Python 0.5.6

Breaking Changes

• tskit now requires Python 3.8, as Python 3.7 became end-of-life on 2023-06-27

Features

• Tree.trmca now accepts >2 nodes and returns nicer errors
  (@hyanwong, :pr:2808, #2801, #2070, #2611)

• Add TreeSequence.genetic_relatedness_weighted stats method.
  (@petrelharp, @brieuclehmann, @jeromekelleher,
  #2785, #1246)

• Add TreeSequence.impute_unknown_mutations_time method to return an
  array of mutation times based on the times of associated nodes
  (@duncanMR, #2760, #2758)

• Add asdict to all dataclasses. These are returned when you access a row or
  other tree sequence object. (@benjeffery, #2759, #2719)

Bugfixes

• Fix incompatibility with jsonschema>4.18.6 which caused
  AttributeError: module jsonschema has no attribute _validators
  (@benjeffery, #2844, #2840)

Python 0.5.5

Performance improvements

• Methods like ts.at() which seek to a specified position on the sequence from
  a new Tree instance are now much faster (@molpopgen, #2661).

Features

• Add __repr__ for variants to return a string representation of the raw data
  without spewing megabytes of text (@chriscrsmith, #2695, #2694)

• Add keep_rows method to table classes to support efficient in-place
  table subsetting (@jeromekelleher, #2700)

Bugfixes

• Fix UnicodeDecodeError when calling Variant.alleles on the emscripten platform.
  (@benjeffery, #2754, #2737)

C API C_1.1.2

Performance improvements

• tsk_tree_seek is now much faster at seeking to arbitrary points along
  the sequence from the null tree (@molpopgen, #2661).

Features

• The struct tsk_treeseq_t now has the variables min_time and max_time,
  which are the minimum and maximum among the node times and mutation times,
  respectively. min_time and max_time can be accessed using the functions
  tsk_treeseq_get_min_time and tsk_treeseq_get_max_time, respectively.
  (@szhan, #2612, #2271)

• Add the TSK_SIMPLIFY_NO_FILTER_NODES option to simplify to allow unreferenced
  nodes be kept in the output (@jeromekelleher, @hyanwong,
  #2606, #2619).

• Add the TSK_SIMPLIFY_NO_UPDATE_SAMPLE_FLAGS option to simplify which ensures
  no node sample flags are changed to allow calling code to manage sample status.
  (@jeromekelleher, #2662, #2663).

• Guarantee that unfiltered tables are not written to unnecessarily
  during simplify (@jeromekelleher #2619).

• Add x_table_keep_rows methods to provide efficient in-place table subsetting
  (@jeromekelleher, #2700).

• Add tsk_tree_seek_index function

Python 0.5.4

Features

• A new Tree.is_root method avoids the need to to search the potentially
  large list of Tree.roots (@hyanwong, #2669, #2620)

• The TreeSequence object now has the attributes min_time and max_time,
  which are the minimum and maximum among the node times and mutation times,
  respectively. (@szhan, #2612, #2271)

• The draw_svg methods now have a max_num_trees parameter to truncate
  the total number of trees shown, giving a readable display for tree
  sequences with many trees (@hyanwong, #2652)

• The draw_svg methods now accept a canvas_size parameter to allow
  extra room on the canvas e.g. for long labels or repositioned graphical
  elements (@hyanwong, #2646, #2645)

• The Tree object now has the method siblings to get
  the siblings of a node. It returns an empty tuple if the node
  has no siblings, is not a node in the tree, is the virtual root,
  or is an isolated non-sample node.
  (@szhan, #2618, #2616)

• The msprime.RateMap class has been ported into tskit: functionality should
  be identical to the version in msprime, apart from minor changes in the formatting
  of tabular text output (@hyanwong, @jeromekelleher, #2678)

• Tskit now supports and has wheels for Python 3.11. This Python version has a significant performance boost. (@benjeffery , #2624 , #2248 )

Breaking Changes

• the filter_populations, filter_individuals, and filter_sites
  parameters to simplify previously defaulted to True but now default
  to None, which is treated as True. Previously, passing None
  would result in an error. (@hyanwong, #2609, #2608)

Python 0.5.3

Fixes

• The Variant object can now be initialized with 64 bit numpy ints as
  returned e.g. from np.where (@hyanwong, #2518, #2514)

• Fix tree.mrca for the case of a tree with multiple roots.
  (@benjeffery, #2533, #2521)

Features

• The ts.nodes method now takes an order parameter so that nodes
  can be visited in time order (@hyanwong, #2471, #2370)

• Add samples argument to TreeSequence.genotype_matrix.
  Default is None, where all the sample nodes are selected.
  (@szhan, #2493, #678)

• ts.draw and the draw_svg methods now have an optional omit_sites
  parameter, aiding drawing large trees with many sites and mutations
  (@hyanwong, #2519, #2516)

Breaking Changes

• Single statistics computed with TreeSequence.general_stat are now
  returned as numpy scalars if windows=None, AND; samples is a single
  list or None (for a 1-way stat), OR indexes is None or a single list of
  length k (instead of a list of length-k lists).
  (@gtsambos, #2417, #2308)

• Accessor methods such as ts.edge(n) and ts.node(n) now allow negative
  indexes (@hyanwong, #2478, #1008)

• ts.subset() produces valid tree sequences even if nodes are shuffled
  out of time order (@hyanwong, #2479, #2473), and the
  same for tables.subset() (@hyanwong, #2489). This involves
  sorting the returned tables, potentially changing the returned edge order.

Performance improvements

• TreeSequence.link_ancestors no longer continues to process edges once all
  of the sample and ancestral nodes have been accounted for, improving memory
  overhead and overall performance
  (@gtsambos, #2456, #2442)

Python 0.5.2

Fixes

• Iterating over ts.variants() could cause a segfault in tree sequences
  with large numbers of alleles or very long alleles
  (@jeromekelleher, #2437, #2429).

• Various circular references fixed, lowering peak memory usage
  (@jeromekelleher, #2424, #2423, #2427).

• Fix bugs in VCF output when there isn't a 1-1 mapping between individuals
  and sample nodes (@jeromekelleher, #2442, #2257,
  #2446, #2448).

Performance improvements

• TreeSequence.site position search performance greatly improved, with much lower
  memory overhead (@jeromekelleher, #2424).

• TreeSequence.samples time/population search performance greatly improved, with
  much lower memory overhead (@jeromekelleher, #2424, #1916).

• The timeasc and timedesc orders for Tree.nodes have much
  improved performance and lower memory overhead
  (@jeromekelleher, #2424, #2423).

Features

• Variant objects now have a .num_missing attribute and .counts() and
  .frequencies methods (@hyanwong, #2390 #2393).

• Add the Tree.num_lineages(t) method to return the number of lineages present
  at time t in the tree (@jeromekelleher, #386, #2422)

• Efficient array access to table data now provided via attributes like
  TreeSequence.nodes_time, etc (@jeromekelleher, #2424).

Breaking Changes

• Previously, accessing (e.g.) tables.edges returned a different instance of
  EdgeTable each time. This has been changed to return the same instance
  for the lifetime of a given TableCollection instance. This is technically
  a breaking change, although it's difficult to see how code would depend
  on the property that (e.g.) tables.edges is not tables.edges.
  (@jeromekelleher, #2441, #2080).

C API C_1.1.1

Bug fixes

• Fix segfault in tsk_variant_restricted_copy in tree sequences with large
  numbers of alleles or very long alleles
  (@jeromekelleher, #2437, #2429).

Python 0.5.1

Fixes

• Copies of a Variant object would cause a segfault when .samples was accessed.
  (@benjeffery, #2400, #2401)

Changes

• Tables in a table collection can be replaced using the replace_with method
  (@hyanwong, #1489 #2389)

• SVG drawing routines now return a special string object that is automatically
  rendered in a Jupyter notebook (@hyanwong, #2377)

Features

• New Site.alleles() method (@hyanwong, #2380, #2385)

• The variants(), haplotypes() and alignments() methods can now
  take a list of sample ids and a left and right position, to restrict the
  size of the output (@hyanwong, #2092, #2397)

C API 1.1.0

Features

• Add num_children to tsk_tree_t an array which contains counts of the number of child
  nodes of each node in the tree. (@GertjanBisschop, #2274, #2316)

• Add edge to tsk_tree_t an array which contains the edge_id of the edge encoding
  the relationship between the child node and its parent for each (child) node in the tree.
  (@GertjanBisschop, #2304, #2340)

Changes

• Reduce the maximum number of rows in a table by 1. This removes edge cases so that a tsk_id_t can be
  used to count the number of rows. (@benjeffery, #2336, #2337)

• Samples are now copied by tsk_variant_restricted_copy. (@benjeffery, #2400, #2401)

Python 0.5.0

Major Feature Release

Breaking Changes

• The JSON metadata codec now interprets the empty string as an empty object. This means
  that applying a schema to an existing table will no longer necessitate modifying the
  existing rows. (@benjeffery, #2064, #2104)

• Remove the previously deprecated as_bytes argument to TreeSequence.variants.
  If you need genotypes in byte form this can be done following the code in the
  to_macs method on line 5573 of trees.py.
  This argument was initially deprecated more than 3 years ago when the code was part of
  msprime.
  (@benjeffery, #605, #2172)

• Arguments after ploidy in write_vcf marked as keyword only
  (@jeromekelleher, #2329, #2315).

• When metadata equal to b'' is printed to text or HTML tables it will render as
  an empty string rather than "b''". (@hyanwong, #2349, #2351)

Changes

• A min_time parameter in draw_svg enables the youngest node as the y axis min
  value, allowing negative times.
  (@hyanwong, #2197, #2215)

• VcfWriter.write now prints the site ID of variants in the ID field of the
  output VCF files.
  (@roohy, #2103, #2107)

• Make dumping of tables and tree sequences to disk a zero-copy operation.
  (@benjeffery, #2111, #2124)

• Add copy argument to TreeSequence.variants which if False reuses the
  returned Variant object for improved performance. Defaults to True.
  (@benjeffery, #605, #2172)

• tree.mrca now takes 2 or more arguments and gives the common ancestor of them all.
  (@savitakartik, #1340, #2121)

• Add a edge attribute to the Mutation class that gives the ID of the
  edge that the mutation falls on.
  (@jeromekelleher, #685, #2279).

• Add the TreeSequence.split_edges operation which inserts nodes into
  edges at a specific time.
  (@jeromekelleher, #2276, #2296).

• Add the TreeSequence.decapitate (and closely related
  TableCollection.delete_older) operation to remove topology and mutations
  older than a give time.
  (@jeromekelleher, #2236, #2302, #2331).

• Add the TreeSequence.individuals_time and TreeSequence.individuals_population
  methods to return arrays of per-individual times and populations, respectively.
  (@petrelharp, #1481, #2298).

• Add the sample_mask and site_mask to write_vcf to allow parts
  of an output VCF to be omitted or marked as missing data. Also add the
  as_vcf convenience function, to return VCF as a string.
  (@jeromekelleher, #2300).

• Add support for missing data to write_vcf, and add the isolated_as_missing
  argument. (@jeromekelleher, #2329, #447).

• Add Tree.num_children_array and Tree.num_children. Returns the counts of
  the number of child nodes for each or a single node in the tree respectively.
  (@GertjanBisschop, #2318, #2319, #2332)

• Add Tree.path_length.
  (@jeremyguez, #2249, #2259).

• Add B1 tree balance index.
  (@jeremyguez, @jeromekelleher, #2251, #2281, #2346).

• Add B2 tree balance index.
  (@jeremyguez, @jeromekelleher, #2252, #2353, #2354).

• Add Sackin tree imbalance index.
  (@jeremyguez, @jeromekelleher, #2246, #2258).

• Add Colless tree imbalance index.
  (@jeremyguez, @jeromekelleher, #2250, #2266, #2344).

• Add direction argument to TreeSequence.edge_diffs, allowing iteration
  over diffs in the reverse direction. NOTE: this comes with a ~10% performance
  regression as the implementation was moved from C to Python for simplicity
  and maintainability. Please open an issue if this affects your application.
  (@jeromekelleher, @benjeffery, #2120).

• Add Tree.edge_array and Tree.edge. Returns the edge id of the edge encoding
  the relationship of each node with its parent.
  (@GertjanBisschop, #2361, #2357)