From 1c10ba3a249f797493cc67da48cbb58398425920 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 9 Oct 2019 12:54:39 +0200
Subject: gnu: python-packaging: Update to 19.2.

* gnu/packages/python-xyz.scm (python-packaging): Update to 19.2.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b0f5ec75881..1ae83dfa876 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12919,14 +12919,14 @@ several utilities, as well as an API for building localization tools.")
 (define-public python-packaging
   (package
     (name "python-packaging")
-    (version "19.0")
+    (version "19.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "packaging" version))
         (sha256
          (base32
-          "1brjhygq9dz6x1kdljivkjfldi3qf5rbkqgck1bpgv9qpv8ab60c"))))
+          "0izwlz9h0bw171a1chr311g2y7n657zjaf4mq4rgm8pp9lbj9f98"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
-- 
cgit v1.3


From 6ba6a1c103ea94f2c9a984db466c3b2829e8f175 Mon Sep 17 00:00:00 2001
From: Jesse Gibbons <jgibbons2357+guix@gmail.com>
Date: Sat, 16 Nov 2019 18:33:05 -0700
Subject: gnu: python-hy: Set HOME to /tmp before install
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes <https://bugs.gnu.org/38241>.

* gnu/packages/python-xyz.scm (python-hy)[arguments]: Add custom
'set-HOME phase before the 'install phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python-xyz.scm | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d2786e48265..5b8b33b87f0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8745,6 +8745,9 @@ with a new public API, and RPython support.")
     (arguments
      '(#:phases
        (modify-phases %standard-phases
+	 (add-before 'install 'set-HOME
+	   (lambda _
+	     (setenv "HOME" "/tmp")))
          (replace 'check
            (lambda _
              ;; Tests require write access to HOME.
-- 
cgit v1.3


From 85cfb0e9e6ccd57715ca6e6bfadfd2b161c08e4d Mon Sep 17 00:00:00 2001
From: Clément Lassieur <clement@lassieur.org>
Date: Tue, 19 Nov 2019 16:09:00 +0100
Subject: gnu: Add python-intelhex.

* gnu/packages/python-xyz.scm (python-intelhex): New variable.
---
 gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5b8b33b87f0..c3999d9cec0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -53,7 +53,7 @@
 ;;; Copyright © 2016, 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018, 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Luther Thompson <lutheroto@gmail.com>
 ;;; Copyright © 2018 Vagrant Cascadian <vagrant@debian.org>
@@ -16887,3 +16887,27 @@ qvarious formats: PDF, PostScript, PNG and even SVG.")
     (description "Pyphen is a pure Python module to hyphenate text using
 existing Hunspell hyphenation dictionaries.")
     (license (list license:gpl2 license:lgpl2.1 license:mpl1.1))))
+
+(define-public python-intelhex
+  (package
+    (name "python-intelhex")
+    (version "2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "intelhex" version))
+       (sha256
+        (base32
+         "0ckqjbxd8gwcg98gfzpn4vq1qxzfvq3rdbrr1hikj1nmw08qb780"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #f))          ;issue with version
+    (home-page "https://pypi.org/project/IntelHex/")
+    (synopsis "Python library for Intel HEX files manipulations")
+    (description "The Intel HEX file format is widely used in microprocessors
+and microcontrollers area (embedded systems etc.) as the de facto standard for
+representation of code to be programmed into microelectronic devices.  This
+package provides an intelhex Python library to read, write, create from
+scratch and manipulate data from Intel HEX file format.  It also includes
+several convenience Python scripts, including \"classic\" hex2bin and bin2hex
+converters and more, those based on the library itself.")
+    (license license:bsd-3)))
-- 
cgit v1.3


From c695f011b31146f68e8b4f86a40aaeef5972005b Mon Sep 17 00:00:00 2001
From: Konrad Hinsen <konrad.hinsen@fastmail.net>
Date: Tue, 19 Nov 2019 19:52:11 +0100
Subject: gnu: python2-scientific: New source code location.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/python-xyz.scm (python2-scientific): New source code location.
Following the annoucement of Bitbucket to delete all
Mercurial repositories in June 2020, the source code has
been migrated to GitHub.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python-xyz.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c3999d9cec0..c16633fba9a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14620,14 +14620,14 @@ is the new Pyro version that is actively developed.")
     (version "2.9.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/khinsen/"
-                           "scientificpython/downloads/ScientificPython-"
-                           version ".tar.gz"))
-       (file-name (string-append "ScientificPython-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/khinsen/ScientificPython")
+             (commit (string-append "rel" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0fc69zhlsn9d2jvbzyjl9ah53vj598h84nkq230c83ahfvgzx5y3"))))
+         "16l48aj9fps9r7jyk8gpxppwrv0fqvlc13sayxskz28r5s6sjwbl"))))
     (build-system python-build-system)
     (inputs
      `(("netcdf" ,netcdf)))
@@ -14645,7 +14645,7 @@ is the new Pyro version that is actively developed.")
              (invoke "python" "setup.py" "build"
                      (string-append "--netcdf_prefix="
                                     (assoc-ref inputs "netcdf"))))))))
-    (home-page "https://bitbucket.org/khinsen/scientificpython")
+    (home-page "http://dirac.cnrs-orleans.fr/ScientificPython")
     (synopsis "Python modules for scientific computing")
     (description "ScientificPython is a collection of Python modules that are
 useful for scientific computing.  Most modules are rather general (Geometry,
-- 
cgit v1.3


From fe9b72c5861fabdf7f37862de393812ff3e423ac Mon Sep 17 00:00:00 2001
From: Konrad Hinsen <konrad.hinsen@fastmail.net>
Date: Tue, 19 Nov 2019 19:52:50 +0100
Subject: gnu: python2-mmtk: Update to 2.7.12.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/python-xyz.scm (python2-mmtk): Update to 2.7.12.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python-xyz.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c16633fba9a..3b28fbb27fc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14657,16 +14657,17 @@ not actively maintained and works only with Python 2 and NumPy < 1.9.")
 (define-public python2-mmtk
   (package
     (name "python2-mmtk")
-    (version "2.7.11")
+    (version "2.7.12")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/khinsen/"
-                           "mmtk/downloads/MMTK-" version ".tar.gz"))
-       (file-name (string-append "MMTK-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/khinsen/MMTK")
+             (commit (string-append "rel" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1d0nnjx4lwsvh8f99vv1r6gi50d93yba0adkz8b4zgv4za4c5862"))))
+         "1fqwh3ba9jd42nigvn5shndgwb1zy7kh9520ncvqci7n8ffjr6p1"))))
     (build-system python-build-system)
     (native-inputs
      `(("netcdf" ,netcdf)))
-- 
cgit v1.3


From 7454078a7c2b6304e98741537419ae974aa1b618 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 14 Nov 2019 18:53:01 +0100
Subject: gnu: python-lazy-object-proxy: Update to 1.4.3.

* gnu/packages/python-xyz.scm (python-lazy-object-proxy): Update to 1.4.3.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3b28fbb27fc..8d53a59c407 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10855,13 +10855,13 @@ it will manage (install/update) them for you.")
 (define-public python-lazy-object-proxy
   (package
     (name "python-lazy-object-proxy")
-    (version "1.4.2")
+    (version "1.4.3")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lazy-object-proxy" version))
               (sha256
                (base32
-                "1wgl0fmddi0ind78a74yyk2qrr9pb5llvj1892cdpp6z6n6mn4zx"))))
+                "1w1aaay424ciz8fz3fkzxb0pxzfxn184f2whpyn4fx72bn50x47k"))))
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm-3.3)))
     (build-system python-build-system)
-- 
cgit v1.3


From 97610a661482cf28d580054d48a26557ee90f877 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 23 Nov 2019 14:48:14 +0100
Subject: gnu: python-whatever: Update to 0.6.

* gnu/packages/python-xyz.scm (python-whatever): Update to 0.6.
---
 gnu/packages/python-xyz.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8d53a59c407..684a41f70c8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14820,15 +14820,14 @@ files, and Makefiles.")
 (define-public python-whatever
   (package
     (name "python-whatever")
-    (version "0.5")
+    (version "0.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/Suor/whatever/archive/" version
                            ".tar.gz"))
        (sha256
-        (base32
-         "1iqvnaf0zpc6b4rvbqq4xy45mszcscyzpzknv8wg6j84pbp22sap"))
+        (base32 "1rchg9hrlvw4sn20lq1zspczr4x1pv57c02gv73igiqx1hqpy2nc"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system python-build-system)
     (arguments
-- 
cgit v1.3


From f9bd82e7a6e4e991be3f3cc6bf8bccd7feeb5241 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 26 Nov 2019 21:01:47 +0100
Subject: gnu: python-seaborn: Add patch to fix tests.

* gnu/packages/python-xyz.scm (python-seaborn)[source]: Add upstream patch to
fix test failures.
---
 gnu/packages/python-xyz.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 684a41f70c8..c89df24dd48 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -6265,7 +6265,19 @@ SVG, EPS, PNG and terminal output.")
        (method url-fetch)
        (uri (pypi-uri "seaborn" version))
        (sha256
-        (base32 "0bqysi3fxfjl1866m5jq8z7mynhqbqnikim74dmzn8539iwkzj3n"))))
+        (base32 "0bqysi3fxfjl1866m5jq8z7mynhqbqnikim74dmzn8539iwkzj3n"))
+       (patches
+        (list (origin
+                (method url-fetch)
+                ;; This has already been merged, but there is no new
+                ;; release including this patch.  It fixes problems
+                ;; with axis rotation that would lead to test
+                ;; failures.
+                (uri "https://patch-diff.githubusercontent.com/raw/mwaskom/seaborn/pull/1716.diff")
+                (sha256
+                 (base32
+                  "1lm870z316n9ivsyr86hpk1gxaraw0mrjvq42lqsm0znhjdp9q9w"))
+                (file-name "seaborn-0.9.0-axis-rotation.patch"))))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.3


From 9e7cb2f1e16fc5b70c6c0e4187443e216767323d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 27 Nov 2019 08:21:12 +0100
Subject: gnu: python-matplotlib: Update to 3.1.2.

* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.1.2.
[arguments]: Disable test_backend_webagg and test_constrainedlayout; skip
other tests tagged with "webagg".
---
 gnu/packages/python-xyz.scm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c89df24dd48..cb74a7ab7f0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3996,14 +3996,14 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
 (define-public python-matplotlib
   (package
     (name "python-matplotlib")
-    (version "3.1.1")
+    (version "3.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "matplotlib" version))
        (sha256
         (base32
-         "14qc109dibp32xfd9lah54djc0rc76fhbsj9cwyb328lzqmd5sqz"))))
+         "1nmshfqh7wyg15i16hx1yiylcvzkws29ivn66n3i0wyqwcpjr3lf"))))
     (build-system python-build-system)
     (propagated-inputs ; the following packages are all needed at run time
      `(("python-cycler" ,python-cycler)
@@ -4068,8 +4068,14 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
              (for-each delete-file
                        ;; test_normal_axes, test_get_tightbbox_polar
                        '("lib/matplotlib/tests/test_axes.py"
+                         ;; We don't use the webagg backend and this test forces it.
+                         "lib/matplotlib/tests/test_backend_webagg.py"
                          ;; test_outward_ticks
                          "lib/matplotlib/tests/test_tightlayout.py"
+                         ;; test_hidden_axes fails with minor extent
+                         ;; differences, possibly due to the use of a
+                         ;; different version of FreeType.
+                         "lib/matplotlib/tests/test_constrainedlayout.py"
                          ;; Fontconfig returns no fonts.
                          "lib/matplotlib/tests/test_font_manager.py"))
              #t))
@@ -4087,7 +4093,7 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (invoke "python" "tests.py" "-v"
-                     "-m" "not network")))
+                     "-m" "not network and not webagg")))
          (add-before 'build 'configure-environment
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let ((cairo (assoc-ref inputs "cairo")))
-- 
cgit v1.3


From a132276537fba4fd8065f85fc2961dfedb5f385b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 27 Nov 2019 09:57:45 +0100
Subject: gnu: python-seaborn: Disable matrix test.

* gnu/packages/python-xyz.scm (python-seaborn)[arguments]: Add phase
"fix-tests".
---
 gnu/packages/python-xyz.scm | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index cb74a7ab7f0..f9e726e8fc4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -6296,6 +6296,12 @@ SVG, EPS, PNG and terminal output.")
                (system (format #f "~a/bin/Xvfb :1 &" xorg-server))
                (setenv "DISPLAY" ":1")
                #t)))
+         (add-after 'unpack 'fix-tests
+           (lambda _
+             ;; test_cbar_ticks fails probably because of matplotlib's
+             ;; expectation of using an older version of FreeType.
+             (delete-file "seaborn/tests/test_matrix.py")
+             #t))
          (replace 'check (lambda _ (invoke "pytest" "seaborn") #t)))))
     (propagated-inputs
      `(("python-pandas" ,python-pandas)
-- 
cgit v1.3


From ff3375251d6a316e3ee05589d70a8bb135ec47a6 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 27 Nov 2019 22:19:13 +0100
Subject: gnu: Use the test-only Xorg variant for tests.

* gnu/packages/education.scm (gcompris-qt)[native-inputs]: Change XORG-SERVER
to XORG-SERVER-FOR-TESTS.
* gnu/packages/engineering.scm (pcb, qucs, openscad)[native-inputs]: Likewise.
* gnu/packages/gnome.scm (libbonoboui, d-feet, gspell, libdazzle, libhandy)[native-inputs]: Likewise.
* gnu/packages/gnupg.scm (parcimonie)[native-inputs]: Likewise.
* gnu/packages/graphics.scm (opensubdiv, rapicorn)[native-inputs]: Likewise.
* gnu/packages/gtk.scm (gtksourceview-2, gtksourceview)[native-inputs]: Likewise.
* gnu/packages/image-processing.scm (opencv)[native-inputs]: Likewise.
* gnu/packages/kde-frameworks.scm (kconfig, kcoreaddons, kwidgetsaddons,
kwindowsystem, kdeclarative)[native-inputs]: Likewise.
* gnu/packages/kde-plasma.scm (kscreenlocker)[native-inputs]: Likewise.
* gnu/packages/messaging.scm (gajim)[native-inputs]: Likewise.
* gnu/packages/python-xyz.scm (python-seaborn)[native-inputs]: Likewise.
---
 gnu/packages/education.scm        |  2 +-
 gnu/packages/engineering.scm      |  6 +++---
 gnu/packages/gnome.scm            | 10 +++++-----
 gnu/packages/gnupg.scm            |  2 +-
 gnu/packages/graphics.scm         |  4 ++--
 gnu/packages/gtk.scm              |  4 ++--
 gnu/packages/image-processing.scm |  2 +-
 gnu/packages/kde-frameworks.scm   | 10 +++++-----
 gnu/packages/kde-plasma.scm       |  2 +-
 gnu/packages/messaging.scm        |  2 +-
 gnu/packages/python-xyz.scm       |  2 +-
 gnu/packages/vim.scm              |  2 +-
 12 files changed, 24 insertions(+), 24 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index c84fa542233..46262fd14b0 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -167,7 +167,7 @@ of categories with some of the activities available in that category.
        ("gettext" ,gettext-minimal)
        ("perl" ,perl)
        ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("openssl" ,openssl)
        ("python-2" ,python-2)
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 294105a757c..c5e2f58aebf 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -373,7 +373,7 @@ features.")))
        ("imagemagick" ,imagemagick)
        ("gerbv" ,gerbv)
        ("ghostscript" ,ghostscript)
-       ("xvfb" ,xorg-server)))
+       ("xvfb" ,xorg-server-for-tests)))
     (home-page "http://pcb.geda-project.org/")
     (synopsis "Design printed circuit board layouts")
     (description
@@ -1771,7 +1771,7 @@ parallel computing platforms.  It also supports serial execution.")
          ("python" ,python-2) ; for tests
          ("matplotlib" ,python2-matplotlib) ; for tests
          ("numpy" ,python2-numpy) ; for tests
-         ("xorg-server" ,xorg-server))) ; for tests
+         ("xorg-server" ,xorg-server-for-tests))) ; for tests
       (inputs
        `(("adms" ,adms)
          ("asco" ,asco)
@@ -2174,7 +2174,7 @@ specification can be downloaded at @url{http://3mf.io/specification/}.")
        ("imagemagick" ,imagemagick)
        ("ps" ,procps)
        ("python" ,python)
-       ("xvfb" ,xorg-server)))
+       ("xvfb" ,xorg-server-for-tests)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index af2558d8144..11ed0359191 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2025,7 +2025,7 @@ since ca. 2006, when GTK+ itself incorporated printing support.")
     (native-inputs
      `(("glib" ,glib "bin")             ; for glib-genmarshal, etc.
        ("intltool" ,intltool)
-       ("xorg-server" ,xorg-server) ; For running the tests
+       ("xorg-server" ,xorg-server-for-tests) ; For running the tests
        ("pkg-config" ,pkg-config)))
     (home-page "https://developer.gnome.org/libbonoboui/")
     (synopsis "Some user interface controls using Bonobo")
@@ -4591,7 +4591,7 @@ principles are simplicity and standards compliance.")
        ("pkg-config" ,pkg-config)
        ("python-pep8" ,python-pep8)
        ("xmllint" ,libxml2)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("gobject-introspection" ,gobject-introspection)
        ("gtk+" ,gtk+)
@@ -7752,7 +7752,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
 
        ;; For tests.
        ("aspell-dict-en" ,aspell-dict-en)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (propagated-inputs
      `(("enchant" ,enchant)))            ;enchant.pc is required by gspell-1.pc
     (home-page "https://wiki.gnome.org/Projects/gspell")
@@ -8167,7 +8167,7 @@ hexadecimal or ASCII.  It is useful for editing binary files in general.")
      `(("glib" ,glib "bin")             ; glib-compile-resources
        ("pkg-config" ,pkg-config)
        ;; For tests.
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("glib" ,glib)
        ("gobject-introspection" ,gobject-introspection)
@@ -8389,9 +8389,9 @@ advanced image management tool")
        ("gtk-doc" ,gtk-doc)
        ("pkg-config" ,pkg-config)
        ("gettext" ,gettext-minimal)
-       ("xorg-server" ,xorg-server)
 
        ;; Test suite dependencies.
+       ("xorg-server" ,xorg-server-for-tests)
        ("hicolor-icon-theme" ,hicolor-icon-theme)))
     (home-page "https://source.puri.sm/Librem5/libhandy")
     (synopsis "Library full of GTK+ widgets for mobile phones")
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 6b6b8f616d9..23d3aba90e2 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -1045,7 +1045,7 @@ files, to verify signatures, and to manage the private and public keys.")
        ("perl-xml-twig" ,perl-xml-twig)
        ("torsocks" ,torsocks)))
     (native-inputs
-     `(("xorg-server" ,xorg-server)))
+     `(("xorg-server" ,xorg-server-for-tests)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index 4f1c50b2729..8795107dcb9 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -758,7 +758,7 @@ realistic reflections, shading, perspective and other effects.")
        ("graphviz" ,graphviz)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)
-       ("xvfb" ,xorg-server)))
+       ("xvfb" ,xorg-server-for-tests)))
     (home-page "https://rapicorn.testbit.org/")
     (synopsis "Toolkit for rapid development of user interfaces")
     (description
@@ -1055,7 +1055,7 @@ requirements.")
                       (setenv "DISPLAY" ":1")
                       #t)))))
     (native-inputs
-     `(("xorg-server" ,xorg-server)))
+     `(("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("glew" ,glew)
        ("libxrandr" ,libxrandr)
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index e6b9042c000..817c03c30ea 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -360,7 +360,7 @@ diagrams.")
        ("glib" ,glib "bin")             ; for glib-genmarshal, etc.
        ("pkg-config" ,pkg-config)
        ;; For testing.
-       ("xorg-server" ,xorg-server)
+       ("xorg-server" ,xorg-server-for-tests)
        ("shared-mime-info" ,shared-mime-info)))
     (propagated-inputs
      ;; As per the pkg-config file.
@@ -431,7 +431,7 @@ printing and other features typical of a source code editor.")
       ("pkg-config" ,pkg-config)
       ("vala" ,vala)
       ;; For testing.
-      ("xorg-server" ,xorg-server)
+      ("xorg-server" ,xorg-server-for-tests)
       ("shared-mime-info" ,shared-mime-info)))
    (propagated-inputs
     ;; gtksourceview-3.0.pc refers to all these.
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 2579da3d6a7..1961b473611 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -373,7 +373,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("xorg-server" ,xorg-server) ; For running the tests
+       ("xorg-server" ,xorg-server-for-tests) ; For running the tests
        ("opencv-extra"
         ,(origin
            (method git-fetch)
diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index ec735d8903b..6f7c5df7b4e 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -483,7 +483,7 @@ Internet).")
        ("extra-cmake-modules" ,extra-cmake-modules)
        ("inetutils" ,inetutils)
        ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
@@ -548,7 +548,7 @@ propagate their changes to their respective configuration files.")
        ("qttools" ,qttools)
        ("shared-mime-info" ,shared-mime-info)
        ;; TODO: FAM: File alteration notification http://oss.sgi.com/projects/fam
-       ("xorg-server" ,xorg-server))) ; for the tests
+       ("xorg-server" ,xorg-server-for-tests))) ; for the tests
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
@@ -1041,7 +1041,7 @@ represented by a QPoint or a QSize.")
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
@@ -1091,7 +1091,7 @@ configuration pages, message boxes, and password requests.")
        ("dbus" ,dbus) ; for the tests
        ("openbox" ,openbox) ; for the tests
        ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server))) ; for the tests
+       ("xorg-server" ,xorg-server-for-tests))) ; for the tests
     (inputs
      `(("libxrender" ,libxrender)
        ("qtbase" ,qtbase)
@@ -2201,7 +2201,7 @@ their settings.")
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("kauth" ,kauth)
        ("kbookmarks" ,kbookmarks)
diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm
index c1731d459a7..d381ae9fb46 100644
--- a/gnu/packages/kde-plasma.scm
+++ b/gnu/packages/kde-plasma.scm
@@ -96,7 +96,7 @@ manager which re-parents a Client window to a window decoration frame.")
 
        ;; For tests.
        ("dbus" ,dbus)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("kcmutils" ,kcmutils)
        ("kcrash" ,kcrash)
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 33e752c9a02..2429bad3e56 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -644,7 +644,7 @@ else [])"))
     (native-inputs
      `(("intltool" ,intltool)
        ("python-docutils" ,python-docutils)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("adwaita-icon-theme" ,adwaita-icon-theme)
        ("gnome-keyring" ,gnome-keyring)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f9e726e8fc4..7343366cd91 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -6310,7 +6310,7 @@ SVG, EPS, PNG and terminal output.")
        ("python-scipy" ,python-scipy)))
     (native-inputs
      `(("python-pytest" ,python-pytest)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (home-page "http://stanford.edu/~mwaskom/software/seaborn/")
     (synopsis "Statistical data visualization")
     (description
diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index ae07bcd9b6f..b360d1fcbe7 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -198,7 +198,7 @@ with the editor vim.")))
                                                     display " &")))))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("xorg-server" ,xorg-server)
+       ("xorg-server" ,xorg-server-for-tests)
        ,@(package-native-inputs vim)))
     (inputs
      `(("acl" ,acl)
-- 
cgit v1.3


From ba5ef9997ba071339473590805331a5eec29b10d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 27 Nov 2019 23:46:21 +0100
Subject: gnu: python-dbus: Update to 1.2.14.

* gnu/packages/python-xyz.scm (python-dbus): Update to 1.2.14.
(python2-dbus)[arguments]: Remove.
---
 gnu/packages/python-xyz.scm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7343366cd91..d2efa742282 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5950,14 +5950,14 @@ parsing (browser/HTTP) user agent strings.")
 (define-public python-dbus
   (package
     (name "python-dbus")
-    (version "1.2.10")
+    (version "1.2.14")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://dbus.freedesktop.org/releases/dbus-python/"
                            "dbus-python-" version ".tar.gz"))
        (sha256
-        (base32 "11nqk01iq5bx2llgb3ksknyinijdp29w4ndj210glm009ayjncyl"))))
+        (base32 "0cdchkgnivlka4lf8q4qfk0yxq483i3r3aqickjf8hfn7nx0c0mi"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -5976,10 +5976,7 @@ implementation of D-Bus.")
     (inputs `(("python" ,python-2)
               ,@(alist-delete "python"
                               (package-inputs python-dbus)
-                              equal?)))
-    ;; FIXME: on Python 2, the test_utf8 fails with:
-    ;; "ValueError: unichr() arg not in range(0x10000) (narrow Python build)"
-    (arguments `(#:tests? #f))))
+                              equal?)))))
 
 (define-public python-notify2
   (package
-- 
cgit v1.3


From 38a404d567dbaed7c9bf3803e2580290d575f1dc Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 28 Nov 2019 16:25:14 +0100
Subject: gnu: python2-matplotlib: Do not inherit test adjustments.

This is a follow-up to commit 9e7cb2f1e16fc5b70c6c0e4187443e216767323d.

* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Do not inherit
the 'fix-and-disable-failing-tests' phase.
---
 gnu/packages/python-xyz.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d2efa742282..a166554f986 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4147,6 +4147,7 @@ toolkits.")
                            (assoc-ref inputs "jquery-ui")
                            "-d" dir))
                  #t))
+             (delete 'fix-and-disable-failing-tests)
              (delete 'check))))) ; These tests weren't run the the past.
       ;; Make sure to use special packages for Python 2 instead
       ;; of those automatically rewritten by package-with-python2.
-- 
cgit v1.3


From c09f598d94af81f326fe1d4cf2ab344d4e720679 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 28 Nov 2019 16:26:51 +0100
Subject: gnu: python-matplotlib: Do not move the 'check' phase.

Running tests after install is now the default in PYTHON-BUILD-SYSTEM.

* gnu/packages/python-xyz.scm (python-matplotlib)[arguments]: Replace 'check'
phase, instead of deleting and adding new phase.
---
 gnu/packages/python-xyz.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a166554f986..fcc3972194c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4088,8 +4088,7 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
                        (assoc-ref inputs "jquery-ui")
                        "-d" dir))
              #t))
-         (delete 'check)
-         (add-after 'install 'check
+         (replace 'check
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (invoke "python" "tests.py" "-v"
-- 
cgit v1.3


From a566231947ef87db830b7ffbd2d3b7c993adb058 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Fri, 29 Nov 2019 11:05:37 +0200
Subject: gnu: python-invoke: Update to 1.3.0.

* gnu/packages/python-xyz.scm (python-invoke): Update to 1.3.0.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fcc3972194c..648f1be963d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12476,13 +12476,13 @@ projects.")
   (package
     (name "python-invoke")
     (home-page "http://www.pyinvoke.org/")
-    (version "1.1.0")
+    (version "1.3.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "invoke" version))
               (sha256
                (base32
-                "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6"))))
+                "1nn7gad0rvy492acpyhkrp01zsk86acf34qhsvq4xmm6x39788n5"))))
     (build-system python-build-system)
     (arguments
      ;; XXX: Requires many dependencies that are not yet in Guix.
-- 
cgit v1.3


From ff3d1b99f2edc40258abeb5e9b87f815f6880686 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 30 Nov 2019 17:33:48 +0100
Subject: gnu: python-pyclipper: Update to 1.1.0.post3.

* gnu/packages/python-xyz.scm (python-pyclipper): Update to 1.1.0.post3.
---
 gnu/packages/python-xyz.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 648f1be963d..24e1e48135c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14381,14 +14381,13 @@ Git.")
 (define-public python-pyclipper
   (package
     (name "python-pyclipper")
-    (version "1.1.0.post1")
+    (version "1.1.0.post3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyclipper" version ".zip"))
        (sha256
-        (base32
-         "0ldbkbnx94an4zzrwb1sxmg6k0jgk4cwmvcdyy8y5k1zslc612wa"))
+        (base32 "164yksvqwqvwzh8f8lq92asg87hd8rvcy2xb5vm4y4ccvd5xgb7i"))
       (modules '((guix build utils)))
       (snippet
        '(begin
-- 
cgit v1.3


From 43ae8f796b4b02106328cb34e90f1d8994ebc7ab Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 30 Nov 2019 17:34:58 +0100
Subject: gnu: python-icalendar: Update to 4.0.4.

* gnu/packages/python-xyz.scm (python-icalendar): Update to 4.0.4.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 24e1e48135c..aef970cd887 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8660,13 +8660,13 @@ minimal and fast API targeting the following uses:
 (define-public python-icalendar
   (package
     (name "python-icalendar")
-    (version "4.0.3")
+    (version "4.0.4")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "icalendar" version))
              (sha256
               (base32
-               "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7"))))
+               "16gjvqv0n05jrb9g228pdjgzd3amz2pdhvcgsn1jypszjg5m2w9l"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)
-- 
cgit v1.3


From 61b77ff307b875bf198dd3d71ef64d1871d0ac6e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 2 Dec 2019 11:01:49 +0200
Subject: gnu: python-pillow: Replace check phase.

* gnu/packages/python-xyz.scm (python-pillow)[arguments]: Since 'check
always come after 'install, replace 'check phase rather than recreate it.
---
 gnu/packages/python-xyz.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index aef970cd887..59f712844f3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4705,8 +4705,7 @@ the OleFileIO module from PIL, the Python Image Library.")
            (lambda _
              (substitute* "setup.py"
                (("\\['/sbin/ldconfig', '-p'\\]") "['true']"))))
-         (delete 'check) ; We must run checks after python-pillow is installed.
-         (add-after 'install 'check-installed
+         (replace 'check
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (begin
                (setenv "HOME" (getcwd))
-- 
cgit v1.3


From 979d8464d4539999a5132caf935cf12fb941b0f4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 2 Dec 2019 11:02:47 +0200
Subject: gnu: python-pillow: Make check phase conditional.

* gnu/packages/python-xyz.scm (python-pillow)[arguments]: Wrap custom
'check phase in check for 'tests?'.
---
 gnu/packages/python-xyz.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 59f712844f3..c628c989d2a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4706,13 +4706,15 @@ the OleFileIO module from PIL, the Python Image Library.")
              (substitute* "setup.py"
                (("\\['/sbin/ldconfig', '-p'\\]") "['true']"))))
          (replace 'check
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             (begin
-               (setenv "HOME" (getcwd))
-               ;; Make installed package available for running the tests.
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "selftest.py" "--installed")
-               (invoke "python" "-m" "pytest" "-vv")))))))
+           (lambda* (#:key outputs inputs tests? #:allow-other-keys)
+             (if tests?
+               (begin
+                 (setenv "HOME" (getcwd))
+                 ;; Make installed package available for running the tests.
+                 (add-installed-pythonpath inputs outputs)
+                 (invoke "python" "selftest.py" "--installed")
+                 (invoke "python" "-m" "pytest" "-vv"))
+               #t))))))
     (home-page "https://python-pillow.org")
     (synopsis "Fork of the Python Imaging Library")
     (description
-- 
cgit v1.3


From 0c4e1c5fbfb6d56aee3a270ed0431790cb67f662 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 2 Dec 2019 11:08:11 +0200
Subject: gnu: python-pillow: Sort inputs alphabetically.

* gnu/packages/python-xyz.scm (python-pillow)[inputs]: Sort
alphabetically.
---
 gnu/packages/python-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c628c989d2a..637a00f4e0c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4691,11 +4691,11 @@ the OleFileIO module from PIL, the Python Image Library.")
     (inputs
      `(("freetype" ,freetype)
        ("lcms"     ,lcms)
-       ("zlib"     ,zlib)
        ("libjpeg"  ,libjpeg)
-       ("openjpeg" ,openjpeg)
        ("libtiff"  ,libtiff)
-       ("libwebp"  ,libwebp)))
+       ("libwebp"  ,libwebp)
+       ("openjpeg" ,openjpeg)
+       ("zlib"     ,zlib)))
     (propagated-inputs
      `(("python-olefile" ,python-olefile)))
     (arguments
-- 
cgit v1.3


From 5fbdd917b73d30ef5ca0aa4e82b8d0a5f81394dd Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 2 Dec 2019 11:13:18 +0200
Subject: gnu: python-pillow: Update to 6.2.1.

* gnu/packages/python-xyz.scm (python-pillow): Update to 6.2.1.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 637a00f4e0c..6d86eb1b22b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4677,14 +4677,14 @@ the OleFileIO module from PIL, the Python Image Library.")
 (define-public python-pillow
   (package
     (name "python-pillow")
-    (version "6.1.0")
+    (version "6.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Pillow" version))
        (sha256
         (base32
-         "1pnrsz0f0n0c819v1pdr8j6rm8xvhc9f3kh1fv9xpdp9n5ygf108"))))
+         "1c8wkzc58f5wdh006jvmwdk3wxld1xgagcbdvj7iv17qi0m9fkmz"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-pytest" ,python-pytest)))
-- 
cgit v1.3


From ca7c365312d3af6f664868690f02c385f07e34a1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 1 Dec 2019 16:42:49 +0100
Subject: gnu: python-scikit-image: Move to (gnu packages python-science).

* gnu/packages/python-xyz.scm (python-scikit-image, python2-scikit-image):
Move these two from here...
* gnu/packages/python-science.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
 gnu/local.mk                    |  1 +
 gnu/packages/python-science.scm | 67 +++++++++++++++++++++++++++++++++++++++++
 gnu/packages/python-xyz.scm     | 37 +----------------------
 3 files changed, 69 insertions(+), 36 deletions(-)
 create mode 100644 gnu/packages/python-science.scm

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/local.mk b/gnu/local.mk
index 9ddd1349daa..e1518db09dc 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -407,6 +407,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/python-check.scm			\
   %D%/packages/python-compression.scm		\
   %D%/packages/python-crypto.scm		\
+  %D%/packages/python-science.scm		\
   %D%/packages/python-web.scm			\
   %D%/packages/python-xyz.scm			\
   %D%/packages/toys.scm				\
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
new file mode 100644
index 00000000000..4636180dfa4
--- /dev/null
+++ b/gnu/packages/python-science.scm
@@ -0,0 +1,67 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
+;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages python-science)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system python))
+
+(define-public python-scikit-image
+  (package
+    (name "python-scikit-image")
+    (version "0.14.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scikit-image" version))
+       (sha256
+        (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
+    (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
+    (propagated-inputs
+     `(("python-cloudpickle" ,python-cloudpickle)
+       ("python-dask" ,python-dask)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)
+       ("python-pillow" ,python-pillow)
+       ("python-pywavelets" ,python-pywavelets)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (home-page "http://scikit-image.org/")
+    (synopsis "Image processing in Python")
+    (description
+     "Scikit-image is a collection of algorithms for image processing.")
+    (license license:bsd-3)))
+
+(define-public python2-scikit-image
+  (package-with-python2 python-scikit-image))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6d86eb1b22b..1d6f0a8367a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -128,6 +128,7 @@
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-compression)
   #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
@@ -3307,42 +3308,6 @@ Mallard using the @command{ducktype} tool.  The yelp-tools package
 provides additional functionality on the produced Mallard documents.")
     (license license:expat)))
 
-(define-public python-scikit-image
-  (package
-    (name "python-scikit-image")
-    (version "0.14.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "scikit-image" version))
-       (sha256
-        (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
-    (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
-    (propagated-inputs
-     `(("python-cloudpickle" ,python-cloudpickle)
-       ("python-dask" ,python-dask)
-       ("python-matplotlib" ,python-matplotlib)
-       ("python-networkx" ,python-networkx)
-       ("python-numpy" ,python-numpy)
-       ("python-pillow" ,python-pillow)
-       ("python-pywavelets" ,python-pywavelets)
-       ("python-scipy" ,python-scipy)
-       ("python-six" ,python-six)))
-    (native-inputs
-     `(("python-cython" ,python-cython)))
-    (home-page "http://scikit-image.org/")
-    (synopsis "Image processing in Python")
-    (description
-     "Scikit-image is a collection of algorithms for image processing.")
-    (license license:bsd-3)))
-
-(define-public python2-scikit-image
-  (package-with-python2 python-scikit-image))
-
 (define-public python-cython
   (package
     (name "python-cython")
-- 
cgit v1.3


From ec1224a73b2c0c0c15a3293261334f3927f6579d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 2 Dec 2019 14:04:39 +0100
Subject: gnu: python-scipy: Move to (gnu packages python-science).

* gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from
here...
* gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here.
* gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm,
gnu/packages/statistics.scm: Adjust module imports.
---
 gnu/packages/bioinformatics.scm   |   1 +
 gnu/packages/machine-learning.scm |   1 +
 gnu/packages/python-science.scm   | 126 ++++++++++++++++++++++++++++++++++++++
 gnu/packages/python-xyz.scm       | 119 -----------------------------------
 gnu/packages/statistics.scm       |   1 +
 5 files changed, 129 insertions(+), 119 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 616fcedc35a..b0d070b4e7f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -105,6 +105,7 @@
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-compression)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index b83b336d841..ab4150cbb1d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -69,6 +69,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages serialization)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4636180dfa4..93fc63c2e7c 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -24,12 +24,138 @@
 (define-module (gnu packages python-science)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system python))
 
+(define-public python-scipy
+  (package
+    (name "python-scipy")
+    (version "1.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scipy" version))
+       (sha256
+        (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pyparsing" ,python-pyparsing)))
+    (inputs
+     `(("lapack" ,lapack)
+       ("openblas" ,openblas)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-sphinx" ,python-sphinx)
+       ("python-numpydoc" ,python-numpydoc)
+       ("gfortran" ,gfortran)
+       ("perl" ,perl)
+       ("which" ,which)))
+    (outputs '("out" "doc"))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-broken-tests
+           (lambda _
+             (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
+               (("^( +)def test_threads_parallel\\(self\\):" m indent)
+                (string-append indent
+                               "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+                               m)))
+             (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
+               (("^def test_parallel_threads\\(\\):" m)
+                (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+                               m)))
+             #t))
+         (add-before 'build 'configure-openblas
+           (lambda* (#:key inputs #:allow-other-keys)
+             (call-with-output-file "site.cfg"
+               (lambda (port)
+                 (format port
+                         "[blas]
+libraries = openblas
+library_dirs = ~a/lib
+include_dirs = ~a/include
+
+# backslash-n to make emacs happy
+\n[atlas]
+library_dirs = ~a/lib
+atlas_libs = openblas
+"
+                         (assoc-ref inputs "openblas")
+                         (assoc-ref inputs "openblas")
+                         (assoc-ref inputs "openblas"))))
+             #t))
+         (add-after 'install 'install-doc
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+                    (doc (string-append data "/doc/" ,name "-" ,version))
+                    (html (string-append doc "/html"))
+                    (pyver ,(string-append "PYVER=" (version-major+minor
+                                                     (package-version python))))
+                    ;; By default it tries to run sphinx-build through the Python
+                    ;; interpreter which won't work with our shell wrapper.
+                    (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
+               ;; Make installed package available for building the
+               ;; documentation
+               (add-installed-pythonpath inputs outputs)
+               (with-directory-excursion "doc"
+                 ;; Fix generation of images for mathematical expressions.
+                 (substitute* (find-files "source" "conf\\.py")
+                   (("pngmath_use_preview = True")
+                    "pngmath_use_preview = False"))
+                 (mkdir-p html)
+                 (invoke "make" "html" pyver sphinxbuild)
+                 (with-directory-excursion "build/html"
+                   (for-each (lambda (file)
+                               (let* ((dir (dirname file))
+                                      (tgt-dir (string-append html "/" dir)))
+                                 (install-file file html)))
+                             (find-files "." ".*")))))
+             #t))
+         ;; Tests can only be run after the library has been installed and not
+         ;; within the source directory.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (with-directory-excursion "/tmp"
+               (invoke "python" "-c"
+                       "import scipy; scipy.test(verbose=2)")))))))
+    (home-page "https://www.scipy.org/")
+    (synopsis "The Scipy library provides efficient numerical routines")
+    (description "The SciPy library is one of the core packages that make up
+the SciPy stack.  It provides many user-friendly and efficient numerical
+routines such as routines for numerical integration and optimization.")
+    (properties `((python2-variant . ,(delay python2-scipy))))
+    (license license:bsd-3)))
+
+;; Version 1.2.2 is the last version to support Python 2
+(define-public python2-scipy
+  (package
+    (inherit (package-with-python2
+              (strip-python2-variant python-scipy)))
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scipy" version))
+       (sha256
+        (base32
+         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
+
 (define-public python-scikit-image
   (package
     (name "python-scikit-image")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1d6f0a8367a..f52d9a410f3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4277,125 +4277,6 @@ those files.  It can also efficiently manipulate ranges of integers using set
 operators such as union, intersection, and difference.")
     (license license:asl2.0)))
 
-(define-public python-scipy
-  (package
-    (name "python-scipy")
-    (version "1.3.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "scipy" version))
-       (sha256
-        (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-numpy" ,python-numpy)
-       ("python-matplotlib" ,python-matplotlib)
-       ("python-pyparsing" ,python-pyparsing)))
-    (inputs
-     `(("lapack" ,lapack)
-       ("openblas" ,openblas)))
-    (native-inputs
-     `(("python-cython" ,python-cython)
-       ("python-pytest" ,python-pytest)
-       ("python-sphinx" ,python-sphinx)
-       ("python-numpydoc" ,python-numpydoc)
-       ("gfortran" ,gfortran)
-       ("perl" ,perl)
-       ("which" ,which)))
-    (outputs '("out" "doc"))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-broken-tests
-           (lambda _
-             (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
-               (("^( +)def test_threads_parallel\\(self\\):" m indent)
-                (string-append indent
-                               "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
-                               m)))
-             (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
-               (("^def test_parallel_threads\\(\\):" m)
-                (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
-                               m)))
-             #t))
-         (add-before 'build 'configure-openblas
-           (lambda* (#:key inputs #:allow-other-keys)
-             (call-with-output-file "site.cfg"
-               (lambda (port)
-                 (format port
-                         "[blas]
-libraries = openblas
-library_dirs = ~a/lib
-include_dirs = ~a/include
-
-# backslash-n to make emacs happy
-\n[atlas]
-library_dirs = ~a/lib
-atlas_libs = openblas
-"
-                         (assoc-ref inputs "openblas")
-                         (assoc-ref inputs "openblas")
-                         (assoc-ref inputs "openblas"))))
-             #t))
-         (add-after 'install 'install-doc
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
-                    (doc (string-append data "/doc/" ,name "-" ,version))
-                    (html (string-append doc "/html"))
-                    (pyver ,(string-append "PYVER=" (version-major+minor
-                                                     (package-version python))))
-                    ;; By default it tries to run sphinx-build through the Python
-                    ;; interpreter which won't work with our shell wrapper.
-                    (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
-               ;; Make installed package available for building the
-               ;; documentation
-               (add-installed-pythonpath inputs outputs)
-               (with-directory-excursion "doc"
-                 ;; Fix generation of images for mathematical expressions.
-                 (substitute* (find-files "source" "conf\\.py")
-                   (("pngmath_use_preview = True")
-                    "pngmath_use_preview = False"))
-                 (mkdir-p html)
-                 (invoke "make" "html" pyver sphinxbuild)
-                 (with-directory-excursion "build/html"
-                   (for-each (lambda (file)
-                               (let* ((dir (dirname file))
-                                      (tgt-dir (string-append html "/" dir)))
-                                 (install-file file html)))
-                             (find-files "." ".*")))))
-             #t))
-         ;; Tests can only be run after the library has been installed and not
-         ;; within the source directory.
-         (delete 'check)
-         (add-after 'install 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             (with-directory-excursion "/tmp"
-               (invoke "python" "-c"
-                       "import scipy; scipy.test(verbose=2)")))))))
-    (home-page "https://www.scipy.org/")
-    (synopsis "The Scipy library provides efficient numerical routines")
-    (description "The SciPy library is one of the core packages that make up
-the SciPy stack.  It provides many user-friendly and efficient numerical
-routines such as routines for numerical integration and optimization.")
-    (properties `((python2-variant . ,(delay python2-scipy))))
-    (license license:bsd-3)))
-
-;; Version 1.2.2 is the last version to support Python 2
-(define-public python2-scipy
-  (package
-    (inherit (package-with-python2
-              (strip-python2-variant python-scipy)))
-    (version "1.2.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "scipy" version))
-       (sha256
-        (base32
-         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
-
 (define-public python-socksipy-branch
   (package
     (name "python-socksipy-branch")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b84b3803ea0..1d6e6aaff53 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -66,6 +66,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sphinx)
-- 
cgit v1.3


From d97cdff18ece9ce3a6caa39e8779d597f535e082 Mon Sep 17 00:00:00 2001
From: Alex Griffin <a@ajgrf.com>
Date: Tue, 26 Nov 2019 13:42:24 -0600
Subject: gnu: python-socksipychain: Update to 2.1.0.

* gnu/packages/python-xyz.scm (python-socksipychain): Update to 2.1.0.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f52d9a410f3..1695f9b11aa 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4308,7 +4308,7 @@ as the original project seems to have been abandoned circa 2007.")
 (define-public python-socksipychain
   (package
     (name "python-socksipychain")
-    (version "2.0.15")
+    (version "2.1.0")
     (source
      (origin
        (method git-fetch)
@@ -4318,7 +4318,7 @@ as the original project seems to have been abandoned circa 2007.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1pkljnh9hfwla8sg7mil4f9zrnsqj0dbhr3crxjw3k8dnjz70dvk"))))
+         "0idm9a050rd2kbgbz2sk9ib9589kj4xh1xdnggs6xbq2v2y8f6zn"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f)) ; Tests try to access the network.
-- 
cgit v1.3


From 13125c5afeeacecdef41e103d9e5f942fcb78c01 Mon Sep 17 00:00:00 2001
From: Alex Griffin <a@ajgrf.com>
Date: Tue, 26 Nov 2019 13:52:21 -0600
Subject: gnu: Remove python2-socksipychain.

* gnu/packages/python-xyz.scm (python2-socksipychain): Remove variable.
---
 gnu/packages/python-xyz.scm | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1695f9b11aa..186e558f2f3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4331,9 +4331,6 @@ TLS/SSL encryption.  It was developed for use in PageKite, and also includes
 a simple netcat replacement with chaining support.")
     (license license:bsd-3)))
 
-(define-public python2-socksipychain
-  (package-with-python2 python-socksipychain))
-
 (define-public python-pycodestyle
   (package
     (name "python-pycodestyle")
-- 
cgit v1.3


From 312ec128af832dc5d22ce4f6ffe66920e69eda8f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 08:56:36 +0100
Subject: gnu: python-pandas: Move to (gnu packages python-science).

* gnu/packages/python-xyz.scm (python-pandas, python2-pandas): Move from
here...
* gnu/packages/python-science.scm (python-pandas, python2-pandas): ...to here.
* gnu/packages/benchmark.scm, gnu/packages/databases.scm,
gnu/packages/graph.scm, gnu/packages/parallel.scm,
gnu/packages/serialization.scm: Import (gnu packages python-science).
---
 gnu/packages/benchmark.scm      |  1 +
 gnu/packages/databases.scm      |  1 +
 gnu/packages/graph.scm          |  1 +
 gnu/packages/parallel.scm       |  1 +
 gnu/packages/python-science.scm | 98 ++++++++++++++++++++++++++++++++++++++++-
 gnu/packages/python-xyz.scm     | 89 -------------------------------------
 gnu/packages/serialization.scm  |  1 +
 7 files changed, 101 insertions(+), 91 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index c513370e74e..8e347879dd2 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -35,6 +35,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages storage)
   #:use-module (ice-9 match))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 4be59120222..8260bfcb431 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -97,6 +97,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 326477730b7..52db619fb39 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 0ad47bca0da..3cb39473fb8 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -44,6 +44,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages tcl)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 93fc63c2e7c..4a262ec7937 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1,10 +1,13 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016 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>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2016, 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,8 +33,10 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages time)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
@@ -191,3 +196,92 @@ routines such as routines for numerical integration and optimization.")
 
 (define-public python2-scikit-image
   (package-with-python2 python-scikit-image))
+
+(define-public python-pandas
+  (package
+    (name "python-pandas")
+    (version "0.25.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pandas" version))
+       (sha256
+        (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build python-build-system)
+                  (ice-9 ftw)
+                  (srfi srfi-26))
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'patch-which
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      (let ((which (assoc-ref inputs "which")))
+                        (substitute* "pandas/io/clipboard/__init__.py"
+                          (("^CHECK_CMD = .*")
+                           (string-append "CHECK_CMD = \"" which "\"\n"))))
+                      #t))
+                  (replace 'check
+                    (lambda _
+                      (let ((build-directory
+                             (string-append
+                              (getcwd) "/build/"
+                              (car (scandir "build"
+                                            (cut string-prefix? "lib." <>))))))
+                        ;; Disable the "strict data files" option which causes
+                        ;; the build to error out if required data files are
+                        ;; not available (as is the case with PyPI archives).
+                        (substitute* "setup.cfg"
+                          (("addopts = --strict-data-files") "addopts = "))
+                        (with-directory-excursion build-directory
+                          ;; Delete tests that require "moto" which is not yet
+                          ;; in Guix.
+                          (for-each delete-file
+                                    '("pandas/tests/io/conftest.py"
+                                      "pandas/tests/io/json/test_compression.py"
+                                      "pandas/tests/io/parser/test_network.py"
+                                      "pandas/tests/io/test_parquet.py"))
+                          (invoke "pytest" "-vv" "pandas" "--skip-slow"
+                                  "--skip-network" "-k"
+                                  ;; XXX: Due to the deleted tests above.
+                                  "not test_read_s3_jsonl"))))))))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-openpyxl" ,python-openpyxl)
+       ("python-pytz" ,python-pytz)
+       ("python-dateutil" ,python-dateutil)
+       ("python-xlrd" ,python-xlrd)))
+    (inputs
+     `(("which" ,which)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-beautifulsoup4" ,python-beautifulsoup4)
+       ("python-lxml" ,python-lxml)
+       ("python-html5lib" ,python-html5lib)
+       ("python-nose" ,python-nose)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-mock" ,python-pytest-mock)))
+    (home-page "https://pandas.pydata.org")
+    (synopsis "Data structures for data analysis, time series, and statistics")
+    (description
+     "Pandas is a Python package providing fast, flexible, and expressive data
+structures designed to make working with structured (tabular,
+multidimensional, potentially heterogeneous) and time series data both easy
+and intuitive.  It aims to be the fundamental high-level building block for
+doing practical, real world data analysis in Python.")
+    (properties `((python2-variant . ,(delay python2-pandas))))
+    (license license:bsd-3)))
+
+;; Pandas 0.24.x are the last versions that support Python 2.
+(define-public python2-pandas
+  (let ((pandas (package-with-python2
+                 (strip-python2-variant python-pandas))))
+    (package/inherit
+     pandas
+     (version "0.24.2")
+     (source (origin
+               (method url-fetch)
+               (uri (pypi-uri "pandas" version))
+               (sha256
+                (base32
+                 "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")))))))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 186e558f2f3..30b84d26b48 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1155,95 +1155,6 @@ human-friendly syntax.")
 (define-public python2-schedule
   (package-with-python2 python-schedule))
 
-(define-public python-pandas
-  (package
-    (name "python-pandas")
-    (version "0.25.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pandas" version))
-       (sha256
-        (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:modules ((guix build utils)
-                  (guix build python-build-system)
-                  (ice-9 ftw)
-                  (srfi srfi-26))
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-which
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      (let ((which (assoc-ref inputs "which")))
-                        (substitute* "pandas/io/clipboard/__init__.py"
-                          (("^CHECK_CMD = .*")
-                           (string-append "CHECK_CMD = \"" which "\"\n"))))
-                      #t))
-                  (replace 'check
-                    (lambda _
-                      (let ((build-directory
-                             (string-append
-                              (getcwd) "/build/"
-                              (car (scandir "build"
-                                            (cut string-prefix? "lib." <>))))))
-                        ;; Disable the "strict data files" option which causes
-                        ;; the build to error out if required data files are
-                        ;; not available (as is the case with PyPI archives).
-                        (substitute* "setup.cfg"
-                          (("addopts = --strict-data-files") "addopts = "))
-                        (with-directory-excursion build-directory
-                          ;; Delete tests that require "moto" which is not yet
-                          ;; in Guix.
-                          (for-each delete-file
-                                    '("pandas/tests/io/conftest.py"
-                                      "pandas/tests/io/json/test_compression.py"
-                                      "pandas/tests/io/parser/test_network.py"
-                                      "pandas/tests/io/test_parquet.py"))
-                          (invoke "pytest" "-vv" "pandas" "--skip-slow"
-                                  "--skip-network" "-k"
-                                  ;; XXX: Due to the deleted tests above.
-                                  "not test_read_s3_jsonl"))))))))
-    (propagated-inputs
-     `(("python-numpy" ,python-numpy)
-       ("python-openpyxl" ,python-openpyxl)
-       ("python-pytz" ,python-pytz)
-       ("python-dateutil" ,python-dateutil)
-       ("python-xlrd" ,python-xlrd)))
-    (inputs
-     `(("which" ,which)))
-    (native-inputs
-     `(("python-cython" ,python-cython)
-       ("python-beautifulsoup4" ,python-beautifulsoup4)
-       ("python-lxml" ,python-lxml)
-       ("python-html5lib" ,python-html5lib)
-       ("python-nose" ,python-nose)
-       ("python-pytest" ,python-pytest)
-       ("python-pytest-mock" ,python-pytest-mock)))
-    (home-page "https://pandas.pydata.org")
-    (synopsis "Data structures for data analysis, time series, and statistics")
-    (description
-     "Pandas is a Python package providing fast, flexible, and expressive data
-structures designed to make working with structured (tabular,
-multidimensional, potentially heterogeneous) and time series data both easy
-and intuitive.  It aims to be the fundamental high-level building block for
-doing practical, real world data analysis in Python.")
-    (properties `((python2-variant . ,(delay python2-pandas))))
-    (license license:bsd-3)))
-
-;; Pandas 0.24.x are the last versions that support Python 2.
-(define-public python2-pandas
-  (let ((pandas (package-with-python2
-                 (strip-python2-variant python-pandas))))
-    (package/inherit
-     pandas
-     (version "0.24.2")
-     (source (origin
-               (method url-fetch)
-               (uri (pypi-uri "pandas" version))
-               (sha256
-                (base32
-                 "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")))))))
-
 (define-public python2-mechanize
   (package
     (name "python2-mechanize")
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 00a8d27387e..a213e4ba0c8 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -46,6 +46,7 @@
   #:use-module (gnu packages lua)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages perl))
 
-- 
cgit v1.3


From 34bf686952e0eb1ce52cea1c1563a94ee693d268 Mon Sep 17 00:00:00 2001
From: Clément Lassieur <clement@lassieur.org>
Date: Thu, 5 Dec 2019 16:50:17 +0100
Subject: gnu: Add python-pykwalify.

* gnu/packages/python-xyz.scm (python-pykwalify): New variable.
---
 gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 89be883cdaf..9dd97a61bd9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16686,3 +16686,28 @@ scratch and manipulate data from Intel HEX file format.  It also includes
 several convenience Python scripts, including \"classic\" hex2bin and bin2hex
 converters and more, those based on the library itself.")
     (license license:bsd-3)))
+
+(define-public python-pykwalify
+  (package
+    (name "python-pykwalify")
+    (version "1.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pykwalify" version))
+       (sha256
+        (base32
+         "1cnfzkg1b01f825ikpw2fhjclf9c8akxjfrbd1vc22x1lg2kk2vy"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #f))          ;missing dependencies
+    (propagated-inputs
+     `(("python-dateutil" ,python-dateutil)
+       ("python-docopt" ,python-docopt)
+       ("python-pyyaml" ,python-pyyaml)))
+    (home-page "https://github.com/grokzen/pykwalify")
+    (synopsis
+     "Python lib/cli for JSON/YAML schema validation")
+    (description
+     "This package provides a parser, schema validator, and data binding tool
+for YAML and JSON.")
+    (license license:expat)))
-- 
cgit v1.3