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-rw-r--r--gnu/packages/python-science.scm72
1 files changed, 64 insertions, 8 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 738b504e3b..b68a2838fc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -14,6 +14,7 @@
;;; Copyright © 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -329,13 +330,13 @@ of the SGP4 satellite tracking algorithm.")
(define-public python-pandas
(package
(name "python-pandas")
- (version "1.3.0")
+ (version "1.3.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
- (base32 "1qi2cv450m05dwccx3p1s373k5b4ncvwi74plnms2pidrz4ycm65"))))
+ (base32 "1pq1nwj2kysy2g3p18wjb1xn8vk1jhcyisxilsnkwyd99aqqqb17"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -453,8 +454,61 @@ doing practical, real world data analysis in Python.")
;; from <https://github.com/pandas-dev/pandas/pull/29294>.
(substitute* "pandas/io/parsers.py"
(("if 'NULL byte' in msg:")
- "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
- #t)))))))
+ "if 'NULL byte' in msg or 'line contains NUL' in msg:"))))))
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build python-build-system)
+ (ice-9 ftw)
+ (srfi srfi-26))
+ #:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack '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"))))))
+ (replace 'check
+ (lambda _
+ (let ((build-directory
+ (string-append
+ (getcwd) "/build/"
+ (car (scandir "build"
+ (cut string-prefix? "lib." <>))))))
+ ;; Disable the "strict data files" option which causes
+ ;; the build to error out if required data files are
+ ;; not available (as is the case with PyPI archives).
+ (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"))))))))
+ (propagated-inputs
+ `(("python-numpy" ,python2-numpy)
+ ("python-openpyxl" ,python2-openpyxl)
+ ("python-pytz" ,python2-pytz)
+ ("python-dateutil" ,python2-dateutil)
+ ("python-xlrd" ,python2-xlrd)))
+ (inputs
+ `(("which" ,which)))
+ (native-inputs
+ `(("python-cython" ,python2-cython)
+ ("python-beautifulsoup4" ,python2-beautifulsoup4)
+ ("python-lxml" ,python2-lxml)
+ ("python-html5lib" ,python2-html5lib)
+ ("python-nose" ,python2-nose)
+ ("python-pytest" ,python2-pytest)
+ ("python-pytest-mock" ,python2-pytest-mock))))))
(define-public python-pyflow
(package
@@ -846,7 +900,7 @@ and more
(define-public python-distributed
(package
(name "python-distributed")
- (version "2021.07.1")
+ (version "2021.09.1")
(source
(origin
;; The test files are not included in the archive on pypi
@@ -857,7 +911,7 @@ and more
(file-name (git-file-name name version))
(sha256
(base32
- "0i55zf3k55sqjxnwlzsyj3h3v1588fn54ng4mj3dfiqzh3nlj0dg"))))
+ "05djzza3f72nw1i1c9qyamgaf93pbf6jxx0migpp1wvvfl0v2j9z"))))
(build-system python-build-system)
(arguments
'(#:phases
@@ -886,9 +940,11 @@ and more
"-m" "not slow and not gpu and not ipython and not avoid_ci"
"-k"
;; TODO: These tests fail for unknown reasons:
- ;; Assertion error.
(string-append
- "not test_version_option"
+ ;; TimeoutExpired
+ "not test_text"
+ ;; AssertionError
+ " and not test_version_option"
;; "The 'distributed' distribution was not found"
" and not test_register_backend_entrypoint"
;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'"