damicore-tree-builder 0.1.0__py3-none-any.whl

damicore_tree_builder/__init__.py

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+from damicore_tree_builder.api import build_tree
+from damicore_tree_builder.config import TreeBuildConfig
+from damicore_tree_builder.errors import TreeBuilderError
+from damicore_tree_builder.models import Tree, TreeBuildResult, TreeEdge, TreeNode
+from damicore_tree_builder.neighbor_joining import neighbor_joining
+
+__all__ = [
+    "build_tree",
+    "neighbor_joining",
+    "TreeBuildConfig",
+    "TreeBuildResult",
+    "Tree",
+    "TreeNode",
+    "TreeEdge",
+    "TreeBuilderError",
+]

damicore_tree_builder/api.py

@@ -0,0 +1,116 @@
+from __future__ import annotations
+
+import time
+from pathlib import Path
+from typing import Literal
+
+import numpy as np
+from pydantic import BaseModel, ConfigDict, ValidationError
+
+from damicore_tree_builder.artifacts import write_tree_artifacts
+from damicore_tree_builder.config import TreeBuildConfig
+from damicore_tree_builder.errors import TreeBuilderError
+from damicore_tree_builder.models import Tree, TreeBuildResult
+from damicore_tree_builder.neighbor_joining import build_neighbor_joining, validate_matrix
+
+
+class _LabelsArtifact(BaseModel):
+    model_config = ConfigDict(frozen=True, extra="forbid", strict=True)
+
+    schema_version: Literal[1]
+    object_ids: tuple[str, ...]
+    labels: tuple[str, ...]
+
+
+def _load_labels(path: Path) -> tuple[list[str], list[str]]:
+    try:
+        artifact = _LabelsArtifact.model_validate_json(path.read_text(encoding="utf-8"))
+        object_ids = list(artifact.object_ids)
+        labels = list(artifact.labels)
+    except (OSError, ValidationError) as exc:
+        raise TreeBuilderError("Invalid labels artifact", code="artifact_validation_error") from exc
+    if (
+        len(object_ids) != len(labels)
+        or len(set(object_ids)) != len(object_ids)
+        or len(set(labels)) != len(labels)
+    ):
+        raise TreeBuilderError(
+            "labels and object_ids must have equal length and unique values",
+            code="artifact_validation_error",
+        )
+    return object_ids, labels
+
+
+def build_tree(
+    matrix_path: str | Path,
+    labels_path: str | Path,
+    output_dir: str | Path,
+    *,
+    config: TreeBuildConfig | None = None,
+) -> TreeBuildResult:
+    """Build and persist a deterministic Neighbor Joining tree."""
+    started = time.monotonic()
+    settings = config or TreeBuildConfig()
+    destination = Path(output_dir).resolve()
+    destination.mkdir(parents=True, exist_ok=True)
+    if (destination / "tree.json").exists() or (destination / "tree.nwk").exists():
+        raise TreeBuilderError(
+            "Tree outputs already exist in the output directory",
+            code="output_directory_conflict_error",
+        )
+    labels, display_labels = _load_labels(Path(labels_path).resolve())
+    try:
+        original = np.load(Path(matrix_path).resolve(), mmap_mode="r", allow_pickle=False)
+    except (OSError, ValueError) as exc:
+        raise TreeBuilderError(
+            "Distance matrix artifact is unreadable",
+            code="artifact_validation_error",
+        ) from exc
+    validate_matrix(original, labels, settings.q_block_size)
+    workspace_path = destination / "tree-work.npy"
+    workspace = np.lib.format.open_memmap(
+        workspace_path, mode="w+", dtype=np.float64, shape=original.shape
+    )
+    try:
+        for start in range(0, original.shape[0], settings.q_block_size):
+            stop = min(start + settings.q_block_size, original.shape[0])
+            workspace[start:stop] = original[start:stop]
+        workspace.flush()
+        tree = build_neighbor_joining(
+            workspace,
+            labels,
+            display_labels,
+            q_block_size=settings.q_block_size,
+        )
+        tree_path, newick_path = write_tree_artifacts(tree, destination)
+        try:
+            validated = Tree.model_validate_json(tree_path.read_text(encoding="utf-8"))
+            if len([node for node in validated.nodes if node.kind == "leaf"]) != len(labels):
+                raise TreeBuilderError(
+                    "Persisted tree lost leaves", code="artifact_validation_error"
+                )
+            newick = newick_path.read_text(encoding="utf-8")
+            # Only the terminator is checked. A semicolon inside a quoted label is data, so
+            # counting them rejects valid output this package itself produces.
+            if not newick.rstrip("\n").endswith(";"):
+                raise TreeBuilderError(
+                    "Persisted Newick artifact is malformed",
+                    code="artifact_validation_error",
+                )
+        except BaseException:
+            # The next run refuses a directory holding either artifact, so a rejected write
+            # must not survive as a file that only manual cleanup can clear.
+            tree_path.unlink(missing_ok=True)
+            newick_path.unlink(missing_ok=True)
+            raise
+        negative = sum(edge.length < 0 for edge in tree.edges)
+    finally:
+        del workspace
+        workspace_path.unlink(missing_ok=True)
+    return TreeBuildResult(
+        tree_path=tree_path,
+        newick_path=newick_path,
+        leaf_count=len(labels),
+        negative_branch_count=negative,
+        timing=time.monotonic() - started,
+    )

damicore_tree_builder/artifacts.py

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+from __future__ import annotations
+
+import json
+import os
+import tempfile
+from pathlib import Path
+
+from damicore_tree_builder.models import Tree
+from damicore_tree_builder.newick import to_newick
+
+
+def _stage(path: Path, payload: str) -> str:
+    """Write `payload` beside `path` and return the temporary name, unrenamed."""
+    descriptor, temporary_name = tempfile.mkstemp(dir=path.parent, prefix=f".{path.name}.")
+    try:
+        with os.fdopen(descriptor, "w", encoding="utf-8", newline="\n") as stream:
+            stream.write(payload)
+            stream.flush()
+            os.fsync(stream.fileno())
+    except BaseException:
+        os.unlink(temporary_name)
+        raise
+    return temporary_name
+
+
+def write_tree_artifacts(tree: Tree, destination: Path) -> tuple[Path, Path]:
+    """Publish both tree artifacts, or neither.
+
+    The two files describe one tree, and the run that follows refuses a directory that already
+    holds either of them. Renaming the first into place before the second exists would
+    therefore let one failed write strand a tree.json that no later run can clear on its own,
+    so both payloads are rendered and staged first and renamed only once both exist.
+    """
+    tree_path = destination / "tree.json"
+    newick_path = destination / "tree.nwk"
+
+    tree_text = (
+        json.dumps(
+            tree.model_dump(mode="json"),
+            indent=2,
+            sort_keys=True,
+            allow_nan=False,
+        )
+        + "\n"
+    )
+    newick_text = to_newick(tree) + "\n"
+
+    tree_temp = _stage(tree_path, tree_text)
+    try:
+        newick_temp = _stage(newick_path, newick_text)
+    except BaseException:
+        os.unlink(tree_temp)
+        raise
+
+    try:
+        os.replace(tree_temp, tree_path)
+    except BaseException:
+        os.unlink(tree_temp)
+        os.unlink(newick_temp)
+        raise
+    try:
+        os.replace(newick_temp, newick_path)
+    except BaseException:
+        # tree.json is already published; withdraw it so the directory is left as found.
+        os.unlink(newick_temp)
+        tree_path.unlink(missing_ok=True)
+        raise
+    return tree_path, newick_path

damicore_tree_builder/config.py

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+from pydantic import BaseModel, ConfigDict, Field
+
+
+class TreeBuildConfig(BaseModel):
+    model_config = ConfigDict(frozen=True, extra="forbid")
+
+    q_block_size: int = Field(default=512, gt=0)

damicore_tree_builder/errors.py

@@ -0,0 +1,10 @@
+from __future__ import annotations
+
+
+class TreeBuilderError(Exception):
+    def __init__(
+        self, message: str, *, code: str = "tree_builder_error", **context: object
+    ) -> None:
+        super().__init__(message)
+        self.code = code
+        self.context = context

damicore_tree_builder/models.py

@@ -0,0 +1,41 @@
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Literal
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class TreeNode(BaseModel):
+    model_config = ConfigDict(frozen=True, extra="forbid", strict=True)
+
+    id: str
+    kind: Literal["leaf", "internal"]
+    label: str | None = None
+
+
+class TreeEdge(BaseModel):
+    model_config = ConfigDict(frozen=True, extra="forbid", strict=True)
+
+    source: str
+    target: str
+    length: float = Field(allow_inf_nan=False)
+
+
+class Tree(BaseModel):
+    model_config = ConfigDict(frozen=True, extra="forbid", strict=True)
+
+    schema_version: Literal[1] = 1
+    root_id: str
+    nodes: tuple[TreeNode, ...]
+    edges: tuple[TreeEdge, ...]
+
+
+class TreeBuildResult(BaseModel):
+    model_config = ConfigDict(frozen=True, extra="forbid", strict=True)
+
+    tree_path: Path
+    newick_path: Path
+    leaf_count: int = Field(ge=0)
+    negative_branch_count: int = Field(ge=0)
+    timing: float = Field(ge=0)

damicore_tree_builder/neighbor_joining.py

@@ -0,0 +1,175 @@
+from __future__ import annotations
+
+import math
+from collections.abc import Sequence
+from typing import Any
+
+import numpy as np
+import numpy.typing as npt
+
+from damicore_tree_builder.errors import TreeBuilderError
+from damicore_tree_builder.models import Tree, TreeEdge, TreeNode
+
+# Section 15.2: two Q scores closer than this, relative to the magnitude of the better one,
+# are one tie for the lexicographic rule to break.
+#
+# An exact float64 comparison asserts a precision the input never had: every distance here is
+# a ratio of integer compressed sizes, so its meaningful digits run out long before the
+# 16th. Worse, the ties the rule exists to break are precisely the ones rounding destroys --
+# with four clusters left, Q(i,j) and Q(k,l) for complementary pairs are algebraically equal
+# for *every* matrix, yet float64 detects that only about 60% of the time, and no summation
+# strategy fixes it because the cancellation happens in the final subtraction rather than in
+# the sums. A relative band restores the rule and makes the choice stable across platforms.
+_TIE_RELATIVE_TOLERANCE = 1e-9
+
+
+def _tie_band(score: float) -> float:
+    """Half-width of the tie band around `score`, scaled to its magnitude."""
+    return _TIE_RELATIVE_TOLERANCE * max(1.0, abs(score))
+
+
+def validate_matrix(
+    matrix: np.ndarray[Any, Any],
+    labels: Sequence[str],
+    block_size: int = 512,
+) -> None:
+    if matrix.ndim != 2 or matrix.shape[0] != matrix.shape[1] or matrix.shape[0] != len(labels):
+        raise TreeBuilderError(
+            "Distance matrix shape does not match labels", code="distance_matrix_validation_error"
+        )
+    if len(labels) < 2 or len(set(labels)) != len(labels):
+        raise TreeBuilderError(
+            "At least two unique labels are required", code="distance_matrix_validation_error"
+        )
+    if matrix.dtype != np.float64:
+        raise TreeBuilderError(
+            "Distance matrix must be float64",
+            code="distance_matrix_validation_error",
+        )
+    size = len(labels)
+    for row_start in range(0, size, block_size):
+        row_stop = min(row_start + block_size, size)
+        if not np.isfinite(matrix[row_start:row_stop]).all():
+            raise TreeBuilderError(
+                "Distance matrix must be finite",
+                code="distance_matrix_validation_error",
+            )
+        for row in range(row_start, row_stop):
+            if float(matrix[row, row]) != 0.0:
+                raise TreeBuilderError(
+                    "Distance matrix diagonal must be exactly zero",
+                    code="distance_matrix_validation_error",
+                )
+            # pyright: ignore is on np.array_equal, whose numpy stub is partially
+            # unknown under strict mode; the arrays themselves are fully typed.
+            symmetric = np.array_equal(  # pyright: ignore[reportUnknownMemberType]
+                matrix[row, :], matrix[:, row]
+            )
+            if not bool(symmetric):
+                raise TreeBuilderError(
+                    "Distance matrix must be bitwise symmetric",
+                    code="distance_matrix_validation_error",
+                )
+
+
+def neighbor_joining(matrix: npt.NDArray[np.floating[Any]], labels: Sequence[str]) -> Tree:
+    """Build a deterministic Neighbor Joining tree, copying the input matrix."""
+    copied = np.array(matrix, dtype=np.float64, copy=True, order="C")
+    validate_matrix(copied, labels)
+    return build_neighbor_joining(copied, list(labels), q_block_size=512)
+
+
+def build_neighbor_joining(
+    work: np.ndarray[Any, Any],
+    labels: list[str],
+    display_labels: list[str] | None = None,
+    *,
+    q_block_size: int,
+) -> Tree:
+    active = list(labels)
+    slots = {label: index for index, label in enumerate(labels)}
+    rendered_labels = display_labels or labels
+    nodes = [
+        TreeNode(id=identifier, kind="leaf", label=rendered_labels[index])
+        for index, identifier in enumerate(labels)
+    ]
+    edges: list[TreeEdge] = []
+    internal_index = 1
+
+    while len(active) > 2:
+        active.sort()
+        count = len(active)
+        # Recomputed from the matrix each round rather than carried forward, so no drift
+        # accumulates across iterations. The cost is O(r^2), which the Q scan below already
+        # pays, so nothing changes asymptotically.
+        row_sums = {
+            node: float(sum(work[slots[node], slots[other]] for other in active if other != node))
+            for node in active
+        }
+        # Section 15.2: the smallest Q wins, and pairs within the tie band are resolved by the
+        # smallest pair of IDs. `active` is sorted and pairs are visited in that order, so the
+        # running pair is always the lexicographically earliest one seen so far; a later pair
+        # therefore replaces it only by winning outright, never by tying with it.
+        best_score = math.inf
+        best_pair: tuple[str, str] | None = None
+        for block_start in range(0, count, q_block_size):
+            block_stop = min(block_start + q_block_size, count)
+            for left_index in range(block_start, block_stop):
+                left = active[left_index]
+                for right in active[left_index + 1 :]:
+                    score = (
+                        (count - 2) * float(work[slots[left], slots[right]])
+                        - row_sums[left]
+                        - row_sums[right]
+                    )
+                    if best_pair is None or score < best_score - _tie_band(best_score):
+                        best_pair = (left, right)
+                        best_score = score
+                    elif score < best_score:
+                        # Inside the band: keep the earlier pair, tighten the band's centre.
+                        best_score = score
+        # `active` holds at least three labels here, so the pair loop above always ran and
+        # `best_pair` is always set; asserting it is how the type narrows without a dead branch.
+        assert best_pair is not None
+        left, right = best_pair
+        left_slot, right_slot = slots[left], slots[right]
+        distance = float(work[left_slot, right_slot])
+        delta = (row_sums[left] - row_sums[right]) / (count - 2)
+        left_length = 0.5 * (distance + delta)
+        right_length = distance - left_length
+        internal = f"nj_{internal_index:06d}"
+        internal_index += 1
+        nodes.append(TreeNode(id=internal, kind="internal"))
+        edges.extend(
+            [
+                TreeEdge(source=internal, target=left, length=left_length),
+                TreeEdge(source=internal, target=right, length=right_length),
+            ]
+        )
+        remaining = [node for node in active if node not in (left, right)]
+        for other in remaining:
+            other_slot = slots[other]
+            left_distance = float(work[left_slot, other_slot])
+            right_distance = float(work[right_slot, other_slot])
+            updated = 0.5 * (left_distance + right_distance - distance)
+            work[left_slot, other_slot] = updated
+            work[other_slot, left_slot] = updated
+        work[left_slot, left_slot] = 0.0
+        slots.pop(left)
+        slots.pop(right)
+        slots[internal] = left_slot
+        active = [*remaining, internal]
+
+    active.sort()
+    left, right = active
+    final_length = float(work[slots[left], slots[right]]) / 2.0
+    root = "nj_root"
+    nodes.append(TreeNode(id=root, kind="internal"))
+    edges.extend(
+        [
+            TreeEdge(source=root, target=left, length=final_length),
+            TreeEdge(source=root, target=right, length=final_length),
+        ]
+    )
+    ordered_edges = tuple(sorted(edges, key=lambda edge: (edge.source, edge.target)))
+    return Tree(root_id=root, nodes=tuple(nodes), edges=ordered_edges)

damicore_tree_builder/newick.py

@@ -0,0 +1,67 @@
+from __future__ import annotations
+
+from damicore_tree_builder.errors import TreeBuilderError
+from damicore_tree_builder.models import Tree
+
+# Underscore is in this set on purpose. Newick converts an unquoted underscore to a blank on
+# reading, and every id this package emits contains one (`column_000001`, `nj_root`), so an
+# unquoted label reaches a conforming viewer with its digits split off from its prefix.
+_MUST_QUOTE = " \t\n\r():;,[]'_"
+
+
+def _escape(identifier: str) -> str:
+    if identifier and all(character not in identifier for character in _MUST_QUOTE):
+        return identifier
+    return "'" + identifier.replace("'", "''") + "'"
+
+
+def to_newick(tree: Tree) -> str:
+    """Render `tree` as a Newick string closed by a single terminator.
+
+    The traversal is iterative because tree depth is not bounded by the object count in any
+    useful way: Neighbor Joining produces a caterpillar of depth n-1 whenever one taxon joins
+    per round, so a recursive renderer exhausts the interpreter stack inside the supported
+    input range rather than at some unreachable extreme.
+
+    Raises
+    ------
+    TreeBuilderError
+        If the edges reach a node already on the current path. A recursive renderer ends such
+        a cycle with RecursionError; an iterative one would otherwise never terminate.
+    """
+    children: dict[str, list[tuple[str, float]]] = {}
+    for edge in tree.edges:
+        children.setdefault(edge.source, []).append((edge.target, edge.length))
+
+    # A node's own branch length belongs to the edge that reaches it, not to the node, so
+    # `body` holds each subtree rendered without it and the length is appended per edge.
+    body: dict[str, str] = {}
+    on_path: set[str] = set()
+    stack: list[tuple[str, bool]] = [(tree.root_id, False)]
+    while stack:
+        node_id, expanded = stack.pop()
+        if expanded:
+            on_path.discard(node_id)
+            descendants = sorted(children.get(node_id, []), key=lambda item: item[0])
+            prefix = ""
+            if descendants:
+                prefix = (
+                    "("
+                    + ",".join(
+                        body[child] + ":" + repr(float(length)) for child, length in descendants
+                    )
+                    + ")"
+                )
+            body[node_id] = prefix + _escape(node_id)
+            continue
+        if node_id in on_path:
+            raise TreeBuilderError(
+                "Tree edges form a cycle",
+                code="artifact_validation_error",
+                node_id=node_id,
+            )
+        on_path.add(node_id)
+        stack.append((node_id, True))
+        stack.extend((child, False) for child, _ in children.get(node_id, []))
+
+    return body[tree.root_id] + ";"

damicore_tree_builder-0.1.0.dist-info/METADATA

@@ -0,0 +1,64 @@
+Metadata-Version: 2.5
+Name: damicore-tree-builder
+Version: 0.1.0
+Summary: Neighbor-Joining tree builder for the DAMICORE pipeline.
+Project-URL: Homepage, https://github.com/Delbem-Research-and-Innovation/damicore
+Project-URL: Repository, https://github.com/Delbem-Research-and-Innovation/damicore
+Project-URL: Issues, https://github.com/Delbem-Research-and-Innovation/damicore/issues
+Project-URL: Documentation, https://github.com/Delbem-Research-and-Innovation/damicore/blob/main/docs/quickstart.md
+Project-URL: Changelog, https://github.com/Delbem-Research-and-Innovation/damicore/blob/main/CHANGELOG.md
+Author-email: Ennio Politi Lopes <enniolopes@users.noreply.github.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: damicore,neighbor-joining,newick,phylogenetics,tree
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Typing :: Typed
+Requires-Python: <3.15,>=3.11
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: pydantic<3,>=2.10
+Description-Content-Type: text/markdown
+
+# damicore-tree-builder
+
+damicore-tree-builder builds a deterministic Neighbor Joining tree from a
+distance matrix and its labels. It is the third stage of the DAMICORE pipeline;
+most users install the aggregate `damicore` distribution, which runs all four
+stages end to end. Install this package alone to build trees without the rest of
+the pipeline.
+
+```bash
+pip install damicore-tree-builder
+```
+
+## Python
+
+```python
+from damicore_tree_builder import build_tree
+
+result = build_tree("distance.npy", "labels.json", "run")
+```
+
+`distance.npy` and `labels.json` are produced by the sibling `damicore-distance`
+distribution; the call writes `tree.json` plus Newick, and `tree.json` is the
+input the sibling `damicore-clusterizer` distribution consumes. The path API
+copies into a temporary memory map, reuses slots, evaluates Q pairwise without
+materializing it, and preserves negative branches. `neighbor_joining(matrix,
+labels)` is available for small in-memory matrices.
+
+## Links
+
+- Repository: <https://github.com/Delbem-Research-and-Innovation/damicore>
+- Issues: <https://github.com/Delbem-Research-and-Innovation/damicore/issues>
+- Documentation:
+  <https://github.com/Delbem-Research-and-Innovation/damicore/blob/main/docs/quickstart.md>
+
+Licensed under Apache-2.0.

damicore_tree_builder-0.1.0.dist-info/RECORD

@@ -0,0 +1,13 @@
+damicore_tree_builder/__init__.py,sha256=9cHjKEzHYzbmKmESFu-GcX4A64AtNum2w-akA96BXt8,486
+damicore_tree_builder/api.py,sha256=YduR7mSNLAIywLNFHJnuB1quHqiBx9fDUMLR_HTfxAU,4651
+damicore_tree_builder/artifacts.py,sha256=vMqQPEfpQ-qewbSxa5XIHB2-WT43xrh7BeOKD0Y_Ui8,2144
+damicore_tree_builder/config.py,sha256=opNdevBGYvWbfHHs5BbQcIEXsN3F_PiTe7sdcsdLMmg,195
+damicore_tree_builder/errors.py,sha256=RIo6uHgniS8kHOhFMoFOKIjntPPyQXGJX7nCQ_bOGrs,278
+damicore_tree_builder/models.py,sha256=HzBKcPtR5Hatlggn8Zp7hI_n9YqEuOVdlgL0Exintxo,977
+damicore_tree_builder/neighbor_joining.py,sha256=E_GtQxCmnBMgc2okybrGErRNbl4fsnYr_jsMFS7ssLI,7808
+damicore_tree_builder/newick.py,sha256=bd9nQPtWZ2LnMOkdV3Pf2Sd8AkMcs-BazopwGNaHtro,2751
+damicore_tree_builder/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+damicore_tree_builder-0.1.0.dist-info/METADATA,sha256=2fWPYz3PF98zPXV2iYjQ1W2_lWod6zXuCiHNYN8obNg,2745
+damicore_tree_builder-0.1.0.dist-info/WHEEL,sha256=zOwg4jB6zX2kU910N-cMawjivD6tO8NEWvE12je1bVk,87
+damicore_tree_builder-0.1.0.dist-info/licenses/LICENSE,sha256=BmVNessiu1YyCBRQp38foYZDCX9oXG_nwFqjbV7ueBA,11348
+damicore_tree_builder-0.1.0.dist-info/RECORD,,

damicore_tree_builder-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.32.0
+Root-Is-Purelib: true
+Tag: py3-none-any

damicore_tree_builder-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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