diff options
Diffstat (limited to 'gnu/packages/python.scm')
| -rw-r--r-- | gnu/packages/python.scm | 118 |
1 files changed, 95 insertions, 23 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a984670f6e..10d8df7b0c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name> ;;; 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, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2015, 2017 Kyle Meyer <kyle@kyleam.com> ;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org> @@ -782,14 +782,14 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of (define-public python-h5py (package (name "python-h5py") - (version "2.7.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (pypi-uri "h5py" version)) (sha256 (base32 - "0433sdv6xc9p7v1xs1gvbxp7p152ywi3nplgjb258q9fvw9469br")))) + "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6")))) (build-system python-build-system) (arguments `(#:tests? #f ; no test target @@ -2218,14 +2218,14 @@ environments and back.") (define-public python-pyyaml (package (name "python-pyyaml") - (version "3.12") + (version "3.13") (source (origin (method url-fetch) (uri (pypi-uri "PyYAML" version)) (sha256 (base32 - "1aqjl8dk9amd4zr99n8v2qxzgmr2hdvqfma4zh7a41rj6336c9sr")))) + "1gx603g484z46cb74j9rzr6sjlh2vndxayicvlyhxdz98lhhkwry")))) (build-system python-build-system) (inputs `(("libyaml" ,libyaml))) @@ -4210,23 +4210,53 @@ support for Python 3 and PyPy. It is based on cffi.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9")))) + "1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9")) + (patches (search-patches "python-cairocffi-dlopen-path.patch")))) (build-system python-build-system) (outputs '("out" "doc")) (inputs - `(("gdk-pixbuf" ,gdk-pixbuf) - ("cairo" ,cairo))) + `(("glib" ,glib) + ("gtk+" ,gtk+) + ("gdk-pixbuf" ,gdk-pixbuf) + ("cairo" ,cairo) + ("pango" ,pango))) (native-inputs `(("pkg-config" ,pkg-config) + ("python-pytest" ,python-pytest) ("python-sphinx" ,python-sphinx) ("python-docutils" ,python-docutils))) (propagated-inputs `(("python-xcffib" ,python-xcffib))) ; used at run time (arguments `(;; FIXME: Tests cannot find 'libcairo.so.2'. - #:tests? #f + #:tests? #t #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* (find-files "." "\\.py$") + (("dlopen\\(ffi, 'cairo'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "cairo") + "/lib/libcairo.so.2'")) + (("dlopen\\(ffi, 'gdk-3'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "gtk+") + "/lib/libgtk-3.so.0'")) + (("dlopen\\(ffi, 'gdk_pixbuf-2.0'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "gdk-pixbuf") + "/lib/libgdk_pixbuf-2.0.so.0'")) + (("dlopen\\(ffi, 'glib-2.0'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "glib") + "/lib/libglib-2.0.so.0'")) + (("dlopen\\(ffi, 'gobject-2.0'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "glib") + "/lib/libgobject-2.0.so.0'")) + (("dlopen\\(ffi, 'pangocairo-1.0'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "pango") + "/lib/libpangocairo-1.0.so.0'")) + (("dlopen\\(ffi, 'pango-1.0'") + (string-append "dlopen(ffi, '" (assoc-ref inputs "pango") + "/lib/libpango-1.0.so.0'"))) + #t)) (add-after 'install 'install-doc (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((data (string-append (assoc-ref outputs "doc") "/share")) @@ -5106,16 +5136,40 @@ of the structure, dynamics, and functions of complex networks.") (define-public python2-networkx2 (package-with-python2 python-networkx2)) +(define-public python-datrie + (package + (name "python-datrie") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "datrie" version)) + (sha256 + (base32 + "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs")))) + (build-system python-build-system) + (native-inputs + `(("python-cython" ,python-cython) + ("python-hypothesis" ,python-hypothesis) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://github.com/kmike/datrie") + (synopsis "Fast, efficiently stored trie for Python") + (description + "This package provides a fast, efficiently stored trie implementation for +Python.") + (license license:lgpl2.1+))) + (define-public snakemake (package (name "snakemake") - (version "4.4.0") + (version "5.2.0") (source (origin (method url-fetch) (uri (pypi-uri "snakemake" version)) (sha256 - (base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv")))) + (base32 "0a1i5v5qxbmmpznp7my9nva8y7pxp8pjrwk2gxgisdskg35sq8s1")))) (build-system python-build-system) (arguments ;; TODO: Package missing test dependencies. @@ -5137,6 +5191,11 @@ of the structure, dynamics, and functions of complex networks.") ("python-requests" ,python-requests) ("python-appdirs" ,python-appdirs) ("python-configargparse" ,python-configargparse) + ("python-datrie" ,python-datrie) + ("python-docutils" ,python-docutils) + ("python-jinja2" ,python-jinja2) + ("python-jsonschema" ,python-jsonschema) + ("python-networkx" ,python-networkx) ("python-pyyaml" ,python-pyyaml) ("python-ratelimiter" ,python-ratelimiter))) (home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home") @@ -5147,6 +5206,24 @@ 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") @@ -6284,14 +6361,14 @@ designed to efficiently cope with extremely large amounts of data.") (define-public python-pyasn1 (package (name "python-pyasn1") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (pypi-uri "pyasn1" version)) (sha256 (base32 - "05bxnr4wmrg62m4qr1pg1p3z7bhwrv74jll3k42pgxwl36kv0n6j")))) + "1z5h38anjzzrxpraa9iq9llffyx2zs8gx0q6dc1g029miwnn50gv")))) (build-system python-build-system) (home-page "http://pyasn1.sourceforge.net/") (synopsis "ASN.1 types and codecs") @@ -6306,14 +6383,14 @@ suitable for a wide range of protocols based on the ASN.1 specification.") (define-public python-pyasn1-modules (package (name "python-pyasn1-modules") - (version "0.0.8") + (version "0.2.2") (source (origin (method url-fetch) (uri (pypi-uri "pyasn1-modules" version)) (sha256 (base32 - "0drqgw81xd3fxdlg89kgd79zzrabvfncvkbybi2wr6w2y4s1jmhh")))) + "0ivm850yi7ajjbi8j115qpsj95bgxdsx48nbjzg0zip788c3xkx0")))) (build-system python-build-system) (propagated-inputs `(("python-pyasn1" ,python-pyasn1))) @@ -12242,14 +12319,14 @@ pure Python module.") (define-public python-xenon (package (name "python-xenon") - (version "0.5.1") + (version "0.5.4") (source (origin (method url-fetch) (uri (pypi-uri "xenon" version)) (sha256 (base32 - "14kby2y48vp3sgwxqlm5d5789yibqwb1qli5fwcmdqg3iayrbklc")))) + "029cbhysg2vr5n4jz8gpg2793f8wkwnqpr1qgv6c1dn685vy31mc")))) (build-system python-build-system) (native-inputs `(("python-pyyaml" ,python-pyyaml) @@ -12261,12 +12338,7 @@ pure Python module.") `(#: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") "")) + (lambda _ ;; Remove httpretty dependency for tests. (substitute* "setup.py" (("httpretty") "")) |