[bug#34882] [PATCH] Update to Pandas, enable Excel writer support

[Marius Bakke]

Hello Maxim,

Overall LGTM, some comments inline.

[...]

> +(define-public python-et-xmlfile
> +  (package
> +    (name "python-et-xmlfile")
> +    (version "1.0.1")
> +    (source
> +      (origin
> +        (method url-fetch)
> +        (uri (pypi-uri "et_xmlfile" version))
> +        (sha256
> +          (base32
> +            "0nrkhcb6jdrlb6pwkvd4rycw34y3s931hjf409ij9xkjsli9fkb1"))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:phases (modify-phases %standard-phases
> +                  (replace 'check
> +                    (lambda _
> +                      (invoke "pytest"))))))
> +    (native-inputs
> +     `(("python-pytest" ,python-pytest)
> +       ("python-lxml" ,python-lxml)))

Should python-lxml be a propagated-input?

> +    (home-page
> +      "https://bitbucket.org/openpyxl/et_xmlfile";)
> +    (synopsis
> +      "Low memory implementation of @code{lxml.xmlfile}")

Please remove the extra newlines in these patches.

> +    (description
> +      "This Python library is based upon the @code{xmlfile} module
> +from @code{lxml}.  It aims to provide a low memory, compatible implementation
> +of @code{xmlfile}.")
> +    (license license:expat)))

[...]
  
> +(define-public python-openpyxl
> +  (package
> +    (name "python-openpyxl")
> +    (version "2.6.0")
> +    (source
> +     (origin
> +       (method hg-fetch)
> +       (uri (hg-reference
> +             (url "https://bitbucket.org/openpyxl/openpyxl";)
> +             (changeset version)))
> +       (file-name (string-append name "-" version "-checkout"))
> +       (sha256
> +        (base32
> +         "1x47ngn7ybaqdbvg90c8h2x0j6yfdfj25gjfinp2w5rf62gsany7"))))

Can you leave a comment about why we take it from this repository
instead of PyPi?

> +    (native-inputs
> +     `(("python-lxml" ,python-lxml)

Why is python-lxml a native-input?

> +       ;; For the test suite.
> +       ("python-pillow" ,python-pillow)
> +       ("python-pytest" ,python-pytest)))
> +    (propagated-inputs
> +     `(("python-et-xmlfile" ,python-et-xmlfile)
> +       ("python-jdcal" ,python-jdcal)))
> +    (home-page "https://openpyxl.readthedocs.io";)
> +    (synopsis
> +     "Python library to read/write Excel 2010 XLSX/XLSM files")
> +    (description
> +     "This Python library allows reading and writing to the Excel XLSX, XLSM,
> +XLTX and XLTM file formats that are defined by the Office Open XML (OOXML)
> +standard.")
> +    (license license:expat)))

[...]

> From ad1f0efe4a5c3d28ee9d7e2e5da275721af9e172 Mon Sep 17 00:00:00 2001
> From: Maxim Cournoyer <address@hidden>
> Date: Sat, 9 Feb 2019 00:25:51 -0500
> Subject: [PATCH 5/5] gnu: python-pandas: Update to 0.24.2.
>
> * gnu/packages/python-xyz.scm (python-pandas): Update to 0.24.2.
> [phases]{patch-which}: Add phase.
> [inputs]: Add WHICH.
> ---
>  gnu/packages/python-xyz.scm | 65 ++++++++++++++++++++++---------------
>  1 file changed, 38 insertions(+), 27 deletions(-)
>
> diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
> index 321c881f4d..bbf1403758 100644
> --- a/gnu/packages/python-xyz.scm
> +++ b/gnu/packages/python-xyz.scm
> @@ -1014,56 +1014,67 @@ human-friendly syntax.")
>  (define-public python-pandas
>    (package
>      (name "python-pandas")
> -    (version "0.23.4")
> +    (version "0.24.2")
>      (source
>       (origin
>         (method url-fetch)
>         (uri (pypi-uri "pandas" version))
>         (sha256
> -        (base32 "1x54pd7hr3y7qahx6b5bf2wzj54xvl8r3s1h4pl254pnmi3wl92v"))))
> +        (base32 "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))))
>      (build-system python-build-system)
>      (arguments
>       `(#:modules ((guix build utils)
>                    (guix build python-build-system)
>                    (ice-9 ftw)
>                    (srfi srfi-26))
> -       #:phases (modify-phases %standard-phases
> -                  (replace 'check
> -                    (lambda _
> -                      (let ((build-directory
> -                             (string-append
> -                              (getcwd) "/build/"
> -                              (car (scandir "build"
> -                                            (cut string-prefix? "lib." 
> <>))))))
> -                        ;; Disable the "strict data files" option which 
> causes
> -                        ;; the build to error out if required data files are 
> not
> -                        ;; available (as is the case with PyPI archives).
> -                        (substitute* "setup.cfg"
> -                          (("addopts = --strict-data-files") "addopts = "))
> -                        (with-directory-excursion build-directory
> -                          ;; Delete tests that require "moto" which is not 
> yet in Guix.
> -                          (for-each delete-file
> -                                    '("pandas/tests/io/conftest.py"
> -                                      
> "pandas/tests/io/json/test_compression.py"
> -                                      
> "pandas/tests/io/parser/test_network.py"
> -                                      "pandas/tests/io/test_parquet.py"))
> -                          (invoke "pytest" "-vv" "pandas" "--skip-slow"
> -                                  "--skip-network" "-k"
> -                                  ;; XXX: Due to the deleted tests above.
> -                                  "not test_read_s3_jsonl"))))))))
> +       #:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'patch-which
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (let ((which (assoc-ref inputs "which")))
> +               (substitute* "pandas/io/clipboard/__init__.py"
> +                 (("^CHECK_CMD = .*")
> +                  (string-append "CHECK_CMD = \"" which "\"\n"))))
> +             #t))
> +         (replace 'check
> +           (lambda _
> +             (let ((build-directory
> +                    (string-append
> +                     (getcwd) "/build/"
> +                     (car (scandir "build"
> +                                   (cut string-prefix? "lib." <>))))))
> +               ;; Disable the "strict data files" option which causes
> +               ;; the build to error out if required data files are not
> +               ;; available (as is the case with PyPI archives).
> +               (substitute* "setup.cfg"
> +                 (("addopts = --strict-data-files") "addopts = "))
> +               (with-directory-excursion build-directory
> +                 ;; Delete tests that require "moto" which is not yet in 
> Guix.
> +                 (for-each delete-file
> +                           '("pandas/tests/io/conftest.py"
> +                             "pandas/tests/io/json/test_compression.py"
> +                             "pandas/tests/io/parser/test_network.py"
> +                             "pandas/tests/io/test_parquet.py"))
> +                 (invoke "pytest" "-vv" "pandas" "--skip-slow"
> +                         "--skip-network" "-k"
> +                         ;; XXX: Due to the deleted tests above.
> +                         "not test_read_s3_jsonl"))))))))

LGTM, although I'd prefer not to reindent the phases section.  It makes
the patch harder to read, and I prefer the "deep" indentation for
logically separate chunks of code anyway (though I am probably in the
minority here..).  YMMV!

Thanks!

>      (propagated-inputs
>       `(("python-numpy" ,python-numpy)
>         ("python-openpyxl" ,python-openpyxl)
>         ("python-pytz" ,python-pytz)
>         ("python-dateutil" ,python-dateutil)
>         ("python-xlrd" ,python-xlrd)))
> +    (inputs
> +     `(("which" ,which)))
>      (native-inputs
>       `(("python-cython" ,python-cython)
>         ("python-beautifulsoup4" ,python-beautifulsoup4)
>         ("python-lxml" ,python-lxml)
>         ("python-html5lib" ,python-html5lib)
>         ("python-nose" ,python-nose)
> -       ("python-pytest" ,python-pytest)))
> +       ("python-pytest" ,python-pytest)
> +       ("python-pytest-mock" ,python-pytest-mock)))
>      (home-page "https://pandas.pydata.org";)
>      (synopsis "Data structures for data analysis, time series, and 
> statistics")
>      (description
> -- 
> 2.20.1

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