(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
`(("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
;; 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
(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
(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.
(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
(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
(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.")
(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
(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
`(("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
(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
(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
(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
(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
(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
(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.")
(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
(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
(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
(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)
(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).")
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-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-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")
- (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