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Changelog

0.2.3 - 2023-05-04

  • Fixed the use of numpy strings for deme names. ({user}terhorst, {user}grahamgower, {issue}495, {pr}505)
  • Added Graph.rename_demes() method to return a graph with renamed demes. ({user}aabiddanda, {pr}499)

0.2.2 - 2022-04-28

Better conformance to the spec. Minor discrepancies between demes-python and the reference implementation have been resolved.

  • Dropped support for Python 3.6 ({user}grahamgower, {issue}445, {pr}446)
  • Reject bad defaults, even if they're not used. ({user}grahamgower, {issue}443, {pr}430)
  • Set encoding to UTF-8 explicitly. This fixes unicode deme names on Windows. ({user}grahamgower, {pr}430)
  • Graph.description and Deme.description can no longer be None. A missing description will now be resolved to the empty string. ({user}grahamgower, {issue}429, {pr}430)
  • Graph.generation_time can no longer be None. When time_units are generations, a missing generation_time will now be resolved to 1 and other values are an error. ({user}grahamgower, {issue}429, {pr}430)
  • Permit selfing_rate + cloning_rate >= 1. Both values must be between zero and one (inclusive), but the selfing_rate is now defined as conditional on sexual reproduction (which occurs at rate 1 - cloning_rate). ({user}grahamgower, {issue}425, {pr}423)

0.2.1 - 2021-12-07

New features:

  • Support for the metadata field at the toplevel of a YAML file. The is a dictionary that may contain arbitrary nested data. ({user}grahamgower, {issue}275, {pr}392).

Bug fixes:

  • The string "Infinity" is now accepted when using load_all(), just like for load() and loads(). This fixes loading fully-resolved models with the CLI. ({user}grahamgower, {issue}394, {pr}395).

Breaking changes:

  • The demes.hypothesis_strategies.graphs() function for generating a random Graph has been removed. This was buggy and not usable as originally intended. ({user}grahamgower, {issue}360, {pr}397).

0.2.0 - 2021-12-01

New features:

  • Add load_all()/dump_all() to support multi-document YAML. ({user}grahamgower, {issue}239, {pr}335)
  • Add CLI. ({user}grahamgower, {pr}339)
  • Add to_ms() function. ({user}grahamgower, {issue}74, {pr}354)
  • Allow for "Infinity" as start times for demes and migrations in input YAMLs and dicts. ({user}apragsdale, {issue}358, {pr}386)

Breaking changes:

  • A pulse event now allows for simultaneous sources and takes arguments sources and proportions instead of source and proportion. The sources and proportions must be provided as a list, even when there is only a single source deme. ({user}apragsdale, {pr}353)
  • Disallow null values and blank entries in input YAML models. ({user}apragsdale, {issue}340, {pr}387)

Bug fixes:

  • Fix various issues in from_ms() with -es/-ej commands. ({user}grahamgower, {issue}350, {issue}351, {pr}352)
  • Fix some pulse edge cases when pulse events occur at the same time. ({user}grahamgower, {issue}328, {issue}357, {pr}362)
  • todict_simplified() now properly handles symmetric migrations when the end times of the demes involved differ. ({user}apragsdale, {issue}384, {pr}385)

0.1.2 - 2021-06-08

New features:

  • Add Graph.migration_matrices() to get the migration matrices for a graph. ({user}grahamgower, {issue}309, {pr}320)
  • Add Deme.size_at() to get the size of a deme at a given time. ({user}grahamgower, {issue}312, {pr}314)
  • Support "linear" as an Epoch.size_function. ({user}noscode, {issue}296, {pr}310)
  • Downstream test code can now use the demes.hypothesis_strategies.graphs() hypothesis strategy to generate a random Graph. This is preliminary, and as such is not yet documented, but is used for testing internally with some success. The API may change in the future in response to requests from downstream application authors. ({user}grahamgower, {issue}217, {pr}294)
  • The string representation for a graph, Graph.__str__(), is now the simplified YAML output. ({user}grahamgower, {issue}235, {pr}293)

Breaking changes:

  • The undocumented msprime and stdpopsim converters have been removed. ({user}grahamgower, {issue}313, {pr}316)
  • The JSON spec doesn't allow serialising infinite float values (although the Python json library does support this by default). So for JSON output we instead use the string "Infinity". ({user}grahamgower, demes-spec#70, {pr}311)

0.1.1 - 2021-04-21

Remove the "demes" console_scripts entry point. This isn't documented/supported and was left in accidentally.

0.1.0 - 2021-04-19

Breaking changes:

  • The interpretation has been changed for symmetric migrations when the start_time (and/or end_time) is not specified. Symmetric migrations are now resolved separately for each pair in the list of participating demes. To accommodate this semantic change, the SymmetricMigration class has been removed, and symmetric migrations are always resolved into pairs of AsymmetricMigration objects. ({user}grahamgower, {issue}263, {pr}268)

  • The size_function field can no longer be an arbitrary string. Only the "constant" and "exponential" strings are recognised. ({issue}262, {pr}278)

New features:

  • The from_ms() function has been added to convert an ms command line into a Graph. ({user}jeromekelleher, {user}grahamgower, {issue}74, {pr}102)

Bug fixes:

  • Graph.in_generations() no longer changes time values for a graph when time_units == "generations" and generation_time is not None. ({user}grahamgower, {issue}273, {pr}274)

0.1.0a4 - 2021-03-22

Breaking changes:

  • The deme id field has been renamed to name. This applies to both the data model (YAML files) and the Deme class. ({pr}246, discussion at popsim-consortium/demes-spec#59)

Bug fixes:

  • Check for multiple pulses causing ancestry proportion > 1. ({user}grahamgower, {issue}250, {pr}251)
  • Check selfing_rate + cloning_rate <= 1. ({user}grahamgower, {issue}242, {pr}251)
  • Check for pulse time edge cases. ({user}grahamgower, {issue}243, {pr}249)
  • Check sum of migration rates entering a deme are <= 1. ({user}grahamgower, {issue}244, {pr}249)
  • Fix migration.end_time in convert.from_msprime. ({user}grahamgower, {pr}241)

0.1.0a3 - 2021-02-25

Bug fixes:

  • Fix Graph.in_generations() to also convert the Deme.start_time field. Thanks to {user}apragsdale for reporting the problem. ({user}grahamgower, {issue}224, {pr}225).
  • Fix assert_close() and is_close() equality checks to compare the deme start_time. ({user}grahamgower, {issue}224, {pr}225).

0.1.0a2 - 2021-02-24

Alpha release for testing. The API and the schema for YAML files have been largely agreed upon. Backwards-incompatible changes before the first stable release are still possible, but are considered unlikely.

0.1.0a1 - 2020-11-12

Initial alpha release to reserve the name 'demes' on pypi.