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

1 files changed, 445 insertions, 109 deletions

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 6b9fe0325c..f1dc2da050 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015, 2017 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Erik Edrosa <erik.edrosa@gmail.com>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
@@ -41,7 +41,7 @@
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017 Kei Kebreau <kei@openmailbox.org>
+;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
 ;;;
@@ -68,6 +68,7 @@
   #:use-module (gnu packages attr)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
@@ -79,6 +80,7 @@
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages icu4c)
@@ -1248,6 +1250,33 @@ datetime module, available in Python 2.3+.")
 (define-public python2-parsedatetime
   (package-with-python2 python-parsedatetime))
 
+(define-public python-schedule
+  (package
+    (name "python-schedule")
+    (version "0.4.3")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (pypi-uri "schedule" version))
+      (sha256
+       (base32
+        "0vplyjcbfrq50sphlwya749z8p2pcyi2nycw3518i0qpd9a6189i"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-mock" ,python-mock)))
+    (home-page "https://github.com/dbader/schedule")
+    (synopsis "Schedule periodic function calls in Python")
+    (description
+     "Schedule is an in-process scheduler for periodic jobs that uses the
+builder pattern for configuration.  Schedule lets you run Python functions (or
+any other callable) periodically at pre-determined intervals using a simple,
+human-friendly syntax.")
+    (license license:expat)))
+
+(define-public python2-schedule
+  (package-with-python2 python-schedule))
+
 (define-public python-pandas
   (package
     (name "python-pandas")
@@ -2811,13 +2840,13 @@ cutting and pasting that code over and over.")
 (define-public python-unidecode
   (package
     (name "python-unidecode")
-    (version "0.04.20")
+    (version "0.04.21")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "Unidecode" version))
              (sha256
               (base32
-               "1q00i8gpsq3d9r0q8wk4b290fxl0kqlsdk7iadvli45in6s1hi7d"))))
+               "0lfhp9c5xrbpjvbpr12ji52g1lx04404bzzdg6pvabhzisw6l2i8"))))
     (build-system python-build-system)
     (home-page "https://pypi.python.org/pypi/Unidecode")
     (synopsis "ASCII transliterations of Unicode text")
@@ -2826,7 +2855,7 @@ cutting and pasting that code over and over.")
 useful when integrating with legacy code that doesn't support Unicode, or for
 ease of entry of non-Roman names on a US keyboard, or when constructing ASCII
 machine identifiers from human-readable Unicode strings that should still be
-somewhat intelligeble.")
+somewhat intelligible.")
     (license license:gpl2+)))
 
 (define-public python2-unidecode
@@ -2835,17 +2864,23 @@ somewhat intelligeble.")
 (define-public python-pyjwt
   (package
     (name "python-pyjwt")
-    (version "1.4.0")
+    (version "1.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "PyJWT" version))
        (sha256
         (base32
-         "1556v2jppd8mjkkj66pxb5rcazm35jq81r233mdl8hfmz9n3icp1"))))
+         "1rxsg14i33vm2i6lz0my628108c81k43v10n4h3p0gx62xdyf2sh"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (for-each delete-file-recursively
+                     (find-files "." "\\.pyc$"))
+           #t))))
     (build-system python-build-system)
     (native-inputs
-     `(("python-pytest" ,python-pytest)
+     `(("python-pytest" ,python-pytest-3.0)
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-pytest-runner" ,python-pytest-runner)))
     (home-page "https://github.com/progrium/pyjwt")
@@ -3030,15 +3065,27 @@ for Python.")
 (define-public python-jinja2
   (package
     (name "python-jinja2")
-    (version "2.8")
+    (version "2.9.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Jinja2" version))
        (sha256
         (base32
-         "1x0v41lp5m1pjix3l46zx02b7lqp2hflgpnxwkywxynvi3zz47xw"))))
+         "1zzrkywhziqffrzks14kzixz7nd4yh2vc0fb04a68vfd2ai03anx"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; These files cannot be built with Python < 3.6.  See
+         ;; https://github.com/pallets/jinja/issues/655
+         ;; FIXME: Remove this when the "python" package is upgraded.
+         (add-after 'unpack 'delete-incompatible-files
+           (lambda _
+             (for-each delete-file
+                       '("jinja2/asyncsupport.py"
+                         "jinja2/asyncfilters.py"))
+             #t)))))
     (propagated-inputs
      `(("python-markupsafe" ,python-markupsafe)))
     (home-page "http://jinja.pocoo.org/")
@@ -3169,14 +3216,14 @@ reStructuredText.")
 (define-public python-pygments
   (package
     (name "python-pygments")
-    (version "2.1.3")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Pygments" version))
        (sha256
         (base32
-         "10axnp2wpjnq9g8wg53fx0c70dfxqrz498jyz8mrdx9a3flwir48"))))
+         "1k78qdvir1yb1c634nkv6rbga8wv4289xarghmsbbvzhvr311bnv"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: Tests require sphinx, which depends on this.
@@ -3611,14 +3658,14 @@ is designed to have a low barrier to entry.")
 (define-public python-cython
   (package
     (name "python-cython")
-    (version "0.26")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cython" version))
        (sha256
         (base32
-         "0riciynnr0r68cvg6r3gbhi9x7h44pdwb7926m6n5vfs5p1f492c"))))
+         "02y0pp1nx77b8s1mpxc6da2dccl6wd31pp4ksi9via479qcvacmr"))))
     (build-system python-build-system)
     ;; we need the full python package and not just the python-wrapper
     ;; because we need libpython3.3m.so
@@ -3673,22 +3720,21 @@ between language specification and implementation aspects.")
 (define-public python-numpy
   (package
     (name "python-numpy")
-    (version "1.12.0")
+    (version "1.13.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://github.com/numpy/numpy/archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (pypi-uri "numpy" version ".zip"))
        (sha256
         (base32
-         "025d4j4aakcp8w5i5diqh812cbbjgac7jszx1j56ivrbi1i8vv7d"))))
+         "1fsgkhh1vdkhmlz8vmdgxnj9n9yaanckxxzz9s0b4p08fqvjic69"))))
     (build-system python-build-system)
     (inputs
      `(("openblas" ,openblas)
        ("lapack" ,lapack)))
     (native-inputs
-     `(("python-cython" ,python-cython)
+     `(("unzip" ,unzip)
+       ("python-cython" ,python-cython)
        ("python-nose" ,python-nose)
        ("gfortran" ,gfortran)))
     (arguments
@@ -3696,6 +3742,8 @@ between language specification and implementation aspects.")
        (modify-phases %standard-phases
         (add-before 'build 'set-environment-variables
          (lambda* (#:key inputs #:allow-other-keys)
+           ;; numpy's distutils uses $SHELL to run external commands.
+          (setenv "SHELL" "bash")
           (call-with-output-file "site.cfg"
             (lambda (port)
               (format port
@@ -3762,6 +3810,71 @@ objects.")
 (define-public python2-munch
   (package-with-python2 python-munch))
 
+(define-public python-colormath
+  (package
+    (name "python-colormath")
+    (version "2.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "colormath" version))
+       (sha256
+        (base32
+         "01wp5xwm0a89wdm1dc9rr1ij90idzdiiipxdj1yslhqzkhnjnfh0"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://github.com/gtaylor/python-colormath")
+    (synopsis "Color math and conversion library")
+    (description
+     "This is a Python library for color math and conversions.")
+    (license license:bsd-3)))
+
+(define-public python2-colormath
+  (package-with-python2 python-colormath))
+
+(define-public python-spectra
+  (package
+    (name "python-spectra")
+    (version "0.0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "spectra" version))
+       (sha256
+        (base32
+         "0n87kzhpkml2s2q91rdkl8wz2kkv5b0bkrgww45lxa5vq34qh6w5"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (zero? (system* "nosetests" "-v")))))))
+    (propagated-inputs
+     `(("python-colormath" ,python-colormath)))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "http://github.com/jsvine/spectra")
+    (synopsis "Color scales and color conversion")
+    (description
+     "This package provides a Python library intended to make color math,
+color scales, and color space conversion easy.  It has support for:
+
+@enumerate
+@item Color scales
+@item Color ranges
+@item Color blending
+@item Brightening/darkening colors
+@item Saturating/desaturating colors
+@item Conversion to/from multiple color spaces.
+@end enumerate\n")
+    (license license:expat)))
+
+(define-public python2-spectra
+  (package-with-python2 python-spectra))
+
 (define-public python2-fastlmm
   (package
     (name "python2-fastlmm")
@@ -4313,33 +4426,56 @@ operators such as union, intersection, and difference.")
 (define-public python-rpy2
   (package
     (name "python-rpy2")
-    (version "2.7.6")
+    (version "2.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rpy2" version))
        (sha256
         (base32
-         "0nhan2qvrw7b7gg5zddwa22kybdv3x1g26vkd7q8lvnkgzrs4dga"))))
+         "0bqihjrdqwj5r1h86shvfb1p5hfr4a6klv1v54bzfr9r144w3rni"))))
     (build-system python-build-system)
     (arguments
-     '(#:phases
+     '(#:modules ((ice-9 ftw)
+                  (srfi srfi-1)
+                  (srfi srfi-26)
+                  (guix build utils)
+                  (guix build python-build-system))
+       #:phases
        (modify-phases %standard-phases
-         (delete 'check)
-         (add-after 'install 'check
+         ;; Without this phase the test loader cannot find the directories, in
+         ;; which it is supposed to look for test files.
+         (add-after 'unpack 'fix-tests
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "rpy/tests.py"
+               (("loader.discover\\(")
+                "loader.discover(rpy_root + '/' +"))
+             #t))
+         (replace 'check
            (lambda* (#:key outputs inputs #:allow-other-keys)
-             ;; It's easier to run tests after install.
-             ;; Make installed package available for running the tests
-             (add-installed-pythonpath inputs outputs)
+             (let ((cwd (getcwd)))
+               (setenv "PYTHONPATH"
+                       (string-append cwd "/build/"
+                                      (find (cut string-prefix? "lib" <>)
+                                            (scandir (string-append cwd "/build")))
+                                      ":"
+                                      (getenv "PYTHONPATH"))))
              (zero? (system* "python" "-m" "rpy2.tests" "-v")))))))
     (propagated-inputs
-     `(("python-six" ,python-six)))
+     `(("python-six" ,python-six)
+       ("python-jinja2" ,python-jinja2)
+       ("python-pytz" ,python-pytz)))
     (inputs
      `(("readline" ,readline)
        ("icu4c" ,icu4c)
        ("pcre" ,pcre)
        ("r-minimal" ,r-minimal)
-       ("r-survival" ,r-survival)))
+       ("r-survival" ,r-survival)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-dplyr" ,r-dplyr)
+       ("r-dbplyr" ,r-dbplyr)
+       ("python-numpy" ,python-numpy)))
     (native-inputs
      `(("zlib" ,zlib)))
     (home-page "http://rpy.sourceforge.net/")
@@ -4348,14 +4484,10 @@ operators such as union, intersection, and difference.")
 low-level interface to R from Python, a proposed high-level interface,
 including wrappers to graphical libraries, as well as R-like structures and
 functions.")
-    (license license:gpl3+)))
-
-(define-public python2-rpy2
-  (let ((rpy2 (package-with-python2 python-rpy2)))
-    (package (inherit rpy2)
-      (propagated-inputs
-       `(("python2-singledispatch" ,python2-singledispatch)
-         ,@(package-propagated-inputs rpy2))))))
+    ;; Any of these licenses can be picked for the R interface.  The whole
+    ;; project is released under GPLv2+ according to the license declaration
+    ;; in "setup.py".
+    (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
 
 (define-public python-scipy
   (package
@@ -5652,13 +5784,13 @@ tools for mocking system commands and recording calls to those.")
 (define-public python-ipython
   (package
     (name "python-ipython")
-    (version "5.2.2")
+    (version "5.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ipython" version ".tar.gz"))
        (sha256
-        (base32 "1qhjwa9cyz1np7rhv3p4ip13lkgbqsad62l24xkwiq1ic2gwiqbf"))))
+        (base32 "079wyjir4a9qx6kvx096b1asm63djbidk65z3ykcbnlngmg62pmz"))))
     (build-system python-build-system)
     (outputs '("out" "doc"))
     (propagated-inputs
@@ -5873,6 +6005,37 @@ and written in Python.")
 (define-public python2-html5lib-0.9
   (package-with-python2 python-html5lib-0.9))
 
+(define-public python-html5-parser
+  (package
+    (name "python-html5-parser")
+    (version "0.4.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "html5-parser" version))
+              (sha256
+               (base32
+                "1d8sxhl41ffh7qlk7wlsy17xw6slzx5v1yna9s72wx5qrpaa3wxr"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libxml2" ,libxml2)))
+    (propagated-inputs
+     `(("python-lxml" ,python-lxml)
+       ("python-beautifulsoup4" ,python-beautifulsoup4)))
+    (home-page "https://html5-parser.readthedocs.io")
+    (synopsis "Fast C-based HTML5 parsing for Python")
+    (description "This package provides a fast implementation of the HTML5
+parsing spec for Python.  Parsing is done in C using a variant of the gumbo
+parser.  The gumbo parse tree is then transformed into an lxml tree, also in
+C, yielding parse times that can be a thirtieth of the html5lib parse times.")
+    ;; src/as-python-tree.[c|h] are licensed GPL3.  The other files
+    ;; indicate ASL2.0, including the LICENSE file for the whole project.
+    (license (list license:asl2.0 license:gpl3))))
+
+(define-public python2-html5-parser
+  (package-with-python2 python-html5-parser))
+
 (define-public python-webencodings
   (package
     (name "python-webencodings")
@@ -6104,6 +6267,16 @@ implementation of D-Bus.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (replace 'build
+           (lambda _
+             (zero?
+              (system* "python" "setup.py" "build" "--enable-all-extensions"))))
+         (add-after 'build 'build-test-helper
+           (lambda _
+             (zero?
+              (system
+               (string-append "gcc -fPIC -shared -o ./testextension.sqlext "
+                              "-I. -Isqlite3 src/testextension.c") ))))
          (delete 'check)
          (add-after 'install 'check
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -6123,14 +6296,14 @@ translate the complete SQLite API into Python.")
 (define-public python-lxml
   (package
     (name "python-lxml")
-    (version "3.6.0")
+    (version "3.8.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "lxml" version))
         (sha256
          (base32
-          "1pvbmiy2m7jwv493kilbghhj2pkh8wy1na3ji350vhzhlwlclx4w"))))
+          "15nvf6n285n282682qyw3wihsncb0x5amdhyi4b83bfa2nz74vvk"))))
     (build-system python-build-system)
     (inputs
       `(("libxml2" ,libxml2)
@@ -7809,14 +7982,14 @@ message digests and key derivation functions.")
 (define-public python-pyopenssl
   (package
     (name "python-pyopenssl")
-    (version "17.2.0")
+    (version "17.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyOpenSSL" version))
        (sha256
         (base32
-         "0d283g4zi0hr9papd24mjl70mi15gyzq6fx618rizi87dgipqqax"))))
+         "0xkc1wfnpg6abzllivg3ylhc63npjdy1v81f4kc08bm8cj80nqr9"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -9096,16 +9269,13 @@ with python-requests.")
 (define-public python-click-threading
   (package
     (name "python-click-threading")
-    (version "0.2.0")
+    (version "0.4.3")
     (source (origin
              (method url-fetch)
-             (uri (string-append
-                    "https://pypi.python.org/packages/"
-                    "fe/b7/e7f609d18a2a351cb71616adcf54df1acd82f83cb9b5936935a4d20e2c23/"
-                    "click-threading-" version ".tar.gz"))
+             (uri (pypi-uri "click-threading" version))
              (sha256
               (base32
-               "18bcqikxwb3drb8rf60cclxkxw52521b38ax3byah6j8cn8y9p4j"))))
+               "0xs4bg2ws0zgyiplk312l049hi23c2zqf1g771rjhh5vr2msk4cg"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-click" ,python-click)))
@@ -9118,13 +9288,13 @@ applications.")
 (define-public python-click-log
   (package
     (name "python-click-log")
-    (version "0.1.8")
+    (version "0.2.0")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "click-log" version))
              (sha256
               (base32
-               "14ikfjfgnzf21mjniq9lfk2igzykgzfvwwrk85nw2b9fq44109sp"))))
+               "1bjrfxji1yv4fj0g78ri2yfgn2wbivn8g69fxfinxvxpmighhshp"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-click" ,python-click)))
@@ -9329,13 +9499,13 @@ processes across test runs.")
 (define-public python-icalendar
   (package
     (name "python-icalendar")
-    (version "3.11.6")
+    (version "3.11.7")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "icalendar" version))
              (sha256
               (base32
-               "1ny9mbm9zgghl612b8wc4ap52bz3kgl486d7f307gxjmlqgz3i64"))))
+               "0ahf1i98wjizhld2qd7v2vmvzsmdw08mmins82bf3fpbnp2sxbgc"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)
@@ -9756,14 +9926,14 @@ Pytest but stripped of Pytest specific details.")
 (define-public python-tox
   (package
    (name "python-tox")
-   (version "2.3.1")
+   (version "2.8.0")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "tox" version))
      (sha256
       (base32
-       "1vj73ar4rimq3fwy5r2z3jv4g9qbh8rmpmncsc00g0k310acqzxz"))))
+       "00lrql2cfzhb712v70inac6mrgdv8s8fmvz7qpggkk623hkm2pgc"))))
    (build-system python-build-system)
    (arguments
     ;; FIXME: Tests require pytest-timeout, which itself requires
@@ -9775,7 +9945,8 @@ Pytest but stripped of Pytest specific details.")
       ("python-virtualenv" ,python-virtualenv)))
    (native-inputs
     `(; FIXME: Missing: ("python-pytest-timeout" ,python-pytest-timeout)
-      ("python-pytest" ,python-pytest)))  ; >= 2.3.5
+      ("python-pytest" ,python-pytest)  ; >= 2.3.5
+      ("python-setuptools-scm" ,python-setuptools-scm)))
    (home-page "http://tox.testrun.org/")
    (synopsis "Virtualenv-based automation of test activities")
    (description "Tox is a generic virtualenv management and test command line
@@ -9815,14 +9986,14 @@ document.")
 (define-public python-botocore
   (package
    (name "python-botocore")
-   (version "1.5.26")
+   (version "1.7.9")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "botocore" version))
      (sha256
       (base32
-       "1b7l48hr88galrrc5q6k21z3sdadzxc87ppzs7k9fz4p1w8bfnvb"))))
+       "02b1bw25r1wdjs5yppb1h9igf11wj092biriv2yg8hzp5r0wrkmg"))))
    (build-system python-build-system)
    (arguments
     ;; FIXME: Many tests are failing.
@@ -9849,14 +10020,14 @@ interface to the Amazon Web Services (AWS) API.")
 (define-public awscli
   (package
    (name "awscli")
-   (version "1.11.63")
+   (version "1.11.151")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri name version))
      (sha256
       (base32
-       "1r8aqv8w27k76lcsfk83w6qw9lz8gk2ibzwacp5wjhpp2gik911m"))))
+       "0h6rirbfy0f9cxm7ikll0kr720dircfmxf2vslmhn4n325831wsp"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-colorama" ,python-colorama)
@@ -11815,20 +11986,22 @@ Wikipedia code samples at
 (define-public python-cleo
   (package
     (name "python-cleo")
-    (version "0.4.1")
+    (version "0.6.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "cleo" version))
               (sha256
                (base32
-                "1k2dcl6mqpn5bljyl6w42rqyd9mb3y9kh2mg7m2x3kfjwvg0rpva"))))
+                "0q1cf0szr0d54am4pypzwdnm74zpladdsinad94c2fz5i06fdpf7"))))
     (build-system python-build-system)
     (native-inputs
      `(;; For testing
        ("python-mock" ,python-mock)
+       ("python-pytest-mock" ,python-pytest-mock)
        ("python-pytest" ,python-pytest)))
     (propagated-inputs
-     `(("python-psutil" ,python-psutil)
+     `(("python-backpack" ,python-backpack)
+       ("python-pastel" ,python-pastel)
        ("python-pylev" ,python-pylev)))
     (home-page "https://github.com/sdispater/cleo")
     (synopsis "Command-line arguments library for Python")
@@ -11989,13 +12162,13 @@ addresses, and phone numbers.")
 (define-public python-pyaml
   (package
     (name "python-pyaml")
-    (version "15.8.2")
+    (version "17.7.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pyaml" version))
               (sha256
                (base32
-                "1f5m28vkh4ksq3d80d8mmd2z8wxvc3mgy2pmrv2751dm2xgznm4w"))))
+                "132grrw0ajq4nrappi3ldbkb952k7yn9b6c7csi2rmvzm1g6ppp2"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-unidecode" ,python-unidecode)))
@@ -12011,6 +12184,32 @@ YAML-serialized data.")
 (define-public python2-pyaml
   (package-with-python2 python-pyaml))
 
+(define-public python-backpack
+  (package
+    (name "python-backpack")
+    (version "0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "backpack" version))
+       (sha256
+        (base32
+         "14rq1mvm0jda90lcx9gyyby9dvq4x3js2cmxvd6vl4686ixwyqh1"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-nose" ,python-nose)))
+    (propagated-inputs
+     `(("python-simplejson" ,python-simplejson)))
+    (home-page "https://github.com/sdispater/backpack")
+    (synopsis "Utilities for working with Python collections")
+    (description "Backpack provides some useful utilities for working with
+collections of data.")
+    (license license:expat)))
+
+(define-public python2-backpack
+  (package-with-python2 python-backpack))
+
 (define-public python-flexmock
   (package
     (name "python-flexmock")
@@ -12032,44 +12231,6 @@ mocks, stubs and fakes.")
 (define-public python2-flexmock
   (package-with-python2 python-flexmock))
 
-(define-public python-orator
-  (package
-    (name "python-orator")
-    (version "0.8.2")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "orator" version))
-              (sha256
-               (base32
-                "1li49irsqha17nrda4nsb48biyy0rarp9pphf0jpqwm5zr8hv569"))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #f)) ; no tests
-    (propagated-inputs
-     `(("python-arrow" ,python-arrow)
-       ("python-blinker" ,python-blinker)
-       ("python-cleo" ,python-cleo)
-       ("python-faker" ,python-faker)
-       ("python-inflection" ,python-inflection)
-       ("python-lazy-object-proxy" ,python-lazy-object-proxy)
-       ("python-pyaml" ,python-pyaml)
-       ("python-simplejson" ,python-simplejson)
-       ("python-wrapt" ,python-wrapt)))
-    (home-page "https://orator-orm.com/")
-    (synopsis "ActiveRecord ORM for Python")
-    (description
-     "Orator provides a simple ActiveRecord-like Object Relational Mapping
-implementation for Python.")
-    (license license:expat)
-    (properties `((python2-variant . ,(delay python2-orator))))))
-
-(define-public python2-orator
-  (let ((base (package-with-python2 (strip-python2-variant python-orator))))
-    (package
-      (inherit base)
-      (propagated-inputs
-       `(("python2-ipaddress" ,python2-ipaddress)
-         ,@(package-propagated-inputs base))))))
-
 (define-public python-prompt-toolkit
  (package
   (name "python-prompt-toolkit")
@@ -13070,16 +13231,40 @@ replay them during future tests.  It is designed to work with python-requests.")
 (define-public python2-betamax
   (package-with-python2 python-betamax))
 
+(define-public python-betamax-matchers
+  (package
+    (name "python-betamax-matchers")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "betamax-matchers" version))
+       (sha256
+        (base32
+         "07qpwjyq2i2aqhz5iwghnj4pqr2ys5n45v1vmpcfx9r5mhwrsq43"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-betamax" ,python-betamax)
+       ("python-requests-toolbelt" ,python-requests-toolbelt)))
+    (home-page "https://github.com/sigmavirus24/betamax_matchers")
+    (synopsis "VCR imitation for python-requests")
+    (description "@code{betamax-matchers} provides a set of Matchers for
+Betamax.")
+    (license license:asl2.0)))
+
+(define-public python2-betamax-matchers
+  (package-with-python2 python-betamax-matchers))
+
 (define-public python-s3transfer
   (package
     (name "python-s3transfer")
-    (version "0.1.10")
+    (version "0.1.11")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "s3transfer" version))
               (sha256
                (base32
-                "1h8g9bknvxflxkpbnxyfxmk8pvgykbbk9ljdvhqh6z4vjc2926ms"))))
+                "0yfrfnf404cxzn3iswibqjxklsl0b1lwgqiml6pwiqj79a7zbwbn"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -13992,7 +14177,22 @@ parse many formal languages.")
          "1i9gik0xrj6jmi95s5w988jl1y265baz5xm5pbqdyvsh8h9ln6yq"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         ;; check phase needs to be run before the build phase. If not,
+         ;; coverage-test-runner looks for tests for the built source files,
+         ;; and fails.
+         (delete 'check)
+         (add-before 'build 'check
+           (lambda _
+             ;; Disable python3 tests
+             (substitute* "check"
+               (("python3") "# python3"))
+             (zero? (system* "./check")))))))
+    (native-inputs
+     `(("python2-coverage-test-runner" ,python2-coverage-test-runner)
+       ("python2-pep8" ,python2-pep8)))
     (propagated-inputs
      `(("python2-pyaml" ,python2-pyaml)))
     (home-page "https://liw.fi/cliapp/")
@@ -14017,8 +14217,20 @@ iterating over input files.")
         (base32
          "0vivqbw7ddhsq1zj3g9cvvv4f0phl0pis2smsnwcr2szz2fk3hl6"))))
     (build-system python-build-system)
+    (native-inputs
+     `(("python2-coverage-test-runner" ,python2-coverage-test-runner)
+       ("python2-pep8" ,python2-pep8)))
     (arguments
-     `(#:python ,python-2))
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         ;; check phase needs to be run before the build phase. If not,
+         ;; coverage-test-runner looks for tests for the built source files,
+         ;; and fails.
+         (delete 'check)
+         (add-before 'build 'check
+           (lambda _
+             (zero? (system* "make" "check")))))))
     (home-page "https://liw.fi/ttystatus/")
     (synopsis "Python library for showing progress reporting and
 status updates on terminals")
@@ -14065,12 +14277,26 @@ happens using the @code{logging} library.")
        (uri (string-append
              "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/larch/snapshot/larch-"
              version ".tar.gz"))
+       (patches (search-patches
+                 "python2-larch-coverage-4.0a6-compatibility.patch"))
        (sha256
         (base32
          "1p4knkkavlqymgciz2wbcnfrdgdbafhg14maplnk4vbw0q8xs663"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         ;; check phase needs to be run before the build phase. If not,
+         ;; coverage-test-runner looks for tests for the built source files,
+         ;; and fails.
+         (delete 'check)
+         (add-before 'build 'check
+           (lambda _
+             (zero? (system* "make" "check")))))))
+    (native-inputs
+     `(("cmdtest" ,cmdtest)
+       ("python2-coverage-test-runner" ,python2-coverage-test-runner)))
     (propagated-inputs
      `(("python2-tracing" ,python2-tracing)))
     (home-page "https://liw.fi/larch/")
@@ -15917,6 +16143,51 @@ pure Python module.")
 (define-public python2-rencode
   (package-with-python2 python-rencode))
 
+(define-public python-xenon
+  (package
+    (name "python-xenon")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "xenon" version))
+       (sha256
+        (base32
+         "14kby2y48vp3sgwxqlm5d5789yibqwb1qli5fwcmdqg3iayrbklc"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pyyaml" ,python-pyyaml)
+       ("python-radon" ,python-radon)
+       ("python-requests" ,python-requests)
+       ("python-flake8" ,python-flake8)
+       ("python-tox" ,python-tox)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'patch-test-requirements
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Update requirements from dependency==version to
+             ;; dependency>=version.
+             (substitute* "requirements.txt"
+               (("==") ">=")
+               ((",<1.5.0") ""))
+             ;; Remove httpretty dependency for tests.
+             (substitute* "setup.py"
+               (("httpretty") ""))
+             #t)))))
+    (home-page "https://xenon.readthedocs.org/")
+    (synopsis "Monitor code metrics for Python on your CI server")
+    (description
+     "Xenon is a monitoring tool based on Radon.  It monitors code complexity.
+Ideally, @code{xenon} is run every time code is committed.  Through command
+line options, various thresholds can be set for the complexity of code.  It
+will fail (i.e.  it will exit with a non-zero exit code) when any of these
+requirements is not met.")
+    (license license:expat)))
+
+(define-public python2-xenon
+  (package-with-python2 python-xenon))
+
 (define-public python-flask-principal
   (package
     (name "python-flask-principal")
@@ -15966,3 +16237,68 @@ authentication for Flask routes.")
 
 (define-public python2-flask-httpauth
   (package-with-python2 python-flask-httpauth))
+
+(define-public python-pysocks
+  (package
+    (name "python-pysocks")
+    (version "1.6.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PySocks" version))
+       (sha256
+        (base32
+         "1krkiss578zqwcg4c8iqz1hwscwhsvy2djp3xyvps5gsgvr2j0yh"))))
+    (build-system python-build-system)
+    (arguments `(#:tests? #f))
+    (home-page "https://github.com/Anorov/PySocks")
+    (synopsis "SOCKS client module")
+    (description "@code{pysocks} is an updated and semi-actively maintained
+version of @code{SocksiPy} with bug fixes and extra features.")
+    (license license:bsd-3)))
+
+(define-public python2-pysocks
+  (package-with-python2 python-pysocks))
+
+(define-public python-pyaes
+  (package
+    (name "python-pyaes")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyaes" version))
+       (sha256
+        (base32
+         "0bp9bjqy1n6ij1zb86wz9lqa1dhla8qr1d7w2kxyn7jbj56sbmcw"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/ricmoo/pyaes")
+    (synopsis "Implementation of AES in Python")
+    (description "This package contains a pure-Python implementation of the
+AES block cipher algorithm and the common modes of operation (CBC, CFB, CTR,
+ECB and OFB).")
+    (license license:expat)))
+
+(define-public python2-pyaes
+  (package-with-python2 python-pyaes))
+
+(define-public python-uritemplate
+  (package
+    (name "python-uritemplate")
+    (version "3.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "uritemplate" version))
+       (sha256
+        (base32
+         "0781gm9g34wa0asc19dx81ng0nqq07igzv3bbvdqmz13pv7469n0"))))
+    (build-system python-build-system)
+    (home-page "https://uritemplate.readthedocs.org")
+    (synopsis "Library to deal with URI Templates")
+    (description "@code{uritemplate} provides Python library to deal with URI
+Templates.")
+    (license license:bsd-2)))
+
+(define-public python2-uritemplate
+  (package-with-python2 python-uritemplate))