From 7509f34fab174e704b4d4d1e465249076502f27e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:28:26 +0100 Subject: gnu: python-pyyaml: Update home page. * gnu/packages/python-xyz.scm (python-pyyaml)[home-page]: Link to the (HTTPS) front page. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f3519b75f6..46b99a4ea5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2337,7 +2337,7 @@ (define-public python-pyyaml (build-system python-build-system) (inputs `(("libyaml" ,libyaml))) - (home-page "http://pyyaml.org/wiki/PyYAML") + (home-page "https://pyyaml.org") (synopsis "YAML parser and emitter for Python") (description "PyYAML is a YAML parser and emitter for Python. PyYAML features a -- cgit v1.2.3 From 58d4e9498f83e89eefb866abc2e7d60cfb7618c3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:23:35 +0100 Subject: gnu: python-pbr: Update home page. * gnu/packages/python-xyz.scm (python-pbr)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 46b99a4ea5..1ea7e3e5e2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1757,7 +1757,7 @@ (define-public python-pbr-minimal (build-system python-build-system) (arguments `(#:tests? #f)) - (home-page "http://docs.openstack.org/developer/pbr/") + (home-page "https://docs.openstack.org/pbr/latest/") (synopsis "Minimal build of python-pbr used for bootstrapping") (description "Used only for bootstrapping python2-pbr, you should not need this.") -- cgit v1.2.3 From b5544cb4d41922c846d3c09bf632f8bdadd3db08 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:57:54 +0100 Subject: gnu: python-invoke: Use HTTPS home page. * gnu/packages/python-xyz.scm (python-invoke)[home-page]: Use HTTPS. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1ea7e3e5e2..4473a0df2c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12326,7 +12326,7 @@ (define-public python2-incremental (define-public python-invoke (package (name "python-invoke") - (home-page "http://www.pyinvoke.org/") + (home-page "https://www.pyinvoke.org/") (version "1.3.0") (source (origin (method url-fetch) -- cgit v1.2.3 From e85af137244924a383f203914467ca6f4b4ebf15 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:00:24 +0100 Subject: gnu: Update pypi.python.org home pages & use HTTPS. * gnu/packages/check.scm (python-unittest2, python-pytest-localserver) (python-discover)[home-page]: Follow (HTTPS) redirections. * gnu/packages/fontutils.scm (python2-defcon)[home-page]: Likewise. * gnu/packages/glib.scm (python2-pygobject-2)[home-page]: Likewise. * gnu/packages/graph.scm (python-igraph)[home-page]: Likewise. * gnu/packages/graphviz.scm (xdot)[home-page]: Likewise. * gnu/packages/pdf.scm (python-poppler-qt5)[home-page]: Likewise. * gnu/packages/python-web.scm (python-zope-event, python-zope-testing) (python-zope-testrunner, python-zope-i18nmessageid, python-zope-schema) (python-zope-configuration, python-zope-proxy, python-zope-location) (python-zope-security))[home-page]: Likewise. * gnu/packages/python-xyz.scm (python-setuptools,python-six) (python2-dogtail, python2-enum, python-enum34, python-unidecode) (python-numpydoc, python-decorator, python-drmaa, python-pathlib2) (python-ly, python-msgpack, python-termcolor, python-colorama) (python-pluggy, python2-pathlib2, python-rfc3987)[home-page]: Likewise. --- gnu/packages/check.scm | 6 +++--- gnu/packages/fontutils.scm | 2 +- gnu/packages/glib.scm | 2 +- gnu/packages/graph.scm | 2 +- gnu/packages/graphviz.scm | 2 +- gnu/packages/pdf.scm | 2 +- gnu/packages/python-web.scm | 18 +++++++++--------- gnu/packages/python-xyz.scm | 34 +++++++++++++++++----------------- 8 files changed, 34 insertions(+), 34 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index fa6575173f..d5a9a9b92a 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -756,7 +756,7 @@ (define-public python-unittest2 (propagated-inputs `(("python-six" ,python-six) ("python-traceback2" ,python-traceback2))) - (home-page "http://pypi.python.org/pypi/unittest2") + (home-page "https://pypi.org/project/unittest2/") (synopsis "Python unit testing library") (description "Unittest2 is a replacement for the unittest module in the Python @@ -1540,7 +1540,7 @@ (define-public python-pytest-localserver (synopsis "Py.test plugin to test server connections locally") (description "Pytest-localserver is a plugin for the pytest testing framework which enables you to test server connections locally.") - (home-page "https://pypi.python.org/pypi/pytest-localserver") + (home-page "https://pypi.org/project/pytest-localserver/") (license license:expat))) (define-public python-pytest-xprocess @@ -1994,7 +1994,7 @@ (define-public python-discover (base32 "0y8d0zwiqar51kxj8lzmkvwc3b8kazb04gk5zcb4nzg5k68zmhq5")))) (build-system python-build-system) - (home-page "http://pypi.python.org/pypi/discover/") + (home-page "https://pypi.org/project/discover/") (synopsis "Python test discovery for unittest") (description diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 8d39730a7b..a8c9e3ddc0 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -678,7 +678,7 @@ (define-public python2-defcon (propagated-inputs `(("python2-fonttools" ,python2-fonttools) ("python2-ufolib" ,python2-ufolib))) - (home-page "https://pypi.python.org/pypi/defcon") + (home-page "https://pypi.org/project/defcon/") (synopsis "Flexible objects for representing @acronym{UFO, unified font object} data") (description "Defcon is a set of @acronym{UFO, unified font object} based objects diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 72d5ea0bdd..03d6be596b 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -670,7 +670,7 @@ (define-public python2-pygobject-2 (arguments `(#:tests? #f ;segfaults during tests #:configure-flags '("LIBS=-lcairo-gobject"))) - (home-page "https://pypi.python.org/pypi/PyGObject") + (home-page "https://pypi.org/project/PyGObject/") (synopsis "Python bindings for GObject") (description "Python bindings for GLib, GObject, and GIO.") diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 63eb36fd7d..ab2bf1daf0 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -119,7 +119,7 @@ (define-public python-igraph (native-inputs `(("pkg-config" ,pkg-config) ("python-pytest" ,python-pytest))) - (home-page "http://pypi.python.org/pypi/python-igraph") + (home-page "https://pypi.org/project/python-igraph/") (synopsis "Python bindings for the igraph network analysis library"))) (define-public r-igraph diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index 365fe1a113..c4f88caa88 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -308,7 +308,7 @@ (define-public xdot ("gtk+" ,gtk+) ("python-pycairo" ,python-pycairo) ("python-pygobject" ,python-pygobject))) - (home-page "https://pypi.python.org/pypi/xdot") + (home-page "https://pypi.org/project/xdot/") (synopsis "Interactive viewer for graphviz dot files") (description "Xdot is an interactive viewer for graphs written in @code{graphviz}’s dot language. Internally, it uses the xdot output format as diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 1ad37706d0..b40940ecab 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -226,7 +226,7 @@ (define-public python-poppler-qt5 ("python-pyqt" ,python-pyqt) ("poppler-qt5" ,poppler-qt5) ("qtbase" ,qtbase))) - (home-page "https://pypi.python.org/pypi/python-poppler-qt5") + (home-page "https://pypi.org/project/python-poppler-qt5/") (synopsis "Python bindings for Poppler-Qt5") (description "This package provides Python bindings for the Qt5 interface of the diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 44f2976ec2..08d75525be 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -972,7 +972,7 @@ (define-public python-zope-event (base32 "1ksbc726av9xacml6jhcfyn828hlhb9xlddpx6fcvnlvmpmpvhk9")))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/zope.event") + (home-page "https://pypi.org/project/zope.event/") (synopsis "Event publishing system for Python") (description "Zope.event provides an event publishing API, intended for use by applications which are unaware of any subscribers to their events. It @@ -1051,7 +1051,7 @@ (define-public python-zope-testing (for-each delete-file (find-files "." "(\\.pyc|~)$")) #t)))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/zope.testing") + (home-page "https://pypi.org/project/zope.testing/") (synopsis "Zope testing helpers") (description "Zope.testing provides a number of testing utilities for HTML forms, HTTP servers, regular expressions, and more.") @@ -1082,7 +1082,7 @@ (define-public python-zope-testrunner ("unzip" ,unzip))) (propagated-inputs `(("python-zope-interface" ,python-zope-interface))) - (home-page "https://pypi.python.org/pypi/zope.testrunner") + (home-page "https://pypi.org/project/zope.testrunner/") (synopsis "Zope testrunner script") (description "Zope.testrunner provides a script for running Python tests.") @@ -1109,7 +1109,7 @@ (define-public python-zope-i18nmessageid (base32 "1rslyph0klk58dmjjy4j0jxy21k03azksixc3x2xhqbkv97cmzml")))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/zope.i18nmessageid") + (home-page "https://pypi.org/project/zope.i18nmessageid/") (synopsis "Message identifiers for internationalization") (description "Zope.i18nmessageid provides facilities for declaring internationalized messages within program source text.") @@ -1140,7 +1140,7 @@ (define-public python-zope-schema `(("python-zope-testing" ,python-zope-testing) ("python-coverage" ,python-coverage) ("python-nose" ,python-nose))) - (home-page "https://pypi.python.org/pypi/zope.schema") + (home-page "https://pypi.org/project/zope.schema/") (synopsis "Zope data schemas") (description "Zope.scheme provides extensions to zope.interface for defining data schemas.") @@ -1165,7 +1165,7 @@ (define-public python-zope-configuration (propagated-inputs `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid) ("python-zope-schema" ,python-zope-schema))) - (home-page "https://pypi.python.org/pypi/zope.configuration") + (home-page "https://pypi.org/project/zope.configuration/") (synopsis "Zope Configuration Markup Language") (description "Zope.configuration implements ZCML, the Zope Configuration Markup Language.") @@ -1190,7 +1190,7 @@ (define-public python-zope-proxy '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. (propagated-inputs `(("python-zope-interface" ,python-zope-interface))) - (home-page "https://pypi.python.org/pypi/zope.proxy") + (home-page "https://pypi.org/project/zope.proxy/") (synopsis "Generic, transparent proxies") (description "Zope.proxy provides generic, transparent proxies for Python. Proxies are special objects which serve as mostly-transparent wrappers around @@ -1219,7 +1219,7 @@ (define-public python-zope-location (propagated-inputs `(("python-zope-proxy" ,python-zope-proxy) ("python-zope-schema" ,python-zope-schema))) - (home-page "https://pypi.python.org/pypi/zope.location/") + (home-page "https://pypi.org/project/zope.location/") (synopsis "Zope location library") (description "Zope.location implements the concept of \"locations\" in Zope3, which are are special objects that have a structural location.") @@ -1253,7 +1253,7 @@ (define-public python-zope-security ("python-zope-location" ,python-zope-location) ("python-zope-testrunner" ,python-zope-testrunner) ("python-zope-testing" ,python-zope-testing))) - (home-page "https://pypi.python.org/pypi/zope.security") + (home-page "https://pypi.org/project/zope.security/") (synopsis "Zope security framework") (description "Zope.security provides a generic mechanism to implement security policies on Python objects.") diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4473a0df2c..3cd1686d28 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -748,7 +748,7 @@ (define-public python-setuptools ;; One could bootstrap with an internal untested setuptools. (arguments `(#:tests? #f)) - (home-page "https://pypi.python.org/pypi/setuptools") + (home-page "https://pypi.org/project/setuptools/") (synopsis "Library designed to facilitate packaging Python projects") (description @@ -1111,7 +1111,7 @@ (define-public python-six (native-inputs `(("python-py" ,python-py) ("python-pytest" ,python-pytest-bootstrap))) - (home-page "https://pypi.python.org/pypi/six/") + (home-page "https://pypi.org/project/six/") (synopsis "Python 2 and 3 compatibility utilities") (description "Six is a Python 2 and 3 compatibility library. It provides utility @@ -1282,7 +1282,7 @@ (define-public python2-dogtail (arguments `(#:python ,python-2 #:tests? #f)) ; invalid command "test" ;; Currently no offical homepage. - (home-page "https://pypi.python.org/pypi/dogtail/") + (home-page "https://pypi.org/project/dogtail/") (synopsis "GUI test tool and automation framework written in Python") (description "Dogtail is a GUI test tool and automation framework written in Python. @@ -1393,7 +1393,7 @@ (define-public python2-enum (build-system python-build-system) (arguments `(#:python ,python-2)) - (home-page "https://pypi.python.org/pypi/enum/") + (home-page "https://pypi.org/project/enum/") (synopsis "Robust enumerated type support in Python") (description "This provides a module for robust enumerations in Python. It has @@ -1414,7 +1414,7 @@ (define-public python-enum34 (base32 "1cgm5ng2gcfrkrm3hc22brl6chdmv67b9zvva9sfs7gn7dwc9n4a")))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/enum34") + (home-page "https://pypi.org/project/enum34/") (synopsis "Backported Python 3.4 Enum") (description "Enum34 is the new Python stdlib enum module available in Python 3.4 @@ -2158,7 +2158,7 @@ (define-public python-unidecode (base32 "1s6cp2lv4m0f00hjckjz8p6m7d3n3v16jvg353llf5ia1iqsnsib")))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/Unidecode") + (home-page "https://pypi.org/project/Unidecode/") (synopsis "ASCII transliterations of Unicode text") (description "Unidecode provides ASCII transliterations of Unicode text. Unidecode is @@ -3827,7 +3827,7 @@ (define-public python-numpydoc `(("python-sphinx" ,python-sphinx))) (native-inputs `(("python-nose" ,python-nose))) - (home-page "https://pypi.python.org/pypi/numpydoc") + (home-page "https://pypi.org/project/numpydoc/") (synopsis "Numpy's Sphinx extensions") (description @@ -4777,7 +4777,7 @@ (define-public python-decorator (sha256 (base32 "0308djallnh00v112y5b7nadl657ysmkp6vc8xn51d6yzc9zm7n3")))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/decorator/") + (home-page "https://pypi.org/project/decorator/") (synopsis "Python module to simplify usage of decorators") (description "The aim of the decorator module is to simplify the usage of decorators @@ -4806,7 +4806,7 @@ (define-public python-drmaa (arguments '(#:tests? #f)) (native-inputs `(("python-nose" ,python-nose))) - (home-page "https://pypi.python.org/pypi/drmaa") + (home-page "https://pypi.org/project/drmaa/") (synopsis "Python bindings for the DRMAA library") (description "A Python package for Distributed Resource Management (DRM) job @@ -5021,7 +5021,7 @@ (define-public python-pathlib2 (propagated-inputs `(("python-scandir" ,python-scandir) ("python-six" ,python-six))) - (home-page "https://pypi.python.org/pypi/pathlib2/") + (home-page "https://pypi.org/project/pathlib2/") (synopsis "Object-oriented file system paths") (description "The goal of pathlib2 is to provide a backport of the standard @code{pathlib} module which tracks the standard library module, so @@ -6928,7 +6928,7 @@ (define-public python-ly (description "This package provides a Python library to parse, manipulate or create documents in LilyPond format. A command line program ly is also provided that can be used to do various manipulations with LilyPond files.") - (home-page "https://pypi.python.org/pypi/python-ly") + (home-page "https://pypi.org/project/python-ly/") (license license:gpl2+))) (define-public python-appdirs @@ -7033,7 +7033,7 @@ (define-public python-msgpack (description "MessagePack is a fast, compact binary serialization format, suitable for similar data to JSON. This package provides CPython bindings for reading and writing MessagePack data.") - (home-page "https://pypi.python.org/pypi/msgpack/") + (home-page "https://pypi.org/project/msgpack/") (license license:asl2.0))) ;; This msgpack library's name changed from "python-msgpack" to "msgpack" with @@ -7526,7 +7526,7 @@ (define-public python-termcolor (arguments ;; There are no tests. `(#:tests? #f)) - (home-page "https://pypi.python.org/pypi/termcolor") + (home-page "https://pypi.org/project/termcolor/") (synopsis "ANSII Color formatting for terminal output") (description "This package provides ANSII Color formatting for output in terminals.") @@ -8780,7 +8780,7 @@ (define-public python-colorama (synopsis "Colored terminal text rendering for Python") (description "Colorama is a Python library for rendering colored terminal text.") - (home-page "https://pypi.python.org/pypi/colorama") + (home-page "https://pypi.org/project/colorama/") (license license:bsd-3))) (define-public python2-colorama @@ -8828,7 +8828,7 @@ (define-public python-pluggy (synopsis "Plugin and hook calling mechanism for Python") (description "Pluggy is an extraction of the plugin manager as used by Pytest but stripped of Pytest specific details.") - (home-page "https://pypi.python.org/pypi/pluggy") + (home-page "https://pypi.org/project/pluggy/") (license license:expat))) (define-public python2-pluggy @@ -9533,7 +9533,7 @@ (define-public python2-pathlib2 (propagated-inputs `(("python2-scandir" ,python2-scandir) ("python2-six" ,python2-six))) - (home-page "https://pypi.python.org/pypi/pathlib2/") + (home-page "https://pypi.org/project/pathlib2/") (synopsis "Object-oriented file system paths - backport of standard pathlib module") (description "The goal of pathlib2 is to provide a backport of standard @@ -13484,7 +13484,7 @@ (define-public python-rfc3987 (base32 "192pclzs2y0yaywqkrlvd0x73740q310kvqvm6jldhi619mq59wi")))) (build-system python-build-system) - (home-page "https://pypi.python.org/pypi/rfc3987") + (home-page "https://pypi.org/project/rfc3987/") (synopsis "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)") (description "@code{rfc3987} provides routines for parsing and validation of URIs (see RFC 3986) and IRIs (see RFC 3987).") -- cgit v1.2.3 From 24ce64216e1f03c14c1693cb9d1051691b758b1f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Mar 2020 21:45:14 +0100 Subject: gnu: python-h5py: Update to 2.10.0. * gnu/packages/python-xyz.scm (python-h5py): Update to 2.10.0. [inputs]: Use hdf5-1.10. [native-inputs]: Add pkg-config. --- gnu/packages/python-xyz.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3cd1686d28..7003f60b15 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -475,14 +475,14 @@ (define-public python2-hdf4 (define-public python-h5py (package (name "python-h5py") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (pypi-uri "h5py" version)) (sha256 (base32 - "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6")))) + "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4")))) (build-system python-build-system) (arguments `(#:tests? #f ; no test target @@ -504,10 +504,11 @@ (define-public python-h5py `(("python-six" ,python-six) ("python-numpy" ,python-numpy))) (inputs - `(("hdf5" ,hdf5))) + `(("hdf5" ,hdf5-1.10))) (native-inputs `(("python-cython" ,python-cython) - ("python-pkgconfig" ,python-pkgconfig))) + ("python-pkgconfig" ,python-pkgconfig) + ("pkg-config" ,pkg-config))) (home-page "https://www.h5py.org/") (synopsis "Read and write HDF5 files from Python") (description -- cgit v1.2.3 From 241409cd8afe45fdecfbd7d24cdeb08aa2a43884 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Mar 2020 21:45:46 +0100 Subject: gnu: Add python-numcodecs. * gnu/packages/python-xyz.scm (python-numcodecs): New variable. --- gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7003f60b15..0642d32631 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15734,6 +15734,31 @@ (define-public python-numba tool).") (license license:bsd-3))) +(define-public python-numcodecs + (package + (name "python-numcodecs") + (version "0.6.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "numcodecs" version)) + (sha256 + (base32 + "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-msgpack" ,python-msgpack))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/zarr-developers/numcodecs") + (synopsis "Buffer compression and transformation codecs") + (description + "This Python package provides buffer compression and transformation +codecs for use in data storage and communication applications.") + (license license:expat))) + (define-public python-anndata (package (name "python-anndata") -- cgit v1.2.3 From 8e04b233f130e01b5b6a41dfcdeb5e622d43f751 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Mar 2020 21:45:55 +0100 Subject: gnu: Add python-asciitree. * gnu/packages/python-xyz.scm (python-asciitree): New variable. --- gnu/packages/python-xyz.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0642d32631..c9865d08e2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15759,6 +15759,23 @@ (define-public python-numcodecs codecs for use in data storage and communication applications.") (license license:expat))) +(define-public python-asciitree + (package + (name "python-asciitree") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asciitree" version)) + (sha256 + (base32 + "0vhgri2m2xlnibhz4xwn4hpbc7xacisxjqrk6k5kyppq96vbk92a")))) + (build-system python-build-system) + (home-page "https://github.com/mbr/asciitree") + (synopsis "Draws ASCII trees") + (description "This package draws tree structures using characters.") + (license license:expat))) + (define-public python-anndata (package (name "python-anndata") -- cgit v1.2.3 From 7032c1cc6040a14e482e71b0cfbdedf957da4f8a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Mar 2020 21:46:05 +0100 Subject: gnu: Add python-zarr. * gnu/packages/python-xyz.scm (python-zarr): New variable. --- gnu/packages/python-xyz.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c9865d08e2..0505ad5f40 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15776,6 +15776,46 @@ (define-public python-asciitree (description "This package draws tree structures using characters.") (license license:expat))) +(define-public python-zarr + (package + (name "python-zarr") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "zarr" version)) + (sha256 + (base32 + "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-service-tests + (lambda _ + (setenv "ZARR_TEST_ABS" "0") + (setenv "ZARR_TEST_MONGO" "0") + (setenv "ZARR_TEST_REDIS" "0") + #t)) + (replace 'check + (lambda _ + (invoke "pytest" "-vv" "-k" "not lmdb") + #t))))) + (propagated-inputs + `(("python-asciitree" ,python-asciitree) + ("python-fasteners" ,python-fasteners) + ("python-numcodecs" ,python-numcodecs) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/zarr-developers/zarr-python") + (synopsis "Chunked, compressed, N-dimensional arrays for Python") + (description + "This package provides an implementation of chunked, compressed, +N-dimensional arrays for Python.") + (license license:expat))) + (define-public python-anndata (package (name "python-anndata") -- cgit v1.2.3 From a098b3498052e046c8338e0630e0166bcb12355d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Mar 2020 21:46:12 +0100 Subject: gnu: python-anndata: Update to 0.7.1. * gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.1. [arguments]: Move check phase after install phase; delete one test. [propagated-inputs]: Add python-importlib-metadata, python-numcodecs, python-packaging, and python-zarr. [native-inputs]: Add python-joblib, python-pytest, and python-setuptools-scm. --- gnu/packages/python-xyz.scm | 27 ++++++++++++++++++++++++--- 1 file changed, 24 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0505ad5f40..bf82f5934f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15819,20 +15819,41 @@ (define-public python-zarr (define-public python-anndata (package (name "python-anndata") - (version "0.6.18") + (version "0.7.1") (source (origin (method url-fetch) (uri (pypi-uri "anndata" version)) (sha256 (base32 - "03x83yjaccbqszj7x4fwwmpil0ai59yx64d1zmf2691za3j03w73")))) + "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-inconvenient-tests + (lambda _ + ;; This test depends on python-scikit-learn. + (delete-file "anndata/tests/test_inplace_subset.py") + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-vv")))))) (propagated-inputs `(("python-h5py" ,python-h5py) + ("python-importlib-metadata" ,python-importlib-metadata) ("python-natsort" ,python-natsort) + ("python-numcodecs" ,python-numcodecs) + ("python-packaging" ,python-packaging) ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + ("python-scipy" ,python-scipy) + ("python-zarr" ,python-zarr))) + (native-inputs + `(("python-joblib" ,python-joblib) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") (description "Anndata is a package for simple (functional) high-level APIs -- cgit v1.2.3