Merge branch 'master' into core-updates.

Conflicts:
	gnu/local.mk
	gnu/packages/build-tools.scm
	gnu/packages/certs.scm
	gnu/packages/check.scm
	gnu/packages/compression.scm
	gnu/packages/cups.scm
	gnu/packages/fontutils.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/guile.scm
	gnu/packages/ibus.scm
	gnu/packages/image-processing.scm
	gnu/packages/linux.scm
	gnu/packages/music.scm
	gnu/packages/nss.scm
	gnu/packages/pdf.scm
	gnu/packages/python-xyz.scm
	gnu/packages/qt.scm
	gnu/packages/ruby.scm
	gnu/packages/shells.scm
	gnu/packages/tex.scm
	gnu/packages/video.scm
	gnu/packages/vulkan.scm
	gnu/packages/web.scm
	gnu/packages/webkit.scm
	gnu/packages/wm.scm

1 files changed, 120 insertions, 45 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 37beb5ed61..c0a1c4794f 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -158,6 +158,57 @@ 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-scikit-allel
+  (package
+    (name "python-scikit-allel")
+    (version "1.3.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scikit-allel" version))
+       (sha256
+        (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+              ;; AttributeError: 'Dataset' object has no attribute 'asstr'
+              "not test_vcf_to_hdf5"
+              " and not test_vcf_to_hdf5_exclude"
+              " and not test_vcf_to_hdf5_rename"
+              " and not test_vcf_to_hdf5_group"
+              " and not test_vcf_to_hdf5_ann"
+              ;; Does not work with recent hmmlearn
+              " and not test_roh_mhmm_0pct"
+              " and not test_roh_mhmm_100pct"))
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'build-ext
+           (lambda _
+             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs
+     (list python-dask
+           python-numpy))
+    (native-inputs
+     (list python-cython
+           ;; The following are all needed for the tests
+           htslib
+           python-h5py
+           python-hmmlearn
+           python-numexpr
+           python-pytest
+           python-scipy
+           python-setuptools-scm
+           python-zarr))
+    (home-page "https://github.com/cggh/scikit-allel")
+    (synopsis "Explore and analyze genetic variation data")
+    (description
+     "This package provides utilities for exploratory analysis of large scale
+genetic variation data.")
+    (license license:expat)))
+
 (define-public python-scikit-fuzzy
   (package
     (name "python-scikit-fuzzy")
@@ -234,53 +285,33 @@ logic, also known as grey logic.")
      "Scikit-image is a collection of algorithms for image processing.")
     (license license:bsd-3)))
 
-(define-public python-scikit-allel
+(define-public python-scikit-optimize
   (package
-    (name "python-scikit-allel")
-    (version "1.3.5")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "scikit-allel" version))
-        (sha256
-         (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
-    (build-system python-build-system)
-    (arguments
-     (list
-       #:phases
-       #~(modify-phases %standard-phases
-           (replace 'check
-             (lambda* (#:key tests? #:allow-other-keys)
-               (when tests?
-                 (invoke "python" "setup.py" "build_ext" "--inplace")
-                 (invoke "python" "-m" "pytest" "-v" "allel"
-                         ;; AttributeError: 'Dataset' object has no attribute 'asstr'
-                         "-k" (string-append
-                                "not test_vcf_to_hdf5"
-                                " and not test_vcf_to_hdf5_exclude"
-                                " and not test_vcf_to_hdf5_rename"
-                                " and not test_vcf_to_hdf5_group"
-                                " and not test_vcf_to_hdf5_ann"))))))))
+    (name "python-scikit-optimize")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "scikit-optimize" version))
+              (sha256
+               (base32
+                "0230ya8bwrzxjwcy2vz23a3hg6caggnnmg2vq1f9zz2797kckn3p"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-dask
-           python-numpy))
+     (list python-joblib
+           python-matplotlib
+           python-numpy
+           python-pyaml
+           python-scikit-learn
+           python-scipy))
     (native-inputs
-     (list python-cython
-           ;; The following are all needed for the tests
-           htslib
-           python-h5py
-           python-hmmlearn
-           python-numexpr
-           python-pytest
-           python-scipy
-           python-setuptools-scm
-           python-zarr))
-    (home-page "https://github.com/cggh/scikit-allel")
-    (synopsis "Explore and analyze genetic variation data")
-    (description
-     "This package provides utilities for exploratory analysis of large scale
-genetic variation data.")
-    (license license:expat)))
+     (list python-pytest))
+    (home-page "https://scikit-optimize.github.io/")
+    (synopsis "Sequential model-based optimization toolbox")
+    (description "Scikit-Optimize, or @code{skopt}, is a simple and efficient
+library to minimize (very) expensive and noisy black-box functions.  It
+implements several methods for sequential model-based optimization.
+@code{skopt} aims to be accessible and easy to use in many contexts.")
+    (license license:bsd-3)))
 
 (define-public python-trimesh
   (package
@@ -1677,6 +1708,50 @@ 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-pylems
+  (package
+    (name "python-pylems")
+    (version "0.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "PyLEMS" version))
+              (sha256
+               (base32
+                "074azbyivjbwi61fs5p8z9n6d8nk8xw6fmln1www13z1dccb3740"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-lxml))
+    (home-page "https://github.com/LEMS/pylems")
+    (synopsis
+     "Python support for the Low Entropy Model Specification language (LEMS)")
+    (description
+     "A LEMS simulator written in Python which can be used to run
+NeuroML2 models.")
+    (license license:lgpl3)))
+
+(define-public python-libneuroml
+  (package
+    (name "python-libneuroml")
+    (version "0.4.1")
+    (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
+                "0mrm4rd6x1sm6hkvhk20mkqp9q53sl3lbvq6hqzyymkw1iqq6bhy"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-lxml python-six))
+    (native-inputs (list python-pytest python-numpy python-tables))
+    (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)))
+    
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar