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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
This commit is contained in:
Ricardo Wurmus
parent
fbe0233575
commit
a8c1d812a0
1 changed files with 58 additions and 56 deletions
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@ -480,71 +480,73 @@ (define-public python-tspex
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(define-public python-pandas
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(package
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(name "python-pandas")
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(version "1.4.4")
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(version "1.5.3")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "pandas" version))
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(sha256
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(base32 "0ryv66s9cvd27q6a985vv556k2qlnlrdna2z7qc7bdhphrrhsv5b"))))
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(build-system python-build-system)
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(base32 "1cdhngylzh352wx5s3sjyznn7a6kmjqcfg97hgqm5h3yb9zgv8vl"))))
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(build-system pyproject-build-system)
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(arguments
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`(#:modules ((guix build utils)
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(guix build python-build-system)
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(ice-9 ftw)
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(srfi srfi-1)
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(srfi srfi-26))
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'enable-parallel-build
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(lambda _
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(substitute* "setup.py"
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(("\"-j\", type=int, default=1")
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(format #f "\"-j\", type=int, default=~a"
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(parallel-job-count))))))
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(add-after 'unpack 'patch-which
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((which (assoc-ref inputs "which")))
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(substitute* "pandas/io/clipboard/__init__.py"
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(("^WHICH_CMD = .*")
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(string-append "WHICH_CMD = \"" which "\"\n"))))))
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(add-before 'check 'prepare-x
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(lambda _
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(system "Xvfb &")
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(setenv "DISPLAY" ":0")
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;; xsel needs to write a log file.
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(setenv "HOME" "/tmp")))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(let ((build-directory
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(string-append
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(getcwd) "/build/"
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(first (scandir "build"
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(cut string-prefix? "lib." <>))))))
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(list
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#:test-flags
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'(list "--pyargs" "pandas"
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"-n" (number->string (parallel-job-count))
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"-m" "not slow and not network and not db"
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"-k"
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(string-append
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;; TODO: Missing input
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"not TestS3"
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" and not s3"
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;; No module named 'pandas.io.sas._sas'
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" and not test_read_expands_user_home_dir"
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" and not test_read_non_existent"
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;; Unknown failures
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" and not test_switch_options"
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;; Crashes
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" and not test_bytes_exceed_2gb"
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;; get_subplotspec() returns None; possibly related to
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;; https://github.com/pandas-dev/pandas/issues/54577
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" and not test_plain_axes"
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;; This test fails when run with pytest-xdist
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;; (see https://github.com/pandas-dev/pandas/issues/39096).
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" and not test_memory_usage"))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'patch-build-system
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(lambda _
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(substitute* "pyproject.toml"
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;; Not all data files are distributed with the tarball.
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(("--strict-data-files ") ""))
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(with-directory-excursion build-directory
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(when tests?
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(invoke "pytest" "-vv" "pandas" "--skip-slow"
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"--skip-network"
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"-n" (number->string (parallel-job-count))
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"-k"
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(string-append
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;; These test access the internet (see:
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;; https://github.com/pandas-dev/pandas/issues/45085).:
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;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml]
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;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree]
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"not test_wrong_url"
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;; TODO: Missing input
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" and not TestS3"
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" and not s3"
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;; This test fails when run with pytest-xdist
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;; (see:
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;; https://github.com/pandas-dev/pandas/issues/39096).
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" and not test_memory_usage"))))))))))
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(("--strict-data-files ") "")
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;; Unknown property "asyncio_mode"
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(("asyncio_mode = \"strict\"") ""))))
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(add-after 'unpack 'patch-which
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "pandas/io/clipboard/__init__.py"
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(("^WHICH_CMD = .*")
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(string-append "WHICH_CMD = \""
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(search-input-file inputs "/bin/which")
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"\"\n")))))
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(add-before 'check 'prepare-x
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(lambda _
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(system "Xvfb &")
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(setenv "DISPLAY" ":0")
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;; xsel needs to write a log file.
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(setenv "HOME" "/tmp")))
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;; The compiled libraries are only in the output at this point,
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;; but they are needed to run tests.
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;; FIXME: This should be handled by the pyargs pytest argument,
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;; but is not for some reason.
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(add-before 'check 'pre-check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(copy-recursively
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(string-append (site-packages inputs outputs)
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"/pandas/_libs")
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"pandas/_libs"))))))
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(propagated-inputs
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(list python-jinja2
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python-matplotlib
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python-numpy
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python-openpyxl
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python-pytz
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@ -554,7 +556,7 @@ (define-public python-pandas
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(inputs
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(list which xclip xsel))
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(native-inputs
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(list python-cython
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(list python-cython-0.29.35
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python-beautifulsoup4
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python-lxml
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python-html5lib
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