import tskit
import json
import warnings
from ._version import *
from .provenance import *
GENOME_TYPE_AUTOSOME = 0
"""
A value used in node metadata ("genome_type") to indicate the node is an autosome.
"""
GENOME_TYPE_X = 1
"""
A value used in node metadata ("genome_type") to indicate the node is an X chromosome.
"""
GENOME_TYPE_Y = 2
"""
A value used in node metadata ("genome_type") to indicate the node is a Y chromosome.
"""
INDIVIDUAL_TYPE_HERMAPHRODITE = -1
"""
A value used in individual metadata ("sex") to indicate the individual is a hermaphrodite.
"""
INDIVIDUAL_TYPE_FEMALE = 0
"""
A value used in individual metadata ("sex") to indicate the individual is a male.
"""
INDIVIDUAL_TYPE_MALE = 1
"""
A value used in individual metadata ("sex") to indicate the individual is a female.
"""
INDIVIDUAL_FLAG_MIGRATED = 0x01
"""
An individual flag indicating the individual is a migrant.
"""
# These are copied from slim_globals.h and modified to be python not json (eg false->False)
_raw_slim_metadata_schemas = {
"tree_sequence" :
{
"$schema": "http://json-schema.org/schema#",
"codec": "json",
"examples": [
{
"SLiM": {
"file_version": "0.8",
"name": "fox",
"description": "foxes on Catalina island",
"cycle": 123,
"tick": 123,
"model_type": "WF",
"nucleotide_based": False,
"separate_sexes": True,
"spatial_dimensionality": "xy",
"spatial_periodicity": "x"
}
}
],
"properties": {
"SLiM": {
"description": "Top-level metadata for a SLiM tree sequence, file format version 0.8",
"properties": {
"file_version": {
"description": "The SLiM 'file format version' of this tree sequence.",
"type": "string"
},
"name": {
"description": "The SLiM species name represented by this tree sequence.",
"type": "string"
},
"description": {
"description": "A user-configurable description of the species represented by this tree sequence.",
"type": "string"
},
"cycle": {
"description": "The 'SLiM cycle' counter when this tree sequence was recorded.",
"type": "integer"
},
"tick": {
"description": "The 'SLiM tick' counter when this tree sequence was recorded.",
"type": "integer"
},
"model_type": {
"description": "The model type used for the last part of this simulation (WF or nonWF).",
"enum": [ "WF", "nonWF" ],
"type": "string"
},
"nucleotide_based": {
"description": "Whether the simulation was nucleotide-based.",
"type": "boolean"
},
"separate_sexes": {
"description": "Whether the simulation had separate sexes.",
"type": "boolean"
},
"spatial_dimensionality": {
"description": "The spatial dimensionality of the simulation.",
"enum": ["", "x", "xy", "xyz"],
"type": "string"
},
"spatial_periodicity": {
"description": "The spatial periodicity of the simulation.",
"enum": ["", "x", "y", "z", "xy", "xz", "yz", "xyz"],
"type": "string"
},
"stage": {
"description": "The stage of the SLiM life cycle when this tree sequence was recorded.",
"type": "string"
}
},
"required": [
"model_type",
"tick",
"file_version",
"spatial_dimensionality",
"spatial_periodicity",
"separate_sexes",
"nucleotide_based"
],
"type": "object"
}
},
"required": ["SLiM"],
"type": "object"
},
"edge" : None,
"site" : None,
"mutation" :
{
"$schema": "http://json-schema.org/schema#",
"additionalProperties": False,
"codec": "struct",
"description": "SLiM schema for mutation metadata.",
"examples": [
{
"mutation_list": [
{
"mutation_type": 1,
"nucleotide": 3,
"selection_coeff": -0.2,
"slim_time": 243,
"subpopulation": 0
}
]
}
],
"properties": {
"mutation_list": {
"items": {
"additionalProperties": False,
"properties": {
"mutation_type": {
"binaryFormat": "i",
"description": "The index of this mutation's mutationType.",
"index": 1,
"type": "integer"
},
"nucleotide": {
"binaryFormat": "b",
"description": "The nucleotide for this mutation (0=A , 1=C , 2=G, 3=T, or -1 for none)",
"index": 5,
"type": "integer"
},
"selection_coeff": {
"binaryFormat": "f",
"description": "This mutation's selection coefficient.",
"index": 2,
"type": "number"
},
"slim_time": {
"binaryFormat": "i",
"description": "The SLiM tick counter when this mutation occurred.",
"index": 4,
"type": "integer"
},
"subpopulation": {
"binaryFormat": "i",
"description": "The ID of the subpopulation this mutation occurred in.",
"index": 3,
"type": "integer"
}
},
"required": [
"mutation_type",
"selection_coeff",
"subpopulation",
"slim_time",
"nucleotide"
],
"type": "object"
},
"noLengthEncodingExhaustBuffer": True,
"type": "array"
}
},
"required": [
"mutation_list"
],
"type": "object"
},
"node" :
{
"$schema": "http://json-schema.org/schema#",
"additionalProperties": False,
"codec": "struct",
"description": "SLiM schema for node metadata.",
"examples": [
{
"genome_type": 0,
"is_null": False,
"slim_id": 123
}
],
"properties": {
"genome_type": {
"binaryFormat": "B",
"description": "The 'type' of this genome (0 for autosome, 1 for X, 2 for Y).",
"index": 2,
"type": "integer"
},
"is_null": {
"binaryFormat": "?",
"description": "Whether this node describes a 'null' (non-existant) chromosome.",
"index": 1,
"type": "boolean"
},
"slim_id": {
"binaryFormat": "q",
"description": "The 'pedigree ID' of this chromosome in SLiM.",
"index": 0,
"type": "integer"
}
},
"required": [
"slim_id",
"is_null",
"genome_type"
],
"type": [
"object",
"null"
]
},
"individual" :
{
"$schema": "http://json-schema.org/schema#",
"additionalProperties": False,
"codec": "struct",
"description": "SLiM schema for individual metadata.",
"examples": [
{
"age": -1,
"flags": 0,
"pedigree_id": 123,
"pedigree_p1": 12,
"pedigree_p2": 23,
"sex": 0,
"subpopulation": 0
}
],
"flags": {
"SLIM_INDIVIDUAL_METADATA_MIGRATED": {
"description": "Whether this individual was a migrant, either in the tick when the tree sequence "
"was written out (if the individual was alive then), or in the tick of the last time "
"they were Remembered (if not).",
"value": 1
}
},
"properties": {
"age": {
"binaryFormat": "i",
"description": "The age of this individual, either when the tree sequence was written out "
"(if the individual was alive then), or the last time they were Remembered (if not).",
"index": 4,
"type": "integer"
},
"flags": {
"binaryFormat": "I",
"description": "Other information about the individual: see 'flags'.",
"index": 7,
"type": "integer"
},
"pedigree_id": {
"binaryFormat": "q",
"description": "The 'pedigree ID' of this individual in SLiM.",
"index": 1,
"type": "integer"
},
"pedigree_p1": {
"binaryFormat": "q",
"description": "The 'pedigree ID' of this individual's first parent in SLiM.",
"index": 2,
"type": "integer"
},
"pedigree_p2": {
"binaryFormat": "q",
"description": "The 'pedigree ID' of this individual's second parent in SLiM.",
"index": 3,
"type": "integer"
},
"sex": {
"binaryFormat": "i",
"description": "The sex of the individual (0 for female, 1 for male, -1 for hermaphrodite).",
"index": 6,
"type": "integer"
},
"subpopulation": {
"binaryFormat": "i",
"description": "The ID of the subpopulation the individual was part of, either when the tree sequence "
"was written out (if the individual was alive then), or the last time they were Remembered (if not).",
"index": 5,
"type": "integer"
}
},
"required": [
"pedigree_id",
"pedigree_p1",
"pedigree_p2",
"age",
"subpopulation",
"sex",
"flags"
],
"type": "object"
},
"population":
{
"$schema": "http://json-schema.org/schema#",
"additionalProperties": True,
"codec": "json",
"description": "SLiM schema for population metadata.",
"examples": [
{
"bounds_x0": 0.0,
"bounds_x1": 100.0,
"bounds_y0": 0.0,
"bounds_y1": 100.0,
"female_cloning_fraction": 0.25,
"male_cloning_fraction": 0.0,
"migration_records": [
{
"migration_rate": 0.9,
"source_subpop": 1
},
{
"migration_rate": 0.1,
"source_subpop": 2
}
],
"selfing_fraction": 0.5,
"sex_ratio": 0.5,
"slim_id": 2,
"name": "p2"
}
],
"properties": {
"bounds_x0": {
"description": "The minimum x-coordinate in this subpopulation.",
"type": "number"
},
"bounds_x1": {
"description": "The maximum x-coordinate in this subpopulation.",
"type": "number"
},
"bounds_y0": {
"description": "The minimum y-coordinate in this subpopulation.",
"type": "number"
},
"bounds_y1": {
"description": "The maximum y-coordinate in this subpopulation.",
"type": "number"
},
"bounds_z0": {
"description": "The minimum z-coordinate in this subpopulation.",
"type": "number"
},
"bounds_z1": {
"description": "The maximum z-coordinate in this subpopulation.",
"type": "number"
},
"description": {
"description": "A description of this subpopulation.",
"type": "string"
},
"female_cloning_fraction": {
"description": "The frequency with which females in this subpopulation reproduce clonally (for WF models).",
"type": "number"
},
"male_cloning_fraction": {
"description": "The frequency with which males in this subpopulation reproduce clonally (for WF models).",
"type": "number"
},
"migration_records": {
"items": {
"properties": {
"migration_rate": {
"description": "The fraction of children in this subpopulation that are composed of 'migrants' from the source subpopulation (in WF models).",
"type": "number"
},
"source_subpop": {
"description": "The ID of the subpopulation migrants come from (in WF models).",
"type": "integer"
}
},
"required": [
"source_subpop",
"migration_rate"
],
"type": "object"
},
"type": "array"
},
"name": {
"description": "A human-readable name for this subpopulation.",
"type": "string"
},
"selfing_fraction": {
"description": "The frequency with which individuals in this subpopulation self (for WF models).",
"type": "number"
},
"sex_ratio": {
"description": "This subpopulation's sex ratio (for WF models).",
"type": "number"
},
"slim_id": {
"description": "The ID of this population in SLiM. Note that this is called a 'subpopulation' in SLiM.",
"type": "integer"
}
},
"required": [],
"type": [
"object",
"null"
]
}
}
slim_metadata_schemas = {k: tskit.MetadataSchema(_raw_slim_metadata_schemas[k]) for k in _raw_slim_metadata_schemas}
"""
A dictionary containing the metadata schemas used by SLiM for each of the tables,
and for top-level metadata.
"""
###########
# Top-level, a.k.a., tree sequence metadata
###########
def set_tree_sequence_metadata(tables,
model_type,
tick,
cycle=None,
spatial_dimensionality='',
spatial_periodicity='',
separate_sexes=False,
nucleotide_based=False,
stage='late',
name='',
description='',
file_version=None,
set_table_schemas=True):
if file_version is None:
file_version = slim_file_version
if isinstance(tables.metadata, bytes):
if len(tables.metadata) > 0:
raise ValueError("Tree sequence has top-level metadata but no schema: this is a problem "
"since pyslim is trying to add to the metadata.")
schema_dict = slim_metadata_schemas['tree_sequence'].schema
metadata_dict = {}
else:
# we need to keep other keys in the metadata (and schema) if there are any
schema_dict = tables.metadata_schema.schema
metadata_dict = tables.metadata
if cycle is None:
cycle = tick
assert(schema_dict['codec'] == 'json')
assert(schema_dict['type'] == 'object')
if "properties" not in schema_dict:
schema_dict["properties"] = {}
schema_dict['properties']['SLiM'] = slim_metadata_schemas['tree_sequence'].schema['properties']['SLiM']
tables.metadata_schema = tskit.MetadataSchema(schema_dict)
metadata_dict['SLiM'] = {
"model_type": model_type,
"tick": tick,
"cycle": cycle,
"file_version": file_version,
"spatial_dimensionality": spatial_dimensionality,
"spatial_periodicity": spatial_periodicity,
"separate_sexes": separate_sexes,
"nucleotide_based": nucleotide_based,
"stage": stage,
"name": name,
"description": description,
}
tables.metadata = metadata_dict
def set_metadata_schemas(tables):
tables.edges.metadata_schema = slim_metadata_schemas['edge']
tables.sites.metadata_schema = slim_metadata_schemas['site']
tables.mutations.metadata_schema = slim_metadata_schemas['mutation']
tables.nodes.metadata_schema = slim_metadata_schemas['node']
tables.individuals.metadata_schema = slim_metadata_schemas['individual']
tables.populations.metadata_schema = slim_metadata_schemas['population']
################################
# Previous versions of metadata schema:
def _old_metadata_schema(name, file_version):
# Returns a metadata schema *if the format has changed*,
# and None otherwise.
ms = None
if (name == "tree_sequence"
and file_version in ["0.1", "0.2", "0.3", "0.4", "0.5", "0.6", "0.7"]):
pre_0_8_tree_sequence = {
"$schema": "http://json-schema.org/schema#",
"codec": "json",
"type": "object",
"properties": {
"SLiM" : {
"description": "Top-level metadata for a SLiM tree sequence, file format version 0.7",
"type": "object",
"properties": {
"model_type" : {
"type": "string",
"enum": ["WF", "nonWF"],
"description": "The model type used for the last part of this simulation (WF or nonWF)."
},
"generation" : {
"type": "integer",
"description": "The 'SLiM generation' counter when this tree sequence was recorded."
},
"stage" : {
"type": "string",
"description": "The stage of the SLiM life cycle when this tree sequence was recorded."
},
"file_version" : {
"type": "string",
"description": "The SLiM 'file format version' of this tree sequence."
},
"spatial_dimensionality": {
"type": "string",
"enum": ["", "x", "xy", "xyz"],
"description": "The spatial dimensionality of the simulation."
},
"spatial_periodicity": {
"type": "string",
"enum": ["", "x", "y", "z", "xy", "xz", "yz", "xyz"],
"description": "The spatial periodicity of the simulation."
},
"separate_sexes": {
"type": "boolean",
"description": "Whether the simulation had separate sexes."
},
"nucleotide_based": {
"type": "boolean",
"description": "Whether the simulation was nucleotide-based."
}
},
"required": ["model_type", "generation", "file_version", "spatial_dimensionality", "spatial_periodicity", "separate_sexes", "nucleotide_based"]
}
},
"required": ["SLiM"],
"examples": [
{
"SLiM" : {
"model_type" : "WF",
"generation" : 123,
"file_version" : "0.7",
"spatial_dimensionality" : "xy",
"spatial_periodicity" : "x",
"separate_sexes" : True,
"nucleotide_based" : False
}
}
]
}
ms = pre_0_8_tree_sequence
if (name == "population"
and file_version in ["0.1", "0.2", "0.3", "0.4", "0.5", "0.6"]):
pre_0_7_population = {
"$schema": "http://json-schema.org/schema#",
"description": "SLiM schema for population metadata.",
"codec": "struct",
"type": ["object", "null"],
"properties": {
"slim_id": {
"type": "integer",
"description": "The ID of this population in SLiM. Note that this is called a 'subpopulation' in SLiM.",
"binaryFormat": "i",
"index": 1},
"selfing_fraction": {
"type": "number",
"description": "The frequency with which individuals in this subpopulation self (for WF models).",
"binaryFormat": "d",
"index": 2},
"female_cloning_fraction": {
"type": "number",
"description": "The frequency with which females in this subpopulation reproduce clonally (for WF models).",
"binaryFormat": "d",
"index": 3},
"male_cloning_fraction": {
"type": "number",
"description": "The frequency with which males in this subpopulation reproduce clonally (for WF models).",
"binaryFormat": "d",
"index": 4},
"sex_ratio": {
"type": "number",
"description": "This subpopulation's sex ratio (for WF models).",
"binaryFormat": "d",
"index": 5},
"bounds_x0": {
"type": "number",
"description": "The minimum x-coordinate in this subpopulation.",
"binaryFormat": "d",
"index": 6},
"bounds_x1": {
"type": "number",
"description": "The maximum x-coordinate in this subpopulation.",
"binaryFormat": "d",
"index": 7},
"bounds_y0": {
"type": "number",
"description": "The minimum y-coordinate in this subpopulation.",
"binaryFormat": "d",
"index": 8},
"bounds_y1": {
"type": "number",
"description": "The maximum y-coordinate in this subpopulation.",
"binaryFormat": "d",
"index": 9},
"bounds_z0": {
"type": "number",
"description": "The minimum z-coordinate in this subpopulation.",
"binaryFormat": "d",
"index": 10},
"bounds_z1": {
"type": "number",
"description": "The maximum z-coordinate in this subpopulation.",
"binaryFormat": "d",
"index": 11},
"migration_records": {
"type": "array",
"index": 13,
"arrayLengthFormat": "I",
"items": {
"type": "object",
"properties": {
"source_subpop": {
"type": "integer",
"description": "The ID of the subpopulation migrants come from (in WF models).",
"binaryFormat": "i",
"index": 1},
"migration_rate": {
"type": "number",
"description": "The fraction of children in this subpopulation that are composed of 'migrants' from the source subpopulation (in WF models).",
"binaryFormat": "d",
"index": 2}
},
"required": ["source_subpop", "migration_rate"],
"additionalProperties": False
}
}
}
}
ms = pre_0_7_population
if (name == "individual"
and file_version in ["0.1", "0.2", "0.3", "0.4", "0.5", "0.6"]):
pre_0_7_individual = {
"$schema": "http://json-schema.org/schema#",
"description": "SLiM schema for individual metadata.",
"codec": "struct",
"type": "object",
"properties": {
"pedigree_id": {
"type": "integer",
"description": "The 'pedigree ID' of this individual in SLiM.",
"binaryFormat": "q",
"index": 1
},
"age": {
"type": "integer",
"description": "The age of this individual, either when the tree sequence was written out (if the individual was alive then), or the last time they were Remembered (if not).",
"binaryFormat": "i",
"index": 2
},
"subpopulation": {
"type": "integer",
"description": "The ID of the subpopulation the individual was part of, either when the tree sequence was written out (if the individual was alive then), or the last time they were Remembered (if not).",
"binaryFormat": "i",
"index": 3
},
"sex": {
"type": "integer",
"description": "The sex of the individual (0 for female, 1 for male, -1 for hermaphrodite).",
"binaryFormat": "i",
"index": 4
},
"flags": {
"type": "integer",
"description": "Other information about the individual: see 'flags'.",
"binaryFormat": "I",
"index": 5
}
},
"required": ["pedigree_id", "age", "subpopulation", "sex", "flags"],
"additionalProperties": False,
"flags": {
"SLIM_INDIVIDUAL_METADATA_MIGRATED": {
"value": 1,
"description": "Whether this individual was a migrant, either in the generation when the tree sequence was written out (if the individual was alive then), or in the generation of the last time they were Remembered (if not)."
}
},
}
ms = pre_0_7_individual
if name == "mutation" and file_version in ["0.1", "0.2"]:
mutation_pre_0_3 = {
"$schema": "http://json-schema.org/schema#",
"description": "SLiM schema for mutation metadata.",
"codec": "struct",
"type": "object",
"properties": {
"mutation_list": {
"type": "array",
"noLengthEncodingExhaustBuffer": True,
"items": {
"type": "object",
"properties": {
"mutation_type": {
"type": "integer",
"description": "The index of this mutation's mutationType.",
"binaryFormat": "i",
"index": 1
},
"selection_coeff": {
"type": "number",
"description": "This mutation's selection coefficient.",
"binaryFormat": "f",
"index": 2
},
"subpopulation": {
"type": "integer",
"description": "The ID of the subpopulation this mutation occurred in.",
"binaryFormat": "i",
"index": 3
},
"slim_time": {
"type": "integer",
"description": "The SLiM generation counter when this mutation occurred.",
"binaryFormat": "i",
"index": 4
},
},
"required": ["mutation_type", "selection_coeff", "subpopulation",
"slim_time"],
"additionalProperties": False
}
}
},
"required": ["mutation_list"],
"additionalProperties": False,
}
ms = mutation_pre_0_3
# everything else's format has remained unchanged
if ms is not None:
ms = tskit.MetadataSchema(ms)
return ms
def is_current_version(ts, _warn=False):
"""
Tests whether the tree sequence or table collection provided is the current
SLiM file format or not. If not, use `pyslim.update( )` to bring it up to
date.
:param TreeSequence ts: The tree sequence or table collection.
:return bool: Whether the tree sequence is the current version.
"""
out = (
isinstance(ts.metadata, dict)
and
('SLiM' in ts.metadata)
and
(ts.metadata['SLiM']['file_version'] == slim_file_version)
)
if _warn and not out:
warnings.warn(
"This tree sequence is not the current SLiM format, "
"so some operations may not work. "
"Use `pyslim.update( )` to update the tree sequence."
)
return out
[docs]def update(ts):
"""
Update a tree sequence produced by a previous verion of SLiM
to the current file version.
:return TreeSequence: The updated tree sequence.
"""
tables = ts.dump_tables()
update_tables(tables)
return tables.tree_sequence()
def update_tables(tables):
"""
Update tables produced by a previous verion of SLiM to the current file version.
Modifies the tables in place.
"""
# First we ensure we can find the file format version number
# in top-level metadata. Then we proceed to fix up the tables as necessary.
if not (isinstance(tables.metadata, dict) and 'SLiM' in tables.metadata):
# Old versions kept information in provenance, not top-level metadata.
# Note this uses defaults on keys not present in provenance,
# which prior to 0.5 was everything but generation and model_type.
values = default_slim_metadata('tree_sequence')['SLiM']
prov = None
file_version = 'unknown'
# use only the last SLiM provenance
for p in tables.provenances:
is_slim, this_file_version = slim_provenance_version(p)
if is_slim:
prov = p
file_version = this_file_version
values['file_version'] = file_version
try:
record = json.loads(prov.record)
if file_version == "0.1":
values['model_type'] = record['model_type']
values['tick'] = record['generation']
values['cycle'] = record['generation']
else:
if 'generation' in record['slim']:
values['tick'] = record['slim']['generation']
values['cycle'] = record['slim']['generation']
for k in values:
if k in record['parameters']:
values[k] = record['parameters'][k]
if k in record['slim']:
values[k] = record['slim'][k]
except:
raise ValueError("Failed to obtain metadata from provenance.")
set_tree_sequence_metadata(tables, **values)
file_version = tables.metadata['SLiM']['file_version']
if file_version != slim_file_version:
warnings.warn("This is a version {} SLiM tree sequence.".format(file_version) +
" When you write this out, " +
"it will be converted to version {}.".format(slim_file_version))
# the only tables to have metadata schema changed thus far
# are populations, individuals, mutations, and top-level:
old_schema = _old_metadata_schema("tree_sequence", file_version)
if old_schema is not None:
md = tables.metadata
new_schema = slim_metadata_schemas["tree_sequence"]
new_properties = new_schema.asdict()['properties']['SLiM']['required']
tables.metadata_schema = new_schema
defaults = default_slim_metadata("tree_sequence")
for k in new_properties:
if k not in md['SLiM']:
if k == "tick":
md['SLiM']['tick'] = md['SLiM']['generation']
md['SLiM']['cycle'] = md['SLiM']['generation']
else:
md['SLiM'][k] = defaults['SLiM'][k]
tables.metadata = md
old_schema = _old_metadata_schema("population", file_version)
if old_schema is not None:
pops = tables.populations.copy()
tables.populations.clear()
if pops.metadata_schema == tskit.MetadataSchema(None):
pops.metadata_schema = old_schema
new_schema = slim_metadata_schemas["population"]
tables.populations.metadata_schema = new_schema
defaults = default_slim_metadata("population")
# just needs recoding
for pop in pops:
tables.populations.append(pop)
old_schema = _old_metadata_schema("individual", file_version)
if old_schema is not None:
inds = tables.individuals.copy()
tables.individuals.clear()
if inds.metadata_schema == tskit.MetadataSchema(None):
inds.metadata_schema = old_schema
new_schema = slim_metadata_schemas["individual"]
tables.individuals.metadata_schema = new_schema
defaults = default_slim_metadata("individual")
d = {}
for k in ["pedigree_p1", "pedigree_p2"]:
d[k] = defaults[k]
for ind in inds:
md = ind.metadata
md.update(d)
tables.individuals.append(ind.replace(metadata=md))
old_schema = _old_metadata_schema("mutation", file_version)
if old_schema is not None:
muts = tables.mutations.copy()
tables.mutations.clear()
if muts.metadata_schema == tskit.MetadataSchema(None):
muts.metadata_schema = old_schema
tables.mutations.metadata_schema = slim_metadata_schemas["mutation"]
for mut in muts:
md = mut.metadata
for ml in md['mutation_list']:
ml['nucleotide'] = -1
tables.mutations.append(mut.replace(metadata=md))
if file_version == "0.1":
# shift times
slim_generation = tables.metadata['SLiM']['tick']
node_times = tables.nodes.time + slim_generation
tables.nodes.set_columns(
flags=tables.nodes.flags,
time=node_times,
population=tables.nodes.population,
individual=tables.nodes.individual,
metadata=tables.nodes.metadata,
metadata_offset=tables.nodes.metadata_offset)
migration_times = tables.migrations.time + slim_generation
tables.migrations.set_columns(
left=tables.migrations.left,
right=tables.migrations.right,
node=tables.migrations.node,
source=tables.migrations.source,
dest=tables.migrations.dest,
time=migration_times)
new_record = {
"schema_version": "1.0.0",
"software": {
"name": "pyslim",
"version": pyslim_version,
},
"parameters": {
"command": ["updrade_tables"],
"old_file_version": file_version,
"new_file_version": slim_file_version,
},
"environment": get_environment(),
}
tskit.validate_provenance(new_record)
tables.provenances.add_row(json.dumps(new_record))
set_metadata_schemas(tables)
md = tables.metadata
md['SLiM']['file_version'] = slim_file_version
tables.metadata = md