Merge branch 'master' into emacs-team

1 files changed, 127 insertions, 2 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 938deaec6a..86ba4209fd 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -50,6 +50,7 @@
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages geo)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages machine-learning)
@@ -209,6 +210,33 @@ routines such as routines for numerical integration and optimization.")
 genetic variation data.")
     (license license:expat)))
 
+(define-public python-scikit-fem
+  (package
+    (name "python-scikit-fem")
+    (version "8.1.0")
+    (source (origin
+              (method git-fetch)        ; no tests in PyPI
+              (uri (git-reference
+                    (url "https://github.com/kinnala/scikit-fem")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1zpn0wpsvls5nkrav5a43z77yg9nc09dpyy9ri0dpmpm2ndh2mhs"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; Examples below require python-autograd and python-pyamg.
+     (list #:test-flags #~(list "-k" "not TestEx32 and not TestEx45")))
+    (propagated-inputs (list python-meshio python-numpy python-scipy))
+    (native-inputs (list python-pytest))
+    (home-page "https://scikit-fem.readthedocs.io/en/latest/")
+    (synopsis "Library for performing finite element assembly")
+    (description
+     "@code{scikit-fem} is a library for performing finite element assembly.
+Its main purpose is the transformation of bilinear forms into sparse matrices
+and linear forms into vectors.")
+    (license license:bsd-3)))
+
 (define-public python-scikit-fuzzy
   (package
     (name "python-scikit-fuzzy")
@@ -1149,7 +1177,7 @@ Mathematics (GLM) library to Python.")
 (define-public python-distributed
   (package
     (name "python-distributed")
-    (version "2023.4.1")
+    (version "2023.7.0")
     (source
      (origin
        ;; The test files are not included in the archive on pypi
@@ -1160,7 +1188,7 @@ Mathematics (GLM) library to Python.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "164xp2dxac95nngmgdhlk0vwnnvbmajqliz994bdvw72xnv1ya18"))))
+         "0b93fpwz7kw31pkzfyihpkw8mzbqshzd6rw5vcwld7n3z2aaaxxb"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1470,6 +1498,103 @@ pandas code.")
 aggregated sum and more.")
     (license license:bsd-3)))
 
+(define-public python-plotnine
+  (package
+    (name "python-plotnine")
+    ;; XXX Version 0.12.x exists, but we can't build it because we're still at
+    ;; matplotlib 3.5.  We'd need at least 3.6.
+    (version "0.10.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/has2k1/plotnine")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0lg53wcm00lj8zbb4q9yj4a0n0fqaqq7c7vj18bda0k56gg0fpwl"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; These all fail because the images are considered to be too different,
+      ;; though they really do look fine.
+      '(list "-k" (string-append
+                   "not TestThemes"
+                   (string-join
+                    (list
+                     ;; Image tests
+                     "test_adjust_text"
+                     "test_annotation_logticks_coord_flip_discrete"
+                     "test_annotation_logticks_faceting"
+                     "test_arrow"
+                     "test_aslabeller_dict_0tag"
+                     "test_caption_simple"
+                     "test_continuous_x"
+                     "test_continuous_x_fullrange"
+                     "test_coord_trans_backtransforms"
+                     "test_coord_trans_se_false"
+                     "test_datetime_scale_limits"
+                     "test_dir_v_ncol"
+                     "test_discrete_x"
+                     "test_discrete_x_fullrange"
+                     "test_facet_grid_drop_false"
+                     "test_facet_grid_expression"
+                     "test_facet_grid_space_ratios"
+                     "test_facet_wrap"
+                     "test_facet_wrap_expression"
+                     "test_facet_wrap_label_both"
+                     "test_label_context_wrap2vars"
+                     "test_labeller_cols_both_grid"
+                     "test_labeller_cols_both_wrap"
+                     "test_labeller_towords"
+                     "test_missing_data_discrete_scale"
+                     "test_ribbon_facetting"
+                     "test_stack_non_linear_scale"
+                     "test_uneven_num_of_lines"
+
+                     ;; Missing optional modules
+                     "test_non_linear_smooth"
+                     "test_non_linear_smooth_no_ci")
+                    " and not " 'prefix)))
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'pre-check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; The data files are referenced by the tests but they are not
+             ;; installed.
+             (copy-recursively "plotnine/data"
+                               (string-append (site-packages inputs outputs)
+                                              "/plotnine/data"))
+             ;; Matplotlib needs to be able to write its configuration file
+             ;; somewhere.
+             (setenv "MPLCONFIGDIR" "/tmp")
+             (setenv "TZ" "UTC")
+             (setenv "TZDIR"
+                     (search-input-directory inputs "share/zoneinfo")))))))
+    (propagated-inputs
+     (list python-adjusttext
+           python-matplotlib
+           python-mizani
+           python-numpy
+           python-patsy
+           python-scipy
+           python-statsmodels))
+    (native-inputs
+     (list python-geopandas
+           python-mock
+           python-pandas
+           python-pytest python-pytest-cov
+           tzdata-for-tests))
+    (home-page "https://github.com/has2k1/plotnine")
+    (synopsis "Grammar of Graphics for Python")
+    (description
+     "Plotnine is a Python implementation of the Grammar of Graphics.
+It is a powerful graphics concept for creating plots and visualizations in a
+structured and declarative manner.  It is inspired by the R package ggplot2
+and aims to provide a similar API and functionality in Python.")
+    (license license:expat)))
+
 (define-public python-pyvista
   (package
     (name "python-pyvista")