gnu: python-coloredlogs: Update to 10.0.

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

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2983425..04d72e2 100644 (file)
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -166,14 +166,13 @@
 (define-public python-psutil
   (package
     (name "python-psutil")
-    (version "5.6.2")
+    (version "5.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psutil" version))
        (sha256
-        (base32
-         "1v95vb5385qscfdvphv8l2w22bmir3d7yhpi02n58v3mlqy1r3l2"))))
+        (base32 "1wv31zly44qj0rp2acg58xbnc7bf6ffyadasq093l455q30qafl6"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: some tests does not return and times out.
@@ -549,14 +548,13 @@ concepts.")
 (define-public python-cftime
   (package
     (name "python-cftime")
-    (version "1.0.3.4")
+    (version "1.0.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cftime" version))
        (sha256
-        (base32
-         "0362dhxbzk593walyjz30dll6y2y79wialik647cbwdsf3ad0x6x"))))
+        (base32 "0w0gi6jnch38hiygl62j4xkcirv4y3dcwrvxl9p7bsk6j27lzihs"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-numpy" ,python-numpy)))
@@ -910,10 +908,18 @@ some helpful Python 2 compatibility convenience methods.")
         (base32
          "09z4d1jiasn7k1hs5af2ckmnrd0i1d1m04bhfjhv7z6svzfdwgg3"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             ;; Do not run pylint plugin test, as astroid is an old
+             ;; unsupported version.
+             (invoke "pytest" "-v" "-k" "not test_pylint_plugin"
+                     "verboselogs/tests.py"))))))
     (native-inputs
      `(("python-mock" ,python-mock)
-       ("python-astroid" ,python-astroid)
-       ("python-pylint" ,python-pylint)))
+       ("python-pytest" ,python-pytest)))
     (home-page "https://verboselogs.readthedocs.io")
     (synopsis "Verbose logging level for Python's logging module")
     (description
@@ -927,14 +933,14 @@ add the log levels NOTICE, SPAM, SUCCESS and VERBOSE.")
 (define-public python-coloredlogs
   (package
     (name "python-coloredlogs")
-    (version "7.3")
+    (version "10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "coloredlogs" version))
        (sha256
         (base32
-         "1blcann6dyg5dhps9pg12rn0q0rjrlajpmmil0gy0j4cbvnl2il9"))))
+         "0dkw6xp0r1dwgz4s2f58npx5nxfq51wf4l6qkm5ib27slgfs4sdq"))))
     (build-system python-build-system)
     (arguments
      `(;Tests require some updated modules
@@ -1916,13 +1922,13 @@ files.")
 (define-public python-pyld
   (package
     (name "python-pyld")
-    (version "1.0.3")
+    (version "1.0.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "PyLD" version))
               (sha256
                (base32
-                "12i2g6xdj30k7xxcibg3sc5y76snwq8l6n8fy9lyi577kgy0h2pm"))))
+                "1ywbdbsrkg533qh8xn9ifjh2mvam6v5msrjyqq73jfpvcp89qvff"))))
     (build-system python-build-system)
     (home-page "https://github.com/digitalbazaar/pyld")
     (synopsis "Python implementation of the JSON-LD specification")
@@ -2992,14 +2998,13 @@ receive files via the SCP1 protocol, as implemented by the OpenSSH
 (define-public python-rst.linker
   (package
     (name "python-rst.linker")
-    (version "1.10")
+    (version "1.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rst.linker" version))
        (sha256
-        (base32
-         "0iqaacp7pj1s8avs4kc0qg0r7dscywaq37y6l9j14glqdikk0wdj"))))
+        (base32 "0pqsfqqx8h0pq21k8l3k62kznrgaj2ala93c64s4d9rpbr4mgkd2"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)
@@ -5212,13 +5217,13 @@ releases.")
 (define-public python-pathpy
   (package
     (name "python-pathpy")
-    (version "11.5.0")
+    (version "11.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "path.py" version))
        (sha256
-        (base32 "1jxkf91syzxlpiwgm83fjfz1m5xh3jrvv4iyl5wjsnkk599pls5n"))))
+        (base32 "0ir9j1haq2jbi7aip6k2fa9l7q1l03k4hp1awxhjhcwzsnwp3ll8"))))
     (outputs '("out" "doc"))
     (build-system python-build-system)
     (propagated-inputs
@@ -5432,13 +5437,13 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
 (define-public python-ipykernel
   (package
     (name "python-ipykernel")
-    (version "5.1.1")
+    (version "5.1.3")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "ipykernel" version))
       (sha256
-       (base32 "173nm29g85w8cac3fg40b27qaq26g41wgg6qn79ql1hq4w2n5sgh"))))
+       (base32 "1a08y677lpn80qzvv7z0smgggmr5m5ayf0bs6vds47xpxl9sss5k"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -5463,8 +5468,9 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
        ;; imported at runtime during connect
        ("python-jupyter-client" ,python-jupyter-client)))
     (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-nose" ,python-nose)))
+     `(("python-flaky" ,python-flaky)
+       ("python-nose" ,python-nose)
+       ("python-pytest" ,python-pytest)))
     (home-page "https://ipython.org")
     (synopsis "IPython Kernel for Jupyter")
     (description
@@ -5618,13 +5624,13 @@ computing.")
 (define-public python-ipython
   (package
     (name "python-ipython")
-    (version "7.5.0")
+    (version "7.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ipython" version ".tar.gz"))
        (sha256
-        (base32 "09mbxq37mfn88xjnib7qfzaq9krr7gf1jxwy1p6mcjr254082h78"))))
+        (base32 "103jkw18z7fnwdal1mdbijjxi1fndzn31g887lmj7ddpf2r07lyz"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-backcall" ,python-backcall)
@@ -5957,15 +5963,20 @@ the GObject Introspection bindings to libnotify for non-GTK applications.")
 (define-public python-lxml
   (package
     (name "python-lxml")
-    (version "4.2.5")
+    (version "4.4.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "lxml" version))
         (sha256
          (base32
-          "0zw0y9hs0nflxhl9cs6ipwwh53szi3w2x06wl0k9cylyqac0cwin"))))
+          "14jnpfcpgqr9sx8ppd286jzcbk0b36hbqsvd8jkvffipzw5v8768"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      (invoke "make" "test"))))))
     (inputs
       `(("libxml2" ,libxml2)
         ("libxslt" ,libxslt)))
@@ -6138,13 +6149,13 @@ Python.")
 (define-public snakemake
   (package
     (name "snakemake")
-    (version "5.2.4")
+    (version "5.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "snakemake" version))
        (sha256
-        (base32 "0gj0xxgiq3mp9qyyrbfzldiaq1giliqw0in64nqiz7vx49myqj7z"))))
+        (base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
     (build-system python-build-system)
     (arguments
      ;; TODO: Package missing test dependencies.
@@ -6162,18 +6173,19 @@ Python.")
                                "/bin/snakemake")))
              #t)))))
     (propagated-inputs
-     `(("python-gitpython" ,python-gitpython)
-       ("python-wrapt" ,python-wrapt)
-       ("python-requests" ,python-requests)
-       ("python-appdirs" ,python-appdirs)
+     `(("python-appdirs" ,python-appdirs)
        ("python-configargparse" ,python-configargparse)
        ("python-datrie" ,python-datrie)
        ("python-docutils" ,python-docutils)
+       ("python-gitpython" ,python-gitpython)
        ("python-jinja2" ,python-jinja2)
        ("python-jsonschema" ,python-jsonschema)
        ("python-networkx" ,python-networkx)
+       ("python-psutil" ,python-psutil)
        ("python-pyyaml" ,python-pyyaml)
-       ("python-ratelimiter" ,python-ratelimiter)))
+       ("python-ratelimiter" ,python-ratelimiter)
+       ("python-requests" ,python-requests)
+       ("python-wrapt" ,python-wrapt)))
     (home-page "https://snakemake.readthedocs.io")
     (synopsis "Python-based execution environment for make-like workflows")
     (description
@@ -6182,24 +6194,6 @@ providing a clean and modern domain specific specification language (DSL) in
 Python style, together with a fast and comfortable execution environment.")
     (license license:expat)))
 
-;; This is currently needed for the pigx-* packages.
-(define-public snakemake-4
-  (package (inherit snakemake)
-    (version "4.4.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "snakemake" version))
-       (sha256
-        (base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
-    (propagated-inputs
-     `(("python-wrapt" ,python-wrapt)
-       ("python-requests" ,python-requests)
-       ("python-appdirs" ,python-appdirs)
-       ("python-configargparse" ,python-configargparse)
-       ("python-pyyaml" ,python-pyyaml)
-       ("python-ratelimiter" ,python-ratelimiter)))))
-
 (define-public python-pyqrcode
   (package
     (name "python-pyqrcode")
@@ -12538,18 +12532,19 @@ clone, while other processes access the original tree.")
 (define-public python-astroid
   (package
     (name "python-astroid")
-    (version "2.1.0")
+    (version "2.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astroid" version))
        (sha256
         (base32
-         "08hz675knh4294bancdapql392fmbjyimhbyrmfkz1ka7l035c1m"))))
+         "0crfhpblcy5a6nh694hc2073gw389f01yilamzqi34si2skgp8q9"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-lazy-object-proxy" ,python-lazy-object-proxy)
        ("python-six" ,python-six)
+       ("python-typed-ast" ,python-typed-ast)
        ("python-wrapt" ,python-wrapt)))
     (native-inputs
      `(("python-dateutil" ,python-dateutil)
@@ -12616,7 +12611,8 @@ builds partial trees by inspecting living objects.")
          ,python2-backports-functools-lru-cache)
         ("python2-enum34" ,python2-enum34)
         ("python2-singledispatch" ,python2-singledispatch)
-        ,@(package-propagated-inputs base))))))
+        ,@(alist-delete "python-typed-ast"
+                        (package-propagated-inputs base)))))))
 
 (define-public python-isort
   (package
@@ -14333,14 +14329,20 @@ such as figshare or Zenodo.")
 (define-public python-pyro4
   (package
     (name "python-pyro4")
-    (version "4.75")
+    (version "4.77")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Pyro4" version))
        (sha256
-        (base32 "1dfpp36imddx19yv0kd28gk1l71ckhpqy6jd590wpm2680jw15rq"))))
+        (base32 "0gsjg869y4gpy265s1gj1f2qy6jn5iz8r2bwwnq78r1r5yi15zib"))))
     (build-system python-build-system)
+    (arguments
+     '(#:tests? #f)) ;FIXME: Some tests require network access.
+    (native-inputs
+     `(("python-cloudpickle" ,python-cloudpickle)
+       ("python-dill" ,python-dill)
+       ("python-msgpack" ,python-msgpack)))
     (propagated-inputs
      `(("python-serpent" ,python-serpent)))
     (home-page "https://pyro4.readthedocs.io")
@@ -14735,14 +14737,16 @@ source bytes using the UTF-8 encoding and then rewrites Python 3.6 style
 (define-public python-typed-ast
   (package
     (name "python-typed-ast")
-    (version "1.3.5")
+    (version "1.4.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "typed-ast" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/python/typed_ast.git")
+             (commit version)))
        (sha256
-        (base32
-         "1m7pr6qpana3cvqwiw7mlvrgvmw27ch5mx1592572xhlki8g85ak"))))
+        (base32 "0l0hz809f7i356kmqkvfsaswiidb98j9hs9rrjnfawzqcbffzgyb"))
+       (file-name (git-file-name name version))))
     (build-system python-build-system)
     (arguments
      `(#:modules ((guix build utils)
@@ -14842,14 +14846,13 @@ Included are implementations of:
 (define-public bpython
   (package
     (name "bpython")
-    (version "0.17.1")
+    (version "0.18")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "bpython" version))
        (sha256
-        (base32
-         "0bxhxi5zxdkrf8b4gwn0d363kdz3qnypjwhm1aydki53ph8ca1w9"))))
+        (base32 "1hl6frgvr2lqaxqczl8amg9xih32b3gzv429vs0qrjb8wpdj1k2n"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -14872,10 +14875,10 @@ Included are implementations of:
     (propagated-inputs
      `(("python-pygments" ,python-pygments)
        ("python-requests" ,python-requests)
-       ("python-babel" ,python-babel) ; optional, for internationalization
+       ("python-babel" ,python-babel)   ; optional, for internationalization
        ("python-curtsies" ,python-curtsies) ; >= 0.1.18
        ("python-greenlet" ,python-greenlet)
-       ("python-urwid" ,python-urwid) ; for bpython-urwid only
+       ("python-urwid" ,python-urwid)   ; for bpython-urwid only
        ("python-six" ,python-six)))
     (native-inputs
      `(("python-sphinx" ,python-sphinx)
@@ -16598,3 +16601,57 @@ It is the recommended replacement for Python's original
 @code{distro} also provides a command-line interface to output the platform
 information in various formats.")
     (license license:asl2.0)))
+
+(define-public python-cairosvg
+  (package
+    (name "python-cairosvg")
+    (version "2.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "CairoSVG" version))
+       (sha256
+        (base32 "1bb7irxbaxxb9ahm3z5wsx1q96mm5gzskc7b6q07h9ikcnb8yrjf"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _ (invoke "pytest"))))))
+    (propagated-inputs
+     `(("python-cairocffi" ,python-cairocffi)
+       ("python-cssselect2" ,python-cssselect2)
+       ("python-defusedxml" ,python-defusedxml)
+       ("python-pillow" ,python-pillow)
+       ("python-tinycss2" ,python-tinycss2)))
+    (native-inputs
+     `(("python-pytest-flake8" ,python-pytest-flake8)
+       ("python-pytest-isort" ,python-pytest-isort)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (home-page "https://cairosvg.org/")
+    (synopsis "SVG to PDF/PS/PNG converter based on Cairo")
+    (description "CairoSVG is a SVG converter based on Cairo.  It can export
+SVG files to PDF, PostScript and PNG files.  The main part of CairoSVG is a
+SVG parser, trying to follow the SVG 1.1 recommendation from the W3C.  Once
+parsed, the result is drawn to a Cairo surface that can be exported to
+qvarious formats: PDF, PostScript, PNG and even SVG.")
+    (license license:lgpl3+)))
+
+(define-public python-pyphen
+  (package
+    (name "python-pyphen")
+    (version "0.9.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Pyphen" version))
+       (sha256
+        (base32 "08c9y69ry9d6m4zalhnalg86lsp9v2j5n1ziw5vxfmiihx83lqrv"))))
+    (build-system python-build-system)
+    ;; TODO: Use the Guix system hyphenation packages hyphen-* rather than the
+    ;; embedded set provided by upstream - like Debian does.
+    (home-page "https://github.com/Kozea/Pyphen")
+    (synopsis "Pure Python module to hyphenate text")
+    (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))))