guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 7ab93dad0e6267344a1f8701ee1d7d2739d76042
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sun Dec 7 21:45:38 2025 +0000
gnu: python-pandas: Update to 2.3.3.
* gnu/packages/python-science.scm (python-pandas-2): Update to 2.3.3 and
rename to python-pandas.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'pre-check, and 'patch-which; use custom 'check.
[inputs]: Remove which, it's implemanted with Python's `shutil.which()'.
[propagated-inputs]: Remove python-jinja2, python-matplotlib,
python-openpyxl, python-xlrd, and python-xlsxwriter.
[native-inputs]: Remove python-beautifulsoup4, python-cython,
python-html5lib, python-matplotlib, python-openpyxl,
python-pytest-localserver, and python-pytest-mock; add meson and
tzdata-for-tests.
(python-pandas-2): Deprecate variable in favor of python-pandas.
Change-Id: Ib4aefbbc33f46f793430ac396cbe5e6c4107ec2f
---
gnu/packages/python-science.scm | 167 +++++++++++++++++-----------------------
1 file changed, 72 insertions(+), 95 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 988c45357e..108dc8dd2f 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -104,6 +104,7 @@
#:use-module (gnu packages xorg)
#:use-module (guix packages)
#:use-module (guix gexp)
+ #:use-module (guix deprecation)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
@@ -4008,72 +4009,33 @@ library.")
tissue-specificity metrics for gene expression.")
(license license:gpl3+)))
-(define-public python-pandas-2
+(define-public python-pandas
(package
(name "python-pandas")
- (version "2.2.3")
+ (version "2.3.3")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pandas-dev/pandas";)
- (commit (string-append "v" version))))
+ (url "https://github.com/pandas-dev/pandas";)
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "00f6jnplwg7iffnxdm4hpfls0ncbarc23933xq1rm5nk5g8dcldx"))
+ (base32 "0qf4frgj31kd9i544n8v03a0bv9mgml3f7n9n1rik187q3r8ygfg"))
(patches (search-patches "python-pandas-2-no-pytz_datetime.patch"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; tests: 174115 passed, 24224 skipped, 990 xfailed, 77 xpassed, 110
warnings
#:test-flags
- #~(list "--pyargs" "pandas"
- ;; "--exitfirst"
- ;; XXX The tests won't even start on my 16 core laptop, but they
- ;; start with 4 processes.
+ #~(list "-m" (string-join
+ (list "not db" "network" "single_cpu" "slow" "slow_arm")
+ " and not ")
"--numprocesses" (number->string (min 4 (parallel-job-count)))
- "-m" "not slow and not network and not db"
- ;; All tests errored.
- "--ignore=pandas/tests/io/test_clipboard.py"
"-k" (string-join
- (list
- "not test_git_version"
- "test_show_versions_console"
- ;; Not testing ~ expansion.
- "test_expand_user"
- "test_get_handle_with_path"
- ;; These test access the internet (see:
- ;; https://github.com/pandas-dev/pandas/issues/45085).:
- ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml]
- ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree]
- "test_wrong_url"
- ;; TODO: Missing input
- "TestS3"
- "s3"
- ;; This test fails when run with pytest-xdist
- ;; (see:
https://github.com/pandas-dev/pandas/issues/39096).
- "test_memory_usage"
- "test_parsing_tzlocal_deprecated"
- ;; PyArrow is optional.
- "test_style_bar_with_pyarrow_NA_values"
- "test_very_negative_exponent"
- "test_usecols_no_header_pyarrow"
- "test_scientific_no_exponent[pyarrow-None]"
- "test_inspect_getmembers"
- ;; SciPy introduces cycle, optional.
- "test_savefig"
- ;; It requires a fresh python-tzdata, including new
- ;; timezones.
- "test_repr"
- ;; Fails with [email protected], fixed on main branch.
- ;; See:
<https://github.com/pandas-dev/pandas/issues/61557>.
- "test_groupby_raises_category_on_category"
- ;; These tests should be skipped on 32bit systems:
- ;; Cannot cast array data from dtype('int64') to
dtype('int32')
- #$@(if (not (target-64bit?))
- #~("test_inf_bound_infinite_recursion"
- "test_reindex_behavior_with_interval_index"
- "test_repeating_interval_index_with_infs")
- #~()))
+ (list "not test_git_version"
+ "test_parsing_tzlocal_deprecated"
+ "test_show_versions_console")
" and not "))
#:phases
#~(modify-phases %standard-phases
@@ -4082,57 +4044,72 @@ tissue-specificity metrics for gene expression.")
(with-output-to-file "_version.py"
(lambda _
(display
- (string-append "__version__ = \""
- #$(package-version this-package)
- "\""))))))
- (add-before 'check 'pre-check
- (lambda _
- (setenv "HOME" ".")
- ;; Skip tests that require lots of resources.
- (setenv "PANDAS_CI" "1")))
- (add-after 'unpack 'patch-which
- (lambda _
- (substitute* "pandas/io/clipboard/__init__.py"
- (("^WHICH_CMD = .*")
- (string-append "WHICH_CMD = \""
- #$(this-package-input "which")
- "/bin/which\"\n")))))
- ;; The compiled libraries are only in the output at this point,
- ;; but they are needed to run tests.
- ;; FIXME: This should be handled by the pyargs pytest argument,
- ;; but is not for some reason.
- (add-before 'check 'pre-check
- (lambda _
- (copy-recursively
- (string-append #$output
- "/lib/python3.11/site-packages/pandas/_libs")
- "pandas/_libs"))))))
+ (string-append "__version__ = \"" #$version "\""))))))
+ (replace 'check
+ (lambda* (#:key inputs outputs test-flags tests?
#:allow-other-keys)
+ (when tests?
+ (setenv "HOME" "/tmp")
+ (with-directory-excursion
+ (string-append (string-append (site-packages inputs
outputs)
+ "/pandas"))
+ (apply invoke "pytest" "-vv" test-flags))))))))
(propagated-inputs
- (list python-dateutil
- python-jinja2
- python-matplotlib
- python-numpy
- python-openpyxl
+ (list python-numpy
+ python-dateutil
python-pytz
python-tzdata
- python-xlrd
- python-xlsxwriter))
+ ;; 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
+ ;; possible.
+ ;;
+ ;; [optional]
+ ;; python-adbc-driver-postgresql
+ ;; python-adbc-driver-sqlite
+ ;; python-beautifulsoup4
+ ;; python-bottleneck
+ ;; python-fastparquet
+ ;; python-fsspec
+ ;; python-gcsfs
+ ;; python-html5lib
+ ;; python-hypothesis
+ ;; python-jinja2
+ ;; python-lxml
+ ;; python-matplotlib
+ ;; python-numba
+ ;; python-numexpr
+ ;; python-odfpy
+ ;; python-openpyxl
+ ;; python-psycopg2
+ ;; python-pyarrow
+ ;; python-pyiceberg
+ ;; python-pymysql
+ ;; python-pyqt5
+ ;; python-pyreadstat
+ ;; python-python-calamine
+ ;; python-pytz
+ ;; python-pyxlsb
+ ;; python-qtpy
+ ;; python-s3fs
+ ;; python-scipy
+ ;; python-sqlalchemy
+ ;; python-tables
+ ;; python-tabulate
+ ;; python-xarray
+ ;; python-xlrd
+ ;; python-xlsxwriter
+ #;python-zstandard))
(inputs
- (list which xclip xsel))
+ (list xclip xsel))
(native-inputs
- (list meson-python
- python-beautifulsoup4
- python-cython
- python-html5lib
+ (list meson
+ meson-python
python-lxml
- python-matplotlib
- python-openpyxl
- python-pytest-asyncio
python-pytest
- python-pytest-localserver
- python-pytest-mock
+ python-pytest-asyncio
python-pytest-xdist
- python-versioneer))
+ python-versioneer
+ tzdata-for-tests))
(home-page "https://pandas.pydata.org";)
(synopsis "Data structures for data analysis, time series, and statistics")
(description
@@ -4143,7 +4120,7 @@ and intuitive. It aims to be the fundamental high-level
building block for
doing practical, real world data analysis in Python.")
(license license:bsd-3)))
-(define-public python-pandas python-pandas-2)
+(define-deprecated/public-alias python-pandas-2 python-pandas)
(define-public python-pandas-stubs
(package
