@@ 399,6 399,35 @@ higher scores.")
one of the fastest libraries for histogramming.")
(license license:bsd-3)))
+(define-public python-bottleneck
+ (package
+ (name "python-bottleneck")
+ (version "1.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "bottleneck" version))
+ (sha256
+ (base32 "1x29yj4yr12v646si63gkxj9b6lx1xk65536wqy4i9fyk4bqx3ps"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'rebuild-ext
+ (lambda _
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ (native-inputs (list python-pytest
+ python-setuptools
+ python-wheel))
+ (propagated-inputs (list python-numpy))
+ (home-page "https://github.com/pydata/bottleneck")
+ (synopsis "Fast NumPy array functions written in C")
+ (description
+ "Bottleneck is a collection of fast, NaN-aware NumPy array functions
+written in C.")
+ (license license:bsd-2)))
+
(define-public python-clarabel
(package
(name "python-clarabel")
@@ 589,6 618,59 @@ it can be used for displaying many qualitatively different samples.")
optimization problems in Python.")
(license license:asl2.0)))
+(define-public python-dask-expr
+ (package
+ (name "python-dask-expr")
+ (version "1.0.14")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dask/dask-expr")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0c2q8w8wl5d2hycbjp9vavkl5f36kaz390wxlis2d8d43jnqhf0d"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #false ;need python-distributed, which needs dask-expr.
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'versioneer
+ (lambda _
+ ;; Our version of versioneer needs setup.cfg. This is adapted
+ ;; from pyproject.toml.
+ (with-output-to-file "setup.cfg"
+ (lambda ()
+ (display "\
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = dask_expr/_version.py
+versionfile_build = dask_expr/_version.py
+tag_prefix =
+parentdir_prefix = dask_expr-
+")))
+ (invoke "versioneer" "install")
+ (substitute* "setup.py"
+ (("versioneer.get_version\\(\\)")
+ (string-append "\"" #$version "\""))))))))
+ (propagated-inputs (list python-pandas python-pyarrow))
+ (native-inputs
+ ;; We use python-dask/bootstrap so that python-dask can propagate this
+ ;; package without creating a mutually recursive dependency.
+ (list python-dask/bootstrap
+ python-pytest
+ python-setuptools
+ python-versioneer
+ python-wheel))
+ (home-page "https://github.com/dask/dask-expr")
+ (synopsis "Dask DataFrames with query optimization")
+ (description "This is a rewrite of Dask DataFrame that includes query
+optimization and generally improved organization.")
+ (license license:bsd-3)))
+
(define-public python-decaylanguage
(package
(name "python-decaylanguage")
@@ 959,6 1041,39 @@ spheres, cubes, etc.")
density maps, both for interactive and non-interactive use.")
(license license:bsd-2)))
+(define-public python-mpsplines
+ ;; No release on PyPI no git tag, use the latest commit.
+ (let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
+ (revision "0"))
+ (package
+ (name "python-mpsplines")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jararias/mpsplines")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1wqfvjp1d6xzb07qnq72h76f0mx7za9pasgw3qp3ciaycmlkvdr3"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ; no tests provided
+ (native-inputs
+ (list python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-scipy
+ python-numpy
+ python-loguru))
+ (home-page "https://github.com/jararias/mpsplines")
+ (synopsis "Mean preserving interpolation with splines")
+ (description
+ "Thi package implements a functionality for mean-preserving
+interpolation of 1D data (for example, time series) with splines.")
+ (license license:bsd-3))))
+
(define-public python-ndindex
(package
(name "python-ndindex")
@@ 1432,6 1547,33 @@ factorization routine for quasi-definite linear system.")
automated with the minimum of fuss and the least effort.")
(license license:expat)))
+(define-public python-salib
+ (package
+ (name "python-salib")
+ (version "1.4.7")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/SALib/SALib")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "18xfyzircsx2q2lmfc9lxb6xvkxicnc83qzghd7df1jsprr5ymch"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-matplotlib
+ python-multiprocess
+ python-numpy
+ python-pandas
+ python-scipy))
+ (native-inputs (list python-hatchling python-pytest python-pytest-cov))
+ (home-page "https://salib.readthedocs.io/en/latest/")
+ (synopsis "Tools for global sensitivity analysis")
+ (description "SALib provides tools for global sensitivity analysis. It
+contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and
+fractional factorial methods.")
+ (license license:expat)))
+
(define-public python-scikit-allel
(package
(name "python-scikit-allel")
@@ 2316,39 2458,6 @@ manipulation and analysis, in the style of the Polygon object in the Shapely
library.")
(license license:expat)))
-(define-public python-mpsplines
- ;; No release on PyPI no git tag, use the latest commit.
- (let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
- (revision "0"))
- (package
- (name "python-mpsplines")
- (version (git-version "0.0.0" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/jararias/mpsplines")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1wqfvjp1d6xzb07qnq72h76f0mx7za9pasgw3qp3ciaycmlkvdr3"))))
- (build-system pyproject-build-system)
- (arguments
- (list #:tests? #f)) ; no tests provided
- (native-inputs
- (list python-setuptools
- python-wheel))
- (propagated-inputs
- (list python-scipy
- python-numpy
- python-loguru))
- (home-page "https://github.com/jararias/mpsplines")
- (synopsis "Mean preserving interpolation with splines")
- (description
- "Thi package implements a functionality for mean-preserving
-interpolation of 1D data (for example, time series) with splines.")
- (license license:bsd-3))))
-
(define-public python-pyamg
(package
(name "python-pyamg")
@@ 3104,35 3213,6 @@ Python module with the same interface, but (hopefully) faster.")
"This package provides a Python package for time series classification.")
(license license:bsd-3)))
-(define-public python-bottleneck
- (package
- (name "python-bottleneck")
- (version "1.4.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "bottleneck" version))
- (sha256
- (base32 "1x29yj4yr12v646si63gkxj9b6lx1xk65536wqy4i9fyk4bqx3ps"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'check 'rebuild-ext
- (lambda _
- (invoke "python" "setup.py" "build_ext" "--inplace"))))))
- (native-inputs (list python-pytest
- python-setuptools
- python-wheel))
- (propagated-inputs (list python-numpy))
- (home-page "https://github.com/pydata/bottleneck")
- (synopsis "Fast NumPy array functions written in C")
- (description
- "Bottleneck is a collection of fast, NaN-aware NumPy array functions
-written in C.")
- (license license:bsd-2)))
-
(define-public python-spin
(package
(name "python-spin")
@@ 3247,6 3327,43 @@ not usually a runtime dependency, but only a type checking, testing, and/or
docs dependency in support of other libraries.")
(license license:bsd-3)))
+(define-public python-unyt
+ (package
+ (name "python-unyt")
+ (version "3.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "unyt" version))
+ (sha256
+ (base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; This is a Numpy DeprecationWarning, remove it on next update.
+ (list #:test-flags ''("-k" "not test_h5_io")))
+ ;; Pint is optional, but we do not propagate it due to its size.
+ (native-inputs
+ (list python-pint
+ python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ ;; Astropy is an optional import, but we do not include it as it creates a
+ ;; module cycle: astronomy->python-science->astronomy.
+ (propagated-inputs
+ (list python-h5py ; optional import
+ python-matplotlib ; optional import
+ python-numpy
+ python-sympy))
+ (home-page "https://unyt.readthedocs.io")
+ (synopsis "Library for working with data that has physical units")
+ (description
+ "@code{unyt} is a Python library working with data that has physical
+units. It defines the @code{unyt.array.unyt_array} and
+@code{unyt.array.unyt_quantity} classes (subclasses of NumPy’s ndarray class)
+for handling arrays and scalars with units,respectively")
+ (license license:bsd-3)))
+
(define-public python-upsetplot
(package
(name "python-upsetplot")
@@ 3301,6 3418,65 @@ geometric calculations on arrays of vectors, rather than one vector at a time
in a Python @code{for} loop.")
(license license:bsd-3)))
+(define-public python-vedo
+ (package
+ (name "python-vedo")
+ (version "2025.5.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/marcomusy/vedo")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hrqyvcxxbc1wz0cnafc8rvsi5mj19kck4b6pmddh25rlhdcr5qb"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; XXX: The whole test suite depends on the data from
+ ;; <https://vedo.embl.es/examples> providing samples which need to be
+ ;; downloaded during tests, find the way how to enable it.
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ ;; vtk does not provide Python metadata.
+ ;;
+ ;; ...checking requirements: ERROR: vedo==2025.5.3
+ ;; DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("\"vtk\",") "")))))))
+ (native-inputs
+ (list pkg-config
+ python-pkgconfig
+ python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-deprecated
+ python-matplotlib
+ python-numpy
+ python-pygments
+ vtk))
+ (home-page "https://github.com/marcomusy/vedo")
+ (synopsis
+ "Analysis and visualization of 3D objects and point clouds")
+ (description
+ "@code{vedo} is a fast and lightweight python module for
+scientific analysis and visualization. The package provides a wide
+range of functionalities for working with three-dimensional meshes and
+point clouds. It can also be used to generate high quality
+two-dimensional renderings such as scatter plots and histograms.
+@code{vedo} is based on @code{vtk} and @code{numpy}.")
+ ;; vedo is released under the Expat license. Included fonts are
+ ;; covered by the OFL license and textures by the CC0 license.
+ ;; The earth images are in the public domain.
+ (license (list license:expat
+ license:silofl1.1
+ license:cc0
+ license:public-domain))))
+
(define-public python-xarray
(package
(name "python-xarray")
@@ 3613,102 3789,6 @@ SCS (Splitting conic solver) library.")
annotations on an existing boxplots and barplots generated by seaborn.")
(license license:expat)))
-(define-public python-unyt
- (package
- (name "python-unyt")
- (version "3.0.3")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "unyt" version))
- (sha256
- (base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni"))))
- (build-system pyproject-build-system)
- (arguments
- ;; This is a Numpy DeprecationWarning, remove it on next update.
- (list #:test-flags ''("-k" "not test_h5_io")))
- ;; Pint is optional, but we do not propagate it due to its size.
- (native-inputs
- (list python-pint
- python-pytest
- python-setuptools
- python-setuptools-scm
- python-wheel))
- ;; Astropy is an optional import, but we do not include it as it creates a
- ;; module cycle: astronomy->python-science->astronomy.
- (propagated-inputs
- (list python-h5py ; optional import
- python-matplotlib ; optional import
- python-numpy
- python-sympy))
- (home-page "https://unyt.readthedocs.io")
- (synopsis "Library for working with data that has physical units")
- (description
- "@code{unyt} is a Python library working with data that has physical
-units. It defines the @code{unyt.array.unyt_array} and
-@code{unyt.array.unyt_quantity} classes (subclasses of NumPy’s ndarray class)
-for handling arrays and scalars with units,respectively")
- (license license:bsd-3)))
-
-(define-public python-vedo
- (package
- (name "python-vedo")
- (version "2025.5.3")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/marcomusy/vedo")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0hrqyvcxxbc1wz0cnafc8rvsi5mj19kck4b6pmddh25rlhdcr5qb"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- ;; XXX: The whole test suite depends on the data from
- ;; <https://vedo.embl.es/examples> providing samples which need to be
- ;; downloaded during tests, find the way how to enable it.
- #:tests? #f
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- ;; vtk does not provide Python metadata.
- ;;
- ;; ...checking requirements: ERROR: vedo==2025.5.3
- ;; DistributionNotFound(Requirement.parse('vtk'), {'vedo'})
- (lambda _
- (substitute* "pyproject.toml"
- (("\"vtk\",") "")))))))
- (native-inputs
- (list pkg-config
- python-pkgconfig
- python-setuptools
- python-wheel))
- (propagated-inputs
- (list python-deprecated
- python-matplotlib
- python-numpy
- python-pygments
- vtk))
- (home-page "https://github.com/marcomusy/vedo")
- (synopsis
- "Analysis and visualization of 3D objects and point clouds")
- (description
- "@code{vedo} is a fast and lightweight python module for
-scientific analysis and visualization. The package provides a wide
-range of functionalities for working with three-dimensional meshes and
-point clouds. It can also be used to generate high quality
-two-dimensional renderings such as scatter plots and histograms.
-@code{vedo} is based on @code{vtk} and @code{numpy}.")
- ;; vedo is released under the Expat license. Included fonts are
- ;; covered by the OFL license and textures by the CC0 license.
- ;; The earth images are in the public domain.
- (license (list license:expat
- license:silofl1.1
- license:cc0
- license:public-domain))))
-
(define-public python-pandas-flavor
(package
(name "python-pandas-flavor")
@@ 3796,59 3876,6 @@ and more
@end itemize")
(license license:gpl3)))
-(define-public python-dask-expr
- (package
- (name "python-dask-expr")
- (version "1.0.14")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/dask/dask-expr")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0c2q8w8wl5d2hycbjp9vavkl5f36kaz390wxlis2d8d43jnqhf0d"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:tests? #false ;need python-distributed, which needs dask-expr.
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'versioneer
- (lambda _
- ;; Our version of versioneer needs setup.cfg. This is adapted
- ;; from pyproject.toml.
- (with-output-to-file "setup.cfg"
- (lambda ()
- (display "\
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = dask_expr/_version.py
-versionfile_build = dask_expr/_version.py
-tag_prefix =
-parentdir_prefix = dask_expr-
-")))
- (invoke "versioneer" "install")
- (substitute* "setup.py"
- (("versioneer.get_version\\(\\)")
- (string-append "\"" #$version "\""))))))))
- (propagated-inputs (list python-pandas python-pyarrow))
- (native-inputs
- ;; We use python-dask/bootstrap so that python-dask can propagate this
- ;; package without creating a mutually recursive dependency.
- (list python-dask/bootstrap
- python-pytest
- python-setuptools
- python-versioneer
- python-wheel))
- (home-page "https://github.com/dask/dask-expr")
- (synopsis "Dask DataFrames with query optimization")
- (description "This is a rewrite of Dask DataFrame that includes query
-optimization and generally improved organization.")
- (license license:bsd-3)))
-
(define-public python-distributed
(package
(name "python-distributed")
@@ 4790,33 4817,6 @@ Out-of-Core DataFrames (similar to Pandas), to visualize and explore big
tabular datasets. This package provides the core modules of Vaex.")
(license license:expat)))
-(define-public python-salib
- (package
- (name "python-salib")
- (version "1.4.7")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/SALib/SALib")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "18xfyzircsx2q2lmfc9lxb6xvkxicnc83qzghd7df1jsprr5ymch"))))
- (build-system pyproject-build-system)
- (propagated-inputs (list python-matplotlib
- python-multiprocess
- python-numpy
- python-pandas
- python-scipy))
- (native-inputs (list python-hatchling python-pytest python-pytest-cov))
- (home-page "https://salib.readthedocs.io/en/latest/")
- (synopsis "Tools for global sensitivity analysis")
- (description "SALib provides tools for global sensitivity analysis. It
-contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and
-fractional factorial methods.")
- (license license:expat)))
-
(define-public python-pylems
(package
(name "python-pylems")