Merge remote-tracking branch 'origin/master' into core-updates

1 files changed, 95 insertions, 9 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index a1e2b57669..79ee7c8bb2 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 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2020, 2021 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>
@@ -9,7 +9,7 @@
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
-;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -36,6 +36,8 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages sphinx)
@@ -240,18 +242,34 @@ logic, also known as grey logic.")
 (define-public python-scikit-image
   (package
     (name "python-scikit-image")
-    (version "0.17.2")
+    (version "0.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scikit-image" version))
        (sha256
-        (base32 "1cyqqbcbrg3prc36wis0sm3q5rjhd7h9bp33jwfyixzhi02lr5dx"))))
+        (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
     (build-system python-build-system)
     (arguments
-     ;; TODO: Some tests require running X11 server. Disable them?
-     '(#:tests? #f))
-    ;; See DEPENDS.txt for the list of build and run time requiremnts
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp")
+             #t))
+         (replace 'build
+           (lambda _
+             (invoke "make")))
+         (replace 'check
+           (lambda _
+             ;; The following tests require online data.
+             (invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
+                     (string-append "not test_ndim"
+                                    " and not test_skin")))))))
+    ;; See requirements/ for the list of build and run time requirements.
+    ;; NOTE: scikit-image has an optional dependency on python-pooch, however
+    ;; propagating it would enable many more tests that require online data.
     (propagated-inputs
      `(("python-cloudpickle" ,python-cloudpickle)
        ("python-dask" ,python-dask)
@@ -262,10 +280,15 @@ logic, also known as grey logic.")
        ("python-pillow" ,python-pillow)
        ("python-pywavelets" ,python-pywavelets)
        ("python-scipy" ,python-scipy)
-       ("python-six" ,python-six)
        ("python-tifffile" ,python-tifffile)))
     (native-inputs
-     `(("python-cython" ,python-cython)))
+     `(("python-codecov" ,python-codecov)
+       ("python-cython" ,python-cython)
+       ("python-flake8" ,python-flake8)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-localserver" ,python-pytest-localserver)
+       ("python-wheel" ,python-wheel)))
     (home-page "https://scikit-image.org/")
     (synopsis "Image processing in Python")
     (description
@@ -531,3 +554,66 @@ serialization and deserialization of numerical and array data types provided
 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-statannot
+  (package
+    (name "python-statannot")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "statannot" version))
+       (sha256
+        (base32
+         "1f8c2sylzr7lpjbyqxsqlp9xi8rj3d8c9hfh98x4jbb83zxc4026"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-seaborn" ,python-seaborn)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pandas" ,python-pandas)
+       ("python-scipy" ,python-scipy)))
+    (home-page
+     "https://github.com/webermarcolivier/statannot")
+    (synopsis "Add annotations to existing plots generated by seaborn")
+    (description
+     "This is a Python package to compute statistical test and add statistical
+annotations on an existing boxplots and barplots generated by seaborn.")
+    (license license:expat)))
+
+(define-public python-upsetplot
+  (package
+    (name "python-upsetplot")
+    (version "0.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "UpSetPlot" version))
+       (sha256
+        (base32
+         "0kwljcmsvrxm33y3ssham2bwv4a5m31mv96y9h18va0cv7s3mqn1"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-versioning
+           (lambda _
+             (substitute* "setup.py"
+               (("pytest-cov<2.6") "pytest-cov"))))
+         (replace 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-v" "--doctest-modules"))))))
+    (propagated-inputs
+     `(("python-matplotlib" ,python-matplotlib)
+       ("python-pandas" ,python-pandas)))
+    (native-inputs
+     `(("python-pytest-runner" ,python-pytest-runner)
+       ("python-pytest-cov" ,python-pytest-cov)))
+    (home-page "https://upsetplot.readthedocs.io")
+    (synopsis "Draw UpSet plots with Pandas and Matplotlib")
+    (description
+     "This is a Python implementation of UpSet plots by Lex et al.
+UpSet plots are used to visualize set overlaps; like Venn diagrams but more
+readable.")
+    (license license:bsd-3)))