Changelog

All notable changes to this project will be documented in this file.

[0.14.1] - 2023-04-16

Bug Fixes

  • Tree now tied to TreeSequence lifetime (#497)

Miscellaneous Tasks

  • Update delegate requirement from 0.8.0 to 0.9.0 (#494)

[0.14.0] - 2023-03-17

Documentation

  • Book section on node defaults (#491)

Features

  • Allow use of bookmark in examples/haploid_wright_fisher (#479)
  • Impl Default for row id types (#484)
  • Impl Default for Bookmark (#486)
  • Implement Builder pattern for flags (#487)
  • Support adding nodes with defaults (#488)

Miscellaneous Tasks

  • [breaking] Bump MSRV to 1.60.0 (#478)

Refactor

  • Remove internal impl Deref/DerefMut for edge diff iterator. (#482)
  • Mod table_view is no longer pub (#483)
  • [breaking] TableCollection::simplify now takes &[NodeId] (#485)
  • Replace macros with fn for adding node table rows (#489)
  • Manually impl Default for NodeDefaultsWithMetadata (#490)

[0.12.0] - 2022-12-23

Documentation

  • Book section on lending row iterators (#406)
  • Advanced metadata topics in book (#407)
  • Book chapter on edge differences (#417)

Features

  • TreeSequence::edge_differences_iter (#410)
  • Add convience functions to get usize from row ids. (#413)
  • Tree::total_branch_length now works. (#429)
  • Add getters/setters for Bookmark. (#437)

Miscellaneous Tasks

  • Update bindgen requirement from 0.61.0 to 0.63.0 (#415)

Refactor

  • [breaking] Replace Deref with delegation of TableViews API (#409)
  • [breaking] Remove TskitTypeAccess trait (#411)
  • Allow TreeSequence::edge_differences_iter to Err. (#412)
  • [breaking] Usize to SizeType conversion is now fallible. (#419)
  • Macros only use newtype public API. (#420)
  • Move newtypes into module (#421)
  • The raw_metadata fn for tables now takes Into. (#425)
  • Add low-level table wrappers to sys (#426)
  • Generalize slice building in sys (#427)
  • Remove many unsafe calls from tree_interface.rs (#428)
  • Add sys::LLTreeSeq. (#430)
  • Sys module no longer depends on TskitError (#431)
  • Move Drop details for TreeSequence to sys. (#432)
  • Add low level owning tables to sys (#433)
  • Tidy up table definitions (#434)

Styling

  • [breaking] Rename all OwnedX tables to OwningX. (#408)
  • Replace column access macro with generic fn (#422)
  • Generic fns for ragged column access (#423)
  • Use fn to get array slices from Trees. (#424)

[0.12.0-alpha.1] - 2022-11-09

Bug Fixes

  • [breaking] MetadataError::RoundtripError now requires Send + Sync (#396)

Documentation

  • Add haploid WF example to book (#397)

Features

  • Add examples/haploid_wright_fisher.rs (#394)
  • Add lending iterators over table row "views" (#398)
  • Impl PartialEq for table row views. (#400)
  • Add ProvenenceTableRowView (#401)
  • Add row_view() for tables (#402)
  • Add row_view() for tables (#402)
  • Column slice getters for tables (#404)

Refactor

  • [breaking] Return &str from provenance table getters (#403)
  • Deprecate NodeTable::flags_array_mut and NodeTable::time_array_mut (#405)

[0.12.0-alpha.0] - 2022-11-06

Documentation

  • Add book sections on table data access (#379)
  • Remove chapter number from book intro (#380)
  • Start book sections on tree sequences (#381)
  • Book section on the tree API. (#382)
  • Add book section on misc. ops on treeseqs (#385)
  • Appendix material for book (#386)
  • Rewrite book intro (#389)
  • Show prelude contents as book appendix (#390)
  • Book sections on metadata (#391)
  • Book section on error handling (#393)

Refactor

  • [breaking] Improve Tree iterator ergonomics (#384)
  • [breaking] Improve Tree interface ergonomics (#388)

[0.11.1] - 2022-11-04

Documentation

Refactor

  • Apply functional style for NodeTable fns (#377)

[0.11.0] - 2022-11-04

Bug Fixes

  • Derive Debug for all table row types (#361)
  • [breaking] Update generic bounds on metadata getters (#370)
  • Impl DerefMut for "owned" tables. (#371)

Documentation

  • Add migration guide (#376)

Features

  • [breaking] Add TskitError::LibraryError (#342)

Refactor

  • Streamline code for generating table rows. (#340)
  • Replace unwrap with expect in _macros.rs (#341)
  • Replace unwrap with errors in table_collection.rs (#343)
  • Remove unwraps in trees source files. (#344)
  • Streamline building individual table rows (#345)
  • Remove unwraps from node_table.rs (#346)
  • Unwrap to expect in error.rs (#347)
  • Remove type info from Display for newtypes. (#349)
  • [breaking] Return None for out-of-range row indexes. (#350)
  • [breaking] Return None for out-of-range row indexes, part II. (#351)
  • [breaking] Return None for out-of-range row indexes, part III. (#355)
  • Improve safety of tsk array access (#362)
  • Tree now stores tsk_tree_t in MBox. (#367)
  • [breaking] Provenance table getters now return Option (#369)
  • [breaking] Remove lifetime annotation from table types (#373)

Styling

  • Fix lints from rust 1.65.0 (#374)
  • Fix lints from nightly (#375)

Testing

  • Rewrite table API tests (#356)
  • Add doc tests for node table (#359)

[0.10.0] - 2022-10-28

Documentation

  • Display feature flags in docs.rs (#338)

Miscellaneous Tasks

  • Set msrv to 1.57.0 (result of cargo msrv) (#322)
  • Fix tag_pattern in cliff.toml (#330)
  • Update github actions (#332)
  • Add github actions to monthly dependabot (#333)
  • Update bindgen requirement from 0.60.1 to 0.61.0 (#336)
  • Bump styfle/cancel-workflow-action from 0.6.0 to 0.11.0 (#334)

Performance

  • Use Bookmark in forward simulation example (#318)

Refactor

  • Streamline internal macros for adding nodes (#309)
  • Remove internal ffi module (#310)
  • Panics compatible with earlier rustc (#311)
  • Remove type name from SizeType Display output. (#315)
  • [breaking] TableCollection::simplify returns Option<&[NodeId]> (#316)
  • [breaking] Conversion from row id to usize is now fallible. (#319)
  • Use clap::Parser in example program. (#320)
  • Remove pontential panic! when instantiating table rows. (#329)
  • Examples/tree_traversals.rs now uses clap derive (#337)

Styling

  • Remove unneeded ( ) from match. (#323)
  • Use auto-deref for pointer deref. (#325)
  • Fix +nightly clippy lints for all targets/features. (#326)

Testing

  • Improve test work flow (#331)

[0.10.0-alpha.1] - 2022-07-31

Bug Fixes

  • Replace crate with $crate in macros (#287)

Features

  • Add tskit::OwnedMutationTable (#281)
  • Add tskit::OwnedSiteTable (#283)
  • Add tskit::OwnedIndividualTable (#284)
  • Add tskit::OwnedMigrationTable (#285)
  • Add tskit::provenance::OwnedProvenanceTable (#286)
  • Set tables in collection from owned tables. (#288)
  • [breaking] Impl Send/Sync for TreeSequence (#297)

Miscellaneous Tasks

  • Update to C API 1.1.1 (#304)

Performance

  • [breaking] Implement slice access to individual data (#292)
  • [breaking] Eliminate several copies from C to rust (#293)

Refactor

  • Deduplicate code for adding node table rows. (#278)
  • Use macros to implement adding table rows. (#279)
  • Add new macro to build owned tables (#282)
  • Separate tree ownership from API. (#300)
  • Bring back generic syntax for adding node table rows. (#302)
  • [breaking] Display for new types now omits type name. (#305)
  • Remove MBox for tsk_treeseq_t storage (#306)

[0.10.0-alpha.0] - 2022-07-19

Bug Fixes

  • Fix memory leak in TreeSequence::simplify (#274)
  • Fix leak in TableCollection::deepcopy (#275)
  • Fix leak in TreeSequence::dump_tables (#276)

Documentation

  • Fix warnings from "cargo doc" (#255)

Features

  • Make load from file generic over AsRef (#254)
  • Add tskit::OwnedPopulationTable (#267)
  • Add tskit::OwnedEdgeTable (#268)
  • Add tskit::OwnedNodeTable (#273)

Miscellaneous Tasks

  • Add cliff.toml (config file for git-cliff) (#257)
  • Prefix "chore: " to dependabot.yml (#258)
  • Use cargo-hack to streamline CI. (#259)
  • Add cargo-valgrind CI workflow (#277)

Refactor

  • Macro metadata_to_vector intputs changed. (#263)
  • Add macros to implement owned tables. (#269)

Testing

  • Add another experimental trait idea for metadata. (#261)
  • Redo doctest: TableCollection::new_from_file (#272)

2022-06-20, Version 0.9.0

Commits

  • [068fdccdea] Bump version to 0.9.0 (Kevin R. Thornton)
  • [d700af7294] doc sorting requirements (#243) (Kevin R. Thornton)
  • [6114d2bd65] Change ffi to private visibility. (#241) (Kevin R. Thornton)
  • [b53105112a] Add new_sample and is_sample to NodeFlags public API. (#238) (Kevin R. Thornton)

2022-05-26, Version 0.8.1

Commits

  • [bd72b689ac] Bump version to 0.8.1 (molpopgen)
  • [b0abdfad5c] impl TryFrom for TreeSequence (#236) (Kevin R. Thornton)
  • [71e927a9bb] TreeSequence::new now takes ownership of the TableCollection. (#235) (Kevin R. Thornton)

2022-05-24, Version 0.8.0

Commits

  • [e463302ced] Bump package version to 0.8.0 (molpopgen)
  • [deffc58127] Replace From for usize with TryFrom. (#234) (Kevin R. Thornton)
  • [a7c04213a1] update to CAPI 1.0.0 (#229) (Kevin R. Thornton)
  • [7c0b6169a3] Add CI for 32 bit Linux builds (#232) (Kevin R. Thornton)
  • [7458d85163] Invoke rust dependency caching after setting up rustc (#233) (Kevin R. Thornton)
  • [203a43a0e8] Only run CI for rust/stable. (#231) (Kevin R. Thornton)
  • [fb2128c0a5] Add dependency caching for CI. (#230) (Kevin R. Thornton)
  • [aff053c786] Improvements to handling of tsk_flags_t: (#227) (Kevin R. Thornton)
  • [5f558cb051] Audit pedantic lints re: integer casts (#223) (Kevin R. Thornton)
  • [609546185c] Fix several "pedantic" lints from clippy: (#222) (Kevin R. Thornton)

2022-03-24, Version 0.7.0

Commits

  • [8427c2fea7] Change order of generics to match argument order for all "add" (#221) (Kevin R. Thornton)
  • [6ef0406731] Fix typo in docstring for TableCollection::full_sort. (#219) (Kevin R. Thornton)
  • [a1a7e12208] Add TableCollection::topological_sort_individuals. (#218) (Kevin R. Thornton)
  • [4c17ca62a2] Update clap requirement from ~3.0.0 to ~3.1.3 (#215) (dependabot[bot])
  • [f40562a56a] Fix lint found by clippy. (#216) (Kevin R. Thornton)
  • [4efddb6f5d] Update clap requirement from ~2.34.0 to ~3.0.0 (#214) (dependabot[bot])

2021-12-15, Version 0.7.0-alpha.1

Fixes various minor issues with the first alpha.

Commits

  • [44965969c0] Bump version to 0.7.0.alpha.1 (molpopgen)
  • [5d6a289490] Fix issues with Time, Position, Location newtypes (#212) (Kevin R. Thornton)
  • [99930e8bb0] Add explicit tests of tree roots. (#211) (Kevin R. Thornton)

2021-12-15, Version 0.7.0-alpha.0

Breaking changes:

  • Update to tskit C API 0.99.15.
  • Add newtypes for Time, Position, and Location.
  • Add newtype SizeType, which wraps tsk_size_t.
  • tsk_id_t and tsk_size_t removed from library prelude.
  • The Provenance trait is removed and all "provenance stuff" is now a first-class table API supported by the TableAccess trait.

New features:

  • Update to tskit C API 0.99.15.
  • tskit C structs are now managed by MBox.
  • Support for virtual tree roots.
  • Add postorder node iterator for Tree

Commits

  • [272d0736e2] bump package version to 0.7.0-alpha.0 (molpopgen)
  • [b5946a4cc4] Redesign provenance feature: (#207) (Kevin R. Thornton)
  • [5699aab37f] Change return time of Tree::num_tracked_samples. (#206) (Kevin R. Thornton)
  • [2391c9e587] Add support for virtual roots (#205) (Kevin R. Thornton)
  • [4cf3496d82] Fix metadata links in lib.rs (#204) (Kevin R. Thornton)
  • [d7f70a7cfd] Use MBox to manage lifetimes of tskit C structs. (#203) (Kevin R. Thornton)
  • [034204ed88] Add newtypes for Time, Position, and for Location. (#199) (Kevin R. Thornton)
  • [4ba44ef0c5] Bump editions to 2021. (#198) (Kevin R. Thornton)
  • [c4cc6e875a] Add tskit::SizeType (#192) (Kevin R. Thornton)
  • [8429cc37d2] Use type erasure for all table row iteration functions. (#189) (Kevin R. Thornton)
  • [f4cb6350e0] Add TableCollection::check_integrity. (#188) (Kevin R. Thornton)
  • [562014b04f] Add preorder node traversal using latest tskit C API. (#186) (Kevin R. Thornton)
  • [db8550f6d7] Replace Box with malloc'd raw pointer for tskit types. (#184) (Kevin R. Thornton)
  • [90a2d84a9d] Update to C API 0.99.15 (breaking) (#183) (Kevin R. Thornton)
  • [58e7c5ed73] Update clap requirement from ~2.33.3 to ~2.34.0 (#176) (dependabot[bot])

2021-11-29, Version 0.6.1

Commits

  • [3eadcb161e] Replace chrono with humantime in provenance doc tests. (#175) (Kevin R. Thornton)
  • [4def777ddf] Add security audit work flow. (#172) (Kevin R. Thornton)

2021-11-23, Version 0.6.0

Commits

  • [b07c035077] bump version to 0.6.0 (molpopgen)
  • [8bb08be83d] Replace chrono dependency with humantime to avoid RUSTSEC-2020-0071 and RUSTSEC-2020-0159 (#171) (Momo Langenstein)
  • [896b5891e0] Implement Display for Id newtypes. (#168) (Kevin R. Thornton)
  • [d2c6383ae9] Update to C API 0.99.14 (#165) (Kevin R. Thornton)

2021-09-03, Version 0.5.0

Commits

Derive macros for table metadata.

  • [41633b60ed] Add metadata type registration via derive macros. (#163) (Kevin R. Thornton)

2021-08-31, Version 0.4.0

The theme of this release is "type safety". This release breaks API due to use of newtypes for row IDs and new metadata marker traits.

Commits

  • [a7d78b16aa] Bump version to 0.4.0 (molpopogen)
  • [b5e2c265dd] Add newtype row IDs to prelude. (#161) (Kevin R. Thornton)
  • [3dbe8c4b5e] Fix implementation of tree preorder stacking. (#160) (Kevin R. Thornton)
  • [fafd457033] Refactor metadata encoding: (#158) (Kevin R. Thornton)
  • [258b4ee5f0] replace IdIsNull trait with associated fn (#156) (Kevin R. Thornton)
  • [9987fc0472] Release build optimizations: (#155) (Kevin R. Thornton)
  • [58ac4a92d7] Refine what "NULL"-ness means for an Id type: (#154) (Kevin R. Thornton)
  • [ad4975fc70] Update bindgen requirement from 0.58.1 to 0.59.1 (#152) (dependabot[bot])
  • [8a553eaa80] fix clippy warnings that showed up in rust 1.54 (#153) (Kevin R. Thornton)
  • [bef4bb6c7a] Allow empty provenance records. (#151) (Kevin R. Thornton)
  • [86df702040] Improve test coverage of "adding rows to table collections" (#143): (Kevin R. Thornton)
  • [036680050b] * Update trees API to use NodeId (#145) (Kevin R. Thornton)
  • [7a716bbe76] Add additional member functions to TableCollection to (#141) (Kevin R. Thornton)
  • [baf6f17430] Fix Into< > type for TableCollection::add_individual_* (#142) (Kevin R. Thornton)
  • [689938eee7] fix link from ProvenanceId to ProvenanceTable in docs (#140) (Kevin R. Thornton)
  • [1203a5d523] strong id type cleanup (#139) (Kevin R. Thornton)
  • [6bae100e61] Add EdgeId (#138) (Kevin R. Thornton)
  • [9baff077b5] Add MigrationId and ProvenanceId (#137) (Kevin R. Thornton)
  • [7713ef669e] Add SiteId and MutationId (#136) (Kevin R. Thornton)
  • [de006a1f0e] Add PopulationId (#135) (Kevin R. Thornton)
  • [630ccd5f5e] Add IndividualId. (#133) (Kevin R. Thornton)
  • [8bf7d4b954] NodeTable::metadata now uses Into. (#134) (Kevin R. Thornton)
  • [3ac3d50f7b] * Establish a pattern for stronger ID types (#129) (Kevin R. Thornton)
  • [e19095d9a9] clippy vs bindgen (#130) (Kevin R. Thornton)
  • [d9abda5bb6] Change links in Cargo.toml to tskit-dev (#127) (Kevin R. Thornton)

2021-05-19, Version 0.3.0

This release has a few API changes, etc., that streamline the public interface.

The C code is updated to 0.99.12.

Commits

  • [ec0adc36ae] streamline API for creating table row objects (#126) (Kevin R. Thornton)
  • [edd36fa886] Add mutable access to NodeTable flag and time arrays. (#125) (Kevin R. Thornton)
  • [634df568af] Fix docs for Tree::total_branch_length. Fixes #114. (#124) (Kevin R. Thornton)
  • [202bcded3f] Give access to TableCollection edge indexes. (#123) (Kevin R. Thornton)
  • [3888fe5f10] update C code to version 0.99.12 (#122) (Kevin R. Thornton)
  • [6fa2057af6] Add prelude.rs (#119) (Kevin R. Thornton)
  • [a592126594] replace crate with $crate for all macros (#113) (Kevin R. Thornton)
  • [b618d75e5b] Add macro to aid returning from MetadataRoundtrip functions. (#110) (Kevin R. Thornton)
  • [79adaa1a4a] Add macro to remove code duplication (#111) (Kevin R. Thornton)
  • [159bbfe926] Add convenience macro to use all public traits. (#106) (Kevin R. Thornton)
  • [e912f7b2c8] Bump bindgen version. (#109) (Kevin R. Thornton)
  • [15fae9327b] Update clap requirement from ~2.27.0 to ~2.33.3 (#107) (dependabot[bot])
  • [55f18a1a4f] Refactor MetadataError: (#105) (Kevin R. Thornton)
  • [fbce6ca894] API fixes. (#104) (Kevin R. Thornton)

2021-04-27, Version 0.2.2

This release fixes issues with the lifetime relationships of Tree and the raw C arrays. Technically, this is an API change, but only with respect to return type and the integer type used to index that return type.

Commits

  • [89d234f674] Replace WrappedTskArray with idiomatic slices. Closes #99 (#101) (Kevin R. Thornton)
  • [ed8329b89e] Completely hide NodeIterator from public name spaces. (#100) (Kevin R. Thornton)

2021-04-26, Version 0.2.1

  • [ff1c7ced82] Add Provenance trait as optional feature (#98). (Kevin R. Thornton)
  • [0fdd30067e] Fix error in transmitting nodes. Closes #96 (#97) (Kevin R. Thornton)
  • [299c83ae35] Update repo/homepage name in Cargo.toml (molpopgen)
  • [35ecf29933] Remove re-exports that are part of existing bitflags types. (#95) (Kevin R. Thornton)

2021-04-21, Version 0.2.0

Commits

  • [daffeda43e] bump version to 0.2.0 (molpopgen)
  • [0dad5e39d2] Update docs (#93) (Kevin R. Thornton)
  • [f905b9c384] Add reverse tree iteration. (#92) (Kevin R. Thornton)
  • [a1a033f901] Add development documentation. (#91) (Kevin R. Thornton)
  • [ce3d8f4849] Refine forward sim example (#90) (Kevin R. Thornton)
  • [b1022e1f59] Refactor how tskit flags are handled. (#89) (Kevin R. Thornton)
  • [56e43cb0ff] Add forward simulation example. Closes #71. (#86) (Kevin R. Thornton)
  • [5530d7b234] Refactor all examples into examples/ (#85) (Kevin R. Thornton)
  • [651e4edcac] Collect public traits in traits.rs. Closes #81. (#84) (Kevin R. Thornton)
  • [11ad49f0e1] Remove mention of use NodeIterator. Closes #68. (#83) (Kevin R. Thornton)
  • [df28231d9a] Add test fixtures module. Closes #73 (#80) (Kevin R. Thornton)
  • [3a8a82637e] Rename Tree::nodes to Tree::traverse_nodes. (#79) (Kevin R. Thornton)
  • [4e7af98ac5] Update GitHub actions. (#78) (Kevin R. Thornton)
  • [43e14bb8a6] Add NodeListGenerator trait bound to TableAccess. Closes #67. (#75) (Kevin R. Thornton)
  • [ae203769f4] add id field to table row types. Closes #76 (#77) (Kevin R. Thornton)
  • [346c804be8] Make tree arrays public. Closes #70 (#74) (Kevin R. Thornton)
  • [a2dfcfe8f6] Add TableCollection and TreeSequence simplification (#64) (Kevin R. Thornton)
  • [c62ccd21aa] Add TableAccess trait and implement for TableCollection and TreeSequence. (#66) (Kevin R. Thornton)
  • [167209466a] Remove duplication of entire table collection when creating a tree sequence. (#65) (Kevin R. Thornton)
  • [df258ad8d1] Fix useless conversion in lib::c_api_version (#63) (Kevin R. Thornton)
  • [fcca8bb682] remove unnecessary function from util (#62) (Kevin R. Thornton)
  • [0ee9f86db4] Merge pull request #61 from molpopgen/add_individual_and_migration_tables (Kevin R. Thornton)
  • [8f072c47d1] Add migrations and individuals tables. (molpopogen)
  • [b2c891300b] Merge pull request #60 from molpopgen/tskit_C_version (Kevin R. Thornton)
  • [f48b2fed57] Add functions to return C API version info (molpopogen)
  • [87593d4bdc] Merge pull request #59 from molpopgen/add_test_metadata_some_columns_only (Kevin R. Thornton)
  • [5ab8e8c9d0] Add test of metadata decoding when not all rows have metadata. (molpopogen)
  • [adcc321cc8] Merge pull request #58 from molpopgen/table_row_access (Kevin R. Thornton)
  • [860a647bf3] * Add ::row for all tables (molpopgen)
  • [6b0a77e106] Add util.rs (molpopgen)
  • [6b9631e1f1] Merge pull request #57 from molpopgen/unify_table_iteration (Kevin R. Thornton)
  • [3d79f8bbfa] Add ability to iterate tables from a TableCollection: (molpopogen)
  • [392ce57e0a] Merge pull request #52 from molpopgen/table_iteration (Kevin R. Thornton)
  • [2fe5912c34] Add table iteration w/optional handling of metadata. (molpopgen)
  • [9a59a148f7] Merge pull request #55 from molpopgen/wrapped_tsk_array_iter_adapter (Kevin R. Thornton)
  • [84b0b496c1] Replace built-in iteration with iterator adapter for WrappedTskArray (molpopgen)
  • [18234998ea] Merge pull request #56 from molpopgen/metadata_macro_fixes (Kevin R. Thornton)
  • [49bbd0f2f4] metadata_to_vector macro is now a simple return (no ? operator). (molpopgen)
  • [6e293acf14] Remove unused paramter to metadata_to_vector. Fixes #54. (molpopgen)
  • [45347a576c] Change log for 0.1.2 (molpopgen)

2021-04-12, Version 0.1.2

Commits

  • [f475a5c624] Bump version to 0.1.2 (molpopgen)
  • [f1887d55e0] Merge pull request #46 from molpopgen/add_important_missing_functions (Kevin R. Thornton)
  • [f5598256dd] Merge pull request #47 from molpopgen/add_changelog (Kevin R. Thornton)
  • [fb85ba9606] Add Tree::num_tracked_samples and Tree::kc_distance. (molpopogen)
  • [08febd5062] Add change log (molpopogen)
  • [e6495a959a] Merge pull request #51 from molpopgen/test_beta_instead_of_nightly (Kevin R. Thornton)
  • [fa7cca91a5] Test beta instead of nightly. (molpopgen)
  • [bd7185eef2] Merge pull request #45 from molpopgen/documentation (Kevin R. Thornton)
  • [2400906762] Add documentation related to Tree/TreeSequence (molpopogen)
  • [550aa76597] Fix typo in function name. (molpopogen)
  • [56eaf875b6] Merge pull request #44 from molpopgen/fix_clippy_warnings (Kevin R. Thornton)
  • [20ffe557ca] Fix warnings from clippy (molpopogen)
  • [0bf1dada4d] Merge pull request #43 from molpopgen/kc_distance (Kevin R. Thornton)
  • [2e8b4c1cfc] Add TreeSequence::kc_distance (molpopogen)
  • [efe5ce2b0b] Merge pull request #42 from molpopgen/fix_tskit_array_access_macro (Kevin R. Thornton)
  • [82bb6ec6a1] Modify unsafe_tsk_column_access to support idiomatic fall-through. (molpopogen)
  • [40e898910d] Merge pull request #41 from molpopgen/sample_list_traversal (Kevin R. Thornton)
  • [cb0e9a4355] Add support for samples iteration: (molpopogen)
  • [f1acfb06f2] Merge pull request #40 from molpopgen/more_node_iteration (Kevin R. Thornton)
  • [22684248d1] * Rename NodeIteration to NodeIterator (molpopogen)
  • [faa105d577] Merge pull request #38 from molpopgen/Tree_API (Kevin R. Thornton)
  • [896f921e91] Several changes to Tree and TreeSequence: (molpopogen)
  • [683ba84b10] Merge pull request #39 from molpopgen/ffi_array_wrapper (Kevin R. Thornton)
  • [dd3df03ca3] Add non-owning wrappers to C arrays. (molpopogen)
  • [85cc4a591f] Merge pull request #37 from molpopgen/add_tree (Kevin R. Thornton)
  • [be97490641] Add minimial Tree interface. (molpopgen)
  • [4b6257ed2c] Merge pull request #36 from molpopgen/streamline_macros (Kevin R. Thornton)
  • [238f652d24] Remove macro redundancy. (molpopgen)
  • [85505887e1] Merge pull request #35 from molpopgen/refine_ffi (Kevin R. Thornton)
  • [2cb4993f07] Refactor the ffi module: (molpopgen)
  • [1b9a054ff0] Merge pull request #34 from molpopgen/improve_error_handling_macro (Kevin R. Thornton)
  • [20a5486132] Add overload of handle_tsk_return_value. (molpopgen)
  • [eae11b4c8a] Merge pull request #33 from molpopgen/add_tree_sequence (Kevin R. Thornton)
  • [a57b947352] Add TskitConsumingType, macro to build one, and convert TreeSequence (molpopgen)
  • [dcb5a02f3c] change dependabot to monthly (molpopgen)
  • [4eb407ac61] Merge pull request #31 from molpopgen/dependabot/add-v2-config-file (Kevin R. Thornton)
  • [a759e0441b] Merge pull request #32 from molpopgen/dependabot/cargo/bindgen-0.57.0 (dependabot-preview[bot])
  • [fb2a56c868] Update bindgen requirement from 0.56.0 to 0.57.0 (dependabot-preview[bot])
  • [a8a0b1aabf] Create Dependabot config file (dependabot-preview[bot])

2021-03-26, Version 0.1.1

Commits

  • [e9d73e4912] Fix crate name in README.md (molpopogen)
  • [28deef7d04] update README (molpopogen)
  • [ef79a446c1] Bump version to 0.1.1 (molpopogen)
  • [d3c31fa0fc] Merge pull request #30 from molpopgen/fix_warnings (Kevin R. Thornton)
  • [bedfa02f76] Merge pull request #29 from molpopgen/metadata_docs (Kevin R. Thornton)
  • [f6f3304d75] Remove Drop constraint on TskitType. (molpopogen)
  • [d8873a7941] Quick fix regarding documenting metadata. Closes #25 (molpopogen)
  • [4518db4946] Merge pull request #28 from molpopgen/update_to_tskit_0_3_5 (Kevin R. Thornton)
  • [80893566ed] Update C files to tskit 0.3.5 (molpopogen)
  • [e81aad0bf6] Merge pull request #27 from molpopgen/fix_example_file_names (Kevin R. Thornton)
  • [dbaf304b38] Fix swapped example file names. Fixes #26 (molpopogen)
  • [30c34c2023] Merge pull request #23 from molpopgen/rename_crate (Kevin R. Thornton)
  • [e01b3e530e] rename crate to tskit (molpopgen)
  • [a7a69ad31d] Merge pull request #20 from molpopgen/metadata (Kevin R. Thornton)
  • [54ac4312a1] clippy and fmt (molpopgen)
  • [a1aea5cd95] add examples of metadata round trips (molpopgen)
  • [7352ca95b5] Update table operations to metadata API. (molpopgen)
  • [275074da30] Add metadata trait and API. (molpopgen)
  • [d89dcd19dd] Merge pull request #18 from molpopgen/tskit_wrapper_trait (Kevin R. Thornton)
  • [3445af368d] TableCollection uses new trait. (molpopgen)
  • [93c43aa2c7] Add trait to define what it means to wrap a tskit type. (molpopgen)