diff options
Diffstat (limited to 'gnu/packages/python.scm')
| -rw-r--r-- | gnu/packages/python.scm | 266 |
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)) + |