gnu: packages/python-science: Sort packages.

* gnu/packages/python-science.scm: (python-asap3, python-baycomp,
python-clarabel, python-hist, python-numpoly, python-particle,
python-uhi, python-vector): Sort variables alphabetically.

Change-Id: Idd202a03a518774d204de6292d74fbe53ea5761e

1 files changed, 236 insertions, 236 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index f7aca11a6a..d4e51ba3f0 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -297,6 +297,25 @@ specification and test suite in Python.")
 supersedes the RTED algorithm for computing the tree edit distance.")
       (license license:expat))))
 
+(define-public python-asap3
+  (package
+    (name "python-asap3")
+    (version "3.13.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asap3" version))
+       (sha256
+        (base32 "0z6m9ybiy4fdnzlkfkvyxich18iwlwlgj1jd99fylyfwf8l160am"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-ase))
+    (native-inputs (list python-setuptools python-wheel which))
+    (home-page "https://wiki.fysik.dtu.dk/asap")
+    (synopsis "ASAP - classical potentials for Molecular Dynamics with ASE.")
+    (description "This package provides accelerated simulations and potentials
+of solids.")
+    (license license:lgpl3)))
+
 (define-public python-ase
   (package
     (name "python-ase")
@@ -327,6 +346,32 @@ setting up, manipulating, running, visualizing and analyzing atomistic
 simulations.")
     (license license:lgpl2.1+)))
 
+(define-public python-baycomp
+  (package
+    (name "python-baycomp")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "baycomp" version))
+       (sha256
+        (base32 "1v6s4mfr6xzjbv9a2v89hywm6fbv5nii0qczvcfjanvdn7bmmcij"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest python-setuptools python-wheel))
+    (propagated-inputs
+     (list python-matplotlib python-numpy python-scipy))
+    (home-page "https://github.com/janezd/baycomp")
+    (synopsis "Library for comparison of Bayesian classifiers")
+    (description
+     "Baycomp is a library for Bayesian comparison of classifiers.  Functions
+in the library compare two classifiers on one or on multiple data sets.  They
+compute three probabilities: the probability that the first classifier has
+higher scores than the second, the probability that differences are within the
+region of practical equivalence (rope), or that the second classifier has
+higher scores.")
+    (license license:expat)))
+
 (define-public python-boost-histogram
   (package
     (name "python-boost-histogram")
@@ -354,6 +399,62 @@ simulations.")
 one of the fastest libraries for histogramming.")
     (license license:bsd-3)))
 
+(define-public python-clarabel
+  (package
+    (name "python-clarabel")
+    (version "0.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "clarabel" version))
+       (sha256
+        (base32 "15k32ynvh45n9q905bxwamh5w5cia9bxzmwz69wbribmyhsv22m3"))
+       (patches
+        (search-patches "python-clarabel-blas.patch"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list
+      #:imported-modules `(,@%cargo-build-system-modules
+                           ,@%pyproject-build-system-modules)
+      #:modules '((guix build cargo-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'build 'build-python-module
+            (assoc-ref py:%standard-phases 'build))
+          (add-after 'build-python-module 'install-python-module
+            (assoc-ref py:%standard-phases 'install)))
+      #:cargo-inputs
+      `(("rust-amd" ,rust-amd-0.2)
+        ("rust-blas" ,rust-blas-0.22)
+        ("rust-cfg-if" ,rust-cfg-if-1)
+        ("rust-derive-builder" ,rust-derive-builder-0.11)
+        ("rust-enum-dispatch" ,rust-enum-dispatch-0.3) ;0.3.8
+        ("rust-itertools" ,rust-itertools-0.11)
+        ("rust-lapack" ,rust-lapack-0.19)
+        ("rust-lazy-static" ,rust-lazy-static-1) ;1.4
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-num-derive" ,rust-num-derive-0.2)
+        ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-pyo3" ,rust-pyo3-0.20)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-serde-json" ,rust-serde-json-1)
+        ("rust-thiserror" ,rust-thiserror-1))
+      #:features '(list "python")
+      #:install-source? #false))
+    (inputs
+     (list maturin))
+    (native-inputs
+     (list python-wrapper))
+    (propagated-inputs (list python-numpy python-scipy))
+    (home-page "https://github.com/oxfordcontrol/Clarabel.rs")
+    (synopsis "Interior-point solver for convex conic optimisation problems")
+    (description "Clarabel.rs is a Rust implementation of an interior point
+numerical solver for convex optimization problems using a novel homogeneous
+embedding.")
+    (license license:asl2.0)))
+
 (define-public python-cmocean
   (package
     (name "python-cmocean")
@@ -632,6 +733,31 @@ constants in the HEP System of Units, as derived from the basic units
 originally defined by the CLHEP project.")
     (license license:bsd-3)))
 
+(define-public python-hist
+  (package
+    (name "python-hist")
+    (version "2.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hist" version))
+       (sha256
+        (base32 "17cd46c0ixq18fr2kgzam09w1sr4qkd9l6nsjdbl4vggw80ck9vx"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-boost-histogram
+                             python-histoprint
+                             python-numpy
+                             python-typing-extensions))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-pytest-mpl))
+    (home-page "https://hist.readthedocs.io/en/latest/")
+    (synopsis "Hist classes and utilities")
+    (description
+     "Hist is an analyst-friendly front-end for @code{boost-histogram}.")
+    (license license:bsd-3)))
+
 (define-public python-histoprint
   (package
     (name "python-histoprint")
@@ -842,6 +968,32 @@ allowing the user to specify whether complex-step, central, forward or
 backward differences are used.")
     (license license:bsd-3)))
 
+(define-public python-numpoly
+  (package
+    (name "python-numpoly")
+    (version "1.2.11")
+    (source (origin
+              (method git-fetch) ;; PyPI is missing some Pytest fixtures
+              (uri (git-reference
+                    (url "https://github.com/jonathf/numpoly")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "01g21v91f4d66xd0bvap0n6d6485w2fnq1636gx6h2s42550rlbd"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-importlib-metadata python-numpy))
+    (native-inputs (list python-pytest python-setuptools python-sympy
+                         python-wheel))
+    (home-page "https://numpoly.readthedocs.io/en/master/")
+    (synopsis "Polynomials as a numpy datatype")
+    (description "Numpoly is a generic library for creating, manipulating and
+evaluating arrays of polynomials based on @code{numpy.ndarray objects}.")
+    ;; Tests fail with dtype mismatches on 32-bit architectures, suggesting
+    ;; that numpoly only supports 64 bit platforms.
+    (supported-systems '("x86_64-linux" "aarch64-linux" "powerpc64le-linux"))
+    (license license:bsd-2)))
+
 (define-public python-numpy-groupies
   (package
     (name "python-numpy-groupies")
@@ -922,6 +1074,34 @@ aggregated sum and more.")
 numerical optimization package.")
     (license license:asl2.0)))
 
+(define-public python-particle
+  (package
+    (name "python-particle")
+    (version "0.25.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "particle" version))
+       (sha256
+        (base32 "0as50k5hinxszsm6lnghnmx2cyjy77c0i2gvzf2q64g2x5b7xkvq"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-attrs
+                             python-hepunits
+                             python-typing-extensions))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pandas
+                         python-pytest
+                         python-pytest-benchmark
+                         python-tabulate))
+    (home-page "https://github.com/scikit-hep/particle")
+    (synopsis "Extended PDG particle data and MC identification codes")
+    (description
+     "@code{Particle} provides a pythonic interface to the Particle Data Group
+(PDG) particle data tables and particle identification codes, with extended
+particle information and extra goodies.")
+    (license license:bsd-3)))
+
 (define-public python-pint
   (package
     (name "python-pint")
@@ -1732,58 +1912,6 @@ its software deployment plugins.")
 Snakemake and its storage plugins.")
     (license license:expat)))
 
-(define-public python-uhi
-  (package
-    (name "python-uhi")
-    (version "0.5.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "uhi" version))
-       (sha256
-        (base32 "0753b7yw0zi06g4azafnk3w8i3q6js9i6wwg3pya464gygrbnncm"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-numpy))
-    (native-inputs (list python-boost-histogram
-                         python-fastjsonschema
-                         python-hatch-vcs
-                         python-hatchling
-                         python-pytest))
-    (home-page "https://github.com/scikit-hep/uhi")
-    (synopsis "Universal Histogram Interface")
-    (description "This is a package meant primarily for documenting histogram
-indexing and the PlottableHistogram Protocol and any future cross-library
-standards.  It also contains the code for the PlottableHistogram Protocol, to
-be used in type checking libraries wanting to conform to the protocol.  It is
-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-hist
-  (package
-    (name "python-hist")
-    (version "2.8.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "hist" version))
-       (sha256
-        (base32 "17cd46c0ixq18fr2kgzam09w1sr4qkd9l6nsjdbl4vggw80ck9vx"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-boost-histogram
-                             python-histoprint
-                             python-numpy
-                             python-typing-extensions))
-    (native-inputs (list python-hatch-vcs
-                         python-hatchling
-                         python-pytest
-                         python-pytest-mpl))
-    (home-page "https://hist.readthedocs.io/en/latest/")
-    (synopsis "Hist classes and utilities")
-    (description
-     "Hist is an analyst-friendly front-end for @code{boost-histogram}.")
-    (license license:bsd-3)))
-
 (define-public python-tdda
   (package
     (name "python-tdda")
@@ -1830,63 +1958,6 @@ reference testing, constraint discovery for data, automatic inference
 of regular expressions from text data and automatic test generation.")
     (license license:expat))) ; MIT License
 
-(define-public python-particle
-  (package
-    (name "python-particle")
-    (version "0.25.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "particle" version))
-       (sha256
-        (base32 "0as50k5hinxszsm6lnghnmx2cyjy77c0i2gvzf2q64g2x5b7xkvq"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-attrs
-                             python-hepunits
-                             python-typing-extensions))
-    (native-inputs (list python-hatch-vcs
-                         python-hatchling
-                         python-pandas
-                         python-pytest
-                         python-pytest-benchmark
-                         python-tabulate))
-    (home-page "https://github.com/scikit-hep/particle")
-    (synopsis "Extended PDG particle data and MC identification codes")
-    (description
-     "@code{Particle} provides a pythonic interface to the Particle Data Group
-(PDG) particle data tables and particle identification codes, with extended
-particle information and extra goodies.")
-    (license license:bsd-3)))
-
-(define-public python-vector
-  (package
-    (name "python-vector")
-    (version "1.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "vector" version))
-       (sha256
-        (base32 "1jhfgx54a6l1cz9as2wlwrph86f8s1882biaakx1cl31igdxjnbf"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; This file requires python-papermill (not yet packaged).
-      #:test-flags #~(list "--ignore" "tests/test_notebooks.py")))
-    (propagated-inputs (list python-numpy python-packaging))
-    (native-inputs (list python-awkward
-                         python-hatch-vcs
-                         python-hatchling
-                         python-pytest
-                         python-sympy))
-    (home-page "https://github.com/scikit-hep/vector")
-    (synopsis "Arrays of 2D, 3D, and Lorentz vectors")
-    (description "Vector is a Python library for 2D and 3D spatial vectors, as
-well as 4D space-time vectors.  It is especially intended for performing
-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-traittypes
   (package
     (name "python-traittypes")
@@ -2863,32 +2934,6 @@ Python module with the same interface, but (hopefully) faster.")
 written in C.")
     (license license:bsd-2)))
 
-(define-public python-numpoly
-  (package
-    (name "python-numpoly")
-    (version "1.2.11")
-    (source (origin
-              (method git-fetch) ;; PyPI is missing some Pytest fixtures
-              (uri (git-reference
-                    (url "https://github.com/jonathf/numpoly")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "01g21v91f4d66xd0bvap0n6d6485w2fnq1636gx6h2s42550rlbd"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-importlib-metadata python-numpy))
-    (native-inputs (list python-pytest python-setuptools python-sympy
-                         python-wheel))
-    (home-page "https://numpoly.readthedocs.io/en/master/")
-    (synopsis "Polynomials as a numpy datatype")
-    (description "Numpoly is a generic library for creating, manipulating and
-evaluating arrays of polynomials based on @code{numpy.ndarray objects}.")
-    ;; Tests fail with dtype mismatches on 32-bit architectures, suggesting
-    ;; that numpoly only supports 64 bit platforms.
-    (supported-systems '("x86_64-linux" "aarch64-linux" "powerpc64le-linux"))
-    (license license:bsd-2)))
-
 (define-public python-spin
   (package
   (name "python-spin")
@@ -2915,32 +2960,6 @@ changed, it made sense to abstract away the nuisance of having to re-learn
 them.")
   (license license:bsd-3)))
 
-(define-public python-baycomp
-  (package
-    (name "python-baycomp")
-    (version "1.0.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "baycomp" version))
-       (sha256
-        (base32 "1v6s4mfr6xzjbv9a2v89hywm6fbv5nii0qczvcfjanvdn7bmmcij"))))
-    (build-system pyproject-build-system)
-    (native-inputs
-     (list python-pytest python-setuptools python-wheel))
-    (propagated-inputs
-     (list python-matplotlib python-numpy python-scipy))
-    (home-page "https://github.com/janezd/baycomp")
-    (synopsis "Library for comparison of Bayesian classifiers")
-    (description
-     "Baycomp is a library for Bayesian comparison of classifiers.  Functions
-in the library compare two classifiers on one or on multiple data sets.  They
-compute three probabilities: the probability that the first classifier has
-higher scores than the second, the probability that differences are within the
-region of practical equivalence (rope), or that the second classifier has
-higher scores.")
-    (license license:expat)))
-
 (define-public python-fastcluster
   (package
     (name "python-fastcluster")
@@ -3022,6 +3041,33 @@ analysis} (PCA), SVD, and eigendecompositions via randomized methods")
 learning frameworks.")
     (license license:expat)))
 
+(define-public python-uhi
+  (package
+    (name "python-uhi")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "uhi" version))
+       (sha256
+        (base32 "0753b7yw0zi06g4azafnk3w8i3q6js9i6wwg3pya464gygrbnncm"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-boost-histogram
+                         python-fastjsonschema
+                         python-hatch-vcs
+                         python-hatchling
+                         python-pytest))
+    (home-page "https://github.com/scikit-hep/uhi")
+    (synopsis "Universal Histogram Interface")
+    (description "This is a package meant primarily for documenting histogram
+indexing and the PlottableHistogram Protocol and any future cross-library
+standards.  It also contains the code for the PlottableHistogram Protocol, to
+be used in type checking libraries wanting to conform to the protocol.  It is
+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-upsetplot
   (package
     (name "python-upsetplot")
@@ -3047,6 +3093,35 @@ UpSet plots are used to visualize set overlaps; like Venn diagrams but more
 readable.")
     (license license:bsd-3)))
 
+(define-public python-vector
+  (package
+    (name "python-vector")
+    (version "1.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "vector" version))
+       (sha256
+        (base32 "1jhfgx54a6l1cz9as2wlwrph86f8s1882biaakx1cl31igdxjnbf"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; This file requires python-papermill (not yet packaged).
+      #:test-flags #~(list "--ignore" "tests/test_notebooks.py")))
+    (propagated-inputs (list python-numpy python-packaging))
+    (native-inputs (list python-awkward
+                         python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-sympy))
+    (home-page "https://github.com/scikit-hep/vector")
+    (synopsis "Arrays of 2D, 3D, and Lorentz vectors")
+    (description "Vector is a Python library for 2D and 3D spatial vectors, as
+well as 4D space-time vectors.  It is especially intended for performing
+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-xarray
   (package
     (name "python-xarray")
@@ -4246,62 +4321,6 @@ visual integration of spatially referenced datasets.")
 to do spectral analysis in Python.")
     (license license:expat)))
 
-(define-public python-clarabel
-  (package
-    (name "python-clarabel")
-    (version "0.7.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "clarabel" version))
-       (sha256
-        (base32 "15k32ynvh45n9q905bxwamh5w5cia9bxzmwz69wbribmyhsv22m3"))
-       (patches
-        (search-patches "python-clarabel-blas.patch"))))
-    (build-system cargo-build-system)
-    (arguments
-     (list
-      #:imported-modules `(,@%cargo-build-system-modules
-                           ,@%pyproject-build-system-modules)
-      #:modules '((guix build cargo-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
-                  (guix build utils))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'build 'build-python-module
-            (assoc-ref py:%standard-phases 'build))
-          (add-after 'build-python-module 'install-python-module
-            (assoc-ref py:%standard-phases 'install)))
-      #:cargo-inputs
-      `(("rust-amd" ,rust-amd-0.2)
-        ("rust-blas" ,rust-blas-0.22)
-        ("rust-cfg-if" ,rust-cfg-if-1)
-        ("rust-derive-builder" ,rust-derive-builder-0.11)
-        ("rust-enum-dispatch" ,rust-enum-dispatch-0.3) ;0.3.8
-        ("rust-itertools" ,rust-itertools-0.11)
-        ("rust-lapack" ,rust-lapack-0.19)
-        ("rust-lazy-static" ,rust-lazy-static-1) ;1.4
-        ("rust-libc" ,rust-libc-0.2)
-        ("rust-num-derive" ,rust-num-derive-0.2)
-        ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-pyo3" ,rust-pyo3-0.20)
-        ("rust-serde" ,rust-serde-1)
-        ("rust-serde-json" ,rust-serde-json-1)
-        ("rust-thiserror" ,rust-thiserror-1))
-      #:features '(list "python")
-      #:install-source? #false))
-    (inputs
-     (list maturin))
-    (native-inputs
-     (list python-wrapper))
-    (propagated-inputs (list python-numpy python-scipy))
-    (home-page "https://github.com/oxfordcontrol/Clarabel.rs")
-    (synopsis "Interior-point solver for convex conic optimisation problems")
-    (description "Clarabel.rs is a Rust implementation of an interior point
-numerical solver for convex optimization problems using a novel homogeneous
-embedding.")
-    (license license:asl2.0)))
-
 (define-public python-climin
   (package
     (name "python-climin")
@@ -4924,25 +4943,6 @@ applications.")
 neuronal models")
     (license license:bsd-3)))
 
-(define-public python-asap3
-  (package
-    (name "python-asap3")
-    (version "3.13.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "asap3" version))
-       (sha256
-        (base32 "0z6m9ybiy4fdnzlkfkvyxich18iwlwlgj1jd99fylyfwf8l160am"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-ase))
-    (native-inputs (list python-setuptools python-wheel which))
-    (home-page "https://wiki.fysik.dtu.dk/asap")
-    (synopsis "ASAP - classical potentials for Molecular Dynamics with ASE.")
-    (description "This package provides accelerated simulations and potentials
-of solids.")
-    (license license:lgpl3)))
-
 (define-public snakemake
   (package
     (name "snakemake")