From 250276a20272dcbf609bb8761b6ef213a2e9f863 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 12 Jul 2018 16:06:28 +0200 Subject: gnu: python-pyyaml: Update to 3.13. * gnu/packages/python.scm (python-pyyaml): Update to 3.13. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c9b22e87ee..057a14c501 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -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))) -- cgit v1.2.3 From 5908818e309280b124b64f5320e4b98210093061 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 15 Jul 2018 00:43:57 +1000 Subject: gnu: python-h5py: Update to 2.8.0. * gnu/packages/python.scm (python-h5py): Update to 2.8.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0fdc53bdca..d350990c67 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -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 -- cgit v1.2.3 From 6c10675928a4485fd4ed83f4a067f22ae06779cc Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 14 Jul 2018 23:19:26 +0300 Subject: gnu: python-xenon: Update to 0.5.4. * gnu/packages/python.scm (python-xenon): Update to 0.5.4. [arguments]: Remove part of custom 'patch-test-requirements phase. --- gnu/packages/python.scm | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d350990c67..38c48288a9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2015, 2016, 2017 Leo Famulari ;;; Copyright © 2015, 2017 Ben Woodcroft ;;; Copyright © 2015, 2016 Erik Edrosa -;;; Copyright © 2015, 2016, 2017 Efraim Flashner +;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2015, 2017 Kyle Meyer ;;; Copyright © 2015, 2016 Chris Marusich ;;; Copyright © 2016 Danny Milosavljevic @@ -12242,14 +12242,14 @@ 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 +12261,7 @@ 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") "")) -- cgit v1.2.3 From 90f38fb66109e7da897fa9e6d56a10079d05c4bf Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 16 Jul 2018 16:44:59 -0400 Subject: gnu: python-pyasn1: Update to 0.4.3. * gnu/packages/python.scm (python-pyasn1, python2-pyasn1): Update to 0.4.3. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 38c48288a9..7e2e194816 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6284,14 +6284,14 @@ 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") -- cgit v1.2.3 From 8e632a6435bb8ea408127833030f7764b78768a9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 16 Jul 2018 16:45:37 -0400 Subject: gnu: python-pyasn1-modules: Update to 0.2.2. * gnu/packages/python.scm (python-pyasn1-modules, python2-pyasn1-modules): Update to 0.2.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7e2e194816..ebf02af22e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6306,14 +6306,14 @@ 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))) -- cgit v1.2.3 From a545090ce5e6b9da1f473f558dabda69f317e461 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Mon, 16 Jul 2018 23:48:24 +0200 Subject: gnu: python-cairocffi: Fix loading of shared libraries. Fixes . * gnu/packages/patches/python-cairocffi-dlopen-path.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-cairocffi)[inputs]: Add glib, gtk+, pango. [native-inputs]: Add python-pytest. [arguments]: Enable tests. [arguments]<#:phases>[patch-paths]: New phase. --- gnu/packages/python.scm | 38 ++++++++++++++++++++++++++++++++++---- 1 file changed, 34 insertions(+), 4 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ebf02af22e..fc1ef3eb2a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -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")) -- cgit v1.2.3 From b62715aa82cd884936124f2060e718957721138b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 14:10:23 +0200 Subject: gnu: snakemake: Update to 5.2.0. * gnu/packages/python.scm (snakemake): Update to 5.2.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fc1ef3eb2a..f20de13720 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5139,13 +5139,13 @@ of the structure, dynamics, and functions of complex networks.") (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. -- cgit v1.2.3 From 216a72a95738d6d643094f156000cbc006cd79f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 15:07:12 +0200 Subject: gnu: Add python-datrie. * gnu/packages/python.scm (python-datrie): New variable. --- gnu/packages/python.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f20de13720..1422ad26a3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5136,6 +5136,30 @@ 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") -- cgit v1.2.3 From 269f100330cf92afdc911bbd7db0644719d6dc3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 15:07:26 +0200 Subject: gnu: snakemake: Add missing dependencies. * gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-datrie, python-docutils, python-jinja2, python-jsonschema, and python-networkx. --- gnu/packages/python.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1422ad26a3..a6e3ebb9d6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5191,6 +5191,11 @@ Python.") ("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") -- cgit v1.2.3 From ed2dfe3955f0144bc858c66fdb751f51e9bd84fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 Jul 2018 15:13:56 +0200 Subject: gnu: Add snakemake-4. * gnu/packages/python.scm (snakemake-4): New variable. * gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq, pigx-chipseq)[inputs]: Use it. --- gnu/packages/python.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a6e3ebb9d6..e9fb9f529f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5206,6 +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") -- cgit v1.2.3