Merge branch 'core-updates'

[jackhill/guix/guix.git] / gnu / packages / python.scm

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index bc00c02..6fe83b2 100644 (file)
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -806,14 +806,14 @@ NetCDF files can also be read and modified.  Python-HDF4 is a fork of
 (define-public python-h5py
   (package
     (name "python-h5py")
-    (version "2.6.0")
+    (version "2.7.0")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "h5py" version))
       (sha256
        (base32
-        "0df46dg7i7xfking9lp221bfm8dbl974yvlrbi1w7r6m61ac7bxj"))))
+        "0433sdv6xc9p7v1xs1gvbxp7p152ywi3nplgjb258q9fvw9469br"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; no test target
@@ -855,14 +855,14 @@ concepts.")
 (define-public python-netcdf4
   (package
     (name "python-netcdf4")
-    (version "1.2.7")
+    (version "1.2.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "netCDF4" version))
        (sha256
         (base32
-         "1fllizmnpw0zkzzm4j9pgamarlzfn3kmv9zrm0w65q1y31h9ni0c"))))
+         "1h6jq338amlbk0ilzvjyl7cck80i0bah9a5spn9in71vy2qxm7i5"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-cython" ,python-cython)))
@@ -3477,7 +3477,7 @@ and is very extensible.")
 (define-public python-scikit-learn
   (package
     (name "python-scikit-learn")
-    (version "0.18.1")
+    (version "0.19.0")
     (source
      (origin
        (method url-fetch)
@@ -3487,7 +3487,7 @@ and is very extensible.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1hwswckdmd27f7k1jvwdc0m4mqrgxl2s245yq1scq34v124bjqgq"))))
+         "0g7q4ri75mj93wpa9bp83a3jmrf3dm5va9h7k4zkbcxr6bgqka15"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -3611,15 +3611,14 @@ is designed to have a low barrier to entry.")
 (define-public python-cython
   (package
     (name "python-cython")
-    (version "0.25.2")
+    (version "0.26")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cython" version))
-       (patches (search-patches "python-cython-fix-tests-32bit.patch"))
        (sha256
         (base32
-         "01h3lrf6d98j07iakifi81qjszh6faa37ibx7ylva1vsqbwx2hgi"))))
+         "0riciynnr0r68cvg6r3gbhi9x7h44pdwb7926m6n5vfs5p1f492c"))))
     (build-system python-build-system)
     ;; we need the full python package and not just the python-wrapper
     ;; because we need libpython3.3m.so
@@ -3630,7 +3629,7 @@ is designed to have a low barrier to entry.")
        (modify-phases %standard-phases
          (add-before 'check 'set-HOME
            ;; some tests require access to "$HOME/.cython"
-           (lambda _ (setenv "HOME" "/tmp")))
+           (lambda _ (setenv "HOME" "/tmp") #t))
          (replace 'check
            (lambda _ (zero? (system* "python" "runtests.py" "-vv")))))))
     (home-page "http://cython.org/")
@@ -3915,14 +3914,14 @@ association studies (GWAS) on extremely large data sets.")
 (define-public python-pygit2
   (package
     (name "python-pygit2")
-    (version "0.25.0")
+    (version "0.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pygit2" version))
        (sha256
         (base32
-         "0wf5rp0fvrw7j3j18dvwjq6xqlbm611wd55aphrfpps0v1gxh3ny"))
+         "1cbc488ra3kg7r3qky17ms0szi3cda2d96qfkv1l9djsy9hnvw57"))
        (patches
         (search-patches "python-pygit2-disable-network-tests.patch"))))
     (build-system python-build-system)
@@ -5231,6 +5230,53 @@ cluster without needing to write any wrapper code yourself.")
 (define-public python2-gridmap
   (package-with-python2 python-gridmap))
 
+(define-public python-honcho
+  (package
+    (name "python-honcho")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/nickstenning/honcho/archive/v"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0zizn61n5z5hq421hkypk9pw8s6fpxw30f4hsg7k4ivwzy3gjw9j"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest-3.0)
+       ("python-mock" ,python-mock)
+       ("python-tox" ,python-tox)
+       ("which" ,which))) ;for tests
+    (propagated-inputs
+     `(("python-jinja2" ,python-jinja2)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             ;; fix honcho path in testsuite
+             (substitute* "tests/conftest.py"
+               (("'honcho'") (string-append "'" (assoc-ref outputs "out")
+                                            "/bin/honcho" "'")))
+             ;; It's easier to run tests after install.
+             ;; Make installed package available for running the tests
+             (add-installed-pythonpath inputs outputs)
+             (zero? (system* "py.test" "-v")))))))
+    (home-page "https://github.com/nickstenning/honcho")
+    (synopsis "Manage Procfile-based applications")
+    (description
+      "A Procfile is a file which describes how to run an application
+consisting of serveral processes. honcho starts all listed processes.
+The output of all running processes is collected by honcho and
+displayed.")
+    (license license:expat)))
+
+(define-public python2-honcho
+  (package-with-python2 python-honcho))
+
 (define-public python-pexpect
   (package
     (name "python-pexpect")
@@ -6565,6 +6611,29 @@ connection to each user.")
          ("python2-singledispatch" ,python2-singledispatch)
           ,@(package-propagated-inputs tornado))))))
 
+(define-public python-tornado-http-auth
+  (package
+    (name "python-tornado-http-auth")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tornado-http-auth" version))
+       (sha256
+        (base32
+         "0znrgqd7k2s4ia474xizi6h3061zj4sn5n6cq76bkwl3wwshifn5"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-tornado" ,python-tornado)))
+    (home-page
+     "https://github.com/gvalkov/tornado-http-auth")
+    (synopsis
+     "Digest and basic authentication module for Tornado")
+    (description
+     "Provides support for adding authentication to services using the Tornado
+web framework, either via the basic or digest authentication schemes.")
+    (license license:asl2.0)))
+
 ;; the python- version can be removed with python-3.5
 (define-public python-backports-abc
   (package
@@ -7273,7 +7342,7 @@ reading and writing MessagePack data.")
 (define-public python-netaddr
   (package
     (name "python-netaddr")
-    (version "0.7.18")
+    (version "0.7.19")
     (source
      (origin
        (method url-fetch)
@@ -7283,7 +7352,7 @@ reading and writing MessagePack data.")
              ".tar.gz"))
        (sha256
          (base32
-          "06dxjlbcicq7q3vqy8agq11ra01kvvd47j4mk6dmghjsyzyckxd1"))))
+          "1zdfadvpq4lmcqzr383gywxn4xyn355kj1n3lk9q2l03vmyfrbiq"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ;; No tests.
     (home-page "https://github.com/drkjam/netaddr/")
@@ -7668,14 +7737,14 @@ responses, rather than doing any computation.")
 (define-public python-cryptography-vectors
   (package
     (name "python-cryptography-vectors")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cryptography_vectors" version))
        (sha256
         (base32
-         "0yvi2cp23rg20bq3hd47ixbvjh0zgxnxrriqx5v17d7vkmliwbsi"))))
+         "1qa117fs1yd50zn2cfxh7d9l999ds0z4h83m9m7j4fk6ffm33f5y"))))
     (build-system python-build-system)
     (home-page "https://github.com/pyca/cryptography")
     (synopsis "Test vectors for the cryptography package")
@@ -7690,14 +7759,14 @@ responses, rather than doing any computation.")
 (define-public python-cryptography
   (package
     (name "python-cryptography")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cryptography" version))
        (sha256
         (base32
-         "1aq6ilnf2zdqshwqai4w8gmb5y6p7ip34qrjp1yb7sz77rkb501p"))))
+         "0fnck37zyvbzmccbp7w3jy27jgmij1992j5wyy3gxhw6a11b4jyh"))))
     (build-system python-build-system)
     (inputs
      `(("openssl" ,openssl)))
@@ -7982,14 +8051,14 @@ Debian-related files, such as:
 (define-public python-nbformat
   (package
     (name "python-nbformat")
-    (version "4.1.0")
+    (version "4.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "nbformat" version))
        (sha256
         (base32
-         "0mq8iki3d4mnx7wy05phss7x98mds4fqydin8lcagidp1knw1xnv"))))
+         "12s7j4qja8b5bs1kyw5dzmrqbjxxj8wk52cyasbiqbv7fblcrssz"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ; no test target
     (propagated-inputs
@@ -13910,7 +13979,7 @@ parse many formal languages.")
 (define-public python2-cliapp
   (package
     (name "python2-cliapp")
-    (version "1.20160724")
+    (version "1.20170823")
     (source
      (origin
        (method url-fetch)
@@ -13919,7 +13988,7 @@ parse many formal languages.")
              version ".tar.gz"))
        (sha256
         (base32
-         "025cyi75vxyghbm4hav8dz4fzwksshddavy9g9fwr440awcvw74f"))))
+         "1i9gik0xrj6jmi95s5w988jl1y265baz5xm5pbqdyvsh8h9ln6yq"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
@@ -13936,7 +14005,7 @@ iterating over input files.")
 (define-public python2-ttystatus
   (package
     (name "python2-ttystatus")
-    (version "0.32")
+    (version "0.35")
     (source
      (origin
        (method url-fetch)
@@ -13945,7 +14014,7 @@ iterating over input files.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0b5g889jj23r2w1hi300cdldx6jvspanp0ybf5n1qvdvl150aamf"))))
+         "0vivqbw7ddhsq1zj3g9cvvv4f0phl0pis2smsnwcr2szz2fk3hl6"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
@@ -14301,10 +14370,12 @@ Pylint has many rules enabled by default, way too much to silence them
 all on a minimally sized program.  It's highly configurable and handle
 pragmas to control it from within your code.  Additionally, it is
 possible to write plugins to add your own checks.")
+    (properties `((python2-variant . ,(delay python2-pylint))))
     (license license:gpl2+)))
 
 (define-public python2-pylint
-  (let ((pylint (package-with-python2 python-pylint)))
+  (let ((pylint (package-with-python2
+                  (strip-python2-variant python-pylint))))
     (package (inherit pylint)
              (propagated-inputs
               `(("python2-backports-functools-lru-cache"
@@ -15542,14 +15613,14 @@ address is valid and really exists.")
 (define-public python-marshmallow
   (package
     (name "python-marshmallow")
-    (version "3.0.0b2")
+    (version "3.0.0b3")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "marshmallow" version))
       (sha256
        (base32
-        "11bnpvfdbczr74177p295zbkdrax2cahvbj5bqhhlprgz2xxi5d9"))))
+        "07mcrij1yvk85lvgx44wwr9pc80xryghvlgayb057g1cazcypysd"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)