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-rw-r--r--gnu/packages/python.scm266
1 files changed, 225 insertions, 41 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index dc7def5507..adb84fc5b7 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -37,6 +37,7 @@
#:use-module (gnu packages openssl)
#:use-module (gnu packages elf)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages ncurses)
#:use-module (gnu packages gcc)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages databases)
@@ -50,6 +51,9 @@
#:use-module (gnu packages fontutils)
#:use-module (gnu packages which)
#:use-module (gnu packages perl)
+ #:use-module (gnu packages xorg)
+ #:use-module (gnu packages glib)
+ #:use-module (gnu packages gtk)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
@@ -614,6 +618,43 @@ get the local timezone information, unless you know the zoneinfo name, and
under several distributions that's hard or impossible to figure out.")
(license cc0)))
+(define-public python-pysam
+ (package
+ (name "python-pysam")
+ (version "0.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://pypi.python.org/packages/source/p/pysam/pysam-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; tests are excluded in the manifest
+ #:phases
+ (alist-cons-before
+ 'build 'set-flags
+ (lambda _
+ (setenv "LDFLAGS" "-lncurses")
+ (setenv "CFLAGS" "-D_CURSES_LIB=1"))
+ %standard-phases)))
+ (inputs
+ `(("python-cython" ,python-cython)
+ ("python-setuptools" ,python-setuptools)
+ ("ncurses" ,ncurses)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/pysam-developers/pysam")
+ (synopsis "Python bindings to the SAMtools C API")
+ (description
+ "Pysam is a Python module for reading and manipulating files in the
+SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
+also includes an interface for tabix.")
+ (license expat)))
+
+(define-public python2-pysam
+ (package-with-python2 python-pysam))
(define-public python2-pysqlite
(package
@@ -2117,10 +2158,35 @@ that client code uses to construct the grammar directly in Python code.")
"0m6v9nwdldlwk22gcd339zg6mny5m301fxgks7z8sb8m9wawg8qp"))))
(build-system python-build-system)
(outputs '("out" "doc"))
+ (propagated-inputs ; the following packages are all needed at run time
+ `(("python-pyparsing" ,python-pyparsing)
+ ("python-pygobject" ,python-pygobject)
+ ("gobject-introspection" ,gobject-introspection)
+ ;; The 'gtk+' package (and 'gdk-pixbuf', 'atk' and 'pango' propagated
+ ;; from 'gtk+') provides the required 'typelib' files used by
+ ;; 'gobject-introspection'. The location of these files is set with the
+ ;; help of the environment variable GI_TYPELIB_PATH. At build time this
+ ;; is done automatically by a 'native-search-path' procedure. However,
+ ;; at run-time the user must set this variable as follows:
+ ;;
+ ;; export GI_TYPELIB_PATH=~/.guix-profile/lib/girepository-1.0
+ ;;
+ ;; 'typelib' files include references to dynamic libraries. Currently
+ ;; the references do not include the full path to the libraries. For
+ ;; this reason the user must set the LD_LIBRARY_PATH to the location of
+ ;; 'libgtk-3.so.0', 'libgdk-3.so.0' and 'libatk-1.0.so.0':
+ ;;
+ ;; export LD_LIBRARY_PATH=~/.guix-profile/lib
+ ("gtk+" ,gtk+)
+ ;; From version 1.4.0 'matplotlib' makes use of 'cairocffi' instead of
+ ;; 'pycairo'. However, 'pygobject' makes use of a 'pycairo' 'context'
+ ;; object. For this reason we need to import both libraries.
+ ;; https://pythonhosted.org/cairocffi/cffi_api.html#converting-pycairo
+ ("python-pycairo" ,python-pycairo)
+ ("python-cairocffi" ,python-cairocffi)))
(inputs
`(("python-setuptools" ,python-setuptools)
("python-dateutil" ,python-dateutil-2)
- ("python-pyparsing" ,python-pyparsing)
("python-six" ,python-six)
("python-pytz" ,python-pytz)
("python-numpy" ,python-numpy-bootstrap)
@@ -2131,10 +2197,10 @@ that client code uses to construct the grammar directly in Python code.")
("libpng" ,libpng)
("imagemagick" ,imagemagick)
("freetype" ,freetype)
+ ("cairo" ,cairo)
+ ("glib" ,glib)
+ ("python-pillow" ,python-pillow)
;; FIXME: Add backends when available.
- ;("python-pygtk" ,python-pygtk)
- ;("python-pycairo" ,python-pycairo)
- ;("python-pygobject" ,python-pygobject)
;("python-wxpython" ,python-wxpython)
;("python-pyqt" ,python-pyqt)
))
@@ -2144,40 +2210,51 @@ that client code uses to construct the grammar directly in Python code.")
("texinfo" ,texinfo)))
(arguments
`(#:phases
- (alist-cons-after
- 'install 'install-doc
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
- (doc (string-append data "/doc/" ,name "-" ,version))
- (info (string-append data "/info"))
- (html (string-append doc "/html")))
- (with-directory-excursion "doc"
- ;; Without setting this variable we get an encoding error.
- (setenv "LANG" "en_US.UTF-8")
- ;; Produce pdf in 'A4' format.
- (substitute* (find-files "." "conf\\.py")
- (("latex_paper_size = 'letter'")
- "latex_paper_size = 'a4'"))
- (mkdir-p html)
- (mkdir-p info)
- ;; The doc recommends to run the 'html' target twice.
- (system* "python" "make.py" "html")
- (system* "python" "make.py" "html")
- (system* "python" "make.py" "latex")
- (system* "python" "make.py" "texinfo")
- (copy-file "build/texinfo/matplotlib.info"
- (string-append info "/matplotlib.info"))
- (copy-file "build/latex/Matplotlib.pdf"
- (string-append doc "/Matplotlib.pdf"))
- (with-directory-excursion "build/html"
- (map (lambda (file)
- (let* ((dir (dirname file))
- (tgt-dir (string-append html "/" dir)))
- (unless (equal? "." dir)
- (mkdir-p tgt-dir))
- (copy-file file (string-append html "/" file))))
- (find-files "." ".*"))))))
- %standard-phases)))
+ (alist-cons-before
+ 'build 'configure-environment
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let ((cairo (assoc-ref inputs "cairo"))
+ (gtk+ (assoc-ref inputs "gtk+")))
+ ;; Setting these directories in the 'basedirlist' of 'setup.cfg'
+ ;; has not effect.
+ ;;
+ ;; FIXME: setting LD_LIBRARY_PATH should be removed once we patch
+ ;; gobject-introspection to include the full path of shared
+ ;; libraries in 'typelib' files.
+ (setenv "LD_LIBRARY_PATH"
+ (string-append cairo "/lib:" gtk+ "/lib"))
+ (setenv "HOME" (getcwd))
+ (call-with-output-file "setup.cfg"
+ (lambda (port)
+ (format port "[rc_options]~%
+backend = GTK3Agg~%")))))
+ (alist-cons-after
+ 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (info (string-append data "/info"))
+ (html (string-append doc "/html")))
+ (with-directory-excursion "doc"
+ ;; Without setting this variable we get an encoding error.
+ (setenv "LANG" "en_US.UTF-8")
+ ;; Produce pdf in 'A4' format.
+ (substitute* (find-files "." "conf\\.py")
+ (("latex_paper_size = 'letter'")
+ "latex_paper_size = 'a4'"))
+ (mkdir-p html)
+ (mkdir-p info)
+ ;; The doc recommends to run the 'html' target twice.
+ (system* "python" "make.py" "html")
+ (system* "python" "make.py" "html")
+ (system* "python" "make.py" "latex")
+ (system* "python" "make.py" "texinfo")
+ (copy-file "build/texinfo/matplotlib.info"
+ (string-append info "/matplotlib.info"))
+ (copy-file "build/latex/Matplotlib.pdf"
+ (string-append doc "/Matplotlib.pdf"))
+ (copy-recursively "build/html" html))))
+ %standard-phases))))
(home-page "http://matplotlib.org")
(synopsis "2D plotting library for Python")
(description
@@ -2193,9 +2270,17 @@ toolkits.")
(package (inherit matplotlib)
;; Make sure we use exactly PYTHON2-NUMPYDOC, which is
;; customized for Python 2.
- (inputs `(("python2-numpydoc" ,python2-numpydoc)
- ,@(alist-delete "python-numpydoc"
- (package-inputs matplotlib)))))))
+ (propagated-inputs
+ `(("python2-py2cairo" ,python2-py2cairo)
+ ("python2-pygobject-2" ,python2-pygobject-2)
+ ,@(alist-delete "python-pycairo"
+ (alist-delete "python-pygobject"
+ (package-propagated-inputs
+ matplotlib)))))
+ (inputs
+ `(("python2-numpydoc" ,python2-numpydoc)
+ ,@(alist-delete "python-numpydoc"
+ (package-inputs matplotlib)))))))
;; Scipy 0.14.0 with Numpy 0.19.X fails several tests. This is known and
;; planned to be fixed in 0.14.1. It is claimed that the failures can safely
@@ -2542,3 +2627,102 @@ a front-end for C compilers or analysis tools.")
(define-public python2-cffi
(package-with-python2 python-cffi))
+
+(define-public python-xcffib
+ (package
+ (name "python-xcffib")
+ (version "0.1.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://pypi.python.org/packages/source/x/"
+ "xcffib/xcffib-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0655hzxv57h1a9ja9kwp0ichbkhf3djw32k33d66xp0q37dq2y81"))))
+ (build-system python-build-system)
+ (inputs
+ `(("libxcb" ,libxcb)
+ ("python-six" ,python-six)))
+ (native-inputs
+ `(("python-setuptools" ,python-setuptools)))
+ (propagated-inputs
+ `(("python-cffi" ,python-cffi))) ; used at run time
+ (arguments
+ `(#:phases
+ (alist-cons-after
+ 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((doc (string-append (assoc-ref outputs "out") "/share"
+ "/doc/" ,name "-" ,version)))
+ (mkdir-p doc)
+ (copy-file "README.md"
+ (string-append doc "/README.md"))))
+ %standard-phases)))
+ (home-page "https://github.com/tych0/xcffib")
+ (synopsis "XCB Python bindings")
+ (description
+ "Xcffib is a replacement for xpyb, an XCB Python bindings. It adds
+support for Python 3 and PyPy. It is based on cffi.")
+ (license expat)))
+
+(define-public python2-xcffib
+ (package-with-python2 python-xcffib))
+
+(define-public python-cairocffi
+ (package
+ (name "python-cairocffi")
+ (version "0.6")
+ (source
+ (origin
+ (method url-fetch)
+ ;; The archive on pypi is missing the 'utils' directory!
+ (uri (string-append "https://github.com/SimonSapin/cairocffi/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "03w5p62sp3nqiccx864sbq0jvh7946277jqx3rcc3dch5xwfvv51"))))
+ (build-system python-build-system)
+ (outputs '("out" "doc"))
+ (inputs
+ `(("gdk-pixbuf" ,gdk-pixbuf)
+ ("cairo" ,cairo)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("python-sphinx" ,python-sphinx)
+ ("python-docutils" ,python-docutils)
+ ("python-setuptools" ,python-setuptools)))
+ (propagated-inputs
+ `(("python-xcffib" ,python-xcffib))) ; used at run time
+ (arguments
+ `(#:phases
+ (alist-cons-after
+ 'install 'install-doc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (html (string-append doc "/html")))
+ (setenv "LD_LIBRARY_PATH"
+ (string-append (assoc-ref inputs "cairo") "/lib" ":"
+ (assoc-ref inputs "gdk-pixbuf") "/lib"))
+ (setenv "LANG" "en_US.UTF-8")
+ (mkdir-p html)
+ (for-each (lambda (file)
+ (copy-file (string-append "." file)
+ (string-append doc file)))
+ '("/README.rst" "/CHANGES" "/LICENSE"))
+ (system* "python" "setup.py" "build_sphinx")
+ (copy-recursively "docs/_build/html" html)))
+ %standard-phases)))
+ (home-page "https://github.com/SimonSapin/cairocffi")
+ (synopsis "Python bindings and object-oriented API for Cairo")
+ (description
+ "Cairocffi is a CFFI-based drop-in replacement for Pycairo, a set of
+Python bindings and object-oriented API for cairo. Cairo is a 2D vector
+graphics library with support for multiple backends including image buffers,
+PNG, PostScript, PDF, and SVG file output.")
+ (license bsd-3)))
+
+(define-public python2-cairocffi
+ (package-with-python2 python-cairocffi))
+
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