Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Wed, 13 Dec 2023 14:41:01 UTC
Severity: normal
Tags: patch
Done: Nicolas Graves <ngraves <at> ngraves.fr>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 67813 <at> debbugs.gnu.org Cc: ngraves <at> ngraves.fr Subject: [bug#67813] [PATCH 12/12] gnu: python-pandas: Update to 2.1.1. Date: Wed, 13 Dec 2023 22:56:32 +0100
* gnu/packages/python-science.scm (python-pandas): Update to 2.1.1.
[source]: Use git origin.
[build-system]: Use pyproject-build-system.
[arguments]:
(modules): Remove argument.
(test-flags): Add required test flags.
(phases): Add phase version-set-by-guix and pre-check.
Remove phase enable-parallel-build. Remove check phase
replacement.
[propagated-inputs]: Add package python-tzdata.
[native-inputs]: Add meson-python, python-versioneer python-matplotlib,
python-openpyxl, python-asyncio, python-pytest-localserver. Replace
python-pytest by python-pytest-next.
---
gnu/packages/python-science.scm | 132 +++++++++++++++++---------------
1 file changed, 72 insertions(+), 60 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2e238dc198..09d130537f 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -468,75 +468,81 @@ (define-public python-tspex
(define-public python-pandas
(package
(name "python-pandas")
- (version "1.4.4")
+ (version "2.1.1")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "pandas" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pandas-dev/pandas")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0ryv66s9cvd27q6a985vv556k2qlnlrdna2z7qc7bdhphrrhsv5b"))))
- (build-system python-build-system)
+ (base32 "1v9j38bvw739csdfl98ga6fqjdm61q3p5a2l7h364kg925nbc9r1"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:modules ((guix build utils)
- (guix build python-build-system)
- (ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'enable-parallel-build
- (lambda _
- (substitute* "setup.py"
- (("\"-j\", type=int, default=1")
- (format #f "\"-j\", type=int, default=~a"
- (parallel-job-count))))))
- (add-after 'unpack 'patch-which
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((which (assoc-ref inputs "which")))
- (substitute* "pandas/io/clipboard/__init__.py"
- (("^WHICH_CMD = .*")
- (string-append "WHICH_CMD = \"" which "\"\n"))))))
- (add-before 'check 'prepare-x
- (lambda _
- (system "Xvfb &")
- (setenv "DISPLAY" ":0")
- ;; xsel needs to write a log file.
- (setenv "HOME" "/tmp")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (let ((build-directory
- (string-append
- (getcwd) "/build/"
- (first (scandir "build"
- (cut string-prefix? "lib." <>))))))
- (substitute* "pyproject.toml"
- ;; Not all data files are distributed with the tarball.
- (("--strict-data-files ") ""))
- (with-directory-excursion build-directory
- (when tests?
- (invoke "pytest" "-vv" "pandas" "--skip-slow"
- "--skip-network"
- "-n" (number->string (parallel-job-count))
- "-k"
- (string-append
- ;; 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]
- "not test_wrong_url"
- ;; TODO: Missing input
- " and not TestS3"
- " and not s3"
- ;; This test fails when run with pytest-xdist
- ;; (see:
- ;; https://github.com/pandas-dev/pandas/issues/39096).
- " and not test_memory_usage"))))))))))
+ (list
+ #:test-flags
+ #~(list "--pyargs" "pandas"
+ ;; "--exitfirst"
+ ;; FIXME "-n" (number->string (parallel-job-count))
+ "-m" "not slow and not network and not db"
+ "-k" (string-append
+ "not test_git_version"
+ " and not test_show_versions_console"
+ ;; Not testing ~ expansion.
+ " and not test_expand_user"
+ " and not 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]
+ " and not test_wrong_url"
+ ;; TODO: Missing input
+ " and not TestS3"
+ " and not s3"
+ ;; This test fails when run with pytest-xdist
+ ;; (see: https://github.com/pandas-dev/pandas/issues/39096).
+ " and not test_memory_usage"
+ " and not test_parsing_tzlocal_deprecated"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'version-set-by-guix
+ (lambda _
+ (with-output-to-file "_version_meson.py"
+ (lambda _
+ (display
+ (string-append "__version__ = \""
+ #$(package-version this-package)
+ "\""))))))
+ (add-before 'check 'prepare-x
+ (lambda _
+ (system "Xvfb &")
+ (setenv "DISPLAY" ":0")
+ (setenv "HOME" ".")))
+ (add-after 'unpack 'patch-which
+ (lambda _
+ (substitute* "pandas/io/clipboard/__init__.py"
+ (("^WHICH_CMD = .*")
+ (string-append "WHICH_CMD = \""
+ #$(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/python3.10/site-packages/pandas/_libs")
+ "pandas/_libs"))))))
(propagated-inputs
(list python-jinja2
python-numpy
python-openpyxl
python-pytz
python-dateutil
+ python-tzdata
python-xlrd
python-xlsxwriter))
(inputs
@@ -546,9 +552,15 @@ (define-public python-pandas
python-beautifulsoup4
python-lxml
python-html5lib
- python-pytest
+ meson-python
+ python-matplotlib
+ python-openpyxl
+ python-pytest-next
+ python-pytest-asyncio
+ python-pytest-localserver
python-pytest-mock
python-pytest-xdist
+ python-versioneer
;; Needed to test clipboard support.
xorg-server-for-tests))
(home-page "https://pandas.pydata.org")
--
2.41.0
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Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.