diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 72 |
1 files changed, 64 insertions, 8 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 738b504e3b..b68a2838fc 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2021 Felix Gruber <felgru@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -329,13 +330,13 @@ of the SGP4 satellite tracking algorithm.") (define-public python-pandas (package (name "python-pandas") - (version "1.3.0") + (version "1.3.3") (source (origin (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "1qi2cv450m05dwccx3p1s373k5b4ncvwi74plnms2pidrz4ycm65")))) + (base32 "1pq1nwj2kysy2g3p18wjb1xn8vk1jhcyisxilsnkwyd99aqqqb17")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -453,8 +454,61 @@ doing practical, real world data analysis in Python.") ;; from <https://github.com/pandas-dev/pandas/pull/29294>. (substitute* "pandas/io/parsers.py" (("if 'NULL byte' in msg:") - "if 'NULL byte' in msg or 'line contains NUL' in msg:")) - #t))))))) + "if 'NULL byte' in msg or 'line contains NUL' in msg:")))))) + (arguments + `(#:modules ((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-26)) + #:python ,python-2 + #: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")))))) + (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")))))))) + (propagated-inputs + `(("python-numpy" ,python2-numpy) + ("python-openpyxl" ,python2-openpyxl) + ("python-pytz" ,python2-pytz) + ("python-dateutil" ,python2-dateutil) + ("python-xlrd" ,python2-xlrd))) + (inputs + `(("which" ,which))) + (native-inputs + `(("python-cython" ,python2-cython) + ("python-beautifulsoup4" ,python2-beautifulsoup4) + ("python-lxml" ,python2-lxml) + ("python-html5lib" ,python2-html5lib) + ("python-nose" ,python2-nose) + ("python-pytest" ,python2-pytest) + ("python-pytest-mock" ,python2-pytest-mock)))))) (define-public python-pyflow (package @@ -846,7 +900,7 @@ and more (define-public python-distributed (package (name "python-distributed") - (version "2021.07.1") + (version "2021.09.1") (source (origin ;; The test files are not included in the archive on pypi @@ -857,7 +911,7 @@ and more (file-name (git-file-name name version)) (sha256 (base32 - "0i55zf3k55sqjxnwlzsyj3h3v1588fn54ng4mj3dfiqzh3nlj0dg")))) + "05djzza3f72nw1i1c9qyamgaf93pbf6jxx0migpp1wvvfl0v2j9z")))) (build-system python-build-system) (arguments '(#:phases @@ -886,9 +940,11 @@ and more "-m" "not slow and not gpu and not ipython and not avoid_ci" "-k" ;; TODO: These tests fail for unknown reasons: - ;; Assertion error. (string-append - "not test_version_option" + ;; TimeoutExpired + "not test_text" + ;; AssertionError + " and not test_version_option" ;; "The 'distributed' distribution was not found" " and not test_register_backend_entrypoint" ;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'" |