@@ 455,6 455,27 @@ numerical solver for convex optimization problems using a novel homogeneous
embedding.")
(license license:asl2.0)))
+(define-public python-climin
+ (package
+ (name "python-climin")
+ (version "0.1a1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "climin" version))
+ (sha256
+ (base32
+ "1wpjisd5zzi5yvjff02hnxn84822k8sdxvvd33lil2x79wdb36rv"))))
+ (build-system python-build-system)
+ (native-inputs (list python-nose))
+ (propagated-inputs (list python-numpydoc python-numpy python-scipy))
+ (home-page "https://github.com/BRML/climin")
+ (synopsis "Optimization for machine learning")
+ (description
+ "@command{climin} is a Python package for optimization,
+heavily biased to machine learning scenarios. It works on top of
+@command{numpy} and (partially) @command{gnumpy}.")
+ (license license:bsd-3)))
+
(define-public python-cmocean
(package
(name "python-cmocean")
@@ 665,6 686,26 @@ that is 7-15x faster than @code{numpy.histogram}, and a 2D histogram function
that is 20-25x faster than @code{numpy.histogram2d}.")
(license license:bsd-3)))
+(define-public python-fastcluster
+ (package
+ (name "python-fastcluster")
+ (version "1.2.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fastcluster" version))
+ (sha256
+ (base32 "19labbgnq85p4r4jbli2p045lgh57larhi2g2anagfxnlzpqdf5a"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-numpy))
+ (native-inputs (list python-scipy python-setuptools python-wheel))
+ (home-page "https://danifold.net/fastcluster.html")
+ (synopsis "Fast hierarchical clustering routines for R and Python")
+ (description "The fastcluster package implements seven common hierarchical
+clustering schemes efficiently. The package is made with two interfaces to
+standard software: R and Python.")
+ (license license:bsd-2)))
+
(define-public python-formulaic
(package
(name "python-formulaic")
@@ 828,6 869,38 @@ Features:
@end itemize")
(license license:bsd-2)))
+(define-public python-libneuroml
+ (package
+ (name "python-libneuroml")
+ (version "0.6.5")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/NeuralEnsemble/libNeuroML.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "04cfff9phm19x87p86xrkhd6wlpxvdwk3rf1c3qgyncfchws0sjh"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-numpy
+ python-setuptools
+ python-tables
+ python-wheel))
+ (propagated-inputs
+ (list python-lxml
+ python-natsort
+ python-networkx))
+ (home-page "https://libneuroml.readthedocs.org/en/latest/")
+ (synopsis
+ "Python library for working with NeuroML descriptions of neuronal models")
+ (description
+ "This package provides a Python library for working with NeuroML descriptions of
+neuronal models")
+ (license license:bsd-3)))
+
(define-public python-meshzoo
(package
(name "python-meshzoo")
@@ 910,6 983,39 @@ density maps, both for interactive and non-interactive use.")
indices of @code{ndarrays}.")
(license license:expat)))
+(define-public python-nibabel
+ (package
+ (name "python-nibabel")
+ (version "5.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "nibabel" version))
+ (sha256
+ (base32 "16snprwgp7qzp51j3mx0zdn7brvx6r14ankldi24ny0w7d8adp0b"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; AttributeError: 'dict' object has no attribute 'add'.
+ #:test-flags #~(list "-k" "not test_first and not test_second")))
+ (propagated-inputs (list python-importlib-resources python-numpy
+ python-packaging python-typing-extensions))
+ (native-inputs (list python-hatch-vcs
+ python-hatchling
+ python-pytest
+ python-pytest-httpserver
+ python-pytest-xdist))
+ (home-page "https://nipy.org/nibabel/")
+ (synopsis "Read and write access to common neuroimaging file formats")
+ (description
+ "@code{nibabel} is a library that provides read and write access to
+common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2
+and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD,
+ECAT and Philips PAR/REC. In addition, NiBabel also supports FreeSurfer’s
+MGH, geometry, annotation and morphometry files, and provides some limited
+support for DICOM.")
+ (license license:expat))) ; and other non-copyleft licenses
+
(define-public python-numdifftools
(package
(name "python-numdifftools")
@@ 1017,6 1123,32 @@ evaluating arrays of polynomials based on @code{numpy.ndarray objects}.")
aggregated sum and more.")
(license license:bsd-3)))
+(define-public python-opt-einsum
+ (package
+ (name "python-opt-einsum")
+ (version "3.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "opt_einsum" version))
+ (sha256
+ (base32
+ "0jb5lia0q742d1713jk33vlj41y61sf52j6pgk7pvhxvfxglgxjr"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-numpy))
+ (native-inputs
+ (list python-pytest python-pytest-cov python-setuptools python-wheel))
+ (home-page "https://github.com/dgasmith/opt_einsum")
+ (synopsis "Optimizing numpys einsum function")
+ (description
+ "Optimized einsum can significantly reduce the overall execution time of
+einsum-like expressions by optimizing the expression's contraction order and
+dispatching many operations to canonical BLAS, cuBLAS, or other specialized
+routines. Optimized einsum is agnostic to the backend and can handle NumPy,
+Dask, PyTorch, Tensorflow, CuPy, Sparse, Theano, JAX, and Autograd arrays as
+well as potentially any library which conforms to a standard API. See the
+documentation for more information.")
+ (license license:expat)))
+
(define-public python-osqp
(package
(name "python-osqp")
@@ 1144,6 1276,56 @@ allows arithmetic operations between them and conversions from and to
different units.")
(license license:bsd-3)))
+(define-public python-pynetdicom
+ (package
+ (name "python-pynetdicom")
+ (version "2.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pynetdicom" version))
+ (sha256
+ (base32
+ "1smzrnc93nmv8jz4np9knas74a46b1nhb3hjpf8n9vfpxypgnwcn"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; Tests takes about 10-15min to complete.
+ ;; Skip tests that require networking.
+ #~(list "-k" (string-append
+ " not TestFindSCP"
+ " and not TestQRGetServiceClass"
+ " and not TestQRMoveServiceClass"
+ " and not TestStoreSCP"
+ " and not test_ae.py"
+ " and not test_echoscp.py"
+ " and not test_qrscp_echo.py"
+ " and not test_storescp.py"
+ " and not test_pr_level_patient"
+ " and not test_pr_level_series"
+ " and not test_scp_cancelled"))))
+ (native-inputs (list python-codespell
+ python-coverage
+ python-poetry-core
+ python-pytest
+ python-pytest-cov
+ python-pytest-xdist
+ python-sphinx
+ python-sphinx-rtd-theme))
+ (propagated-inputs (list python-mypy
+ python-numpydoc
+ python-pydicom
+ python-pyfakefs
+ python-sqlalchemy))
+ (home-page "https://github.com/pydicom/pynetdicom")
+ (synopsis "Python implementation of the DICOM networking protocol")
+ (description
+ "@code{pynetdicom} is a Python package that implements the DICOM
+networking protocol. It allows the easy creation of DICOM
+@acronym{SCUs,Service Class Users} and @acronym{SCPs,Service Class
+Providers}.")
+ (license license:expat)))
+
(define-public python-pyzx
(package
(name "python-pyzx")
@@ 1219,6 1401,37 @@ or as a TikZ file for use in LaTeX documents;
factorization routine for quasi-definite linear system.")
(license license:asl2.0)))
+(define-public python-ruffus
+ (package
+ (name "python-ruffus")
+ (version "2.8.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ruffus" version))
+ (sha256
+ (base32
+ "1ai673k1s94s8b6pyxai8mk17p6zvvyi87rl236fs6ls8mpdklvc"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "ruffus/test"
+ (invoke "bash" "run_all_unit_tests3.cmd"))))))))
+ (native-inputs
+ (list python-pytest))
+ (home-page "http://www.ruffus.org.uk")
+ (synopsis "Light-weight computational pipeline management")
+ (description
+ "Ruffus is designed to allow scientific and other analyses to be
+automated with the minimum of fuss and the least effort.")
+ (license license:expat)))
+
(define-public python-scikit-allel
(package
(name "python-scikit-allel")
@@ 1746,6 1959,25 @@ the SciPy stack. It provides many user-friendly and efficient numerical
routines such as routines for numerical integration and optimization.")
(license license:bsd-3)))
+(define-public python-simple-pid
+ (package
+ (name "python-simple-pid")
+ (version "2.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "simple_pid" version))
+ (sha256
+ (base32
+ "17p9bgka5yv5lbnbk374yjccrlizm572wv3xb479072lahf7cwap"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest python-setuptools python-wheel))
+ (home-page "https://github.com/m-lundberg/simple-pid")
+ (synopsis "Easy to use PID controller")
+ (description "This package provides a simple and easy-to-use @acronym{PID,
+proportional-integral-derivative} controller.")
+ (license license:expat)))
+
(define-public python-snakemake-interface-common
(package
(name "python-snakemake-interface-common")
@@ 2212,39 2444,6 @@ interpolation of 1D data (for example, time series) with splines.")
Evapotranspiration using various standard methods.")
(license license:expat)))
-(define-public python-nibabel
- (package
- (name "python-nibabel")
- (version "5.3.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "nibabel" version))
- (sha256
- (base32 "16snprwgp7qzp51j3mx0zdn7brvx6r14ankldi24ny0w7d8adp0b"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- ;; AttributeError: 'dict' object has no attribute 'add'.
- #:test-flags #~(list "-k" "not test_first and not test_second")))
- (propagated-inputs (list python-importlib-resources python-numpy
- python-packaging python-typing-extensions))
- (native-inputs (list python-hatch-vcs
- python-hatchling
- python-pytest
- python-pytest-httpserver
- python-pytest-xdist))
- (home-page "https://nipy.org/nibabel/")
- (synopsis "Read and write access to common neuroimaging file formats")
- (description
- "@code{nibabel} is a library that provides read and write access to
-common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2
-and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD,
-ECAT and Philips PAR/REC. In addition, NiBabel also supports FreeSurfer’s
-MGH, geometry, annotation and morphometry files, and provides some limited
-support for DICOM.")
- (license license:expat))) ; and other non-copyleft licenses
-
(define-public python-tspex
(package
(name "python-tspex")
@@ 2960,26 3159,6 @@ changed, it made sense to abstract away the nuisance of having to re-learn
them.")
(license license:bsd-3)))
-(define-public python-fastcluster
- (package
- (name "python-fastcluster")
- (version "1.2.6")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "fastcluster" version))
- (sha256
- (base32 "19labbgnq85p4r4jbli2p045lgh57larhi2g2anagfxnlzpqdf5a"))))
- (build-system pyproject-build-system)
- (propagated-inputs (list python-numpy))
- (native-inputs (list python-scipy python-setuptools python-wheel))
- (home-page "https://danifold.net/fastcluster.html")
- (synopsis "Fast hierarchical clustering routines for R and Python")
- (description "The fastcluster package implements seven common hierarchical
-clustering schemes efficiently. The package is made with two interfaces to
-standard software: R and Python.")
- (license license:bsd-2)))
-
(define-public python-fbpca
(package
(name "python-fbpca")
@@ 3381,37 3560,6 @@ by numpy using the highly efficient @code{msgpack} format. Serialization of
Python's native complex data types is also supported.")
(license license:bsd-3)))
-(define-public python-ruffus
- (package
- (name "python-ruffus")
- (version "2.8.4")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ruffus" version))
- (sha256
- (base32
- "1ai673k1s94s8b6pyxai8mk17p6zvvyi87rl236fs6ls8mpdklvc"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (delete 'check)
- (add-after 'install 'check
- (lambda* (#:key tests? inputs outputs #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "ruffus/test"
- (invoke "bash" "run_all_unit_tests3.cmd"))))))))
- (native-inputs
- (list python-pytest))
- (home-page "http://www.ruffus.org.uk")
- (synopsis "Light-weight computational pipeline management")
- (description
- "Ruffus is designed to allow scientific and other analyses to be
-automated with the minimum of fuss and the least effort.")
- (license license:expat)))
-
(define-public python-scs
(package
(name "python-scs")
@@ 4321,27 4469,6 @@ visual integration of spatially referenced datasets.")
to do spectral analysis in Python.")
(license license:expat)))
-(define-public python-climin
- (package
- (name "python-climin")
- (version "0.1a1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "climin" version))
- (sha256
- (base32
- "1wpjisd5zzi5yvjff02hnxn84822k8sdxvvd33lil2x79wdb36rv"))))
- (build-system python-build-system)
- (native-inputs (list python-nose))
- (propagated-inputs (list python-numpydoc python-numpy python-scipy))
- (home-page "https://github.com/BRML/climin")
- (synopsis "Optimization for machine learning")
- (description
- "@command{climin} is a Python package for optimization,
-heavily biased to machine learning scenarios. It works on top of
-@command{numpy} and (partially) @command{gnumpy}.")
- (license license:bsd-3)))
-
(define-public python-paramz
(package
(name "python-paramz")
@@ 4562,25 4689,6 @@ of use as pickling or @code{numpy.save}, but with the language
interoperability offered by HDF5.")
(license license:bsd-3))))
-(define-public python-simple-pid
- (package
- (name "python-simple-pid")
- (version "2.0.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "simple_pid" version))
- (sha256
- (base32
- "17p9bgka5yv5lbnbk374yjccrlizm572wv3xb479072lahf7cwap"))))
- (build-system pyproject-build-system)
- (native-inputs
- (list python-pytest python-setuptools python-wheel))
- (home-page "https://github.com/m-lundberg/simple-pid")
- (synopsis "Easy to use PID controller")
- (description "This package provides a simple and easy-to-use @acronym{PID,
-proportional-integral-derivative} controller.")
- (license license:expat)))
-
(define-public python-supersmoother
(package
(name "python-supersmoother")
@@ 4611,32 4719,6 @@ Friedman's SuperSmoother} based in Python. It makes use of numpy for fast
numerical computation.")
(license license:bsd-2)))
-(define-public python-opt-einsum
- (package
- (name "python-opt-einsum")
- (version "3.3.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "opt_einsum" version))
- (sha256
- (base32
- "0jb5lia0q742d1713jk33vlj41y61sf52j6pgk7pvhxvfxglgxjr"))))
- (build-system pyproject-build-system)
- (propagated-inputs (list python-numpy))
- (native-inputs
- (list python-pytest python-pytest-cov python-setuptools python-wheel))
- (home-page "https://github.com/dgasmith/opt_einsum")
- (synopsis "Optimizing numpys einsum function")
- (description
- "Optimized einsum can significantly reduce the overall execution time of
-einsum-like expressions by optimizing the expression's contraction order and
-dispatching many operations to canonical BLAS, cuBLAS, or other specialized
-routines. Optimized einsum is agnostic to the backend and can handle NumPy,
-Dask, PyTorch, Tensorflow, CuPy, Sparse, Theano, JAX, and Autograd arrays as
-well as potentially any library which conforms to a standard API. See the
-documentation for more information.")
- (license license:expat)))
-
(define-public python-vaex-core
(package
(name "python-vaex-core")
@@ 4755,56 4837,6 @@ fractional factorial methods.")
NeuroML2 models.")
(license license:lgpl3)))
-(define-public python-pynetdicom
- (package
- (name "python-pynetdicom")
- (version "2.1.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "pynetdicom" version))
- (sha256
- (base32
- "1smzrnc93nmv8jz4np9knas74a46b1nhb3hjpf8n9vfpxypgnwcn"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- ;; Tests takes about 10-15min to complete.
- ;; Skip tests that require networking.
- #~(list "-k" (string-append
- " not TestFindSCP"
- " and not TestQRGetServiceClass"
- " and not TestQRMoveServiceClass"
- " and not TestStoreSCP"
- " and not test_ae.py"
- " and not test_echoscp.py"
- " and not test_qrscp_echo.py"
- " and not test_storescp.py"
- " and not test_pr_level_patient"
- " and not test_pr_level_series"
- " and not test_scp_cancelled"))))
- (native-inputs (list python-codespell
- python-coverage
- python-poetry-core
- python-pytest
- python-pytest-cov
- python-pytest-xdist
- python-sphinx
- python-sphinx-rtd-theme))
- (propagated-inputs (list python-mypy
- python-numpydoc
- python-pydicom
- python-pyfakefs
- python-sqlalchemy))
- (home-page "https://github.com/pydicom/pynetdicom")
- (synopsis "Python implementation of the DICOM networking protocol")
- (description
- "@code{pynetdicom} is a Python package that implements the DICOM
-networking protocol. It allows the easy creation of DICOM
-@acronym{SCUs,Service Class Users} and @acronym{SCPs,Service Class
-Providers}.")
- (license license:expat)))
-
(define-public python-pynrrd
(package
(name "python-pynrrd")
@@ 4911,38 4943,6 @@ and PySide6. It is intended for use in mathematics, scientific or engineering
applications.")
(license license:expat)))
-(define-public python-libneuroml
- (package
- (name "python-libneuroml")
- (version "0.6.5")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/NeuralEnsemble/libNeuroML.git")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "04cfff9phm19x87p86xrkhd6wlpxvdwk3rf1c3qgyncfchws0sjh"))))
- (build-system pyproject-build-system)
- (native-inputs
- (list python-pytest
- python-numpy
- python-setuptools
- python-tables
- python-wheel))
- (propagated-inputs
- (list python-lxml
- python-natsort
- python-networkx))
- (home-page "https://libneuroml.readthedocs.org/en/latest/")
- (synopsis
- "Python library for working with NeuroML descriptions of neuronal models")
- (description
- "This package provides a Python library for working with NeuroML descriptions of
-neuronal models")
- (license license:bsd-3)))
-
(define-public snakemake
(package
(name "snakemake")