From d9134b8b4b0607b9f66a05d77b0def8dad60428d Mon Sep 17 00:00:00 2001 From: Tom White Date: Mon, 23 Jun 2025 16:04:07 +0100 Subject: [PATCH 1/2] Remove unused dask distributed dependency --- .github/scripts/upstream_install.py | 1 - pyproject.toml | 1 - requirements-numpy1.txt | 1 - requirements.txt | 1 - 4 files changed, 4 deletions(-) diff --git a/.github/scripts/upstream_install.py b/.github/scripts/upstream_install.py index cb8e7a28c..972344447 100644 --- a/.github/scripts/upstream_install.py +++ b/.github/scripts/upstream_install.py @@ -15,7 +15,6 @@ def install_deps() -> None: ) upstream_deps = ( "git+https://github.com/dask/dask.git#egg=dask[array,dataframe]", - "git+https://github.com/dask/distributed.git#egg=distributed", "git+https://github.com/pandas-dev/pandas#egg=pandas", "git+https://github.com/pangeo-data/rechunker.git#egg=rechunker", "git+https://github.com/pydata/xarray.git#egg=xarray", diff --git a/pyproject.toml b/pyproject.toml index eb3a10384..0ace3b2e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,6 @@ dependencies = [ "numpy < 2.2", "xarray < 2025.03.1", "dask[array,dataframe] >= 2022.01.0, <= 2024.8.0", - "distributed >= 2022.01.0, <= 2024.8.0", "scipy < 1.16", "zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3", "numba", diff --git a/requirements-numpy1.txt b/requirements-numpy1.txt index 1b093dc6d..509b8d9e5 100644 --- a/requirements-numpy1.txt +++ b/requirements-numpy1.txt @@ -1,7 +1,6 @@ numpy < 2 xarray < 2025.03.1 dask[array,dataframe] >= 2023.01.0, <= 2024.8.0 -distributed >= 2023.01.0, <= 2024.8.0 scipy < 1.16 typing-extensions numba diff --git a/requirements.txt b/requirements.txt index 6e87fc554..74a6b97b9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,6 @@ numpy < 2.2 xarray < 2025.03.1 dask[array,dataframe] >= 2023.01.0, <= 2024.8.0 -distributed >= 2023.01.0, <= 2024.8.0 scipy < 1.16 typing-extensions numba From cd314b3adc1302ddbd0cec45949468dd008a0532 Mon Sep 17 00:00:00 2001 From: Tom White Date: Mon, 23 Jun 2025 16:09:28 +0100 Subject: [PATCH 2/2] Remove typing-extensions dependency and just use standard library --- pyproject.toml | 2 -- requirements-numpy1.txt | 1 - requirements.txt | 1 - sgkit/distance/api.py | 2 +- sgkit/stats/aggregation.py | 3 +-- sgkit/stats/genedrop.py | 3 +-- sgkit/stats/grm.py | 3 +-- sgkit/stats/ibs.py | 3 +-- sgkit/stats/pca.py | 3 +-- sgkit/stats/pedigree.py | 3 +-- 10 files changed, 7 insertions(+), 17 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0ace3b2e6..7ef0d03c4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,6 @@ dependencies = [ "scipy < 1.16", "zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3", "numba", - "typing-extensions", "fsspec != 2021.6.*", "scikit-learn", "pandas", @@ -97,7 +96,6 @@ known_third_party = [ "sgkit_plink", "sklearn", "sphinx", - "typing_extensions", "xarray", "yaml", "zarr", diff --git a/requirements-numpy1.txt b/requirements-numpy1.txt index 509b8d9e5..b4da65449 100644 --- a/requirements-numpy1.txt +++ b/requirements-numpy1.txt @@ -2,7 +2,6 @@ numpy < 2 xarray < 2025.03.1 dask[array,dataframe] >= 2023.01.0, <= 2024.8.0 scipy < 1.16 -typing-extensions numba zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3 fsspec != 2021.6.* diff --git a/requirements.txt b/requirements.txt index 74a6b97b9..8b130d40d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,6 @@ numpy < 2.2 xarray < 2025.03.1 dask[array,dataframe] >= 2023.01.0, <= 2024.8.0 scipy < 1.16 -typing-extensions numba zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3 fsspec != 2021.6.* diff --git a/sgkit/distance/api.py b/sgkit/distance/api.py index 4593984ea..fb0518584 100644 --- a/sgkit/distance/api.py +++ b/sgkit/distance/api.py @@ -1,8 +1,8 @@ import typing +from typing import Literal import dask.array as da import numpy as np -from typing_extensions import Literal from sgkit.typing import ArrayLike diff --git a/sgkit/stats/aggregation.py b/sgkit/stats/aggregation.py index 9f3862985..e11eb6e7e 100644 --- a/sgkit/stats/aggregation.py +++ b/sgkit/stats/aggregation.py @@ -1,8 +1,7 @@ -from typing import Hashable +from typing import Hashable, Literal import numpy as np import xarray as xr -from typing_extensions import Literal from xarray import Dataset import sgkit.distarray as da diff --git a/sgkit/stats/genedrop.py b/sgkit/stats/genedrop.py index 1d928904b..1d0e48f85 100644 --- a/sgkit/stats/genedrop.py +++ b/sgkit/stats/genedrop.py @@ -1,9 +1,8 @@ -from typing import Hashable, Optional +from typing import Hashable, Literal, Optional import dask.array as da import numpy as np import xarray as xr -from typing_extensions import Literal from xarray import Dataset from sgkit import variables diff --git a/sgkit/stats/grm.py b/sgkit/stats/grm.py index c8b5a380a..1eab4626a 100644 --- a/sgkit/stats/grm.py +++ b/sgkit/stats/grm.py @@ -1,8 +1,7 @@ -from typing import Hashable, Optional, Tuple +from typing import Hashable, Literal, Optional, Tuple import dask.array as da import numpy as np -from typing_extensions import Literal from xarray import Dataset from sgkit import variables diff --git a/sgkit/stats/ibs.py b/sgkit/stats/ibs.py index 964615bb8..3d8bc0429 100644 --- a/sgkit/stats/ibs.py +++ b/sgkit/stats/ibs.py @@ -1,7 +1,6 @@ -from typing import Hashable +from typing import Hashable, Literal import dask.array as da -from typing_extensions import Literal from xarray import Dataset from sgkit import variables diff --git a/sgkit/stats/pca.py b/sgkit/stats/pca.py index 653f3100b..96be389a8 100644 --- a/sgkit/stats/pca.py +++ b/sgkit/stats/pca.py @@ -1,10 +1,9 @@ -from typing import Any, Optional, Union +from typing import Any, Literal, Optional, Union import numpy as np import xarray as xr from sklearn.base import BaseEstimator from sklearn.pipeline import Pipeline -from typing_extensions import Literal from xarray import DataArray, Dataset import sgkit.distarray as da diff --git a/sgkit/stats/pedigree.py b/sgkit/stats/pedigree.py index a040fc6de..bff889407 100644 --- a/sgkit/stats/pedigree.py +++ b/sgkit/stats/pedigree.py @@ -1,10 +1,9 @@ import warnings -from typing import Hashable, Tuple +from typing import Hashable, Literal, Optional, Tuple import dask.array as da import numpy as np import xarray as xr -from typing_extensions import Literal, Optional from xarray import Dataset from sgkit import variables