demes-rs

demes:

[0.6.0] - 2024-04-16

Documentation

• Cleanup internal references (#380)

Features

• Add fn Deme::ancestor_indexes (#352)
• Add demes::ffi module (#339)

Miscellaneous Tasks

• Bump serde_json from 1.0.105 to 1.0.107 (#324)
• Bump serde_json from 1.0.107 to 1.0.108 (#330)
• Bump serde_json from 1.0.108 to 1.0.110 (#349)
• Bump version number of all crates (#354)
• Bump serde_json from 1.0.110 to 1.0.113 (#360)
• Bump serde_json from 1.0.113 to 1.0.114 (#366)

Refactor

• [breaking] Epoch::size_at returns Option upon success. (#353)
• [breaking] Deme::get_epoch now returns Option<&Epoch> (#358)

Styling

• Fix clippy lints for rust 1.74 (#336)

demes-forward:

[0.5.0] - 2024-04-16

Features

• Add ForwardGraph::demes_graph (#376)

Miscellaneous Tasks

• Bump version number of all crates (#354)

Styling

• Fix unnecessary use of fallible conversion (#337)
• Fix clippy lints for rust 1.75 (#346)

demes-forward-capi:

[0.5.0] - 2024-04-16

Features

• Add forward_graph_get_demes_graph (#377)

Miscellaneous Tasks

• Bump version number of all crates (#354)

Testing

• Run demes-forward-capi tests through valgrind (#379)

demes [0.5.0] - 2023-09-26

Documentation

• Document Err for Epoch::size_at and Demes::size_at (#282)
• Fix broken intra-doc links (#313)
• Add example to README.md (#316)

Features

• Add size_at methods for demes::Deme and demes::Epoch (#256)
• Copy/Clone/Debug for DemeId (#271)
• Impl Clone for demes::Graph and demes_forward::Graph (#281)
• Add fn to return deme names from graph (#294)
• Impl several traits for all "input" newtypes. (#314)
• Impl Add, Sub, Mul, Div for all newtypes. (#317)

Miscellaneous Tasks

• Bump MSRV to 1.60.0 (#279)
• Bump serde_json from 1.0.96 to 1.0.105 (#297)

Refactor

• [breaking] Mark SizeFunction non_exhaustive (#258)
• Graph::get_deme takes Into as argument (#266)
• Uncouple demes::Graph::get_deme input/output lifetimes (#269)
• [breaking] Improve strictness of all newtypes (#272)
• Remove code not covered by tests (#274)
• Remove code duplication in Epoch::size_at (#283)
• Demes::Error uses thiserror decorators instead of custom impl (#308)
• [breaking] Streamling builder API for adding migrations. (#310)
• Use generics to improve builder ergonomics (#312)
• Reduce migration builder API to a single type. (#315)
• Use IntoIterator instead of Deref for builder API. (#319)

Styling

• Fix lints from clippy/nightly (#291)
• Fix clippy lints from 1.72.0 (#304)

Testing

• Update demes-spec submodule (#259)
• Use build.rs to generate demes-spec tests (#289)

demes-forward [0.4.0] - 2023-09-26

Documentation

• Fix broken intra-doc links (#313)

Features

• Add demes-forward::ForwardGraph::size_at (#264)
• Impl Clone for demes::Graph and demes_forward::Graph (#281)
• Add ForwardGraph::deme_size_history (#270)
• Add utility fns for ForwardGraph (#286)
• Add fn to return deme names from graph (#294)

Miscellaneous Tasks

• Bump MSRV to 1.60.0 (#279)

Refactor

• [breaking] Mark SizeFunction non_exhaustive (#258)
• Graph::get_deme takes Into as argument (#266)
• [breaking] Improve strictness of all newtypes (#272)
• Use Vec instead of ndarray internally (#275)
• Fix invalid demes::Time during deme updates (#276)
• ForwardGraph::deme_size_history now works by explicit (#288)
• Use enums to abstract over input time types (#293)
• Demes_forward::Error uses thiserror decorators instead of custom impl (#309)

Testing

• Test all size changes for test added in #253 (#255)

demes-forward-capi [0.4.1] - 2023-09-26

Styling

• Fix clippy lints from 1.72.0 (#304)

Testing

• Fix stacked borrow UB found by miri (#292)

[0.4.0-alpha.2] - 2022-10-28

Documentation

• Pass rustdoc-args on docs.rs (#211)

[0.4.0-alpha.1] - 2022-10-28

Documentation

• Build all features on docs.rs (#210)

[0.4.0-alpha.0] - 2022-10-28

Bug Fixes

• [breaking] Graph::generation_time() now returns GenerationTime. (#204)

Documentation

• Hide setup code in demes::load example (#205)
• Document json cargo feature (#209)

Features

• Add several pub fns and an example. (#201)
• Add JSON support via cargo feature (#206)

Miscellaneous Tasks

• Update github actions (#208)

Styling

• Fix lints from nightly clippy (#200)

Testing

• Use cargo hack to run tests (#207)

[0.3.1] - 2022-10-27

Miscellaneous Tasks

• Fix tag_pattern in cliff.toml (#194)
• Add dependabot update for github-actions. (#195)
• Bump actions/checkout from 2 to 3 (#196)
• Bump styfle/cancel-workflow-action from 0.6.0 to 0.11.0 (#197)

Refactor

• Remove type name from impl Display for newtypes. (#199)

[0.3.0] - 2022-10-25

Documentation

• Remove link to private type (#189)

Features

• Impl Display for Graph, add Graph::as_string (#139)
• Add Deme::most_recent_deme_start_time (#191)
• Add Epoch::start_time() (#192)
• [breaking] Add iterators over epoch times/sizes in a Deme (#193)

Miscellaneous Tasks

• Git-cliff support (#138)
• Bump crate version to 0.3.0
• Update serde_yaml requirement from ~0.8 to ~0.9 (#140)
• Fix clippy lints (#148)
• Remove obsolete doc sections about panics (#179)

Refactor

• Metadata now uses custom deserializer (#142)
• Remove use of Option<_> in AsymmetricMigration (#145)
• Remove possible panics in TryFrom for Migration. (#147)
• Remove potential panics during Deme time resolution. (#149)
• Avoid copies when applying deme defaults (#151)
• Convert panics to Err in UnresolvedMigration. (#153)
• Conver panics to Err in impl Pulse. (#154)
• Convert panics to Err in impl Epoch (#155)
• Replace panic with Err in impl Deme (#156)
• Replace panic with Err in impl Graph (#158)
• [breaking] Metadata::as_yaml_string returns Result (#160)
• Remove code duplication from Pulse validation. (#162)
• Replace assert with Err during migration resolution.
• Streamline Epoch resolution (#163)
• Tidy up impl Deme (#164)
• Streamline Epoch size_function validation. (#165)
• Pass deme name and epoch index to epoch validation. (#166)
• [breaking] Separate Pulse and unresolved/HDM pulse types. (#168)
• Move migration resolution/validation fns to HDM types (#170)
• [breaking] Change internal storage for Deme. (#172)
• Remove use of itertools crate (#174)
• [breaking] Separate HDM/MDM demes (#175)
• Separate HDM/MDM Epoch types (#177)
• Remove last unwraps from Deme (#178)
• Settle on UnresolvedX for HDM types (#180)
• Streamline impl of UnresolvedEpoch (#181)
• Move time-related types to separate module (#182)
• Move MigrationRate to separate module (#183)
• Move SelfingRate to separate module (#184)
• Move CloningRate to separate module (#185)
• Move DemeSize to separte module (#186)
• Move Proportion to separate module (#187)
• Move TimeInterval to time.rs (#188)
• [breaking] Audit serde derive use (#190)

2022-06-19, Version 0.2.2

Commits

• [26d3426856] Bump version to 0.2.2 (Kevin R. Thornton)
• [9b103bcaf7] Fix bug in converting to integer generations for (#129) (Kevin R. Thornton)
• [cac0a1c6ee] Clean up comments from tests in specification.rs (#130) (Kevin R. Thornton)

2022-06-17, Version 0.2.1

Fix GitHub issues #126 and #127.

Commits

• [a9b445f0a5] Bump version to 0.2.1 (Kevin R. Thornton)
• [e2133cbfb7] Fix bugs in converting Graph to generations: (#128) (Kevin R. Thornton)

2022-06-17, Version 0.2.0

Commits

• [fec9c650f2] rewrite main crate docs (#124) (Kevin R. Thornton)
• [8eab302e80] Add Graph::to_integer_generations (#123) (Kevin R. Thornton)
• [f613234e8c] Add Graph::to_generations() (#120) (Kevin R. Thornton)
• [a1860410e4] Document specification.rs (#119) (Kevin R. Thornton)
• [4e4c762ea2] document lib.rs (#118) (Kevin R. Thornton)
• [381bdf14a9] Document builder.rs (#113) (Kevin R. Thornton)
• [de22f5d9d7] clean up commented-out code (#117) (Kevin R. Thornton)
• [abaa835e91] Remove unnecessary uses of TryFrom (#116) (Kevin R. Thornton)
• [ca58cc4a61] All newtypes are now From instead of TryFrom. (#115) (Kevin R. Thornton)
• [5d28bb1959] Document DemesError (#111) (Kevin R. Thornton)
• [05240cddc1] Apply naming consitency to unresolved spec types. (#110) (Kevin R. Thornton)
• [ad6b86b6fd] Separate resolved/unresolved Pulse using newtypes. (#109) (Kevin R. Thornton)
• [6a25123ff0] Define the public exports (#106) (Kevin R. Thornton)
• [fea785c90a] newtypes may now be compared to f64 (#105) (Kevin R. Thornton)
• [b6cf1157db] DemeData visibility changed to pub(crate). (#104) (Kevin R. Thornton)
• [b70787efae] GraphBuilder::add_deme no longer returns Result. (#103) (Kevin R. Thornton)
• [1003786d98] Add convenience constructor to GraphBuilder for time_units: generations (#102) (Kevin R. Thornton)
• [cdcc26ce07] GraphBuilder::new now accepts generation time and top-level defaults. (#101) (Kevin R. Thornton)
• [300be5a017] Add GraphBuilder::add_pulse (#100) (Kevin R. Thornton)
• [6e6b9892fc] Add GraphBuilder::add_migration (#99) (Kevin R. Thornton)
• [8c03dcd8df] Refactor Deme to reduce code duplication. (#98) (Kevin R. Thornton)
• [69071efcbe] Add functionality to add a Deme to a Builder. (#89) (Kevin R. Thornton)
• [2d4c47b265] Streamline internal code for serializing deme-level defaults. (#96) (molpopgen)
• [1b0f5bebaf] Add fn to return crate version. (#92) (Kevin R. Thornton)
• [9f137c2c03] Package version bump to 0.2.0 (molpopgen)
• [fb8b3d2e90] Use SnakeCase formatting for enum fields (#91) (Kevin R. Thornton)
• [19495067ac] Add minimal features to construct GraphBuilder. (#88) (Kevin R. Thornton)
• [2db891fc2b] Merge GenerationTimeError into GraphError (#87) (Kevin R. Thornton)
• [8c0539e437] rename ToplevelError to GraphError (#86) (Kevin R. Thornton)
• [1405ce86fc] fix typo in README. (Kevin R. Thornton)