tskit 1.0.0b1__cp313-cp313-win_amd64.whl → 1.0.0b2__cp313-cp313-win_amd64.whl

tskit/_version.py

@@ -1,4 +1,4 @@
 # Definitive location for the version number.
 # During development, should be x.y.z.devN
 # For beta should be x.y.zbN
-tskit_version = "1.0.0b1"
+tskit_version = "1.0.0b2"

tskit/jit/numba.py

@@ -0,0 +1,674 @@
+import functools
+import os
+
+import numpy as np
+
+import tskit
+
+try:
+    import numba
+
+except ImportError:
+    raise ImportError(
+        "Numba is not installed. Please install it with `pip install numba` "
+        "or `conda install numba` to use the tskit.jit.numba module."
+    )
+
+
+FORWARD = 1  #: Direction constant for forward tree traversal
+REVERSE = -1  #: Direction constant for reverse tree traversal
+
+# Retrieve these here to avoid lookups in tight loops
+NODE_IS_SAMPLE = tskit.NODE_IS_SAMPLE
+NULL = tskit.NULL
+
+edge_range_spec = [
+    ("start", numba.int32),
+    ("stop", numba.int32),
+    ("order", numba.int32[:]),
+]
+
+parent_index_spec = [
+    ("edge_index", numba.int32[:]),
+    ("index_range", numba.int32[:, :]),
+]
+
+
+@numba.experimental.jitclass(edge_range_spec)
+class EdgeRange:
+    """
+    Represents a range of edges during tree traversal.
+
+    This class encapsulates information about a contiguous range of edges
+    that are either being removed or added to step from one tree to another.
+    The ``start`` and ``stop`` indices, when applied to the order array,
+    define the ids of edges to process.
+
+    Attributes
+    ----------
+    start : int
+        Starting index of the edge range (inclusive).
+    stop : int
+        Stopping index of the edge range (exclusive).
+    order : numpy.ndarray
+        Array (dtype=np.int32) containing edge IDs in the order they should be processed.
+        The edge ids in this range are order[start:stop].
+    """
+
+    def __init__(self, start, stop, order):
+        self.start = start
+        self.stop = stop
+        self.order = order
+
+
+@numba.experimental.jitclass(parent_index_spec)
+class ParentIndex:
+    """
+    Simple data container for parent index information.
+
+    This class provides access to all edges where a given node is the child.
+    Since edges are not sorted by child in the tskit edge table, a custom index
+    (edge_index) is built that sorts edge IDs by child node. `index_range`
+    then contains the [start, stop) range of edges for each child node in `edge_index`.
+
+    Attributes
+    ----------
+    edge_index : numpy.ndarray
+        Array (dtype=np.int32) of edge IDs sorted by child node and left coordinate.
+    index_range : numpy.ndarray
+        Array (dtype=np.int32, shape=(num_nodes, 2)) where each row contains the
+        [start, stop) range in edge_index where this node is the child.
+    """
+
+    def __init__(self, edge_index, index_range):
+        self.edge_index = edge_index
+        self.index_range = index_range
+
+
+class TreeIndex:
+    """
+    Traverse trees in a numba compatible tree sequence.
+
+    This class provides efficient forward and backward iteration through
+    the trees in a tree sequence. It provides the tree interval,
+    edge changes to create the current tree, along with its sites and mutations.
+    A full pass over the trees using repeated `next` or `prev` requires O(E + M + S) time
+    complexity.
+
+    It should not be instantiated directly, but is returned by the `tree_index` method
+    of `NumbaTreeSequence`.
+
+
+    Attributes
+    ----------
+    ts : NumbaTreeSequence
+        Reference to the tree sequence being traversed.
+    index : int
+        Current tree index. -1 indicates no current tree (null state).
+    direction : int
+        Traversal direction: tskit.FORWARD or tskit.REVERSE. tskit.NULL
+        if uninitialised.
+    interval : tuple
+        Genomic interval (left, right) covered by the current tree.
+    in_range : EdgeRange
+        Edges being added to form this current tree, relative to the last state
+    out_range : EdgeRange
+        Edges being removed to form this current tree, relative to the last state
+    site_range : tuple
+        Range of sites in the current tree (start, stop).
+    mutation_range : tuple
+        Range of mutations in the current tree (start, stop).
+
+    Example
+    --------
+    >>> tree_index = numba_ts.tree_index()
+    >>> num_edges = 0
+    >>> while tree_index.next():
+            num_edges += (tree_index.in_range.stop - tree_index.in_range.start)
+            num_edges -= (tree_index.out_range.stop - tree_index.out_range.start)
+            print(f"Tree {tree_index.index}: {num_edges} edges")
+    """
+
+    def __init__(self, ts):
+        self.ts = ts
+        self.index = -1
+        self.direction = NULL
+        self.interval = (0, 0)
+        self.in_range = EdgeRange(0, 0, np.zeros(0, dtype=np.int32))
+        self.out_range = EdgeRange(0, 0, np.zeros(0, dtype=np.int32))
+        self.site_range = (0, 0)
+        self.mutation_range = (0, 0)
+
+    def set_null(self):
+        """
+        Reset the tree index to null state.
+        """
+        self.index = -1
+        self.interval = (0, 0)
+        self.site_range = (0, 0)
+        self.mutation_range = (0, 0)
+
+    def next(self):  # noqa: A003
+        """
+        Move to the next tree in forward direction.
+
+        Updates the tree index to the next tree in the sequence,
+        computing the edges that need to be added and removed to
+        transform from the previous tree to the current tree.
+        On the first call, this initializes the iterator and moves to tree 0.
+
+        :return: True if successfully moved to next tree, False if the end
+            of the tree sequence is reached. When False is returned, the iterator
+            is in null state (index=-1).
+        :rtype: bool
+        """
+        M = self.ts.num_edges
+        NS = self.ts.num_sites
+        NM = self.ts.num_mutations
+        breakpoints = self.ts.breakpoints
+        left_coords = self.ts.edges_left
+        left_order = self.ts.indexes_edge_insertion_order
+        right_coords = self.ts.edges_right
+        right_order = self.ts.indexes_edge_removal_order
+        sites_position = self.ts.sites_position
+        mutations_site = self.ts.mutations_site
+
+        if self.index == -1:
+            self.interval = (self.interval[0], 0)
+            self.out_range.stop = 0
+            self.in_range.stop = 0
+            self.direction = FORWARD
+            self.site_range = (0, 0)
+            self.mutation_range = (0, 0)
+
+        if self.direction == FORWARD:
+            left_current_index = self.in_range.stop
+            right_current_index = self.out_range.stop
+        else:
+            left_current_index = self.out_range.stop + 1
+            right_current_index = self.in_range.stop + 1
+
+        left = self.interval[1]
+
+        j = right_current_index
+        self.out_range.start = j
+        while j < M and right_coords[right_order[j]] == left:
+            j += 1
+        self.out_range.stop = j
+        self.out_range.order = right_order
+
+        j = left_current_index
+        self.in_range.start = j
+        while j < M and left_coords[left_order[j]] == left:
+            j += 1
+        self.in_range.stop = j
+        self.in_range.order = left_order
+
+        self.direction = FORWARD
+        self.index += 1
+        if self.index == self.ts.num_trees:
+            self.set_null()
+        else:
+            right = breakpoints[self.index + 1]
+            self.interval = (left, right)
+
+            # Find sites in current tree interval [left, right)
+            old_site_left, old_site_right = self.site_range
+            j = old_site_right
+            while j < NS and sites_position[j] < right:
+                j += 1
+            self.site_range = (old_site_right, j)
+
+            # Find mutations for sites in this interval
+            old_mutation_left, old_mutation_right = self.mutation_range
+            k = old_mutation_right
+            while k < NM and mutations_site[k] < j:
+                k += 1
+            self.mutation_range = (old_mutation_right, k)
+
+        return self.index != -1
+
+    def prev(self):
+        """
+        Move to the previous tree in reverse direction.
+
+        Updates the tree index to the previous tree in the sequence,
+        computing the edges that need to be added and removed to
+        transform from the next tree to the current tree.
+        On the first call, this initializes the iterator and moves to the most
+        rightward tree.
+
+        :return: True if successfully moved to previous tree, False if the beginning
+            of the tree sequence is reached. When False is returned, the iterator
+            is in null state (index=-1).
+        :rtype: bool
+        """
+        M = self.ts.num_edges
+        NS = self.ts.num_sites
+        NM = self.ts.num_mutations
+        breakpoints = self.ts.breakpoints
+        right_coords = self.ts.edges_right
+        right_order = self.ts.indexes_edge_removal_order
+        left_coords = self.ts.edges_left
+        left_order = self.ts.indexes_edge_insertion_order
+        sites_position = self.ts.sites_position
+        mutations_site = self.ts.mutations_site
+
+        if self.index == -1:
+            self.index = self.ts.num_trees
+            self.interval = (self.ts.sequence_length, self.interval[1])
+            self.in_range.stop = M - 1
+            self.out_range.stop = M - 1
+            self.direction = REVERSE
+            self.site_range = (NS, NS)
+            self.mutation_range = (NM, NM)
+
+        if self.direction == REVERSE:
+            left_current_index = self.out_range.stop
+            right_current_index = self.in_range.stop
+        else:
+            left_current_index = self.in_range.stop - 1
+            right_current_index = self.out_range.stop - 1
+
+        right = self.interval[0]
+
+        j = left_current_index
+        self.out_range.start = j
+        while j >= 0 and left_coords[left_order[j]] == right:
+            j -= 1
+        self.out_range.stop = j
+        self.out_range.order = left_order
+
+        j = right_current_index
+        self.in_range.start = j
+        while j >= 0 and right_coords[right_order[j]] == right:
+            j -= 1
+        self.in_range.stop = j
+        self.in_range.order = right_order
+
+        self.direction = REVERSE
+        self.index -= 1
+        if self.index == -1:
+            self.set_null()
+        else:
+            left = breakpoints[self.index]
+            self.interval = (left, right)
+
+            # Find sites in current tree interval [left, right) going backward
+            old_site_left, old_site_right = self.site_range
+            j = old_site_left - 1
+            while j >= 0 and sites_position[j] >= left:
+                j -= 1
+            self.site_range = (j + 1, old_site_left)
+
+            # Find mutations for sites in this interval going backward
+            old_mutation_left, old_mutation_right = self.mutation_range
+            k = old_mutation_left - 1
+            while k >= 0 and mutations_site[k] >= self.site_range[0]:
+                k -= 1
+            self.mutation_range = (k + 1, old_mutation_left)
+
+        return self.index != -1
+
+
+class NumbaTreeSequence:
+    """
+    A Numba-compatible representation of a tree sequence.
+
+    This class provides access a tree sequence class that can be used
+    from within Numba "njit" compiled functions. :meth:`jitwrap` should
+    be used to JIT compile this class from a :class:`tskit.TreeSequence` object,
+    before it is passed to a Numba function.
+
+    Attributes
+    ----------
+    num_trees : int
+        Number of trees in the tree sequence.
+    num_nodes : int
+        Number of nodes in the tree sequence.
+    num_samples : int
+        Number of samples in the tree sequence.
+    num_edges : int
+        Number of edges in the tree sequence.
+    num_sites : int
+        Number of sites in the tree sequence.
+    num_mutations : int
+        Number of mutations in the tree sequence.
+    sequence_length : float
+        Total sequence length of the tree sequence.
+    edges_left : numpy.ndarray
+        Array (dtype=np.float64) of left coordinates of edges.
+    edges_right : numpy.ndarray
+        Array (dtype=np.float64) of right coordinates of edges.
+    edges_parent : numpy.ndarray
+        Array (dtype=np.int32) of parent node IDs for each edge.
+    edges_child : numpy.ndarray
+        Array (dtype=np.int32) of child node IDs for each edge.
+    nodes_time : numpy.ndarray
+        Array (dtype=np.float64) of time values for each node.
+    nodes_flags : numpy.ndarray
+        Array (dtype=np.uint32) of flag values for each node.
+    nodes_population : numpy.ndarray
+        Array (dtype=np.int32) of population IDs for each node.
+    nodes_individual : numpy.ndarray
+        Array (dtype=np.int32) of individual IDs for each node.
+    individuals_flags : numpy.ndarray
+        Array (dtype=np.uint32) of flag values for each individual.
+    sites_position : numpy.ndarray
+        Array (dtype=np.float64) of positions of sites along the sequence.
+    mutations_site : numpy.ndarray
+        Array (dtype=np.int32) of site IDs for each mutation.
+    mutations_node : numpy.ndarray
+        Array (dtype=np.int32) of node IDs for each mutation.
+    mutations_parent : numpy.ndarray
+        Array (dtype=np.int32) of parent mutation IDs.
+    mutations_time : numpy.ndarray
+        Array (dtype=np.float64) of time values for each mutation.
+    breakpoints : numpy.ndarray
+        Array (dtype=np.float64) of genomic positions where trees change.
+    indexes_edge_insertion_order : numpy.ndarray
+        Array (dtype=np.int32) specifying the order in which edges are inserted
+        during tree building.
+    indexes_edge_removal_order : numpy.ndarray
+        Array (dtype=np.int32) specifying the order in which edges are removed
+        during tree building.
+
+    """
+
+    def __init__(
+        self,
+        num_trees,
+        num_nodes,
+        num_samples,
+        num_edges,
+        num_sites,
+        num_mutations,
+        sequence_length,
+        edges_left,
+        edges_right,
+        indexes_edge_insertion_order,
+        indexes_edge_removal_order,
+        individuals_flags,
+        nodes_time,
+        nodes_flags,
+        nodes_population,
+        nodes_individual,
+        edges_parent,
+        edges_child,
+        sites_position,
+        sites_ancestral_state,
+        mutations_site,
+        mutations_node,
+        mutations_parent,
+        mutations_time,
+        mutations_derived_state,
+        mutations_inherited_state,
+        breakpoints,
+        max_ancestral_length,
+        max_derived_length,
+        max_inherited_length,
+    ):
+        self.num_trees = num_trees
+        self.num_nodes = num_nodes
+        self.num_samples = num_samples
+        self.num_edges = num_edges
+        self.num_sites = num_sites
+        self.num_mutations = num_mutations
+        self.sequence_length = sequence_length
+        self.edges_left = edges_left
+        self.edges_right = edges_right
+        self.indexes_edge_insertion_order = indexes_edge_insertion_order
+        self.indexes_edge_removal_order = indexes_edge_removal_order
+        self.individuals_flags = individuals_flags
+        self.nodes_time = nodes_time
+        self.nodes_flags = nodes_flags
+        self.nodes_population = nodes_population
+        self.nodes_individual = nodes_individual
+        self.edges_parent = edges_parent
+        self.edges_child = edges_child
+        self.sites_position = sites_position
+        self.sites_ancestral_state = sites_ancestral_state
+        self.mutations_site = mutations_site
+        self.mutations_node = mutations_node
+        self.mutations_parent = mutations_parent
+        self.mutations_time = mutations_time
+        self.mutations_derived_state = mutations_derived_state
+        self.mutations_inherited_state = mutations_inherited_state
+        self.breakpoints = breakpoints
+        self.max_ancestral_length = max_ancestral_length
+        self.max_derived_length = max_derived_length
+        self.max_inherited_length = max_inherited_length
+
+    def tree_index(self):
+        """
+        Create a :class:`TreeIndex` for traversing this tree sequence.
+
+        :return: A new tree index initialized to the null tree.
+            Use next() or prev() to move to an actual tree.
+        :rtype: TreeIndex
+        """
+        # This method will be overriden when the concrete JIT class TreeIndex
+        # is defined in `jitwrap`.
+        return TreeIndex(self)  # pragma: no cover
+
+    def child_index(self):
+        """
+        Create child index array for finding child edges of nodes. This operation
+        requires a linear pass over the edge table and therefore has a time
+        complexity of O(E).
+
+        :return: A numpy array (dtype=np.int32, shape=(num_nodes, 2)) where each row
+            contains the [start, stop) range of edges where this node is the parent.
+        :rtype: numpy.ndarray
+        """
+        child_range = np.full((self.num_nodes, 2), -1, dtype=np.int32)
+        edges_parent = self.edges_parent
+        if self.num_edges == 0:
+            return child_range
+
+        # Find ranges in tskit edge ordering
+        last_parent = -1
+        for edge_id in range(self.num_edges):
+            parent = edges_parent[edge_id]
+            if parent != last_parent:
+                child_range[parent, 0] = edge_id
+            if last_parent != -1:
+                child_range[last_parent, 1] = edge_id
+            last_parent = parent
+
+        if last_parent != -1:
+            child_range[last_parent, 1] = self.num_edges
+
+        return child_range
+
+    def parent_index(self):
+        """
+        Create a :class:`ParentIndex` for finding parent edges of nodes.
+
+        Edges within each child's group are not guaranteed to be in any
+        specific order. This operation uses a two-pass algorithm with
+        O(N + E) time complexity and O(N) auxiliary space.
+
+        :return: A new parent index container that can be used to
+            efficiently find all edges where a given node is the child.
+        :rtype: ParentIndex
+        """
+        num_nodes = self.num_nodes
+        num_edges = self.num_edges
+        edges_child = self.edges_child
+
+        child_counts = np.zeros(num_nodes, dtype=np.int32)
+        edge_index = np.zeros(num_edges, dtype=np.int32)
+        index_range = np.zeros((num_nodes, 2), dtype=np.int32)
+
+        if num_edges == 0:
+            return ParentIndex(edge_index, index_range)
+
+        # Count how many children each node has
+        for child_node in edges_child:
+            child_counts[child_node] += 1
+
+        # From the counts build the index ranges, we set both the start and the
+        # end index to the start - this lets us use the end index as a tracker
+        # for where we should insert the next edge for that node - when all
+        # edges are done these values will be the correct end values!
+        current_start = 0
+        for i in range(num_nodes):
+            index_range[i, :] = current_start
+            current_start += child_counts[i]
+
+        # Now go over the edges, inserting them at the index pointed to
+        # by the node's current end value, then increment.
+        for edge_id in range(num_edges):
+            child = edges_child[edge_id]
+            pos = index_range[child, 1]
+            edge_index[pos] = edge_id
+            index_range[child, 1] += 1
+
+        return ParentIndex(edge_index, index_range)
+
+
+# We cache these classes to avoid repeated JIT compilation
+@functools.lru_cache(None)
+def _jitwrap(max_ancestral_length, max_derived_length, max_inherited_length):
+    # We have a circular dependency in JIT compilation between NumbaTreeSequence
+    # and NumbaTreeIndex so we used a deferred type to break it
+    tree_sequence_type = numba.deferred_type()
+
+    # We run this code on CI with this env var set so we can get coverage
+    # of the jitted functions. EdgeRange doesn't have a class_type
+    # in this case, so we skip the spec entirely.
+    if os.environ.get("NUMBA_DISABLE_JIT") == "1":
+        tree_index_spec = []
+    else:
+        tree_index_spec = [
+            ("ts", tree_sequence_type),
+            ("index", numba.int32),
+            ("direction", numba.int32),
+            ("interval", numba.types.UniTuple(numba.float64, 2)),
+            ("in_range", EdgeRange.class_type.instance_type),
+            ("out_range", EdgeRange.class_type.instance_type),
+            ("site_range", numba.types.UniTuple(numba.int32, 2)),
+            ("mutation_range", numba.types.UniTuple(numba.int32, 2)),
+        ]
+
+    JittedTreeIndex = numba.experimental.jitclass(tree_index_spec)(TreeIndex)
+
+    tree_sequence_spec = [
+        ("num_trees", numba.int32),
+        ("num_nodes", numba.int32),
+        ("num_samples", numba.int32),
+        ("num_edges", numba.int32),
+        ("num_sites", numba.int32),
+        ("num_mutations", numba.int32),
+        ("sequence_length", numba.float64),
+        ("edges_left", numba.float64[:]),
+        ("edges_right", numba.float64[:]),
+        ("indexes_edge_insertion_order", numba.int32[:]),
+        ("indexes_edge_removal_order", numba.int32[:]),
+        ("individuals_flags", numba.uint32[:]),
+        ("nodes_time", numba.float64[:]),
+        ("nodes_flags", numba.uint32[:]),
+        ("nodes_population", numba.int32[:]),
+        ("nodes_individual", numba.int32[:]),
+        ("edges_parent", numba.int32[:]),
+        ("edges_child", numba.int32[:]),
+        ("sites_position", numba.float64[:]),
+        ("sites_ancestral_state", numba.types.UnicodeCharSeq(max_ancestral_length)[:]),
+        ("mutations_site", numba.int32[:]),
+        ("mutations_node", numba.int32[:]),
+        ("mutations_parent", numba.int32[:]),
+        ("mutations_time", numba.float64[:]),
+        ("mutations_derived_state", numba.types.UnicodeCharSeq(max_derived_length)[:]),
+        (
+            "mutations_inherited_state",
+            numba.types.UnicodeCharSeq(max_inherited_length)[:],
+        ),
+        ("breakpoints", numba.float64[:]),
+        ("max_ancestral_length", numba.int32),
+        ("max_derived_length", numba.int32),
+        ("max_inherited_length", numba.int32),
+    ]
+
+    # The `tree_index` method on NumbaTreeSequence uses NumbaTreeIndex
+    # which is the uncompiled version of the class. The compiled version isn't
+    # known till now, so replace the method with this definition.
+
+    class _NumbaTreeSequence(NumbaTreeSequence):
+        def tree_index(self):
+            return JittedTreeIndex(self)
+
+    JittedTreeSequence = numba.experimental.jitclass(tree_sequence_spec)(
+        _NumbaTreeSequence
+    )
+
+    # Now both classes are setup we can resolve the deferred type
+    if os.environ.get("NUMBA_DISABLE_JIT") != "1":
+        tree_sequence_type.define(JittedTreeSequence.class_type.instance_type)
+
+    return JittedTreeSequence
+
+
+def jitwrap(ts):
+    """
+    Convert a TreeSequence to a Numba-compatible format.
+
+    Creates a NumbaTreeSequence object that can be used within
+    Numba-compiled functions.
+
+    :param tskit.TreeSequence ts: The tree sequence to convert.
+    :return: A Numba-compatible representation of the input tree sequence.
+        Contains all necessary data arrays and metadata for tree traversal.
+    :rtype: NumbaTreeSequence
+    """
+    max_ancestral_length = max(1, max(map(len, ts.sites_ancestral_state), default=1))
+    max_derived_length = max(1, max(map(len, ts.mutations_derived_state), default=1))
+    max_inherited_length = max(
+        1, max(map(len, ts.mutations_inherited_state), default=1)
+    )
+
+    JittedTreeSequence = _jitwrap(
+        max_ancestral_length, max_derived_length, max_inherited_length
+    )
+
+    # Create the tree sequence instance
+    numba_ts = JittedTreeSequence(
+        num_trees=ts.num_trees,
+        num_nodes=ts.num_nodes,
+        num_samples=ts.num_samples,
+        num_edges=ts.num_edges,
+        num_sites=ts.num_sites,
+        num_mutations=ts.num_mutations,
+        sequence_length=ts.sequence_length,
+        edges_left=ts.edges_left,
+        edges_right=ts.edges_right,
+        indexes_edge_insertion_order=ts.indexes_edge_insertion_order,
+        indexes_edge_removal_order=ts.indexes_edge_removal_order,
+        individuals_flags=ts.individuals_flags,
+        nodes_time=ts.nodes_time,
+        nodes_flags=ts.nodes_flags,
+        nodes_population=ts.nodes_population,
+        nodes_individual=ts.nodes_individual,
+        edges_parent=ts.edges_parent,
+        edges_child=ts.edges_child,
+        sites_position=ts.sites_position,
+        sites_ancestral_state=ts.sites_ancestral_state.astype(
+            f"U{max_ancestral_length}"
+        ),
+        mutations_site=ts.mutations_site,
+        mutations_node=ts.mutations_node,
+        mutations_parent=ts.mutations_parent,
+        mutations_time=ts.mutations_time,
+        mutations_derived_state=ts.mutations_derived_state.astype(
+            f"U{max_derived_length}"
+        ),
+        mutations_inherited_state=ts.mutations_inherited_state.astype(
+            f"U{max_inherited_length}"
+        ),
+        breakpoints=ts.breakpoints(as_array=True),
+        max_ancestral_length=max_ancestral_length,
+        max_derived_length=max_derived_length,
+        max_inherited_length=max_inherited_length,
+    )
+
+    return numba_ts

{tskit-1.0.0b1.dist-info → tskit-1.0.0b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tskit
-Version: 1.0.0b1
+Version: 1.0.0b2
 Summary: The tree sequence toolkit.
 Author-email: Tskit Developers <admin@tskit.dev>
 License: MIT

{tskit-1.0.0b1.dist-info → tskit-1.0.0b2.dist-info}/RECORD

@@ -1,7 +1,7 @@
-_tskit.cp313-win_amd64.pyd,sha256=wLrIgLHXs9j4e5j7O3ulrQq-ieqUeq5qHITa46x6d5c,570368
+_tskit.cp313-win_amd64.pyd,sha256=iFUQmw0SHS9ZSf48xJzIb65Uc04NpRw42hdZ7jkjsig,570368
 tskit/__init__.py,sha256=iw2dYlGVXcJUCDUpIuzj-x6h9SvF-j2wvbWkx5LUsSI,3312
 tskit/__main__.py,sha256=Dnv25YfzrMDwYSW3pHqOdoa7EZI3oUEw81vU6x3qY_c,71
-tskit/_version.py,sha256=uhZFyLeOUoG8Pt-iWUoxiDdmzQWOiFgkUjSCJhSWF38,148
+tskit/_version.py,sha256=TAaXO78UDuZn2Q6kyb5R2HZANmJaZnESfTFS6_Psu70,148
 tskit/cli.py,sha256=kcWbw-lujEAYT5GQXU2gzcZOW3RHhcegH1D7S1-RNFE,9029
 tskit/combinatorics.py,sha256=q0Wf95djp5dYv5NqMzx6hAiKfmNtauiFFAqFim5v9LQ,57227
 tskit/drawing.py,sha256=SVG2r0IOne57oEKwLb7rPOhoXpz8v9r6lJmKj7rfeXs,114112
@@ -17,9 +17,11 @@ tskit/text_formats.py,sha256=ZDGEhAhar9Z8Zjjg3SZwm5-AQxHVSTjZy4kifZqTNtQ,15262
 tskit/trees.py,sha256=VNYpyGQk3ahF2950x6eDmBN35utM_SQUbdH2EZZ3SWY,502418
 tskit/util.py,sha256=OYlDi5phgNiirgiG62_MMzyiMC1CSKI4IGrY4gbj4i4,36448
 tskit/vcf.py,sha256=U6IqXuw8mWO7K5DgjmKH9s7GjSJHrnCDK53sMoq9UNQ,8814
-tskit-1.0.0b1.dist-info/licenses/LICENSE,sha256=h92w-U3mbrRNLntc2_9qHbCB2MmJsvDSBia6BTUCwLE,1099
-tskit-1.0.0b1.dist-info/METADATA,sha256=y9r31ja-D18FCOwrxKrJCXOJs6VcXVNwslX1ZU9wCIY,4645
-tskit-1.0.0b1.dist-info/WHEEL,sha256=qV0EIPljj1XC_vuSatRWjn02nZIz3N1t8jsZz7HBr2U,101
-tskit-1.0.0b1.dist-info/entry_points.txt,sha256=3Zik1X8C9Io1WvmTRBao5yEG5Kwy_xhFdM-ABC9TkWQ,47
-tskit-1.0.0b1.dist-info/top_level.txt,sha256=6GsXJYqSCR5Uhb4Js0BBzC0EFXE0FA5ywslsixSbwGM,13
-tskit-1.0.0b1.dist-info/RECORD,,
+tskit/jit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tskit/jit/numba.py,sha256=vyH3Hpa1_a3PJMGLli9Zw8_t8nPJx7pO46z5PFd7xP4,25453
+tskit-1.0.0b2.dist-info/licenses/LICENSE,sha256=h92w-U3mbrRNLntc2_9qHbCB2MmJsvDSBia6BTUCwLE,1099
+tskit-1.0.0b2.dist-info/METADATA,sha256=TAY19u828s_IqIjncv0hn5wqH0ev2vsIsdsaWT6PZQU,4645
+tskit-1.0.0b2.dist-info/WHEEL,sha256=qV0EIPljj1XC_vuSatRWjn02nZIz3N1t8jsZz7HBr2U,101
+tskit-1.0.0b2.dist-info/entry_points.txt,sha256=3Zik1X8C9Io1WvmTRBao5yEG5Kwy_xhFdM-ABC9TkWQ,47
+tskit-1.0.0b2.dist-info/top_level.txt,sha256=6GsXJYqSCR5Uhb4Js0BBzC0EFXE0FA5ywslsixSbwGM,13
+tskit-1.0.0b2.dist-info/RECORD,,