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fix: support numpy 2 #4798

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merged 2 commits into from
Sep 30, 2024
Merged

fix: support numpy 2 #4798

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e8b774c
fix: support numpy 2
RogerHYang Sep 29, 2024
753868d
fix uv
RogerHYang Sep 29, 2024
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7 changes: 4 additions & 3 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,12 @@ classifiers = [
]
dependencies = [
"scikit-learn",
"numpy<2", # https://github.com/TutteInstitute/fast_hdbscan/issues/17#issuecomment-2380859314
"numpy!=2.0.0", # https://github.com/lmcinnes/umap/issues/1138
"pandas>=1.0",
"jinja2",
"umap-learn",
"fast-hdbscan",
"hdbscan>=0.8.38",
"numba>=0.60.0", # https://github.com/astral-sh/uv/issues/6281
"starlette",
"uvicorn",
"psutil",
Expand Down Expand Up @@ -385,7 +386,7 @@ exclude = [

[[tool.mypy.overrides]]
module = [
"fast_hdbscan",
"hdbscan",
"umap",
"numba.*",
"scipy.*",
Expand Down
2 changes: 1 addition & 1 deletion src/phoenix/pointcloud/clustering.py
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Expand Up @@ -17,7 +17,7 @@ class Hdbscan:
cluster_selection_epsilon: float = 0.0

def find_clusters(self, mat: Matrix) -> List[RawCluster]:
from fast_hdbscan import HDBSCAN
from hdbscan import HDBSCAN

cluster_ids: npt.NDArray[np.int_] = HDBSCAN(**asdict(self)).fit_predict(mat)
ans: List[RawCluster] = [set() for _ in range(np.max(cluster_ids) + 1)]
Expand Down
11 changes: 5 additions & 6 deletions src/phoenix/pointcloud/projectors.py
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Expand Up @@ -6,12 +6,6 @@
import numpy.typing as npt
from typing_extensions import TypeAlias

with warnings.catch_warnings():
from numba.core.errors import NumbaWarning

warnings.simplefilter("ignore", category=NumbaWarning)
from umap import UMAP

Matrix: TypeAlias = npt.NDArray[np.float64]


Expand All @@ -25,6 +19,11 @@ class Umap:
min_dist: float = 0.1

def project(self, mat: Matrix, n_components: int) -> Matrix:
with warnings.catch_warnings():
from numba.core.errors import NumbaWarning

warnings.simplefilter("ignore", category=NumbaWarning)
from umap import UMAP
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delayed import could save 3s when they're not needed

Screenshot 2024-09-29 at 6 01 00 PM

config = asdict(self)
config["n_components"] = n_components
if len(mat) <= n_components:
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