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47/53: gnu: python-pandas: Update to 1.5.3.
From: |
guix-commits |
Subject: |
47/53: gnu: python-pandas: Update to 1.5.3. |
Date: |
Thu, 11 Jan 2024 09:43:04 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit 7fa4db842310b1cc0fe26b67c2add13c0a6d22b2
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Jan 11 10:13:17 2024 +0100
gnu: python-pandas: Update to 1.5.3.
* gnu/packages/python-science.scm (python-pandas): Update to 1.5.3.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; move test flags to #:test-flags; add phase
'patch-build-system; fix substitution of "which" executable; remove
'enable-parallel-build; remove custom 'check phase; add 'pre-check phase.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Replace python-cython with python-cython-0.29.35.
Change-Id: I9d09971f707b925f469e29be67fe040c181314ff
---
gnu/packages/python-science.scm | 114 ++++++++++++++++++++--------------------
1 file changed, 58 insertions(+), 56 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c2388f9eb6..e5c424584c 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -480,71 +480,73 @@ tissue-specificity metrics for gene expression.")
(define-public python-pandas
(package
(name "python-pandas")
- (version "1.4.4")
+ (version "1.5.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
- (base32 "0ryv66s9cvd27q6a985vv556k2qlnlrdna2z7qc7bdhphrrhsv5b"))))
- (build-system python-build-system)
+ (base32 "1cdhngylzh352wx5s3sjyznn7a6kmjqcfg97hgqm5h3yb9zgv8vl"))))
+ (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." <>))))))
+ (list
+ #:test-flags
+ '(list "--pyargs" "pandas"
+ "-n" (number->string (parallel-job-count))
+ "-m" "not slow and not network and not db"
+ "-k"
+ (string-append
+ ;; TODO: Missing input
+ "not TestS3"
+ " and not s3"
+ ;; No module named 'pandas.io.sas._sas'
+ " and not test_read_expands_user_home_dir"
+ " and not test_read_non_existent"
+ ;; Unknown failures
+ " and not test_switch_options"
+ ;; Crashes
+ " and not test_bytes_exceed_2gb"
+ ;; get_subplotspec() returns None; possibly related to
+ ;; https://github.com/pandas-dev/pandas/issues/54577
+ " and not test_plain_axes"
+ ;; This test fails when run with pytest-xdist
+ ;; (see https://github.com/pandas-dev/pandas/issues/39096).
+ " and not test_memory_usage"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-build-system
+ (lambda _
(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"))))))))))
+ (("--strict-data-files ") "")
+ ;; Unknown property "asyncio_mode"
+ (("asyncio_mode = \"strict\"") ""))))
+ (add-after 'unpack 'patch-which
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "pandas/io/clipboard/__init__.py"
+ (("^WHICH_CMD = .*")
+ (string-append "WHICH_CMD = \""
+ (search-input-file inputs "/bin/which")
+ "\"\n")))))
+ (add-before 'check 'prepare-x
+ (lambda _
+ (system "Xvfb &")
+ (setenv "DISPLAY" ":0")
+ ;; xsel needs to write a log file.
+ (setenv "HOME" "/tmp")))
+ ;; 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* (#:key inputs outputs #:allow-other-keys)
+ (copy-recursively
+ (string-append (site-packages inputs outputs)
+ "/pandas/_libs")
+ "pandas/_libs"))))))
(propagated-inputs
(list python-jinja2
+ python-matplotlib
python-numpy
python-openpyxl
python-pytz
@@ -554,7 +556,7 @@ tissue-specificity metrics for gene expression.")
(inputs
(list which xclip xsel))
(native-inputs
- (list python-cython
+ (list python-cython-0.29.35
python-beautifulsoup4
python-lxml
python-html5lib
- 45/53: gnu: datasette: Update to 1.0a7., (continued)
- 45/53: gnu: datasette: Update to 1.0a7., guix-commits, 2024/01/11
- 49/53: gnu: python-adjusttext: Disable tests., guix-commits, 2024/01/11
- 24/53: gnu: python-cleanlab: Disable test_aux_inputs, enable other tests., guix-commits, 2024/01/11
- 22/53: gnu: Add python-pytest-nunit., guix-commits, 2024/01/11
- 20/53: gnu: python-matplotlib: Update to 3.8.2., guix-commits, 2024/01/11
- 09/53: gnu: python-lazy-loader: Update to 0.3., guix-commits, 2024/01/11
- 21/53: gnu: python-seaborn: Update to 0.13.1., guix-commits, 2024/01/11
- 26/53: gnu: python-captum: Update to 0.7.0., guix-commits, 2024/01/11
- 38/53: gnu: python-fit-nbinom: Disable tests., guix-commits, 2024/01/11
- 40/53: gnu: python-hicmatrix: Update to 17.1., guix-commits, 2024/01/11
- 47/53: gnu: python-pandas: Update to 1.5.3.,
guix-commits <=
- 11/53: gnu: python-scikit-image: Update to 0.22.0., guix-commits, 2024/01/11
- 19/53: gnu: Add python-contourpy., guix-commits, 2024/01/11
- 41/53: gnu: python-hicexplorer: Make compatible with latest scipy., guix-commits, 2024/01/11
- 10/53: gnu: python-imageio: Update to 2.33.1., guix-commits, 2024/01/11
- 13/53: gnu: python-matplotx: Disable test_png test., guix-commits, 2024/01/11
- 17/53: gnu: Add python-cppy., guix-commits, 2024/01/11
- 23/53: gnu: python-scanpy: Update to 1.9.6., guix-commits, 2024/01/11
- 04/53: gnu: Add python-pyproject-metadata-0.7., guix-commits, 2024/01/11
- 07/53: gnu: python-scipy: Update to 1.11.4., guix-commits, 2024/01/11
- 14/53: gnu: python-scikit-learn: Update to 1.3.2., guix-commits, 2024/01/11