From 1c10ba3a249f797493cc67da48cbb58398425920 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 9 Oct 2019 12:54:39 +0200 Subject: gnu: python-packaging: Update to 19.2. * gnu/packages/python-xyz.scm (python-packaging): Update to 19.2. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b0f5ec7588..1ae83dfa87 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12919,14 +12919,14 @@ (define-public python2-translate-toolkit (define-public python-packaging (package (name "python-packaging") - (version "19.0") + (version "19.2") (source (origin (method url-fetch) (uri (pypi-uri "packaging" version)) (sha256 (base32 - "1brjhygq9dz6x1kdljivkjfldi3qf5rbkqgck1bpgv9qpv8ab60c")))) + "0izwlz9h0bw171a1chr311g2y7n657zjaf4mq4rgm8pp9lbj9f98")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From 6ba6a1c103ea94f2c9a984db466c3b2829e8f175 Mon Sep 17 00:00:00 2001 From: Jesse Gibbons Date: Sat, 16 Nov 2019 18:33:05 -0700 Subject: gnu: python-hy: Set HOME to /tmp before install MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/packages/python-xyz.scm (python-hy)[arguments]: Add custom 'set-HOME phase before the 'install phase. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d2786e4826..5b8b33b87f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8745,6 +8745,9 @@ (define-public python-hy (arguments '(#:phases (modify-phases %standard-phases + (add-before 'install 'set-HOME + (lambda _ + (setenv "HOME" "/tmp"))) (replace 'check (lambda _ ;; Tests require write access to HOME. -- cgit v1.2.3 From 85cfb0e9e6ccd57715ca6e6bfadfd2b161c08e4d Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Tue, 19 Nov 2019 16:09:00 +0100 Subject: gnu: Add python-intelhex. * gnu/packages/python-xyz.scm (python-intelhex): New variable. --- gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5b8b33b87f..c3999d9cec 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -53,7 +53,7 @@ ;;; Copyright © 2016, 2018 Tomáš Čech ;;; Copyright © 2018, 2019 Nicolas Goaziou ;;; Copyright © 2018 Oleg Pykhalov -;;; Copyright © 2018 Clément Lassieur +;;; Copyright © 2018, 2019 Clément Lassieur ;;; Copyright © 2018, 2019 Maxim Cournoyer ;;; Copyright © 2018 Luther Thompson ;;; Copyright © 2018 Vagrant Cascadian @@ -16887,3 +16887,27 @@ (define-public python-pyphen (description "Pyphen is a pure Python module to hyphenate text using existing Hunspell hyphenation dictionaries.") (license (list license:gpl2 license:lgpl2.1 license:mpl1.1)))) + +(define-public python-intelhex + (package + (name "python-intelhex") + (version "2.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "intelhex" version)) + (sha256 + (base32 + "0ckqjbxd8gwcg98gfzpn4vq1qxzfvq3rdbrr1hikj1nmw08qb780")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ;issue with version + (home-page "https://pypi.org/project/IntelHex/") + (synopsis "Python library for Intel HEX files manipulations") + (description "The Intel HEX file format is widely used in microprocessors +and microcontrollers area (embedded systems etc.) as the de facto standard for +representation of code to be programmed into microelectronic devices. This +package provides an intelhex Python library to read, write, create from +scratch and manipulate data from Intel HEX file format. It also includes +several convenience Python scripts, including \"classic\" hex2bin and bin2hex +converters and more, those based on the library itself.") + (license license:bsd-3))) -- cgit v1.2.3 From c695f011b31146f68e8b4f86a40aaeef5972005b Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Tue, 19 Nov 2019 19:52:11 +0100 Subject: gnu: python2-scientific: New source code location. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz.scm (python2-scientific): New source code location. Following the annoucement of Bitbucket to delete all Mercurial repositories in June 2020, the source code has been migrated to GitHub. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c3999d9cec..c16633fba9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14620,14 +14620,14 @@ (define-public python2-scientific (version "2.9.4") (source (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/khinsen/" - "scientificpython/downloads/ScientificPython-" - version ".tar.gz")) - (file-name (string-append "ScientificPython-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/khinsen/ScientificPython") + (commit (string-append "rel" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0fc69zhlsn9d2jvbzyjl9ah53vj598h84nkq230c83ahfvgzx5y3")))) + "16l48aj9fps9r7jyk8gpxppwrv0fqvlc13sayxskz28r5s6sjwbl")))) (build-system python-build-system) (inputs `(("netcdf" ,netcdf))) @@ -14645,7 +14645,7 @@ (define-public python2-scientific (invoke "python" "setup.py" "build" (string-append "--netcdf_prefix=" (assoc-ref inputs "netcdf")))))))) - (home-page "https://bitbucket.org/khinsen/scientificpython") + (home-page "http://dirac.cnrs-orleans.fr/ScientificPython") (synopsis "Python modules for scientific computing") (description "ScientificPython is a collection of Python modules that are useful for scientific computing. Most modules are rather general (Geometry, -- cgit v1.2.3 From fe9b72c5861fabdf7f37862de393812ff3e423ac Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Tue, 19 Nov 2019 19:52:50 +0100 Subject: gnu: python2-mmtk: Update to 2.7.12. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz.scm (python2-mmtk): Update to 2.7.12. Signed-off-by: Ludovic Courtès --- gnu/packages/python-xyz.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c16633fba9..3b28fbb27f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14657,16 +14657,17 @@ (define-public python2-scientific (define-public python2-mmtk (package (name "python2-mmtk") - (version "2.7.11") + (version "2.7.12") (source (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/khinsen/" - "mmtk/downloads/MMTK-" version ".tar.gz")) - (file-name (string-append "MMTK-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/khinsen/MMTK") + (commit (string-append "rel" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1d0nnjx4lwsvh8f99vv1r6gi50d93yba0adkz8b4zgv4za4c5862")))) + "1fqwh3ba9jd42nigvn5shndgwb1zy7kh9520ncvqci7n8ffjr6p1")))) (build-system python-build-system) (native-inputs `(("netcdf" ,netcdf))) -- cgit v1.2.3 From 7454078a7c2b6304e98741537419ae974aa1b618 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Nov 2019 18:53:01 +0100 Subject: gnu: python-lazy-object-proxy: Update to 1.4.3. * gnu/packages/python-xyz.scm (python-lazy-object-proxy): Update to 1.4.3. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3b28fbb27f..8d53a59c40 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10855,13 +10855,13 @@ (define-public poetry (define-public python-lazy-object-proxy (package (name "python-lazy-object-proxy") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (pypi-uri "lazy-object-proxy" version)) (sha256 (base32 - "1wgl0fmddi0ind78a74yyk2qrr9pb5llvj1892cdpp6z6n6mn4zx")))) + "1w1aaay424ciz8fz3fkzxb0pxzfxn184f2whpyn4fx72bn50x47k")))) (native-inputs `(("python-setuptools-scm" ,python-setuptools-scm-3.3))) (build-system python-build-system) -- cgit v1.2.3 From 97610a661482cf28d580054d48a26557ee90f877 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 23 Nov 2019 14:48:14 +0100 Subject: gnu: python-whatever: Update to 0.6. * gnu/packages/python-xyz.scm (python-whatever): Update to 0.6. --- gnu/packages/python-xyz.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8d53a59c40..684a41f70c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14820,15 +14820,14 @@ (define-public python2-gyp (define-public python-whatever (package (name "python-whatever") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/Suor/whatever/archive/" version ".tar.gz")) (sha256 - (base32 - "1iqvnaf0zpc6b4rvbqq4xy45mszcscyzpzknv8wg6j84pbp22sap")) + (base32 "1rchg9hrlvw4sn20lq1zspczr4x1pv57c02gv73igiqx1hqpy2nc")) (file-name (string-append name "-" version ".tar.gz")))) (build-system python-build-system) (arguments -- cgit v1.2.3 From f9bd82e7a6e4e991be3f3cc6bf8bccd7feeb5241 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 26 Nov 2019 21:01:47 +0100 Subject: gnu: python-seaborn: Add patch to fix tests. * gnu/packages/python-xyz.scm (python-seaborn)[source]: Add upstream patch to fix test failures. --- gnu/packages/python-xyz.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 684a41f70c..c89df24dd4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6265,7 +6265,19 @@ (define-public python-seaborn (method url-fetch) (uri (pypi-uri "seaborn" version)) (sha256 - (base32 "0bqysi3fxfjl1866m5jq8z7mynhqbqnikim74dmzn8539iwkzj3n")))) + (base32 "0bqysi3fxfjl1866m5jq8z7mynhqbqnikim74dmzn8539iwkzj3n")) + (patches + (list (origin + (method url-fetch) + ;; This has already been merged, but there is no new + ;; release including this patch. It fixes problems + ;; with axis rotation that would lead to test + ;; failures. + (uri "https://patch-diff.githubusercontent.com/raw/mwaskom/seaborn/pull/1716.diff") + (sha256 + (base32 + "1lm870z316n9ivsyr86hpk1gxaraw0mrjvq42lqsm0znhjdp9q9w")) + (file-name "seaborn-0.9.0-axis-rotation.patch")))))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From 9e7cb2f1e16fc5b70c6c0e4187443e216767323d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Nov 2019 08:21:12 +0100 Subject: gnu: python-matplotlib: Update to 3.1.2. * gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.1.2. [arguments]: Disable test_backend_webagg and test_constrainedlayout; skip other tests tagged with "webagg". --- gnu/packages/python-xyz.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c89df24dd4..cb74a7ab7f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3996,14 +3996,14 @@ (define-public python2-colorspacious (define-public python-matplotlib (package (name "python-matplotlib") - (version "3.1.1") + (version "3.1.2") (source (origin (method url-fetch) (uri (pypi-uri "matplotlib" version)) (sha256 (base32 - "14qc109dibp32xfd9lah54djc0rc76fhbsj9cwyb328lzqmd5sqz")))) + "1nmshfqh7wyg15i16hx1yiylcvzkws29ivn66n3i0wyqwcpjr3lf")))) (build-system python-build-system) (propagated-inputs ; the following packages are all needed at run time `(("python-cycler" ,python-cycler) @@ -4068,8 +4068,14 @@ (define-public python-matplotlib (for-each delete-file ;; test_normal_axes, test_get_tightbbox_polar '("lib/matplotlib/tests/test_axes.py" + ;; We don't use the webagg backend and this test forces it. + "lib/matplotlib/tests/test_backend_webagg.py" ;; test_outward_ticks "lib/matplotlib/tests/test_tightlayout.py" + ;; test_hidden_axes fails with minor extent + ;; differences, possibly due to the use of a + ;; different version of FreeType. + "lib/matplotlib/tests/test_constrainedlayout.py" ;; Fontconfig returns no fonts. "lib/matplotlib/tests/test_font_manager.py")) #t)) @@ -4087,7 +4093,7 @@ (define-public python-matplotlib (lambda* (#:key outputs inputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) (invoke "python" "tests.py" "-v" - "-m" "not network"))) + "-m" "not network and not webagg"))) (add-before 'build 'configure-environment (lambda* (#:key outputs inputs #:allow-other-keys) (let ((cairo (assoc-ref inputs "cairo"))) -- cgit v1.2.3 From a132276537fba4fd8065f85fc2961dfedb5f385b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Nov 2019 09:57:45 +0100 Subject: gnu: python-seaborn: Disable matrix test. * gnu/packages/python-xyz.scm (python-seaborn)[arguments]: Add phase "fix-tests". --- gnu/packages/python-xyz.scm | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cb74a7ab7f..f9e726e8fc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6296,6 +6296,12 @@ (define-public python-seaborn (system (format #f "~a/bin/Xvfb :1 &" xorg-server)) (setenv "DISPLAY" ":1") #t))) + (add-after 'unpack 'fix-tests + (lambda _ + ;; test_cbar_ticks fails probably because of matplotlib's + ;; expectation of using an older version of FreeType. + (delete-file "seaborn/tests/test_matrix.py") + #t)) (replace 'check (lambda _ (invoke "pytest" "seaborn") #t))))) (propagated-inputs `(("python-pandas" ,python-pandas) -- cgit v1.2.3 From ff3375251d6a316e3ee05589d70a8bb135ec47a6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 27 Nov 2019 22:19:13 +0100 Subject: gnu: Use the test-only Xorg variant for tests. * gnu/packages/education.scm (gcompris-qt)[native-inputs]: Change XORG-SERVER to XORG-SERVER-FOR-TESTS. * gnu/packages/engineering.scm (pcb, qucs, openscad)[native-inputs]: Likewise. * gnu/packages/gnome.scm (libbonoboui, d-feet, gspell, libdazzle, libhandy)[native-inputs]: Likewise. * gnu/packages/gnupg.scm (parcimonie)[native-inputs]: Likewise. * gnu/packages/graphics.scm (opensubdiv, rapicorn)[native-inputs]: Likewise. * gnu/packages/gtk.scm (gtksourceview-2, gtksourceview)[native-inputs]: Likewise. * gnu/packages/image-processing.scm (opencv)[native-inputs]: Likewise. * gnu/packages/kde-frameworks.scm (kconfig, kcoreaddons, kwidgetsaddons, kwindowsystem, kdeclarative)[native-inputs]: Likewise. * gnu/packages/kde-plasma.scm (kscreenlocker)[native-inputs]: Likewise. * gnu/packages/messaging.scm (gajim)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-seaborn)[native-inputs]: Likewise. --- gnu/packages/education.scm | 2 +- gnu/packages/engineering.scm | 6 +++--- gnu/packages/gnome.scm | 10 +++++----- gnu/packages/gnupg.scm | 2 +- gnu/packages/graphics.scm | 4 ++-- gnu/packages/gtk.scm | 4 ++-- gnu/packages/image-processing.scm | 2 +- gnu/packages/kde-frameworks.scm | 10 +++++----- gnu/packages/kde-plasma.scm | 2 +- gnu/packages/messaging.scm | 2 +- gnu/packages/python-xyz.scm | 2 +- gnu/packages/vim.scm | 2 +- 12 files changed, 24 insertions(+), 24 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index c84fa54223..46262fd14b 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -167,7 +167,7 @@ (define-public gcompris-qt ("gettext" ,gettext-minimal) ("perl" ,perl) ("qttools" ,qttools) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("openssl" ,openssl) ("python-2" ,python-2) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 294105a757..c5e2f58aeb 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -373,7 +373,7 @@ (define-public pcb ("imagemagick" ,imagemagick) ("gerbv" ,gerbv) ("ghostscript" ,ghostscript) - ("xvfb" ,xorg-server))) + ("xvfb" ,xorg-server-for-tests))) (home-page "http://pcb.geda-project.org/") (synopsis "Design printed circuit board layouts") (description @@ -1771,7 +1771,7 @@ (define-public qucs ("python" ,python-2) ; for tests ("matplotlib" ,python2-matplotlib) ; for tests ("numpy" ,python2-numpy) ; for tests - ("xorg-server" ,xorg-server))) ; for tests + ("xorg-server" ,xorg-server-for-tests))) ; for tests (inputs `(("adms" ,adms) ("asco" ,asco) @@ -2174,7 +2174,7 @@ (define-public openscad ("imagemagick" ,imagemagick) ("ps" ,procps) ("python" ,python) - ("xvfb" ,xorg-server))) + ("xvfb" ,xorg-server-for-tests))) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index af2558d814..11ed035919 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2025,7 +2025,7 @@ (define-public libbonoboui (native-inputs `(("glib" ,glib "bin") ; for glib-genmarshal, etc. ("intltool" ,intltool) - ("xorg-server" ,xorg-server) ; For running the tests + ("xorg-server" ,xorg-server-for-tests) ; For running the tests ("pkg-config" ,pkg-config))) (home-page "https://developer.gnome.org/libbonoboui/") (synopsis "Some user interface controls using Bonobo") @@ -4591,7 +4591,7 @@ (define-public d-feet ("pkg-config" ,pkg-config) ("python-pep8" ,python-pep8) ("xmllint" ,libxml2) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("gobject-introspection" ,gobject-introspection) ("gtk+" ,gtk+) @@ -7752,7 +7752,7 @@ (define-public gspell ;; For tests. ("aspell-dict-en" ,aspell-dict-en) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (propagated-inputs `(("enchant" ,enchant))) ;enchant.pc is required by gspell-1.pc (home-page "https://wiki.gnome.org/Projects/gspell") @@ -8167,7 +8167,7 @@ (define-public libdazzle `(("glib" ,glib "bin") ; glib-compile-resources ("pkg-config" ,pkg-config) ;; For tests. - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("glib" ,glib) ("gobject-introspection" ,gobject-introspection) @@ -8389,9 +8389,9 @@ (define-public libhandy ("gtk-doc" ,gtk-doc) ("pkg-config" ,pkg-config) ("gettext" ,gettext-minimal) - ("xorg-server" ,xorg-server) ;; Test suite dependencies. + ("xorg-server" ,xorg-server-for-tests) ("hicolor-icon-theme" ,hicolor-icon-theme))) (home-page "https://source.puri.sm/Librem5/libhandy") (synopsis "Library full of GTK+ widgets for mobile phones") diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 6b6b8f616d..23d3aba90e 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -1045,7 +1045,7 @@ (define-public parcimonie ("perl-xml-twig" ,perl-xml-twig) ("torsocks" ,torsocks))) (native-inputs - `(("xorg-server" ,xorg-server))) + `(("xorg-server" ,xorg-server-for-tests))) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 4f1c50b272..8795107dcb 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -758,7 +758,7 @@ (define-public rapicorn ("graphviz" ,graphviz) ("intltool" ,intltool) ("pkg-config" ,pkg-config) - ("xvfb" ,xorg-server))) + ("xvfb" ,xorg-server-for-tests))) (home-page "https://rapicorn.testbit.org/") (synopsis "Toolkit for rapid development of user interfaces") (description @@ -1055,7 +1055,7 @@ (define-public opensubdiv (setenv "DISPLAY" ":1") #t))))) (native-inputs - `(("xorg-server" ,xorg-server))) + `(("xorg-server" ,xorg-server-for-tests))) (inputs `(("glew" ,glew) ("libxrandr" ,libxrandr) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index e6b9042c00..817c03c30e 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -360,7 +360,7 @@ (define-public gtksourceview-2 ("glib" ,glib "bin") ; for glib-genmarshal, etc. ("pkg-config" ,pkg-config) ;; For testing. - ("xorg-server" ,xorg-server) + ("xorg-server" ,xorg-server-for-tests) ("shared-mime-info" ,shared-mime-info))) (propagated-inputs ;; As per the pkg-config file. @@ -431,7 +431,7 @@ (define-public gtksourceview ("pkg-config" ,pkg-config) ("vala" ,vala) ;; For testing. - ("xorg-server" ,xorg-server) + ("xorg-server" ,xorg-server-for-tests) ("shared-mime-info" ,shared-mime-info))) (propagated-inputs ;; gtksourceview-3.0.pc refers to all these. diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 2579da3d6a..1961b47361 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -373,7 +373,7 @@ (define-public opencv (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp))))))))) (native-inputs `(("pkg-config" ,pkg-config) - ("xorg-server" ,xorg-server) ; For running the tests + ("xorg-server" ,xorg-server-for-tests) ; For running the tests ("opencv-extra" ,(origin (method git-fetch) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index ec735d8903..6f7c5df7b4 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -483,7 +483,7 @@ (define-public kconfig ("extra-cmake-modules" ,extra-cmake-modules) ("inetutils" ,inetutils) ("qttools" ,qttools) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("qtbase" ,qtbase))) (arguments @@ -548,7 +548,7 @@ (define-public kcoreaddons ("qttools" ,qttools) ("shared-mime-info" ,shared-mime-info) ;; TODO: FAM: File alteration notification http://oss.sgi.com/projects/fam - ("xorg-server" ,xorg-server))) ; for the tests + ("xorg-server" ,xorg-server-for-tests))) ; for the tests (inputs `(("qtbase" ,qtbase))) (arguments @@ -1041,7 +1041,7 @@ (define-public kwidgetsaddons (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) ("qttools" ,qttools) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("qtbase" ,qtbase))) (arguments @@ -1091,7 +1091,7 @@ (define-public kwindowsystem ("dbus" ,dbus) ; for the tests ("openbox" ,openbox) ; for the tests ("qttools" ,qttools) - ("xorg-server" ,xorg-server))) ; for the tests + ("xorg-server" ,xorg-server-for-tests))) ; for the tests (inputs `(("libxrender" ,libxrender) ("qtbase" ,qtbase) @@ -2201,7 +2201,7 @@ (define-public kdeclarative (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) ("pkg-config" ,pkg-config) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("kauth" ,kauth) ("kbookmarks" ,kbookmarks) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index c1731d459a..d381ae9fb4 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -96,7 +96,7 @@ (define-public kscreenlocker ;; For tests. ("dbus" ,dbus) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("kcmutils" ,kcmutils) ("kcrash" ,kcrash) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 33e752c9a0..2429bad3e5 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -644,7 +644,7 @@ (define-public gajim (native-inputs `(("intltool" ,intltool) ("python-docutils" ,python-docutils) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (inputs `(("adwaita-icon-theme" ,adwaita-icon-theme) ("gnome-keyring" ,gnome-keyring) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f9e726e8fc..7343366cd9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6310,7 +6310,7 @@ (define-public python-seaborn ("python-scipy" ,python-scipy))) (native-inputs `(("python-pytest" ,python-pytest) - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-for-tests))) (home-page "http://stanford.edu/~mwaskom/software/seaborn/") (synopsis "Statistical data visualization") (description diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index ae07bcd9b6..b360d1fcbe 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -198,7 +198,7 @@ (define-public vim-full display " &"))))))))))) (native-inputs `(("pkg-config" ,pkg-config) - ("xorg-server" ,xorg-server) + ("xorg-server" ,xorg-server-for-tests) ,@(package-native-inputs vim))) (inputs `(("acl" ,acl) -- cgit v1.2.3 From ba5ef9997ba071339473590805331a5eec29b10d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 27 Nov 2019 23:46:21 +0100 Subject: gnu: python-dbus: Update to 1.2.14. * gnu/packages/python-xyz.scm (python-dbus): Update to 1.2.14. (python2-dbus)[arguments]: Remove. --- gnu/packages/python-xyz.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7343366cd9..d2efa74228 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5950,14 +5950,14 @@ (define-public python2-user-agents (define-public python-dbus (package (name "python-dbus") - (version "1.2.10") + (version "1.2.14") (source (origin (method url-fetch) (uri (string-append "https://dbus.freedesktop.org/releases/dbus-python/" "dbus-python-" version ".tar.gz")) (sha256 - (base32 "11nqk01iq5bx2llgb3ksknyinijdp29w4ndj210glm009ayjncyl")))) + (base32 "0cdchkgnivlka4lf8q4qfk0yxq483i3r3aqickjf8hfn7nx0c0mi")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -5976,10 +5976,7 @@ (define-public python2-dbus (inputs `(("python" ,python-2) ,@(alist-delete "python" (package-inputs python-dbus) - equal?))) - ;; FIXME: on Python 2, the test_utf8 fails with: - ;; "ValueError: unichr() arg not in range(0x10000) (narrow Python build)" - (arguments `(#:tests? #f)))) + equal?))))) (define-public python-notify2 (package -- cgit v1.2.3 From 38a404d567dbaed7c9bf3803e2580290d575f1dc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 28 Nov 2019 16:25:14 +0100 Subject: gnu: python2-matplotlib: Do not inherit test adjustments. This is a follow-up to commit 9e7cb2f1e16fc5b70c6c0e4187443e216767323d. * gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Do not inherit the 'fix-and-disable-failing-tests' phase. --- gnu/packages/python-xyz.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d2efa74228..a166554f98 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4147,6 +4147,7 @@ (define-public python2-matplotlib (assoc-ref inputs "jquery-ui") "-d" dir)) #t)) + (delete 'fix-and-disable-failing-tests) (delete 'check))))) ; These tests weren't run the the past. ;; Make sure to use special packages for Python 2 instead ;; of those automatically rewritten by package-with-python2. -- cgit v1.2.3 From c09f598d94af81f326fe1d4cf2ab344d4e720679 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 28 Nov 2019 16:26:51 +0100 Subject: gnu: python-matplotlib: Do not move the 'check' phase. Running tests after install is now the default in PYTHON-BUILD-SYSTEM. * gnu/packages/python-xyz.scm (python-matplotlib)[arguments]: Replace 'check' phase, instead of deleting and adding new phase. --- gnu/packages/python-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a166554f98..fcc3972194 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4088,8 +4088,7 @@ (define-public python-matplotlib (assoc-ref inputs "jquery-ui") "-d" dir)) #t)) - (delete 'check) - (add-after 'install 'check + (replace 'check (lambda* (#:key outputs inputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) (invoke "python" "tests.py" "-v" -- cgit v1.2.3 From a566231947ef87db830b7ffbd2d3b7c993adb058 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 29 Nov 2019 11:05:37 +0200 Subject: gnu: python-invoke: Update to 1.3.0. * gnu/packages/python-xyz.scm (python-invoke): Update to 1.3.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fcc3972194..648f1be963 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12476,13 +12476,13 @@ (define-public python-invoke (package (name "python-invoke") (home-page "http://www.pyinvoke.org/") - (version "1.1.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (pypi-uri "invoke" version)) (sha256 (base32 - "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6")))) + "1nn7gad0rvy492acpyhkrp01zsk86acf34qhsvq4xmm6x39788n5")))) (build-system python-build-system) (arguments ;; XXX: Requires many dependencies that are not yet in Guix. -- cgit v1.2.3 From ff3d1b99f2edc40258abeb5e9b87f815f6880686 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 30 Nov 2019 17:33:48 +0100 Subject: gnu: python-pyclipper: Update to 1.1.0.post3. * gnu/packages/python-xyz.scm (python-pyclipper): Update to 1.1.0.post3. --- gnu/packages/python-xyz.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 648f1be963..24e1e48135 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14381,14 +14381,13 @@ (define-public python-setuptools-git (define-public python-pyclipper (package (name "python-pyclipper") - (version "1.1.0.post1") + (version "1.1.0.post3") (source (origin (method url-fetch) (uri (pypi-uri "pyclipper" version ".zip")) (sha256 - (base32 - "0ldbkbnx94an4zzrwb1sxmg6k0jgk4cwmvcdyy8y5k1zslc612wa")) + (base32 "164yksvqwqvwzh8f8lq92asg87hd8rvcy2xb5vm4y4ccvd5xgb7i")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 43ae8f796b4b02106328cb34e90f1d8994ebc7ab Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 30 Nov 2019 17:34:58 +0100 Subject: gnu: python-icalendar: Update to 4.0.4. * gnu/packages/python-xyz.scm (python-icalendar): Update to 4.0.4. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 24e1e48135..aef970cd88 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8660,13 +8660,13 @@ (define-public python2-execnet (define-public python-icalendar (package (name "python-icalendar") - (version "4.0.3") + (version "4.0.4") (source (origin (method url-fetch) (uri (pypi-uri "icalendar" version)) (sha256 (base32 - "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7")))) + "16gjvqv0n05jrb9g228pdjgzd3amz2pdhvcgsn1jypszjg5m2w9l")))) (build-system python-build-system) (propagated-inputs `(("python-dateutil" ,python-dateutil) -- cgit v1.2.3 From 61b77ff307b875bf198dd3d71ef64d1871d0ac6e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 2 Dec 2019 11:01:49 +0200 Subject: gnu: python-pillow: Replace check phase. * gnu/packages/python-xyz.scm (python-pillow)[arguments]: Since 'check always come after 'install, replace 'check phase rather than recreate it. --- gnu/packages/python-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index aef970cd88..59f712844f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4705,8 +4705,7 @@ (define-public python-pillow (lambda _ (substitute* "setup.py" (("\\['/sbin/ldconfig', '-p'\\]") "['true']")))) - (delete 'check) ; We must run checks after python-pillow is installed. - (add-after 'install 'check-installed + (replace 'check (lambda* (#:key outputs inputs #:allow-other-keys) (begin (setenv "HOME" (getcwd)) -- cgit v1.2.3 From 979d8464d4539999a5132caf935cf12fb941b0f4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 2 Dec 2019 11:02:47 +0200 Subject: gnu: python-pillow: Make check phase conditional. * gnu/packages/python-xyz.scm (python-pillow)[arguments]: Wrap custom 'check phase in check for 'tests?'. --- gnu/packages/python-xyz.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 59f712844f..c628c989d2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4706,13 +4706,15 @@ (define-public python-pillow (substitute* "setup.py" (("\\['/sbin/ldconfig', '-p'\\]") "['true']")))) (replace 'check - (lambda* (#:key outputs inputs #:allow-other-keys) - (begin - (setenv "HOME" (getcwd)) - ;; Make installed package available for running the tests. - (add-installed-pythonpath inputs outputs) - (invoke "python" "selftest.py" "--installed") - (invoke "python" "-m" "pytest" "-vv"))))))) + (lambda* (#:key outputs inputs tests? #:allow-other-keys) + (if tests? + (begin + (setenv "HOME" (getcwd)) + ;; Make installed package available for running the tests. + (add-installed-pythonpath inputs outputs) + (invoke "python" "selftest.py" "--installed") + (invoke "python" "-m" "pytest" "-vv")) + #t)))))) (home-page "https://python-pillow.org") (synopsis "Fork of the Python Imaging Library") (description -- cgit v1.2.3 From 0c4e1c5fbfb6d56aee3a270ed0431790cb67f662 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 2 Dec 2019 11:08:11 +0200 Subject: gnu: python-pillow: Sort inputs alphabetically. * gnu/packages/python-xyz.scm (python-pillow)[inputs]: Sort alphabetically. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c628c989d2..637a00f4e0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4691,11 +4691,11 @@ (define-public python-pillow (inputs `(("freetype" ,freetype) ("lcms" ,lcms) - ("zlib" ,zlib) ("libjpeg" ,libjpeg) - ("openjpeg" ,openjpeg) ("libtiff" ,libtiff) - ("libwebp" ,libwebp))) + ("libwebp" ,libwebp) + ("openjpeg" ,openjpeg) + ("zlib" ,zlib))) (propagated-inputs `(("python-olefile" ,python-olefile))) (arguments -- cgit v1.2.3 From 5fbdd917b73d30ef5ca0aa4e82b8d0a5f81394dd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 2 Dec 2019 11:13:18 +0200 Subject: gnu: python-pillow: Update to 6.2.1. * gnu/packages/python-xyz.scm (python-pillow): Update to 6.2.1. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 637a00f4e0..6d86eb1b22 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4677,14 +4677,14 @@ (define-public python2-olefile (define-public python-pillow (package (name "python-pillow") - (version "6.1.0") + (version "6.2.1") (source (origin (method url-fetch) (uri (pypi-uri "Pillow" version)) (sha256 (base32 - "1pnrsz0f0n0c819v1pdr8j6rm8xvhc9f3kh1fv9xpdp9n5ygf108")))) + "1c8wkzc58f5wdh006jvmwdk3wxld1xgagcbdvj7iv17qi0m9fkmz")))) (build-system python-build-system) (native-inputs `(("python-pytest" ,python-pytest))) -- cgit v1.2.3 From ca7c365312d3af6f664868690f02c385f07e34a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Dec 2019 16:42:49 +0100 Subject: gnu: python-scikit-image: Move to (gnu packages python-science). * gnu/packages/python-xyz.scm (python-scikit-image, python2-scikit-image): Move these two from here... * gnu/packages/python-science.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. --- gnu/local.mk | 1 + gnu/packages/python-science.scm | 67 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/python-xyz.scm | 37 +---------------------- 3 files changed, 69 insertions(+), 36 deletions(-) create mode 100644 gnu/packages/python-science.scm (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 9ddd1349da..e1518db09d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -407,6 +407,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/python-check.scm \ %D%/packages/python-compression.scm \ %D%/packages/python-crypto.scm \ + %D%/packages/python-science.scm \ %D%/packages/python-web.scm \ %D%/packages/python-xyz.scm \ %D%/packages/toys.scm \ diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm new file mode 100644 index 0000000000..4636180dfa --- /dev/null +++ b/gnu/packages/python-science.scm @@ -0,0 +1,67 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2015 Ricardo Wurmus +;;; Copyright © 2015 Federico Beffa +;;; Copyright © 2016 Hartmut Goebel +;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2018 Marius Bakke +;;; Copyright © 2019 Tobias Geerinckx-Rice +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages python-science) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages) + #:use-module (gnu packages python-xyz) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix utils) + #:use-module (guix build-system python)) + +(define-public python-scikit-image + (package + (name "python-scikit-image") + (version "0.14.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit-image" version)) + (sha256 + (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s")))) + (build-system python-build-system) + (arguments + ;; TODO: Some tests require running X11 server. Disable them? + '(#:tests? #f)) + ;; See DEPENDS.txt for the list of build and run time requiremnts + (propagated-inputs + `(("python-cloudpickle" ,python-cloudpickle) + ("python-dask" ,python-dask) + ("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) + ("python-numpy" ,python-numpy) + ("python-pillow" ,python-pillow) + ("python-pywavelets" ,python-pywavelets) + ("python-scipy" ,python-scipy) + ("python-six" ,python-six))) + (native-inputs + `(("python-cython" ,python-cython))) + (home-page "http://scikit-image.org/") + (synopsis "Image processing in Python") + (description + "Scikit-image is a collection of algorithms for image processing.") + (license license:bsd-3))) + +(define-public python2-scikit-image + (package-with-python2 python-scikit-image)) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6d86eb1b22..1d6f0a8367 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -128,6 +128,7 @@ (define-module (gnu packages python-xyz) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages qt) #:use-module (gnu packages readline) @@ -3307,42 +3308,6 @@ (define-public mallard-ducktype provides additional functionality on the produced Mallard documents.") (license license:expat))) -(define-public python-scikit-image - (package - (name "python-scikit-image") - (version "0.14.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scikit-image" version)) - (sha256 - (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s")))) - (build-system python-build-system) - (arguments - ;; TODO: Some tests require running X11 server. Disable them? - '(#:tests? #f)) - ;; See DEPENDS.txt for the list of build and run time requiremnts - (propagated-inputs - `(("python-cloudpickle" ,python-cloudpickle) - ("python-dask" ,python-dask) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-pillow" ,python-pillow) - ("python-pywavelets" ,python-pywavelets) - ("python-scipy" ,python-scipy) - ("python-six" ,python-six))) - (native-inputs - `(("python-cython" ,python-cython))) - (home-page "http://scikit-image.org/") - (synopsis "Image processing in Python") - (description - "Scikit-image is a collection of algorithms for image processing.") - (license license:bsd-3))) - -(define-public python2-scikit-image - (package-with-python2 python-scikit-image)) - (define-public python-cython (package (name "python-cython") -- cgit v1.2.3 From ec1224a73b2c0c0c15a3293261334f3927f6579d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Dec 2019 14:04:39 +0100 Subject: gnu: python-scipy: Move to (gnu packages python-science). * gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from here... * gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here. * gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm, gnu/packages/statistics.scm: Adjust module imports. --- gnu/packages/bioinformatics.scm | 1 + gnu/packages/machine-learning.scm | 1 + gnu/packages/python-science.scm | 126 ++++++++++++++++++++++++++++++++++++++ gnu/packages/python-xyz.scm | 119 ----------------------------------- gnu/packages/statistics.scm | 1 + 5 files changed, 129 insertions(+), 119 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 616fcedc35..b0d070b4e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -105,6 +105,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-compression) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index b83b336d84..ab4150cbb1 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -69,6 +69,7 @@ (define-module (gnu packages machine-learning) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages serialization) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 4636180dfa..93fc63c2e7 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -24,12 +24,138 @@ (define-module (gnu packages python-science) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) + #:use-module (gnu packages base) + #:use-module (gnu packages check) + #:use-module (gnu packages gcc) + #:use-module (gnu packages maths) + #:use-module (gnu packages perl) + #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages sphinx) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system python)) +(define-public python-scipy + (package + (name "python-scipy") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scipy" version)) + (sha256 + (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-matplotlib" ,python-matplotlib) + ("python-pyparsing" ,python-pyparsing))) + (inputs + `(("lapack" ,lapack) + ("openblas" ,openblas))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-sphinx" ,python-sphinx) + ("python-numpydoc" ,python-numpydoc) + ("gfortran" ,gfortran) + ("perl" ,perl) + ("which" ,which))) + (outputs '("out" "doc")) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-broken-tests + (lambda _ + (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py" + (("^( +)def test_threads_parallel\\(self\\):" m indent) + (string-append indent + "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + m))) + (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py" + (("^def test_parallel_threads\\(\\):" m) + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + m))) + #t)) + (add-before 'build 'configure-openblas + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "site.cfg" + (lambda (port) + (format port + "[blas] +libraries = openblas +library_dirs = ~a/lib +include_dirs = ~a/include + +# backslash-n to make emacs happy +\n[atlas] +library_dirs = ~a/lib +atlas_libs = openblas +" + (assoc-ref inputs "openblas") + (assoc-ref inputs "openblas") + (assoc-ref inputs "openblas")))) + #t)) + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (html (string-append doc "/html")) + (pyver ,(string-append "PYVER=" (version-major+minor + (package-version python)))) + ;; By default it tries to run sphinx-build through the Python + ;; interpreter which won't work with our shell wrapper. + (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build")) + ;; Make installed package available for building the + ;; documentation + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "doc" + ;; Fix generation of images for mathematical expressions. + (substitute* (find-files "source" "conf\\.py") + (("pngmath_use_preview = True") + "pngmath_use_preview = False")) + (mkdir-p html) + (invoke "make" "html" pyver sphinxbuild) + (with-directory-excursion "build/html" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append html "/" dir))) + (install-file file html))) + (find-files "." ".*"))))) + #t)) + ;; Tests can only be run after the library has been installed and not + ;; within the source directory. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "/tmp" + (invoke "python" "-c" + "import scipy; scipy.test(verbose=2)"))))))) + (home-page "https://www.scipy.org/") + (synopsis "The Scipy library provides efficient numerical routines") + (description "The SciPy library is one of the core packages that make up +the SciPy stack. It provides many user-friendly and efficient numerical +routines such as routines for numerical integration and optimization.") + (properties `((python2-variant . ,(delay python2-scipy)))) + (license license:bsd-3))) + +;; Version 1.2.2 is the last version to support Python 2 +(define-public python2-scipy + (package + (inherit (package-with-python2 + (strip-python2-variant python-scipy))) + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scipy" version)) + (sha256 + (base32 + "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4")))))) + (define-public python-scikit-image (package (name "python-scikit-image") diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1d6f0a8367..f52d9a410f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4277,125 +4277,6 @@ (define-public python2-pysnptools operators such as union, intersection, and difference.") (license license:asl2.0))) -(define-public python-scipy - (package - (name "python-scipy") - (version "1.3.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scipy" version)) - (sha256 - (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0")))) - (build-system python-build-system) - (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-pyparsing" ,python-pyparsing))) - (inputs - `(("lapack" ,lapack) - ("openblas" ,openblas))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-sphinx" ,python-sphinx) - ("python-numpydoc" ,python-numpydoc) - ("gfortran" ,gfortran) - ("perl" ,perl) - ("which" ,which))) - (outputs '("out" "doc")) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'disable-broken-tests - (lambda _ - (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py" - (("^( +)def test_threads_parallel\\(self\\):" m indent) - (string-append indent - "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m))) - (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py" - (("^def test_parallel_threads\\(\\):" m) - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m))) - #t)) - (add-before 'build 'configure-openblas - (lambda* (#:key inputs #:allow-other-keys) - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "[blas] -libraries = openblas -library_dirs = ~a/lib -include_dirs = ~a/include - -# backslash-n to make emacs happy -\n[atlas] -library_dirs = ~a/lib -atlas_libs = openblas -" - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas")))) - #t)) - (add-after 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (pyver ,(string-append "PYVER=" (version-major+minor - (package-version python)))) - ;; By default it tries to run sphinx-build through the Python - ;; interpreter which won't work with our shell wrapper. - (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build")) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "doc" - ;; Fix generation of images for mathematical expressions. - (substitute* (find-files "source" "conf\\.py") - (("pngmath_use_preview = True") - "pngmath_use_preview = False")) - (mkdir-p html) - (invoke "make" "html" pyver sphinxbuild) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (install-file file html))) - (find-files "." ".*"))))) - #t)) - ;; Tests can only be run after the library has been installed and not - ;; within the source directory. - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "/tmp" - (invoke "python" "-c" - "import scipy; scipy.test(verbose=2)"))))))) - (home-page "https://www.scipy.org/") - (synopsis "The Scipy library provides efficient numerical routines") - (description "The SciPy library is one of the core packages that make up -the SciPy stack. It provides many user-friendly and efficient numerical -routines such as routines for numerical integration and optimization.") - (properties `((python2-variant . ,(delay python2-scipy)))) - (license license:bsd-3))) - -;; Version 1.2.2 is the last version to support Python 2 -(define-public python2-scipy - (package - (inherit (package-with-python2 - (strip-python2-variant python-scipy))) - (version "1.2.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scipy" version)) - (sha256 - (base32 - "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4")))))) - (define-public python-socksipy-branch (package (name "python-socksipy-branch") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b84b3803ea..1d6e6aaff5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -66,6 +66,7 @@ (define-module (gnu packages statistics) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages sphinx) -- cgit v1.2.3 From d97cdff18ece9ce3a6caa39e8779d597f535e082 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Tue, 26 Nov 2019 13:42:24 -0600 Subject: gnu: python-socksipychain: Update to 2.1.0. * gnu/packages/python-xyz.scm (python-socksipychain): Update to 2.1.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f52d9a410f..1695f9b11a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4308,7 +4308,7 @@ (define-public python2-socksipy-branch (define-public python-socksipychain (package (name "python-socksipychain") - (version "2.0.15") + (version "2.1.0") (source (origin (method git-fetch) @@ -4318,7 +4318,7 @@ (define-public python-socksipychain (file-name (git-file-name name version)) (sha256 (base32 - "1pkljnh9hfwla8sg7mil4f9zrnsqj0dbhr3crxjw3k8dnjz70dvk")))) + "0idm9a050rd2kbgbz2sk9ib9589kj4xh1xdnggs6xbq2v2y8f6zn")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; Tests try to access the network. -- cgit v1.2.3 From 13125c5afeeacecdef41e103d9e5f942fcb78c01 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Tue, 26 Nov 2019 13:52:21 -0600 Subject: gnu: Remove python2-socksipychain. * gnu/packages/python-xyz.scm (python2-socksipychain): Remove variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1695f9b11a..186e558f2f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4331,9 +4331,6 @@ (define-public python-socksipychain a simple netcat replacement with chaining support.") (license license:bsd-3))) -(define-public python2-socksipychain - (package-with-python2 python-socksipychain)) - (define-public python-pycodestyle (package (name "python-pycodestyle") -- cgit v1.2.3 From 312ec128af832dc5d22ce4f6ffe66920e69eda8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 4 Dec 2019 08:56:36 +0100 Subject: gnu: python-pandas: Move to (gnu packages python-science). * gnu/packages/python-xyz.scm (python-pandas, python2-pandas): Move from here... * gnu/packages/python-science.scm (python-pandas, python2-pandas): ...to here. * gnu/packages/benchmark.scm, gnu/packages/databases.scm, gnu/packages/graph.scm, gnu/packages/parallel.scm, gnu/packages/serialization.scm: Import (gnu packages python-science). --- gnu/packages/benchmark.scm | 1 + gnu/packages/databases.scm | 1 + gnu/packages/graph.scm | 1 + gnu/packages/parallel.scm | 1 + gnu/packages/python-science.scm | 98 ++++++++++++++++++++++++++++++++++++++++- gnu/packages/python-xyz.scm | 89 ------------------------------------- gnu/packages/serialization.scm | 1 + 7 files changed, 101 insertions(+), 91 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index c513370e74..8e347879dd 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -35,6 +35,7 @@ (define-module (gnu packages benchmark) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages python) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages storage) #:use-module (ice-9 match)) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 4be5912022..8260bfcb43 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -97,6 +97,7 @@ (define-module (gnu packages databases) #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages rdf) #:use-module (gnu packages readline) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 326477730b..52db619fb3 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -43,6 +43,7 @@ (define-module (gnu packages graph) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 0ad47bca0d..3cb39473fb 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -44,6 +44,7 @@ (define-module (gnu packages parallel) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages tcl) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 93fc63c2e7..4a262ec793 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1,10 +1,13 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ricardo Wurmus +;;; Copyright © 2015, 2016 Ricardo Wurmus ;;; Copyright © 2015 Federico Beffa +;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2016, 2018 Marius Bakke +;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke ;;; Copyright © 2019 Tobias Geerinckx-Rice +;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2019 Giacomo Leidi ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,8 +33,10 @@ (define-module (gnu packages python-science) #:use-module (gnu packages maths) #:use-module (gnu packages perl) #:use-module (gnu packages python) + #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages sphinx) + #:use-module (gnu packages time) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) @@ -191,3 +196,92 @@ (define-public python-scikit-image (define-public python2-scikit-image (package-with-python2 python-scikit-image)) + +(define-public python-pandas + (package + (name "python-pandas") + (version "0.25.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pandas" version)) + (sha256 + (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa")))) + (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 + (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")))))))) + (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-mock" ,python-pytest-mock))) + (home-page "https://pandas.pydata.org") + (synopsis "Data structures for data analysis, time series, and statistics") + (description + "Pandas is a Python package providing fast, flexible, and expressive data +structures designed to make working with structured (tabular, +multidimensional, potentially heterogeneous) and time series data both easy +and intuitive. It aims to be the fundamental high-level building block for +doing practical, real world data analysis in Python.") + (properties `((python2-variant . ,(delay python2-pandas)))) + (license license:bsd-3))) + +;; 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)))) + (package/inherit + pandas + (version "0.24.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "pandas" version)) + (sha256 + (base32 + "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))))))) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 186e558f2f..30b84d26b4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1155,95 +1155,6 @@ (define-public python-schedule (define-public python2-schedule (package-with-python2 python-schedule)) -(define-public python-pandas - (package - (name "python-pandas") - (version "0.25.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa")))) - (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 - (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")))))))) - (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-mock" ,python-pytest-mock))) - (home-page "https://pandas.pydata.org") - (synopsis "Data structures for data analysis, time series, and statistics") - (description - "Pandas is a Python package providing fast, flexible, and expressive data -structures designed to make working with structured (tabular, -multidimensional, potentially heterogeneous) and time series data both easy -and intuitive. It aims to be the fundamental high-level building block for -doing practical, real world data analysis in Python.") - (properties `((python2-variant . ,(delay python2-pandas)))) - (license license:bsd-3))) - -;; 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)))) - (package/inherit - pandas - (version "0.24.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 - "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))))))) - (define-public python2-mechanize (package (name "python2-mechanize") diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 00a8d27387..a213e4ba0c 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -46,6 +46,7 @@ (define-module (gnu packages serialization) #:use-module (gnu packages lua) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages perl)) -- cgit v1.2.3 From 34bf686952e0eb1ce52cea1c1563a94ee693d268 Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 5 Dec 2019 16:50:17 +0100 Subject: gnu: Add python-pykwalify. * gnu/packages/python-xyz.scm (python-pykwalify): New variable. --- gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 89be883cda..9dd97a61bd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16686,3 +16686,28 @@ (define-public python-intelhex several convenience Python scripts, including \"classic\" hex2bin and bin2hex converters and more, those based on the library itself.") (license license:bsd-3))) + +(define-public python-pykwalify + (package + (name "python-pykwalify") + (version "1.7.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pykwalify" version)) + (sha256 + (base32 + "1cnfzkg1b01f825ikpw2fhjclf9c8akxjfrbd1vc22x1lg2kk2vy")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ;missing dependencies + (propagated-inputs + `(("python-dateutil" ,python-dateutil) + ("python-docopt" ,python-docopt) + ("python-pyyaml" ,python-pyyaml))) + (home-page "https://github.com/grokzen/pykwalify") + (synopsis + "Python lib/cli for JSON/YAML schema validation") + (description + "This package provides a parser, schema validator, and data binding tool +for YAML and JSON.") + (license license:expat))) -- cgit v1.2.3