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authorPjotr Prins2019-08-01 08:59:33 -0500
committerPjotr Prins2019-08-01 08:59:33 -0500
commita5a1e75c1379d9c26c0a0f9dbb9fb069c7bf7f18 (patch)
tree198824fa4435adb7bc850f129fff600d607eaa22 /gn/packages/python.scm
parentfd06a7a744cb2368d410e131b4f8c6bc7738cc94 (diff)
parent25db4463972bc8729436d84d8be003ea7eacad71 (diff)
downloadguix-bioinformatics-a5a1e75c1379d9c26c0a0f9dbb9fb069c7bf7f18.tar.gz
Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages/python.scm')
-rw-r--r--gn/packages/python.scm453
1 files changed, 334 insertions, 119 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 651a635..ee32a61 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -30,6 +30,7 @@
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages statistics)
+ #:use-module (gnu packages tcl)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages time)
@@ -134,31 +135,75 @@ functions.")
(license license:expat))
)
+(define-public python-plotly-3.2.1
+ (package
+ (inherit python-plotly)
+ (name "python-plotly")
+ (version "3.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "plotly" version))
+ (sha256
+ (base32
+ "1ay1plgsckfi7fddl99kvbcx5nifh48ahvszkqvb4d7r008m8sxk"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-decorator" ,python-decorator)
+ ("python-nbformat" ,python-nbformat)
+ ("python-pytz" ,python-pytz)
+ ("python-requests" ,python-requests)
+ ("python-retrying" ,python-retrying)
+ ("python-six" ,python-six)))))
+
+(define-public python-retrying
+ (package
+ (name "python-retrying")
+ (version "1.3.3")
+ (source
+ (origin
+ ;; pypi release doesn't have test library
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rholder/retrying")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1kqipkbdaw5s1xg0gi29awm03vp1x8dz24pjidgxagvkvrjpzhi7"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-six" ,python-six)))
+ (home-page "https://github.com/rholder/retrying")
+ (synopsis "General-purpose retrying library")
+ (description "Retrying is a general-purpose retrying library, written in
+Python, to simplify the task of adding retry behavior to just about anything.
+The simplest use case is retrying a flaky function whenever an Exception occurs
+until a value is returned.")
+ (license license:asl2.0)))
+
(define-public python-bagit; guix candidate
-(package
- (name "python-bagit")
- (version "1.7.0")
- (source
- (origin
- (method url-fetch)
- (uri "https://files.pythonhosted.org/packages/ee/11/7a7fa81c0d43fb4d449d418eba57fc6c77959754c5c2259a215152810555/bagit-1.7.0.tar.gz")
- (sha256
- (base32
+ (package
+ (name "python-bagit")
+ (version "1.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "bagit" version))
+ (sha256
+ (base32
"1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
- (build-system python-build-system)
- (inputs
+ (build-system python-build-system)
+ (inputs
`(("python-setuptools-scm" ,python-setuptools-scm)
- ("python-coverage" ,python-coverage)
- ("python-mock" ,python-mock)
- ))
- (arguments `(#:tests? #f)) ;; No tests.
- (home-page "https://pypi.python.org/pypi/bagit")
- (synopsis
- "Python bagit.")
- (description
- "Python bagit.")
- (license license:gpl2))
-)
+ ("python-coverage" ,python-coverage)
+ ("python-mock" ,python-mock)))
+ (arguments `(#:tests? #f)) ;; No tests.
+ (home-page "https://pypi.python.org/pypi/bagit")
+ (synopsis "Create and validate BagIt packages")
+ (description
+ "Create and validate BagIt packages")
+ (license license:gpl2)))
(define-public python-prov ; guix candidate
(package
@@ -188,44 +233,43 @@ functions.")
(license license:expat)))
(define-public python-typing-extensions; guix candidate
-(package
- (name "python-typing-extensions")
- (version "3.6.6")
- (source
- (origin
- (method url-fetch)
- (uri "https://files.pythonhosted.org/packages/fc/e6/3d2f306b12f01bde2861d67458d32c673e206d6fcc255537bf452db8f80c/typing_extensions-3.6.6.tar.gz")
- (sha256
- (base32
+ (package
+ (name "python-typing-extensions")
+ (version "3.6.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "typing_extensions" version))
+ (sha256
+ (base32
"07vhddjnd3mhdijyc3s0mwi9jgfjp3rr056nxqiavydbvkrvgrsi"))))
- (build-system python-build-system)
- (home-page "https://pypi.python.org/pypi/typing_extensions")
- (synopsis
- "Python typing_extensions.")
- (description
- "Python typing_extensions.")
- (license license:gpl2))
+ (build-system python-build-system)
+ (home-page "https://pypi.python.org/pypi/typing_extensions")
+ (synopsis "Python typing_extensions.")
+ (description
+ "Python typing_extensions.")
+ (license license:gpl2))
)
(define-public python-subprocess32 ; guix candidate
-(package
- (name "python-subprocess32")
- (version "0.2.9")
- (source
- (origin
- (method url-fetch)
- (uri "https://files.pythonhosted.org/packages/be/2b/beeba583e9877e64db10b52a96915afc0feabf7144dcbf2a0d0ea68bf73d/subprocess32-3.5.3.tar.gz")
- (sha256
- (base32
+ (package
+ (name "python-subprocess32")
+ (version "3.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "subprocess32" version))
+ (sha256
+ (base32
"1hr5fan8i719hmlmz73hf8rhq74014w07d8ryg7krvvf6692kj3b"))))
- (build-system python-build-system)
- (arguments `(#:tests? #f)) ;; No tests.
- (home-page "https://pypi.python.org/pypi/subprocess32")
- (synopsis
- "Python subprocess32.")
- (description
- "Python subprocess32.")
- (license license:gpl2))
+ (build-system python-build-system)
+ (arguments `(#:tests? #f)) ;; No tests.
+ (home-page "https://pypi.python.org/pypi/subprocess32")
+ (synopsis
+ "Python subprocess32.")
+ (description
+ "Python subprocess32.")
+ (license license:gpl2))
)
(define-public python-inotify ; guix candidate
@@ -447,30 +491,25 @@ Python 3 support.")
(package-with-python2 python-avro))
(define-public python-shellescape ; guix ready
-(package
- (name "python-shellescape")
- (version "3.4.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/s/shellescape/shellescape-"
- version
- ".tar.gz"))
- (sha256
- (base32
+ (package
+ (name "python-shellescape")
+ (version "3.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "shellescape" version))
+ (sha256
+ (base32
"0n5ky1b2vw2y0d4xl3qybyp2rk0gq5frjs8nr8ak6mgj2fyb4676"))))
- (build-system python-build-system)
- (inputs
- `(("python-setuptools" ,python-setuptools)))
- (home-page
- "https://github.com/chrissimpkins/shellescape")
- (synopsis
- "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)")
- (description
- "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)")
- (license expat))
-)
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-setuptools" ,python-setuptools)))
+ (home-page "https://github.com/chrissimpkins/shellescape")
+ (synopsis
+ "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)")
+ (description
+ "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)")
+ (license license:expat)))
(define-public python2-shellescape
(package-with-python2 python-shellescape))
@@ -533,59 +572,68 @@ project)")
(define-public python2-pil1 ; guix obsolete
(package
(name "python2-pil1")
- (version "1.1.6")
+ (version "1.1.7")
(source (origin
(method url-fetch)
- (uri (string-append
- "http://files.genenetwork.org/software/contrib/Imaging-"
- version "-gn.tar.gz"))
+ (uri (string-append "http://effbot.org/downloads/Imaging-"
+ version ".tar.gz"))
(sha256
(base32
- "0jhinbcq2k899c76m1jc5a3z39k6ajghiavpzi6991hbg6xhxdzg"))
+ "04aj80jhfbmxqzvmq40zfi4z3cw6vi01m3wkk6diz3lc971cfnw9"))
(modules '((guix build utils)))
(snippet
- ;; Adapt to newer freetype. As the package is unmaintained upstream,
- ;; there is no use in creating a patch and reporting it.
- '(substitute* "_imagingft.c"
- (("freetype/")
- "freetype2/freetype/")))))
+ ;; Adapt to newer freetype and lcms. As the package is unmaintained
+ ;; upstream, there is no use in creating a patch and reporting it.
+ '(begin (substitute* "_imagingft.c"
+ (("freetype/")
+ "freetype2/freetype/"))
+ (substitute* '("setup.py"
+ "_imagingcms.c")
+ (("lcms.h") "lcms2.h"))))))
(build-system python-build-system)
(inputs
- `(("freetype" ,freetype)
- ("libjpeg" ,libjpeg)
- ("libtiff" ,libtiff)
- ("python2-setuptools" ,python2-setuptools)
- ("zlib" ,zlib)))
+ `(("freetype" ,freetype)
+ ("lcms" ,lcms) ; not fully supported
+ ("libjpeg" ,libjpeg)
+ ("libtiff" ,libtiff)
+ ("tcl" ,tcl)
+ ("zlib" ,zlib)))
(arguments
;; Only the fork python-pillow works with Python 3.
`(#:python ,python-2
#:tests? #f ; no check target
+ #:use-setuptools? #f
#:phases
- (alist-cons-before
- 'build 'configure
- ;; According to README and setup.py, manual configuration is
- ;; the preferred way of "searching" for inputs.
- ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter.
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((jpeg (assoc-ref inputs "libjpeg"))
- (zlib (assoc-ref inputs "zlib"))
- (tiff (assoc-ref inputs "libtiff"))
- (freetype (assoc-ref inputs "freetype")))
- (substitute* "setup.py"
- (("JPEG_ROOT = None")
- (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")"))
- (("ZLIB_ROOT = None")
- (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")"))
- (("TIFF_ROOT = None")
- (string-append "TIFF_ROOT = libinclude(\"" tiff "\")"))
- (("FREETYPE_ROOT = None")
- (string-append "FREETYPE_ROOT = libinclude(\""
- freetype "\")")))))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'link-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((freetype (assoc-ref inputs "freetype"))
+ (jpeg (assoc-ref inputs "libjpeg"))
+ (lcms (assoc-ref inputs "lcms"))
+ (tcl (assoc-ref inputs "tcl"))
+ (tiff (assoc-ref inputs "libtiff"))
+ (zlib (assoc-ref inputs "zlib")))
+ (substitute* "setup.py"
+ (("FREETYPE_ROOT .*")
+ (string-append "FREETYPE_ROOT = libinclude(\"" freetype "\")\n"))
+ (("JPEG_ROOT .*")
+ (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")\n"))
+ (("LCMS_ROOT .*")
+ (string-append "LCMS_ROOT = libinclude(\"" lcms "\")\n"))
+ (("^TCL_ROOT .*")
+ (string-append "TCL_ROOT = libinclude(\"" tcl "\")\n"))
+ (("TIFF_ROOT .*")
+ (string-append "TIFF_ROOT = libinclude(\"" tiff "\")\n"))
+ (("ZLIB_ROOT .*")
+ (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")\n"))))
+ #t)))))
(home-page "http://www.pythonware.com/products/pil/")
(synopsis "Python Imaging Library")
- (description "The Python Imaging Library (PIL) adds image processing
-capabilities to the Python interpreter.")
+ (description "The @dfn{Python Imaging Library} (PIL) adds image processing
+capabilities to your Python interpreter. This library supports many file
+formats, and provides powerful image processing and graphics capabilities.
+
+NOTE: This package is superseded by python-pillow")
(license (license:x11-style
"file://README"
"See 'README' in the distribution."))))
@@ -618,6 +666,34 @@ version ".tgz"))
(description #f)
(license #f)))
+(define-public python2-piddle-1.0.15
+ (package
+ (name "python2-piddle")
+ (version "1.0.15")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/piddle/piddle/"
+ version "/piddle-" version ".zip"))
+ (sha256
+ (base32
+ "0jaxfsrcgqb5cf2wznxnpdws5khlrdixmg85lrhq2zl9cy6dfdya"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:use-setuptools? #f
+ #:tests? #f)) ; tests are interactive
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (propagated-inputs
+ `(("python2-pil" ,python2-pil1)))
+ (home-page "http://www.strout.net/info/coding/python/piddle/")
+ (synopsis "Plug-In Drawing, Does Little Else")
+ (description "PIDDLE is designed for vector graphics -- i.e., drawing of
+primitives such as lines and ellipses, rather than manipulation of individual
+pixels.")
+ (license license:gpl2+)))
+
(define-public python2-parallel ; guix fix number of things
(package
(name "python2-parallel")
@@ -695,7 +771,7 @@ the older versions.")
(define-public python-htmlgen
(package
(name "python-htmlgen")
- (version "1.0.0")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
@@ -704,8 +780,10 @@ the older versions.")
version ".tar.gz"))
(sha256
(base32
- "1rwgqxhmc93l60wf4ay7ph619710kvyp73s22i0snjpm5i0bhc46"))))
+ "0w3pcvm68jfdhnsxwwwifwhqqj9kqg3195b52hqd23qza480xilx"))))
(build-system python-build-system)
+ (propagated-inputs
+ `(("python-typing" ,python-typing)))
(arguments
`(#:tests? #f))
(synopsis "Python HTML 5 Generator")
@@ -713,6 +791,9 @@ the older versions.")
(home-page "https://github.com/srittau/python-htmlgen")
(license license:expat)))
+(define-public python2-htmlgen
+ (package-with-python2 python-htmlgen))
+
(define-public python-version
(let ((commit "e5aadc720bb74c535f29e5a2de5cd9697efe8d7c"))
(package
@@ -730,7 +811,6 @@ the older versions.")
(base32
"1rc8kf72v180qlygkh1y0jwv2fxqpx7n97bqfhbwgnn31iwai9g3"))))
(build-system python-build-system)
- (build-system python-build-system)
(propagated-inputs
`(
("python-more-itertools" ,python-more-itertools)
@@ -784,3 +864,138 @@ the older versions.")
"arcp (Archive and Package) URI parser and generator")
(license license:asl2.0))
)
+
+(define-public python2-pp
+ (package
+ (name "python2-pp")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://www.parallelpython.com/downloads/pp/pp-" version ".zip"))
+ (sha256
+ (base32
+ "0qkxcyclz3vgwpl6xvsrg76q59dj0wwy8qx15567bafv659ypyb1"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:use-setuptools? #f
+ #:tests? #f)) ; no tests
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://www.parallelpython.com")
+ (synopsis "Parallel and distributed programming for Python")
+ (description "PP is a python module which provides mechanism for parallel
+execution of python code on SMP (systems with multiple processors or cores) and
+clusters (computers connected via network).")
+ (license license:bsd-3)))
+
+(define GN1-thirdparty-sources
+ (origin
+ (method url-fetch/tarbomb)
+ ;; ipfs get QmTPwYT2pehdxdG1TiHEzVzLgbeuhJ4utXShuz3twA84AB
+ (uri "file:///gnu/store/p33a2sh3x2nhiiphdw9nly80njg6p8fi-thirdparty.tgz")
+ (file-name "GN1-thirdparty")
+ (sha256
+ (base32
+ "0nnp6g412hjfrcn3k2yrfb14sxv06k0149whc7qmv678nyj5zhfa"))))
+
+(define-public python2-json-GN1
+ (package
+ (name "python2-json-GN1")
+ (version "GN1")
+ (source GN1-thirdparty-sources)
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (delete 'check)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (sitedir (string-append out "/lib/python2.7/site-packages/json/")))
+ (mkdir-p sitedir)
+ (copy-recursively "thirdparty/json" sitedir)
+ #t))))))
+ (home-page "")
+ (synopsis "")
+ (description "")
+ (license license:lgpl2.1+)))
+
+(define-public python2-pyx-GN1
+ (package
+ (name "python2-pyx-GN1")
+ (version "0.8")
+ (source GN1-thirdparty-sources)
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (delete 'check)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (sitedir (string-append out "/lib/python2.7/site-packages/pyx/")))
+ (mkdir-p sitedir)
+ (copy-recursively "thirdparty/pyx" sitedir)
+ #t))))))
+ (home-page "")
+ (synopsis "")
+ (description "")
+ (license license:gpl2+)))
+
+(define-public python2-pyxlwriter
+ (package
+ (name "python2-pyxlwriter")
+ (version "0.4a3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/pyxlwriter/pyxlwriter/"
+ version "/pyXLWriter-" version ".zip"))
+ (sha256
+ (base32
+ "1kfsi6la9y53rwayszgayfmkjfknpp650v69a0hwd1fcfk1df735"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:use-setuptools? #f
+ #:tests? #f)) ; no tests
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "https://sourceforge.net/projects/pyxlwriter/")
+ (synopsis "Python library for generating Excel compatible spreadsheets")
+ (description "PyXLWriter is a Python library for generating Excel compatible
+spreadsheets. It's a port of John McNamara's Perl @code{Spreadsheet::WriteExcel}
+module version 1.01 to Python. It allows writing of Excel compatible
+spreadsheets without the need for COM objects.")
+ (license license:lgpl2.1+)))
+
+(define-public python2-svg-GN1
+ (package
+ (name "python2-svg-GN1")
+ (version "1.0")
+ (source GN1-thirdparty-sources)
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (delete 'check)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (sitedir (string-append out "/lib/python2.7/site-packages/svg/")))
+ (mkdir-p sitedir)
+ (copy-recursively "thirdparty/svg" sitedir)
+ #t))))))
+ (home-page "")
+ (synopsis "")
+ (description "")
+ (license license:bsd-4)))