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-rw-r--r--gnu/packages/python-science.scm129
1 files changed, 109 insertions, 20 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2f7516b9f6..3d6d4e909e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -8,6 +8,7 @@
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -37,7 +38,9 @@
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages time)
+ #:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
+ #:use-module (gnu packages xorg)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
@@ -198,13 +201,13 @@ Cython.")
(define-public python-scikit-image
(package
(name "python-scikit-image")
- (version "0.14.2")
+ (version "0.17.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scikit-image" version))
(sha256
- (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
+ (base32 "1cyqqbcbrg3prc36wis0sm3q5rjhd7h9bp33jwfyixzhi02lr5dx"))))
(build-system python-build-system)
(arguments
;; TODO: Some tests require running X11 server. Disable them?
@@ -231,13 +234,13 @@ Cython.")
(define-public python-pandas
(package
(name "python-pandas")
- (version "0.25.2")
+ (version "1.0.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
- (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
+ (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -249,8 +252,15 @@ Cython.")
(lambda* (#:key inputs #:allow-other-keys)
(let ((which (assoc-ref inputs "which")))
(substitute* "pandas/io/clipboard/__init__.py"
- (("^CHECK_CMD = .*")
- (string-append "CHECK_CMD = \"" which "\"\n"))))
+ (("^WHICH_CMD = .*")
+ (string-append "WHICH_CMD = \"" which "\"\n"))))
+ #t))
+ (add-before 'check 'prepare-x
+ (lambda _
+ (system "Xvfb &")
+ (setenv "DISPLAY" ":0")
+ ;; xsel needs to write a log file.
+ (setenv "HOME" "/tmp")
#t))
(replace 'check
(lambda _
@@ -265,25 +275,19 @@ Cython.")
(substitute* "setup.cfg"
(("addopts = --strict-data-files") "addopts = "))
(with-directory-excursion build-directory
- ;; Delete tests that require "moto" which is not yet
- ;; in Guix.
- (for-each delete-file
- '("pandas/tests/io/conftest.py"
- "pandas/tests/io/json/test_compression.py"
- "pandas/tests/io/parser/test_network.py"
- "pandas/tests/io/test_parquet.py"))
(invoke "pytest" "-vv" "pandas" "--skip-slow"
- "--skip-network" "-k"
- ;; XXX: Due to the deleted tests above.
- "not test_read_s3_jsonl"))))))))
+ "--skip-network"))))))))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
+ `(("python-jinja2" ,python-jinja2)
+ ("python-numpy" ,python-numpy)
("python-openpyxl" ,python-openpyxl)
("python-pytz" ,python-pytz)
("python-dateutil" ,python-dateutil)
("python-xlrd" ,python-xlrd)))
(inputs
- `(("which" ,which)))
+ `(("which" ,which)
+ ("xclip" ,xclip)
+ ("xsel" ,xsel)))
(native-inputs
`(("python-cython" ,python-cython)
("python-beautifulsoup4" ,python-beautifulsoup4)
@@ -291,7 +295,9 @@ Cython.")
("python-html5lib" ,python-html5lib)
("python-nose" ,python-nose)
("python-pytest" ,python-pytest)
- ("python-pytest-mock" ,python-pytest-mock)))
+ ("python-pytest-mock" ,python-pytest-mock)
+ ;; Needed to test clipboard support.
+ ("xorg-server" ,xorg-server-for-tests)))
(home-page "https://pandas.pydata.org")
(synopsis "Data structures for data analysis, time series, and statistics")
(description
@@ -303,10 +309,33 @@ doing practical, real world data analysis in Python.")
(properties `((python2-variant . ,(delay python2-pandas))))
(license license:bsd-3)))
+(define-public python-pandas-0.25
+ (package
+ (inherit python-pandas)
+ (version "0.25.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pandas" version))
+ (sha256
+ (base32
+ "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments python-pandas)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace 'patch-which
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((which (assoc-ref inputs "which")))
+ (substitute* "pandas/io/clipboard/__init__.py"
+ (("^CHECK_CMD = .*")
+ (string-append "CHECK_CMD = \"" which "\"\n"))))
+ #t))
+ (delete 'prepare-x)))))))
+
;; Pandas 0.24.x are the last versions that support Python 2.
(define-public python2-pandas
(let ((pandas (package-with-python2
- (strip-python2-variant python-pandas))))
+ (strip-python2-variant python-pandas-0.25))))
(package
(inherit pandas)
(version "0.24.2")
@@ -325,3 +354,63 @@ doing practical, real world data analysis in Python.")
(("if 'NULL byte' in msg:")
"if 'NULL byte' in msg or 'line contains NUL' in msg:"))
#t)))))))
+
+(define-public python-xarray
+ (package
+ (name "python-xarray")
+ (version "0.15.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "xarray" version))
+ (sha256
+ (base32
+ "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-pytest" ,python-pytest)))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "pytest"))))))
+ (home-page "https://github.com/pydata/xarray")
+ (synopsis "N-D labeled arrays and datasets")
+ (description "Xarray (formerly xray) makes working with labelled
+multi-dimensional arrays simple, efficient, and fun!
+
+Xarray introduces labels in the form of dimensions, coordinates and attributes
+on top of raw NumPy-like arrays, which allows for a more intuitive, more
+concise, and less error-prone developer experience. The package includes a
+large and growing library of domain-agnostic functions for advanced analytics
+and visualization with these data structures.")
+ (license license:asl2.0)))
+
+(define-public python-msgpack-numpy
+ (package
+ (name "python-msgpack-numpy")
+ (version "0.4.6.post0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "msgpack-numpy" version))
+ (sha256
+ (base32
+ "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-msgpack" ,python-msgpack)
+ ("python-numpy" ,python-numpy)))
+ (home-page "https://github.com/lebedov/msgpack-numpy")
+ (synopsis
+ "Numpy data serialization using msgpack")
+ (description
+ "This package provides encoding and decoding routines that enable the
+serialization and deserialization of numerical and array data types provided
+by numpy using the highly efficient @code{msgpack} format. Serialization of
+Python's native complex data types is also supported.")
+ (license license:bsd-3)))
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-15 16:36:32 +0000