diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/python-science.scm | 65 |
2 files changed, 50 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 784fff7c09..b24266159b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -943,7 +943,9 @@ Python.") ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py) - ("python-pandas" ,python-pandas))) + ;; FIXME: Upgrade to pandas 1.0 when + ;; https://github.com/biocore/biom-format/issues/837 is resolved. + ("python-pandas" ,python-pandas-0.25))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 2f7516b9f6..55fc1be4f9 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org> +;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -37,7 +38,9 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages sphinx) #:use-module (gnu packages time) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xml) + #:use-module (gnu packages xorg) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) @@ -231,13 +234,13 @@ Cython.") (define-public python-pandas (package (name "python-pandas") - (version "0.25.2") + (version "1.0.5") (source (origin (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa")))) + (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -249,8 +252,15 @@ Cython.") (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")))) + (("^WHICH_CMD = .*") + (string-append "WHICH_CMD = \"" which "\"\n")))) + #t)) + (add-before 'check 'prepare-x + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0") + ;; xsel needs to write a log file. + (setenv "HOME" "/tmp") #t)) (replace 'check (lambda _ @@ -265,25 +275,19 @@ Cython.") (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")))))))) + "--skip-network")))))))) (propagated-inputs - `(("python-numpy" ,python-numpy) + `(("python-jinja2" ,python-jinja2) + ("python-numpy" ,python-numpy) ("python-openpyxl" ,python-openpyxl) ("python-pytz" ,python-pytz) ("python-dateutil" ,python-dateutil) ("python-xlrd" ,python-xlrd))) (inputs - `(("which" ,which))) + `(("which" ,which) + ("xclip" ,xclip) + ("xsel" ,xsel))) (native-inputs `(("python-cython" ,python-cython) ("python-beautifulsoup4" ,python-beautifulsoup4) @@ -291,7 +295,9 @@ Cython.") ("python-html5lib" ,python-html5lib) ("python-nose" ,python-nose) ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock))) + ("python-pytest-mock" ,python-pytest-mock) + ;; Needed to test clipboard support. + ("xorg-server" ,xorg-server-for-tests))) (home-page "https://pandas.pydata.org") (synopsis "Data structures for data analysis, time series, and statistics") (description @@ -303,10 +309,33 @@ doing practical, real world data analysis in Python.") (properties `((python2-variant . ,(delay python2-pandas)))) (license license:bsd-3))) +(define-public python-pandas-0.25 + (package + (inherit python-pandas) + (version "0.25.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "pandas" version)) + (sha256 + (base32 + "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj")))) + (arguments + (substitute-keyword-arguments (package-arguments python-pandas) + ((#:phases phases) + `(modify-phases ,phases + (replace '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)) + (delete 'prepare-x))))))) + ;; Pandas 0.24.x are the last versions that support Python 2. (define-public python2-pandas (let ((pandas (package-with-python2 - (strip-python2-variant python-pandas)))) + (strip-python2-variant python-pandas-0.25)))) (package (inherit pandas) (version "0.24.2") |