guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 60a4443859168134c5b94de204618176b9509e06
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Tue Jun 16 01:51:08 2026 +0100
gnu: python-pandas: Update to 3.0.3.
This update includes releases since 2.3.3 (2025-09-29):
- 3.0.3 (2026-05-11):
<https://pandas.pydata.org/docs/whatsnew/v3.0.3.html>
- 3.0.2 (2026-03-30):
<https://pandas.pydata.org/docs/whatsnew/v3.0.2.html>
- 3.0.1 (2026-02-17):
<https://pandas.pydata.org/docs/whatsnew/v3.0.1.html>
- 3.0.0 (2026-01-21):
<https://pandas.pydata.org/docs/whatsnew/v3.0.0.html>
* gnu/packages/python-science.scm (python-pandas): Update to 3.0.3.
[source] <patches>: Drop all.
[arguments] <test-flags>: Run more tests and provide extra options.
<phases>: Fix custom 'check phase.
[propagated-inputs]: Remove python-pytz and python-tzdata; add
python-bottleneck, python-lxml, python-numba, and python-numexpr.
[native-inputs]: Remove python-lxml and python-pytest-asyncio; add
python-hypothesis, python-pytest-localserver, and python-pytz.
Fixes: guix/guix#9244
Change-Id: I59a51ef1ba264905fc5fee44e894f1963cbd866d
---
gnu/packages/python-science.scm | 60 ++++++++++++++++++-----------------------
1 file changed, 26 insertions(+), 34 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4898fde840..f5de68b0eb 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4306,7 +4306,7 @@ tissue-specificity metrics for gene expression.")
(define-public python-pandas
(package
(name "python-pandas")
- (version "2.3.3")
+ (version "3.0.3")
(source
(origin
(method git-fetch)
@@ -4315,35 +4315,25 @@ tissue-specificity metrics for gene expression.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0qf4frgj31kd9i544n8v03a0bv9mgml3f7n9n1rik187q3r8ygfg"))
- (patches (search-patches "python-pandas-2-no-pytz_datetime.patch"))))
+ (base32 "1qagfjf4rrpx4xdw0bwg3q9g4k5vjplvifnx6k2frm8z2ws9hgds"))))
(build-system pyproject-build-system)
(arguments
(list
- ;; tests: 173093 passed, 24265 skipped, 990 xfailed, 77 xpassed, 110
warnings
+ ;; tests: 185854 passed, 12827 skipped, 776 xfailed, 86 xpassed
#:test-flags
#~(list "-m" (string-join
(list "not db" "network" "single_cpu" "slow" "slow_arm")
" and not ")
+ "-vv"
+ ;; See: <https://github.com/pandas-dev/pandas/issues/54907>.
+ "--no-strict-data-files"
"--numprocesses" (number->string (min 4 (parallel-job-count)))
"-k" (string-join
(list "not test_git_version"
- "test_parsing_tzlocal_deprecated"
"test_show_versions_console"
- ;; XXX: Introduced by NumPy 2.4.6 and Cython 3.2.5:
- ;; NotImplementedError
- ;; See:
- ;;
<https://github.com/pandas-dev/pandas/issues/62820>,
- ;;
<https://github.com/pandas-dev/pandas/issues/63078>.
- "test_categorical_block_pickle"
- "test_pickle"
- "test_pickle_freq"
- "test_pickle_preserves_block_ndim"
- "test_pickle_preserves_name"
- "test_pickle_round_trip"
- "test_pickle_roundtrip"
- "test_pickle_roundtrip_containers"
- "test_round_trip_current"
+ ;; DeprecationWarning: Bitwise inversion '~' on bool
+ ;; is deprecated and will be removed in Python 3.16.
+ "test_scalar_unary[numexpr-pandas]"
;; AssertionError: Series are different.
#$@(if (target-64bit?)
'()
@@ -4360,18 +4350,20 @@ tissue-specificity metrics for gene expression.")
(("git_version =.*")
(format #f "git_version = ~s~%" #$version)))))
(replace 'check
- (lambda* (#:key inputs outputs test-flags tests?
#:allow-other-keys)
+ (lambda* (#:key test-flags tests? #:allow-other-keys)
(when tests?
+ ;; Tests don't work with "--pyargs pandas" or changing
+ ;; directory to output, script is taken from pyproject.toml
+ ;; file.
(setenv "HOME" "/tmp")
- (with-directory-excursion
- (string-append (string-append (site-packages inputs
outputs)
- "/pandas"))
- (apply invoke "pytest" "-vv" test-flags))))))))
+ (delete-file-recursively "pandas")
+ (invoke "python" "-c" (format #f "~a; ~a=[~{'~a', ~}]);"
+ "import pandas as pd"
+ "pd.test(extra_args"
+ test-flags))))))))
(propagated-inputs
(list python-numpy
python-dateutil
- python-pytz
- python-tzdata
;; XXX: Pandas lists a lot of optional dependencies which are not
;; hard requirements, leave them listed here and commented out for
;; the reference purpose. Try to keep closure as bare minimal as
@@ -4381,17 +4373,17 @@ tissue-specificity metrics for gene expression.")
;; python-adbc-driver-postgresql
;; python-adbc-driver-sqlite
;; python-beautifulsoup4
- ;; python-bottleneck
+ python-bottleneck
;; python-fastparquet
;; python-fsspec
;; python-gcsfs
;; python-html5lib
;; python-hypothesis
;; python-jinja2
- ;; python-lxml
+ python-lxml
;; python-matplotlib
- ;; python-numba
- ;; python-numexpr
+ python-numba
+ python-numexpr
;; python-odfpy
;; python-openpyxl
;; python-psycopg2
@@ -4401,7 +4393,6 @@ tissue-specificity metrics for gene expression.")
;; python-pyqt5
;; python-pyreadstat
;; python-python-calamine
- ;; python-pytz
;; python-pyxlsb
;; python-qtpy
;; python-s3fs
@@ -4416,11 +4407,12 @@ tissue-specificity metrics for gene expression.")
(inputs
(list xclip xsel))
(native-inputs
- (list python-meson
- python-lxml
+ (list python-hypothesis
+ python-meson
python-pytest
- python-pytest-asyncio
+ python-pytest-localserver
python-pytest-xdist
+ python-pytz
python-versioneer
tzdata-for-tests))
(home-page "https://pandas.pydata.org";)
