Changelogs

[1.2.0b1] - 2026-09-26

This is a beta release for the upcoming 1.2.0, to support the beta release of SLiM v6.

Major update release to support the release of SLiM v6.0. The main update to SLiM is support for traits, which accompanied a number of changes to metadata, particularly mutation metadata. For more information see https://tskit.dev/pyslim/docs/latest/previous_versions.html

Breaking changes:

• The release of SLiM 6.0, changes to metadata (see below) mean that accessing top-level metadata (e.g., ts.metadata[“SLiM”]) more than a few times in a script will take a long time. Scripts that previously ran quickly may take a prohibitively long. See the documentation for simple changes that fix the problem: https://tskit.dev/pyslim/docs/latest/previous_versions.html

• The SLiM tree sequence file version number has changed to 1.0. Use pyslim.update to convert your tree sequence file to this format.

• Metadata for SLiM’s mutations are no longer stored along with the tskit mutations, because mutation stacking allows each tskit mutation to be associated with more than one SLiM mutation. Now, metadata for each unique mutation is stored in top-level metadata, under ts.metadata[“SLiM_mutation_list”]. The recommended way to access this information is by obtaining the SLiM ID-to-metadata dict returned by pyslim.mutation_metadata(ts).

• The SLiM mutation IDs represented by each tskit mutation should no longer be read in from the derived_state property, but instead from the tskit mutation’s metadata. (However, SLiM still writes these out in text to the derived_state entry as before.)

• Previously, msprime.sim_mutations with the msprime.SLiMMutationModel would record SLiM metadata along with each new mutation. However, msprime does not modify top-level metadata, and so the method add_mutation_metadata should be used after adding SLiM mutations.

• This is a SLiM change, but top-level metadata is now encoded using the json+struct codec now provided by tskit (so that the mutation metadata is not too large/slow).

• The top-level and individual metadata schemas now depend on the number of traits in the model. The methods slim_tree_sequence_metadata_schema and slim_individual_metadata_schema can be used to produce correct schema.

• Individual metadata no longer has a flags component; the one flag we did set here (pyslim.INDIVIDUAL_FLAG_MIGRATED) is now recorded, as pyslim.INDIVIDUAL_MIGRATED, in individual.flags (rather than individual.metadata[‘flags’]).

• The default sex ratio for populations is now 0.5 instead of 0.0. (#339, @petrelharp)

Bug fixes:

• pyslim.annotate now has a num_chromosomes argument. Previously it could not be easily used to annotate multichromosome simulations with more than 8 chromosomes. (It also now has a num_traits argument.)

• In some previous versions, converting files produced by a yet-older version of SLiM to the previously-current file version dropped some information from metadata: nucleotide values for mutations, and pedigree parent IDs for individuals. This only may have affected users using pyslim.convert(ts) in a previous version of pyslim on a tree sequence ts with SLiM file version prior to 0.9.

• Since verison 1.1, the value of pyslim.INDIVIDUAL_FLAG_MIGRATED has been 2, when in fact it should have been 1, so code using this flag to detect migrants would have been wrong (and should have found no migrants, ever). (Also, this flag is now deprecated; see above.)

New features:

• SLiM now includes in metadata information about the effects of mutations on quantitative traits, the values of traits for individuals, and the values of various “tags” defined in SLiM.

• default_slim_metadata can now take additional arguments to modify the returned values.

[1.1.1] - 2026-03-06

Maintenance release.

• Improved performance on remove_vacant (#393)

• Require Python >= 3.11

[1.1.0] - 2025-08-16

Major update release to support the release of SLiM v5.0. The main update here is support for multiple chromosomes, which entailed a change to the node table metadata that records “vacancy” for chromosomes not diploid in a given individual. Changes are minimal if you’re simulating a single, diploid chromosome; for more information see https://tskit.dev/pyslim/docs/latest/previous_versions.html

Breaking changes:

• SLiM tree sequence file version number has changed to 0.9.

• This is a change in SLiM, really, but top-level SLiM metadata now requires a “this_chromosome” entry.

• Similarly, node metadata no longer has genome_type or is_null; instead they have is_vacant, and the chromosome type is in top-level metadata, under metadata[‘SLiM’][‘this_chromosome’].

• pyslim.slim_metadata_schemas[“node”] has an appropriate metadata schema

  for a single-chromosome simulation (not a breaking change), but users wishing to set up a multi-chromosome simulation should use instead pyslim.slim_node_metadata_schema (which has the appropriate value in [“properties”][“is_vacant”][“length”]) (@petrelharp, #367).

• Previously, pyslim.annotate would leave existing node and individual

  metadata, even if this metadata came from a different schema. This could silently create garbage metadata. Now, annotate removes any existing metadata, and warns if this occurs (@petrelharp, #390).

Notable changes:

• pyslim.individual_parents and pyslim.has_individual_parents are no

  longer needed, as this information can be more reliably extracted from the parents column/attribute of individuals, so they are now deprecated and will be removed in the future.

New features:

• pyslim.set_slim_state will adjust times and “alive” flags so

  that when the tree sequence is loaded into SLiM it will have a specified set of individuals alive at a particular time. (@petrelharp, #384)

• Functions pyslim.node_is_vacant and pyslim.has_vacant_samples

  test for vacancy in the current chromosome. (@petrelharp, #367)

• pyslim.remove_vacant and pyslim.restore_vacant, respectively,

  remove and restore vacant samples nodes, necessary for recapitation and other operations. Also, corresponding pyslim.remove_vacant_tables and pyslim.restore_vacant_tables. (@petrelharp, #367)

• pyslim.recapitate by default removes the sample flags on vacant nodes,

  but this behavior is controlled by an argument, keep_vacant. (@petrelharp, #367)

• pyslim.set_metadata_schemas now includes a num_chromosomes argument

  (@petrelharp, #367)

Bugfixes:

• Recapitation on tree sequences with null genomes would attempt to simulate

  the history of those null genomes; this would in all but exceptional cases fail with an error (“not all roots are at the time expected”). Now, null genomes are “vacant” (see above) and recapitate removes their sample flags before recapitating (and optionally puts them back) as described in pyslim.remove_vacant (@petrelharp, #367).

• Previously, recapitation would require the roots of all trees to be

  at the same time (roughly) as the ‘tick’ stored in the top-level metadata; however, this would not be the case if the first population was added later than the first tick. The requirement has therefore been removed. (@petrelharp, #382)

• The generated_nucleotides method now sets the nucleotide_based entry

  in top-level metadata to True. (@petrelharp, #385)

• The individual flags INDIVIDUAL_ALIVE, INDIVIDUAL_REMEMBERED,

  and INDIVIDUAL_RETAINED were signed integers, but the flags in the individual table they apply to are unsigned, so using the bitwise negation operator ~ could result in an error. Now, they are np.uint32 values. (@petrelharp, #378)

[1.0.4] - 2023-08-01

Bugfixes:

• The last bugfix introduced a small bug: recapitation on a tree sequence

  whose roots are at least 100,000 ticks ago would produce an msprime error: “Attempt to sample a lineage from an inactive population”. Reported by Meaghan Clark. (@petrelharp, #322)

[1.0.3] - 2023-06-21

Bugfixes:

• From 1.0.1 back to 0.700, there was a bug in recapitate when using the

  ancestral_Ne parameter that introduced a bottleneck to diploid size Ne=1 for each SLiM subpopulation for 1 or 2 generations unless either (a) it was a WF simulation, with calls to addSubPop() in first() or early() and treeSeqOutput() in late(), or (b) it was a nonWF simulation, with calls to addSubPop() in first() and treeSeqOutput() in early() or late(). The fix correctly starts the msprime population with effective size ancestral_Ne at the time of the roots, which might be at the value of ts.metadata[‘SLiM’][‘tick’], this value minus 1, or this value minus 2. Furthermore, recapitate now throws an error if any roots of any trees are not at the same time as the others. (@petrelharp, #308)

[1.0.2] - 2023-06-20

This was a bugfix release that was pushed out without the actual bug fix. Please don’t use this one.

[1.0.1] - 2022-09-23

• Documentation of how to empirically measure generation time

  and check that it is correct (@silastittes, @petrelharp, #301, #293).

• Minor modifications to convert_alleles and generate_nucleotides

  so that they run in a reasonable amount of time (@petrelharp, #299).

• Addition of method to find the next SLiM mutation ID,

  pyslim.next_slim_id (@mufernando, #290).

[1.0] - 2022-08-12

Breaking changes:

• Removed SlimTreeSequence class entirely (it was previously deprecated).

  All its methods are either available in tskit.TreeSequence or are now called by pyslim.fn(ts, …) instead of ts.fn(…).

• TODO: Deprecated util.unique_labels_by_group.

• Moved some methods of SlimTreeSequence to pyslim:

  • instead of slim_ts.slim_time(t) do pyslim.slim_time(ts, t)

  • instead of slim_ts.individuals_alive_at(t) do pyslim.individuals_alive_at(ts, t)

  • instead of slim_ts.individuals_parents(t) do pyslim.individuals_parents(ts, t)

  • instead of slim_ts.individuals_ages(t) do pyslim.individuals_ages(ts, t)

• The methods slim_ts.mutation_at( ) and slim_ts.nucleotide_at( )

  are now methods of pyslim, whose first argument is the tree sequence.

• In SLiM v4 “generation” has been renamed to “tick”, and so corresponding things in pyslim have been renamed: top-level metadata now has ts.metadata[“SLiM”][“tick”] instead of ts.metadata[“SLiM”][“generation”]

• Renamed pyslim.annotate_defaults() to pyslim.annotate(), with slight changes in behavior: since msprime.sim_ancestry() now simulates individuals by default, annotation does not set up individuals: if you have a tree sequence without individuals (e.g., produced by msprime.simulate()) then you need to set up those individuals yourself.

• To update a tree sequence produced by an old version of SLiM to the current one, use pyslim.update( ). (However, note that reading it in to SLiM and writing it out again might be even easier.)

• The method pyslim.set_tree_sequence_metadata now has arguments tick and cycle instead of generation.

• Removed pyslim.make_slim_provenance_dict.

Other notable changes:

• Top-level metadata now has a tick attribute that is (for now) a synonym

  for generation; the latter will be deprecated at some point in the future.

• Methods for getting time, population, and location information about individuals are now in tskit:

  • SlimTreeSequence.individual_times is now TreeSequence.individuals_time()

  • SlimTreeSequence.individual_populations is now TreeSequence.individuals_population()

  • SlimTreeSequence.individual_locations is now TreeSequence.individuals_location()

  However, this will be invisible to the user. In each case note the the location of the “s” has moved (to “individual*s* time” instead of “individual time*s*”), but the original version remains an undocumented alias.

New features:

• Methods like pyslim.individuals_alive_at( ) now deal with the new stage=”first”.

[0.700] - 2021-12-20

Breaking changes:

• pyslim.recapitate is updated to use new demography features in msprime 1.0,

  and differs from SlimTreeSequence.recapitate() (now deprecated). Since the backend is now msprime.sim_ancestry() instead of msprime.simulate(), the argument Ne should be replaced with ancestral_Ne.

• reference_sequence is now a tskit TreeSequence attribute, no longer managed

  by pyslim. It is no longer mutable on tree sequences (only TableCollections), and previous calls to ts.reference_sequence to get the actual sequence should be replaced by ts.reference_sequence.data.

• Old-style “legacy” metadata (previously deprecated) has been removed.

  See the documentation for instructions on migrating your code.

New features:

• Added pyslim.population_size( ) to compute an array giving numbers of

  individuals across a grid of space and time bins. ({user}giliapatterson)

[0.600] - 2021-02-24

New features:

• Added ts.individual_parents(), a way to get the IDs of individual’s parents

  when both of them are present in the tree sequence. :user:@petrelharp

• Added and documented TSK_INDIVIDUAL_RETAINED flag to reflect the additional

  of “retained” individuals in SLiM v3.6. :user:@hyanwong, :user:@petrelharp

Bugfix:

• Modified recaptiate to not error with the current msprime 1.0 alpha release.

[0.501] - 2020-12-08

Bugfix:

• Making .slim_generation derive from the tree sequence’s top-level metadata

  had the unanticipated consequence that it could not be modified, which some people were doing. This restores the previous behavior, but in the future, modifying .slim_generation on a tree sequence will be deprecated - instead, this should be modified in the metadata of the TableCollection.

[0.500] - 2020-12-07

Breaking changes:

• “First generation” individuals no longer need to be retained by SLiM to recapitate, thanks to the “keep_input_roots” argument to simplify (new in tskit 0.3.0). The FIRST_GEN flag and .first_generation_individuals() methods are now deprecated, and if you want these to remain in the tree sequence you must explicitly Remember them. (However, their nodes will remain if necessary for recapitation.) If you wish to simplify an un-recapitated tree sequence you now can, but you must pass keep_input_roots=True. This should only cause breakages if you made explicit use of the first generation individuals, without explicitly Remembering them.

• Information about the tree sequence is now stored in top-level metadata, accessible through ts.metadata[‘SLiM’]. Previous interfaces remain: for instance, ts.slim_generation is now redundant with ts.metadata[‘SLiM’][‘generation’]. This should not cause breakages, but will cause warnings where none were previously: for instance, pyslim.SlimTreeSequence(msprime.mutate(ts)) may throw a warning because msprime.mutate( ) does not preserve top-level metadata, and so SLiM-relevant information is retrieved from provenance (as in previous file versions).

Notable changes:

• Switched to using tskit native encoding/decoding of metadata via schemas.

• added to conda-forge (@winni2k)

New features:

• added samples_only and population arguments to ts.individuals_alive_at()

• added the ts.slim_time() method

• enabled dumping the reference sequence for nucleotide models

[0.403] - 2020-08-27

BUGFIX: if a tree had all first generation individuals removed

(e.g., if it had been simplified) then individuals_alive_at( ) failed.

[0.402] - 2020-08-27

This is a compatibility release, for the tskit 0.3.0 release.

New features:

• added has_individual_parents, a method to find individuals with all parents are also recorded as individuals

• Provenance handling:

  • added the .slim_provenances property to return all SLiM provenance entries

  • added the slim_provenance_version and parse_provenance methods to tell if

    provenance entries come from SLiM and to parse them

• documentation for recapitation with a nonuniform map by :user:@TeresaPegan

Bug fixes:

• fixed differential time offset for tree sequences saved out in early versus late:

  prior to this, mutation_at and nucleotides_at would have been sometimes wrong if the tree sequence was saved out during late

• initialises correctly to work with tskit 0.3.0

[0.401] - 2020-03-27

Bug fixes:

• checks for the ability to simulate with a discrete recombination map

  in the available version of msprime, and sets the default flat recombination map in recapitate appropriately

[0.400] - 2020-03-24

New features:

• updated to take and output SLiM file version 0.4, which only differs from 0.3

  in minor aspects of provenance

[0.314] - 2019-10-31

New features:

• allows passing in of a recombination map to recapitate (@mufernando)

• added first_generation_individuals() function

• defined individual ages for WF ages

• added mutation_at() and fixed up nucleotide_at() functions