diff --git a/.github/scripts/upstream_install.py b/.github/scripts/upstream_install.py index 334795790..cb8e7a28c 100644 --- a/.github/scripts/upstream_install.py +++ b/.github/scripts/upstream_install.py @@ -14,9 +14,8 @@ def install_deps() -> None: "--upgrade", ) upstream_deps = ( - "git+https://github.com/dask/dask.git#egg=dask[array]", + "git+https://github.com/dask/dask.git#egg=dask[array,dataframe]", "git+https://github.com/dask/distributed.git#egg=distributed", - "git+https://github.com/dask/dask-ml.git#egg=dask-ml", "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/requirements-numpy2.txt b/requirements-numpy2.txt index 491e63fb8..8cfa612d5 100644 --- a/requirements-numpy2.txt +++ b/requirements-numpy2.txt @@ -1,8 +1,7 @@ numpy < 2.1 xarray -dask[array] >= 2023.01.0, <= 2024.8.0 +dask[array,dataframe] >= 2023.01.0, <= 2024.8.0 distributed >= 2023.01.0, <= 2024.8.0 -dask-ml scipy typing-extensions numba diff --git a/requirements.txt b/requirements.txt index dcc24d89b..c4af1fd9c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,8 +1,7 @@ numpy < 2 xarray -dask[array] >= 2023.01.0, <= 2024.8.0 +dask[array,dataframe] >= 2023.01.0, <= 2024.8.0 distributed >= 2023.01.0, <= 2024.8.0 -dask-ml scipy typing-extensions numba diff --git a/setup.cfg b/setup.cfg index 9ae850220..2a5afa9b6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -29,9 +29,8 @@ python_requires = >=3.10 install_requires = numpy < 2 xarray - dask[array] >= 2022.01.0, <= 2024.8.0 + dask[array,dataframe] >= 2022.01.0, <= 2024.8.0 distributed >= 2022.01.0, <= 2024.8.0 - dask-ml scipy zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3 numba diff --git a/sgkit/stats/pca.py b/sgkit/stats/pca.py index 6754b3aa2..4290d12ed 100644 --- a/sgkit/stats/pca.py +++ b/sgkit/stats/pca.py @@ -219,7 +219,7 @@ def pca( Principal axes defined as eigenvectors for sample covariance matrix. In the context of SVD, these are equivalent to the right singular vectors in the decomposition of a (N, M) matrix, - i.e. ``dask_ml.decomposition.TruncatedSVD.components_``. + i.e. ``sgkit.stats.truncated_svd.TruncatedSVD.components_``. sample_pca_loading : [array-like, shape: (M, C)] Principal axes scaled by square root of eigenvalues. These values can also be interpreted as the correlation between the @@ -227,10 +227,10 @@ def pca( sample_pca_explained_variance : [array-like, shape: (C,)] Variance explained by each principal component. These values are equivalent to eigenvalues that result from the eigendecomposition of a (N, M) matrix, - i.e. ``dask_ml.decomposition.TruncatedSVD.explained_variance_``. + i.e. ``sgkit.stats.truncated_svd.TruncatedSVD.explained_variance_``. sample_pca_explained_variance_ratio : [array-like, shape: (C,)] Ratio of variance explained to total variance for each principal component, - i.e. ``dask_ml.decomposition.TruncatedSVD.explained_variance_ratio_``. + i.e. ``sgkit.stats.truncated_svd.TruncatedSVD.explained_variance_ratio_``. Examples -------- diff --git a/sgkit/variables.py b/sgkit/variables.py index 1e8166355..253306258 100644 --- a/sgkit/variables.py +++ b/sgkit/variables.py @@ -701,7 +701,7 @@ def _check_field( kind="f", __doc__="""Principal axes defined as eigenvectors for sample covariance matrix. In the context of SVD, these are equivalent to the right singular vectors in -the decomposition of a (N, M) matrix., i.e. ``dask_ml.decomposition.TruncatedSVD.components_``.""", +the decomposition of a (N, M) matrix., i.e. ``sgkit.stats.truncated_svd.TruncatedSVD.components_``.""", ) ) @@ -715,7 +715,7 @@ def _check_field( kind="f", __doc__="""Variance explained by each principal component. These values are equivalent to eigenvalues that result from the eigendecomposition of a (N, M) matrix, -i.e. ``dask_ml.decomposition.TruncatedSVD.explained_variance_``.""", +i.e. ``sgkit.stats.truncated_svd.TruncatedSVD.explained_variance_``.""", ) ) @@ -728,7 +728,7 @@ def _check_field( dims=("components",), kind="f", __doc__="""Ratio of variance explained to total variance for each principal component, -i.e. ``dask_ml.decomposition.TruncatedSVD.explained_variance_ratio_``.""", +i.e. ``sgkit.stats.truncated_svd.TruncatedSVD.explained_variance_ratio_``.""", ) )