method for TACT.
  • Various internal improvements and dependency updates.

tact 0.6.0

  • There are no user-facing changes in this release of TACT.
  • The minimum required version of Python is 3.10.
  • Updates NumPy to 2.2.
  • Updates SciPy to 1.14.
  • Updates the version of PyPy in the Docker image to use Python 3.10.

tact 0.5.0

  • TACT has a new documentation website, available at tact.jonathanchang.org.
  • Adds an experimental command, tact_add_config. This uses a configuration-based approach to specify nodes of interest where unsampled species will be placed. This feature is currently undocumented and is expected to have many bugs.
  • Adds a --version option to most commands.
  • Uses a new interval bounds checker to ensure that the union of all possible age constraints on a clade is itself an atomic (single) interval, rather than a disjunction of multiple such intervals.
  • Checks for a valid taxonomy tree are moved from tact_build_taxonomic_tree to tact_add_taxa, ensuring that taxonomic trees generated outside of TACT can still be appropriately validated.
  • Drops support for Python 3.7.
  • Adds support for Python 3.11.
  • Updates NumPy to 1.24.
  • Updates SciPy to 1.10.
  • Updates DendroPy to 4.6.
  • Updates the version of PyPy in the Docker image to use Python 3.9.

tact 0.4.1

  • Extreme age ranges when using the Yule or birth-death models should now cause fewer optimization issues (reported by Alexandre Siqueira).

tact 0.4.0

  • Drops support for Python 3.6.
  • tact_add_taxa gains --ultrametricity-precision to control the precision of ultrametricity checks (reported by Miao Sun, #230).

tact 0.3.4

  • Introduces a new dual-optimizer algorithm, which uses simulated annealing to estimate diversification rates when the standard optimizer fails. This should address optimization problems that occur when estimating parameters on particularly species-rich or species-poor groups.
  • Rate estimation is now optimized for cherries (by not estimating them at all).
  • Improved reporting of which species in the backbone are breaking desired taxonomic monophyly.
  • Full support for Python 3.9.

tact 0.3.3

  • TACT now uses DendroPy 4.5.1.

tact 0.3.2

  • Fixes a numerical precision issue in certain phylogenies with zero length branches (reported by Marcio Pie).
  • Logs now have a more standardized format.

tact 0.3.1

tact 0.3.0

  • tact_build_taxonomic_tree now sorts its input on the user's behalf (suggested by Marcio Pie).
  • tact_build_taxonomic_tree automatically generates unique rank names.
  • tact_build_taxonomic_tree detects and warns on empty input cells.
  • tact_build_taxonomic_tree checks that the phylogeny it produces is valid.
  • tact_add_taxa now has fewer annoying warnings.

tact 0.2.7

  • Fixes some DendroPy messages in tact_add_taxa that were erroneously passed to the user.

tact 0.2.6

  • Internal automation improvements.

tact 0.2.5

  • Fixes a rare optimization bug when using the Yule model
  • Fixes a rare optimization bug when analysing particularly small phylogenies.

tact 0.2.4

  • Internal automation improvements.

tact 0.2.3

  • tact_add_taxa now correctly restores terminal settings when quitting (reported by Joseph W. Brown, #101).
  • tact_add_taxa now assumes in more places that its input trees are rooted.

tact 0.2.2

tact 0.2.1

  • Updates to TACT's unit tests and dependencies.

tact 0.2.0

  • tact_add_taxa gains a --yule option for pure-birth rate estimation.
  • Fall back to arbitrary-precision math in more circumstances.

tact 0.1.4

  • Update NumPy dependency to 1.17.

tact 0.1.3

  • Migrate to Poetry build system
  • Remove poor-performing parallel MRCA rate calculation algorithm

tact 0.1.2

  • Adds example taxonomy and backbone files to the distribution.
  • This is the version that was reviewed for Chang et al. (2019).

tact 0.1.1

  • Fixes a phylogeny generation bug in tact_build_taxonomic_tree.

tact 0.1.0