From a4d52f07d7fd0e4d9997b3021192685d4a3b0b71 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 4 Dec 2022 00:54:55 -0500 Subject: gnu: jami: Apply a patch to fix a crash when using SIP. * gnu/packages/patches/jami-sipaccount-segfault.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/jami.scm (%jami-sources): Apply it. --- gnu/local.mk | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 1bfbe28bde..1602225330 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1345,6 +1345,7 @@ dist_patch_DATA = \ %D%/packages/patches/jami-fix-unit-tests-build.patch \ %D%/packages/patches/jami-libjami-headers-search.patch \ %D%/packages/patches/jami-no-webengine.patch \ + %D%/packages/patches/jami-sipaccount-segfault.patch \ %D%/packages/patches/jami-sip-contacts.patch \ %D%/packages/patches/jami-sip-unregister.patch \ %D%/packages/patches/jami-xcb-link.patch \ -- cgit 1.4.1 From 3a52318e60fa71b18b8473ca99e1e83d16c35d01 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Fri, 18 Nov 2022 12:29:24 +0800 Subject: gnu: Add libapparmor. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/apparmor.scm: New file. (libapparmor): New variable. * gnu/local.mk (GNU_SYSTEM_MODULES): Add the file. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/apparmor.scm | 112 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 113 insertions(+) create mode 100644 gnu/packages/apparmor.scm (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 1602225330..2d3329712b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -116,6 +116,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/anthy.scm \ %D%/packages/antivirus.scm \ %D%/packages/apl.scm \ + %D%/packages/apparmor.scm \ %D%/packages/apr.scm \ %D%/packages/arcan.scm \ %D%/packages/aspell.scm \ diff --git a/gnu/packages/apparmor.scm b/gnu/packages/apparmor.scm new file mode 100644 index 0000000000..ac97580640 --- /dev/null +++ b/gnu/packages/apparmor.scm @@ -0,0 +1,112 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2022 Hilton Chain +;;; +;;; 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 apparmor) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages autotools) + #:use-module (gnu packages base) + #:use-module (gnu packages bison) + #:use-module (gnu packages dejagnu) + #:use-module (gnu packages flex) + #:use-module (gnu packages gawk) + #:use-module (gnu packages gettext) + #:use-module (gnu packages linux) + #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) + #:use-module (gnu packages ruby) + #:use-module (gnu packages swig) + #:use-module (guix build-system gnu) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module (guix packages) + #:use-module (guix utils)) + +(define-public libapparmor + (package + (name "libapparmor") + (version "3.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/apparmor/apparmor") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1h77a7ww0rxfv5nsi1iy4fffklxdr2vq6r7kdsqm15yysglhbjyi")))) + (build-system gnu-build-system) + (arguments + (list #:configure-flags + #~(list (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib") + "--with-perl" "--with-python" "--with-ruby") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (for-each patch-shebang + '("common/list_af_names.sh" + "common/list_capabilities.sh")) + (for-each (lambda (file) + (substitute* file + (("/usr") "") + (("/bin/\\<(pod2man|pod2html|podchecker|prove)\\>" path) + (search-input-file inputs path)) + (("/include/linux/capability.h" path) + (search-input-file inputs path)))) + '("common/Make-po.rules" + "common/Make.rules" + "binutils/Makefile" + "parser/Makefile" + "parser/tst/Makefile" + "profiles/Makefile" + "utils/Makefile" + "utils/python-tools-setup.py" + "utils/vim/Makefile")))) + (add-after 'fix-paths 'change-directory + (lambda _ + (chdir "libraries/libapparmor")))))) + (native-inputs + (list autoconf + automake + bison + dejagnu + flex + libtool + perl + python-minimal + ruby + swig + which)) + (home-page "https://apparmor.net") + (synopsis "Linux kernel security module") + (description + "AppArmor is an effective and easy-to-use Linux application security +system. + +AppArmor proactively protects the operating system and applications from +external or internal threats, even zero-day attacks, by enforcing good +behavior and preventing both known and unknown application flaws from being +exploited. + +AppArmor supplements the traditional Unix discretionary access control (DAC) +model by providing mandatory access control (MAC). It has been included in +the mainline Linux kernel since version 2.6.36 and its development has been +supported by Canonical since 2009.") + (license license:lgpl2.1))) -- cgit 1.4.1 From b2a848d23d37f31496e1ff664f1dcf6abcdcc388 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Thu, 1 Dec 2022 13:20:51 +0000 Subject: tests: Add gdm tests. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/tests/gdm.scm: New file. * gnu/local.mk: Register it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/tests/gdm.scm | 127 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 gnu/tests/gdm.scm (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 2d3329712b..3329801fa6 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -760,6 +760,7 @@ GNU_SYSTEM_MODULES = \ %D%/tests/docker.scm \ %D%/tests/file-sharing.scm \ %D%/tests/ganeti.scm \ + %D%/tests/gdm.scm \ %D%/tests/guix.scm \ %D%/tests/monitoring.scm \ %D%/tests/nfs.scm \ diff --git a/gnu/tests/gdm.scm b/gnu/tests/gdm.scm new file mode 100644 index 0000000000..70a86b9065 --- /dev/null +++ b/gnu/tests/gdm.scm @@ -0,0 +1,127 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2022 Bruno Victal . +;;; +;;; 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 tests gdm) + #:use-module (gnu tests) + #:use-module (gnu packages freedesktop) + #:use-module (gnu services) + #:use-module (gnu services desktop) + #:use-module (gnu services xorg) + #:use-module (gnu system) + #:use-module (gnu system file-systems) + #:use-module (gnu system vm) + #:use-module (guix gexp) + #:use-module (ice-9 format) + #:export (%test-gdm-x11 + %test-gdm-wayland + %test-gdm-wayland-tmpfs)) + +(define* (make-os #:key wayland? tmp-tmpfs?) + (operating-system + (inherit %simple-os) + (services + (modify-services %desktop-services + (gdm-service-type config => (gdm-configuration + (inherit config) + (wayland? wayland?))))) + (file-systems (if tmp-tmpfs? (cons (file-system + (mount-point "/tmp") + (device "none") + (type "tmpfs") + (flags '(no-dev no-suid)) + (check? #f)) + %base-file-systems) + %base-file-systems)))) + +(define* (run-gdm-test #:key wayland? tmp-tmpfs?) + "Run tests in a vm which has gdm running." + (define os + (marionette-operating-system + (make-os #:wayland? wayland? #:tmp-tmpfs? tmp-tmpfs?) + #:imported-modules '((gnu services herd)))) + + (define vm + (virtual-machine + (operating-system os) + (memory-size 1024))) + + (define name (format #f "gdm-~:[x11~;wayland~]~:[~;-tmpfs~]" wayland? tmp-tmpfs?)) + + (define test + (with-imported-modules '((gnu build marionette)) + #~(begin + (use-modules (gnu build marionette) + (ice-9 format) + (srfi srfi-64)) + + (let* ((marionette (make-marionette (list #$vm))) + (expected-session-type #$(if wayland? "wayland" "x11"))) + + (test-runner-current (system-test-runner #$output)) + (test-begin #$name) + + ;; service for gdm is called xorg-server + (test-assert "service is running" + (marionette-eval + '(begin + (use-modules (gnu services herd)) + (start-service 'xorg-server)) + marionette)) + + (test-assert "gdm ready" + (wait-for-file "/var/run/gdm/gdm.pid" marionette)) + + (test-equal (string-append "session-type is " expected-session-type) + expected-session-type + (marionette-eval + '(begin + (use-modules (ice-9 popen) + (ice-9 rdelim)) + + (let* ((loginctl #$(file-append elogind "/bin/loginctl")) + (get-session-cmd (string-join `(,loginctl "show-user" "gdm" + "--property Display" "--value"))) + (session (call-with-port (open-input-pipe get-session-cmd) read-line)) + (get-type-cmd (string-join `(,loginctl "show-session" ,session + "--property Type" "--value"))) + (type (call-with-port (open-input-pipe get-type-cmd) read-line))) + type)) + marionette)) + + (test-end))))) + + (gexp->derivation (string-append name "-test") test)) + +(define %test-gdm-x11 + (system-test + (name "gdm-x11") + (description "Basic tests for the GDM service. (X11)") + (value (run-gdm-test)))) + +(define %test-gdm-wayland + (system-test + (name "gdm-wayland") + (description "Basic tests for the GDM service. (Wayland)") + (value (run-gdm-test #:wayland? #t)))) + +(define %test-gdm-wayland-tmpfs + (system-test + ;; See . + (name "gdm-wayland-tmpfs") + (description "Basic tests for the GDM service. (Wayland, /tmp as tmpfs)") + (value (run-gdm-test #:wayland? #t #:tmp-tmpfs? #t)))) -- cgit 1.4.1 From 02d591206259b30462764cb2f978ae214dea0449 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 8 Dec 2022 12:06:47 +0200 Subject: gnu: julia: Update to 1.8.3. * gnu/packages/julia.scm (julia): Update to 1.8.3. [source]: Remove one patch. [arguments]: Adjust 'prepare-deps phase to changes in inputs. Remove custom 'use-system-libwhich, 'change-number-of-precompiled-statements, 'symlink-libraries phases. In 'fix-include-and-link-paths phase remove substitution for utf8proc linking and adjust libuv linking. Fix reference to shell in 'replace-default-shell phase. Adjust the 'shared-objects-path phase to changes in the source. Change the 'enable-parallel-tests phase for upstream changes. Adjust the 'adjust-test-suite phase to be more robust. Change the 'disable-broken-tests phase to help the test suite pass. Rename 'symlink-llvm-utf8proc phase to 'symlink-missing-libraries and add two more. Adjust make-flags for changes in shared system libraries. Reorder make-flags to changes in the source. Except for aarch64, use the defaults for choosing to use 64-bit blas. [inputs]: Add libblastrampoline. Replace libgit-1.1 with libgit-1.3, utf8proc-2.7.1 with utf8proc-2.8.0. [native-inputs]: Replace python-2 with python. (libunwind-julia): Update to 1.5.0. [source]: Update patches. * gnu/packages/libevent.scm (libuv-julia): Update to 2.0.0-4.e6f0e49. [arguments]: Also build static library, build position-independent-code. * gnu/packages/llvm.scm (llvm-julia): Update to llvm-13, following upstream's build instructions. * gnu/packages/maths.scm (openlibm): Update to 0.8.1. * gnu/packages/textutils.scm (utf8proc-2.7.1): Update and rename to utf8proc-2.8.0. [native-inputs]: Update unicode to 14.0.0. * gnu/packages/tls.scm (mbedtls-apache): Update to 2.28.0. [source]: Remove snippet. [arguments]: Remove trailing #t from phases. * gnu/packages/patches/julia-allow-parallel-build.patch, (julia-patch): Update version string to 1.8.2. gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: Remove files. * gnu/local.mk (dist_patch_DATA): Remove them. Co-authored-by: Akira Kyle --- gnu/local.mk | 2 - gnu/packages/julia.scm | 246 ++++++++++----------- gnu/packages/libevent.scm | 11 +- gnu/packages/llvm.scm | 133 ++--------- gnu/packages/maths.scm | 4 +- .../patches/julia-SOURCE_DATE_EPOCH-mtime.patch | 5 +- .../patches/julia-allow-parallel-build.patch | 32 --- .../libunwind-julia-fix-GCC10-fno-common.patch | 40 ---- gnu/packages/textutils.scm | 10 +- gnu/packages/tls.scm | 38 ++-- 10 files changed, 166 insertions(+), 355 deletions(-) delete mode 100644 gnu/packages/patches/julia-allow-parallel-build.patch delete mode 100644 gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 3329801fa6..af570125bd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1377,7 +1377,6 @@ dist_patch_DATA = \ %D%/packages/patches/jsoncpp-pkg-config-version.patch \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ %D%/packages/patches/julia-tracker-16-compat.patch \ - %D%/packages/patches/julia-allow-parallel-build.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ %D%/packages/patches/libobjc2-unbundle-robin-map.patch \ @@ -1467,7 +1466,6 @@ dist_patch_DATA = \ %D%/packages/patches/libtirpc-hurd.patch \ %D%/packages/patches/libtommath-fix-linkage.patch \ %D%/packages/patches/libtool-skip-tests2.patch \ - %D%/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch \ %D%/packages/patches/libusb-0.1-disable-tests.patch \ %D%/packages/patches/libusb-for-axoloti.patch \ %D%/packages/patches/libutils-add-includes.patch \ diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 75a38c016e..d35901eadb 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2021, 2022 Jean-Baptiste Volatier ;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2022 Akira Kyle ;;; ;;; This file is part of GNU Guix. ;;; @@ -61,7 +62,7 @@ (package (inherit libunwind) (name "libunwind-julia") - (version "1.3.1") + (version "1.5.0") (source (origin (method url-fetch) @@ -69,31 +70,27 @@ version ".tar.gz")) (sha256 (base32 - "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3")) + "05qhzcg1xag3l5m3c805np6k342gc0f3g087b7g16jidv59pccwh")) (patches - (append - ;; Fix linker issue for i686-linux because GCC10 changed default - ;; (see '-fno-common' option). - (search-patches "libunwind-julia-fix-GCC10-fno-common.patch") - (list - (julia-patch "libunwind-prefer-extbl" - "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1") - (julia-patch "libunwind-static-arm" - "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") - (julia-patch "libunwind-cfa-rsp" - "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z")))))) + (list + (julia-patch "libunwind-prefer-extbl" + "0pf3lsq6zxlmqn86lk4fcj1xwdan9gbxyabrwgxcb59p8jjwsl8r") + (julia-patch "libunwind-static-arm" + "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") + (julia-patch "libunwind-cfa-rsp" + "0qs5b1h5lsr5qakkv6sddgy5ghlxpjrn2jiqcvg7bkczy24klr6j"))))) (arguments (substitute-keyword-arguments (package-arguments libunwind) ;; Skip tests on this older and patched version of libunwind. ((#:tests? _ #t) #f))) - (home-page "https://github.com/JuliaLang/tree/master/deps/"))) + (home-page "https://github.com/JuliaLang/julia/tree/master/deps/"))) (define (julia-patch-url version name) (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version "/deps/patches/" name ".patch")) (define-public (julia-patch name sha) - (let ((version "1.6.1")) + (let ((version "1.8.2")) (origin (method url-fetch) (uri (julia-patch-url version name)) (sha256 (base32 sha)) @@ -143,7 +140,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (define-public julia (package (name "julia") - (version "1.6.7") + (version "1.8.3") (source (origin (method url-fetch) (uri (string-append @@ -151,10 +148,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") version "/julia-" version ".tar.gz")) (sha256 (base32 - "0q9xgdpvdkskpzl294w215f6c15c5jk276c9dah5f5w4np3ivbvl")) - (patches - (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch" - "julia-allow-parallel-build.patch")))) + "0jf8dr5j7y8cjnr65kn38xps5h9m2qvi8g1yd8qgiip5r87ld3ad")) + (patches (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -188,7 +183,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") '("curl" "dsfmt" "gmp" "lapack" "libssh2" "libnghttp2" "libgit2" - "mbedtls" "mpfr" + "libblastrampoline" + "mbedtls-apache" "mpfr" "openblas" "openlibm" "pcre2" "suitesparse" "gfortran:lib")) ":")))) @@ -202,25 +198,10 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (string-append line "\n")) (("src ui doc deps") "src ui deps")))) - (add-after 'unpack 'use-system-libwhich - (lambda* (#:key inputs #:allow-other-keys) - ;; don't build it - (substitute* "deps/Makefile" - (("DEP_LIBS \\+= libwhich") "")) - ;; call our version - (substitute* "base/Makefile" - (("\\$\\$\\(build_depsbindir\\)/libwhich") - (search-input-file inputs "/bin/libwhich"))))) (add-after 'unpack 'activate-gnu-source-for-loader (lambda _ (substitute* "cli/Makefile" (("LOADER_CFLAGS =") "LOADER_CFLAGS = -D_GNU_SOURCE")))) - (add-after 'unpack 'change-number-of-precompile-statements - (lambda _ - ;; Remove nss-certs drops the number of statements below 1200, - ;; causing the build to fail prematurely. - (substitute* "contrib/generate_precompile.jl" - (("1200") "1100")))) ;; libquadmath is not available on all architectures. ;; https://github.com/JuliaLang/julia/issues/41613 (add-after 'unpack 'make-libquadmath-optional @@ -232,30 +213,16 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (lambda _ (setenv "HOME" "/tmp"))) (add-before 'build 'fix-include-and-link-paths (lambda* (#:key inputs #:allow-other-keys) - ;; LIBUTF8PROC is a linker flag, not a build target. It is - ;; included in the LIBFILES_* variable which is used as a - ;; collection of build targets and a list of libraries to link - ;; against. - (substitute* "src/flisp/Makefile" - (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)") - "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)") - (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)") - "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)")) - ;; The REPL must be linked with libuv. (substitute* "cli/Makefile" (("JLDFLAGS \\+= ") (string-append "JLDFLAGS += " - (assoc-ref %build-inputs "libuv") - "/lib/libuv.so "))) - - (substitute* "base/Makefile" - (("\\$\\(build_includedir\\)/uv/errno.h") - (search-input-file inputs "/include/uv/errno.h"))))) + (assoc-ref inputs "libuv") + "/lib/libuv.so "))))) (add-before 'build 'replace-default-shell - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (substitute* "base/client.jl" - (("/bin/sh") (which "sh"))))) + (("/bin/sh") (search-input-file inputs "/bin/sh"))))) (add-before 'build 'shared-objects-paths (lambda* (#:key inputs #:allow-other-keys) (let ((jlpath @@ -268,8 +235,12 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (to (lambda* (pkg libname #:optional libname_jl) (string-append - "const " (or libname_jl libname) "= \"" + "const " (or libname_jl libname) " = \"" (assoc-ref inputs pkg) "/lib/" libname ".so")))) + (substitute* (jlpath "CompilerSupportLibraries") + (((from "libgfortran")) + (string-append "const libgfortran = string(\"" + (search-input-file inputs "/lib/libgfortran.so")))) (substitute* (jlpath "dSFMT") (((from "libdSFMT")) (to "dsfmt" "libdSFMT"))) (substitute* (jlpath "GMP") @@ -290,11 +261,9 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* (jlpath "MPFR") (((from "libmpfr")) (to "mpfr" "libmpfr"))) (substitute* (jlpath "MbedTLS") - ;; For the newer version of mbedtls-apache: - (("libmbedcrypto.so.5") "libmbedcrypto.so.6") - (((from "libmbedcrypto")) (to "mbedtls" "libmbedcrypto")) - (((from "libmbedtls")) (to "mbedtls" "libmbedtls")) - (((from "libmbedx509")) (to "mbedtls" "libmbedx509"))) + (((from "libmbedcrypto")) (to "mbedtls-apache" "libmbedcrypto")) + (((from "libmbedtls")) (to "mbedtls-apache" "libmbedtls")) + (((from "libmbedx509")) (to "mbedtls-apache" "libmbedx509"))) (substitute* (jlpath "nghttp2") (((from "libnghttp2")) (to "libnghttp2" "libnghttp2"))) (substitute* (jlpath "OpenBLAS") @@ -302,7 +271,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* (jlpath "OpenLibm") (((from "libopenlibm")) (to "openlibm" "libopenlibm"))) (substitute* (jlpath "PCRE2") - (((from "libpcre2")) (to "pcre2" "libpcre2" "libpcre2_8"))) + (((from "libpcre2_8")) (to "pcre2" "libpcre2-8" "libpcre2_8"))) (substitute* (jlpath "SuiteSparse") (((from "libamd")) (to "suitesparse" "libamd")) (((from "libbtf")) (to "suitesparse" "libbtf")) @@ -319,40 +288,36 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (to "suitesparse" "libsuitesparseconfig")) (((from "libumfpack")) (to "suitesparse" "libumfpack"))) (substitute* (jlpath "Zlib") - (((from "libz")) (to "zlib" "libz")))))) + (((from "libz")) (to "zlib" "libz"))) + (substitute* (jlpath "libblastrampoline") + (("libblastrampoline\\.so") + (search-input-file inputs "/lib/libblastrampoline.so")))))) (add-after 'unpack 'enable-parallel-tests (lambda* (#:key parallel-tests? #:allow-other-keys) - (setenv "JULIA_CPU_THREADS" (if parallel-tests? - (number->string (parallel-job-count)) - "1")) - (format #t "JULIA_CPU_THREADS environment variable set to ~a~%" - (getenv "JULIA_CPU_THREADS")))) + (when parallel-tests? + (setenv "JULIA_TEST_USE_MULTIPLE_WORKERS" "true")))) (add-after 'unpack 'adjust-test-suite (lambda* (#:key inputs #:allow-other-keys) - (let ((pcre2 (assoc-ref inputs "pcre2")) - (mbedtls-apache (assoc-ref inputs "mbedtls")) - (mpfr (assoc-ref inputs "mpfr")) - (gmp (assoc-ref inputs "gmp")) - (nghttp2 (assoc-ref inputs "libnghttp2")) - (zlib (assoc-ref inputs "zlib")) - (suitesparse (assoc-ref inputs "suitesparse"))) - ;; Some tests only check to see if the input is the correct version. - (substitute* "stdlib/PCRE2_jll/test/runtests.jl" - (("10.40.0") ,(package-version pcre2))) - (substitute* "stdlib/MbedTLS_jll/test/runtests.jl" - (("2.24.0") ,(package-version mbedtls-apache))) - (substitute* "stdlib/MPFR_jll/test/runtests.jl" - (("4.1.0") ,(package-version mpfr))) - (substitute* "stdlib/GMP_jll/test/runtests.jl" - (("6.2.0") ,(package-version gmp))) - (substitute* "stdlib/nghttp2_jll/test/runtests.jl" - (("1.41.0") ,(package-version nghttp2))) - (substitute* "stdlib/Zlib_jll/test/runtests.jl" - (("1.2.12") ,(package-version zlib))) - (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl" - (("5004") ,(string-replace-substring - (version-major+minor - (package-version suitesparse)) "." "0")))))) + (substitute* "test/spawn.jl" + (("shcmd = `sh`") (string-append "shcmd = `" (which "sh") "`"))) + ;; Some tests only check to see if the input is the correct version. + (substitute* "stdlib/PCRE2_jll/test/runtests.jl" + (("10.40.0") ,(package-version (this-package-input "pcre2")))) + (substitute* "stdlib/MbedTLS_jll/test/runtests.jl" + (("2.28.0") ,(package-version (this-package-input "mbedtls-apache")))) + (substitute* "stdlib/MPFR_jll/test/runtests.jl" + (("4.1.0") ,(package-version (this-package-input "mpfr")))) + (substitute* "stdlib/GMP_jll/test/runtests.jl" + (("6.2.1") ,(package-version (this-package-input "gmp")))) + (substitute* "stdlib/nghttp2_jll/test/runtests.jl" + (("1.48.0") ,(package-version (this-package-input "libnghttp2")))) + (substitute* "stdlib/Zlib_jll/test/runtests.jl" + (("1.2.12") ,(package-version (this-package-input "zlib")))) + (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl" + (("5010") ,(string-replace-substring + (version-major+minor + (package-version + (this-package-input "suitesparse"))) "." "0"))))) (add-before 'check 'disable-broken-tests (lambda _ ;; disabling REPL tests because they require a stdin @@ -360,6 +325,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ;; https://github.com/JuliaLang/julia/pull/41614 ;; https://github.com/JuliaLang/julia/issues/41156 (substitute* "test/choosetests.jl" + (("\"cmdlineargs\",") "") (("\"precompile\",") "")) ;; Dates/io tests fail on master when networking is unavailable ;; https://github.com/JuliaLang/julia/issues/34655 @@ -371,7 +337,7 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) (("@test isfile\\(MozillaCACerts_jll.cacert\\)") "@test_broken isfile(MozillaCACerts_jll.cacert)")) ;; since certificate is not present some tests are failing in network option - (substitute* "usr/share/julia/stdlib/v1.6/NetworkOptions/test/runtests.jl" + (substitute* "usr/share/julia/stdlib/v1.8/NetworkOptions/test/runtests.jl" (("@test isfile\\(bundled_ca_roots\\(\\)\\)") "@test_broken isfile(bundled_ca_roots())") (("@test ispath\\(ca_roots_path\\(\\)\\)") @@ -390,29 +356,35 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ;; @test_broken cannot be used because if the test randomly ;; passes, then it also raises an error. (("@test isinf\\(log1p\\(-one\\(T\\)\\)\\)") - " ")))) - (add-before 'install 'symlink-libraries - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((link - (lambda (pkgname dir pred) - (map (lambda (file) - (unless (file-exists? - (string-append dir (basename file))) - (symlink file (string-append dir (basename file))))) - (find-files (string-append (assoc-ref inputs pkgname) - "/lib") pred))))) - (link "curl" "usr/lib/" "\\.so") ; missing libpthreads libLLVM-11jl - (link "suitesparse" "usr/lib/julia/" "libbtf\\.so") - (link "suitesparse" "usr/lib/julia/" "libklu\\.so") - (link "suitesparse" "usr/lib/julia/" "libldl\\.so") - (link "suitesparse" "usr/lib/julia/" "librbio\\.so") - (link "gmp" "usr/lib/julia/" "libgmpxx\\.so") - (link "libuv" "usr/lib/julia/" "libuv\\.so") - (link "zlib" "usr/lib/julia/" "libz\\.so") - (link "libunwind" "usr/lib/julia/" "libunwind\\.so") - (symlink (string-append (assoc-ref inputs "p7zip") "/bin/7z") - "usr/libexec/7z")))) - (add-after 'install 'symlink-llvm-utf8proc + " ")) + + ;; These are new test failures for 1.8: + ;; This test passes on some architectures and fails on others. + (substitute* "stdlib/LinearAlgebra/test/lu.jl" + (("@test String") "@test_skip String")) + + (substitute* "stdlib/InteractiveUtils/test/runtests.jl" + (("@test !occursin\\(\"Environment") + "@test_broken !occursin(\"Environment") + (("@test occursin\\(\"Environment") + "@test_broken occursin(\"Environment")) + (substitute* "usr/share/julia/stdlib/v1.8/Statistics/test/runtests.jl" + (("@test cov\\(A") "@test_skip cov(A") + (("@test isfinite") "@test_skip isfinite")) + ;; LoadError: SuiteSparse threads test failed with nthreads == 4 + (substitute* "usr/share/julia/stdlib/v1.8/SuiteSparse/test/runtests.jl" + (("Base\\.USE_GPL_LIBS") "false")) + ;; Got exception outside of a @test + ;; LinearAlgebra.LAPACKException(16) + ;; eliminate all the test bits. + (substitute* "stdlib/LinearAlgebra/test/schur.jl" + (("f = schur\\(A, B\\)") "f = schur(A, A)") + (("@test f\\.Q\\*f\\.S\\*f\\.Z'.*") "\n") + (("@test f\\.Q\\*f\\.T\\*f\\.Z'.*") "\n")) + (substitute* "test/threads.jl" + (("@test success") "@test_broken success")))) + ;; Doesn't this just mean they weren't linked correctly? + (add-after 'install 'symlink-missing-libraries (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (link @@ -425,8 +397,10 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) (basename file))))) (find-files (string-append (assoc-ref inputs pkgname) "/lib") pred))))) - (link "llvm" "libLLVM-11jl\\.so") - (link "utf8proc" "libutf8proc\\.so")))) + (link "libunwind" "libunwind\\.so") + (link "llvm" "libLLVM-13jl\\.so") + (link "utf8proc" "libutf8proc\\.so") + (link "zlib" "libz\\.so")))) (add-after 'install 'make-wrapper (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -462,18 +436,19 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) "CONFIG_SHELL=bash -x" ; needed to build bundled libraries "USE_BINARYBUILDER=0" ;; list (and order!) of "USE_SYSTEM_*" is here: - ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc + ;; https://github.com/JuliaLang/julia/blob/v1.8.2/Make.inc "USE_SYSTEM_CSL=1" "USE_SYSTEM_LLVM=1" "USE_SYSTEM_LIBUNWIND=1" "USE_SYSTEM_PCRE=1" "USE_SYSTEM_OPENLIBM=1" "USE_SYSTEM_DSFMT=1" + "USE_SYSTEM_LIBBLASTRAMPOLINE=1" "USE_SYSTEM_BLAS=1" "USE_SYSTEM_LAPACK=1" "USE_SYSTEM_GMP=1" "USE_SYSTEM_MPFR=1" - "USE_SYSTEM_SUITESPARSE=1" + "USE_SYSTEM_LIBSUITESPARSE=1" "USE_SYSTEM_LIBUV=1" "USE_SYSTEM_UTF8PROC=1" "USE_SYSTEM_MBEDTLS=1" @@ -482,27 +457,29 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) "USE_SYSTEM_CURL=1" "USE_SYSTEM_LIBGIT2=1" "USE_SYSTEM_PATCHELF=1" + "USE_SYSTEM_LIBWHICH=1" "USE_SYSTEM_ZLIB=1" "USE_SYSTEM_P7ZIP=1" + "USE_LLVM_SHLIB=1" + "NO_GIT=1" ; build from release tarball. - "USE_BLAS64=0" ; needed when USE_SYSTEM_BLAS=1 + "USE_GPL_LIBS=1" ; proudly + + ,@(if (target-aarch64?) + `("USE_BLAS64=0") + '()) + "LIBBLAS=-lopenblas" "LIBBLASNAME=libopenblas" - (string-append "SUITESPARSE_INC=-I " - (assoc-ref %build-inputs "suitesparse") - "/include") - "USE_GPL_LIBS=1" ; proudly (string-append "UTF8PROC_INC=" (assoc-ref %build-inputs "utf8proc") "/include") - "LLVM_VER=11.0.0" - - "USE_LLVM_SHLIB=1" + ;; Make.inc expects a static library for libuv. (string-append "LIBUV=" (assoc-ref %build-inputs "libuv") - "/lib/libuv.so") + "/lib/libuv.a") (string-append "LIBUV_INC=" (assoc-ref %build-inputs "libuv") "/include")))) @@ -514,20 +491,21 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ("gfortran:lib" ,gfortran "lib") ("gmp" ,gmp) ("lapack" ,lapack) - ("libgit2" ,libgit2-1.1) + ("libblastrampoline" ,libblastrampoline) + ("libgit2" ,libgit2-1.3) ("libnghttp2" ,nghttp2 "lib") ("libssh2" ,libssh2) ("libunwind" ,libunwind-julia) ("libuv" ,libuv-julia) ("llvm" ,llvm-julia) - ("mbedtls" ,mbedtls-apache) + ("mbedtls-apache" ,mbedtls-apache) ("mpfr" ,mpfr) ("openblas" ,openblas) ("openlibm" ,openlibm) ("p7zip" ,p7zip) ("pcre2" ,pcre2) ("suitesparse" ,suitesparse) - ("utf8proc" ,utf8proc-2.6.1) + ("utf8proc" ,utf8proc-2.7.0) ("wget" ,wget) ("which" ,which) ("zlib" ,zlib) @@ -540,7 +518,7 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ("perl" ,perl) ("patchelf" ,patchelf) ("pkg-config" ,pkg-config) - ("python" ,python-2))) + ("python" ,python))) (native-search-paths (list (search-path-specification (variable "JULIA_LOAD_PATH") @@ -548,8 +526,8 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) (search-path-specification (variable "JULIA_DEPOT_PATH") (files (list "share/julia/"))))) - ;; Julia is not officially released for ARM and MIPS. - ;; See https://github.com/JuliaLang/julia/issues/10639 + ;; Julia only officially supports some of our platforms: + ;; https://julialang.org/downloads/#supported_platforms (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux")) (home-page "https://julialang.org/") (synopsis "High-performance dynamic language for technical computing") diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index 176e66cf42..f9722e4469 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -158,10 +158,10 @@ resolution, asynchronous file system operations, and threading primitives.") (properties '((hidden? . #t))))) (define-public libuv-julia - (let ((commit "fb3e3364c33ae48c827f6b103e05c3f0e78b79a9") - (revision "3")) + (let ((commit "e6f0e4900e195c8352f821abe2b3cffc3089547b") + (revision "4")) ;; When upgrading Julia, also upgrade this. Get the commit from - ;; https://github.com/JuliaLang/julia/blob/v1.6.1/deps/libuv.version + ;; https://github.com/JuliaLang/julia/blob/v1.8.2/deps/libuv.version (package (inherit libuv) (name "libuv-julia") @@ -174,7 +174,10 @@ resolution, asynchronous file system operations, and threading primitives.") (file-name (git-file-name name version)) (sha256 (base32 - "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr")))) + "0ib2cprvbyviwrzm0fw6dqvlbm9akf2kj3vjzp82q3gii74cv3c9")))) + (arguments + '(#:configure-flags '("--with-pic") + #:tests? #f)) (home-page "https://github.com/JuliaLang/libuv") (properties '((hidden? . #t)))))) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 9ffdf8761b..7de7177b77 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -62,7 +62,6 @@ #:use-module (gnu packages bootstrap) ;glibc-dynamic-linker #:use-module (gnu packages check) ;python-lit #:use-module (gnu packages compression) - #:use-module (gnu packages julia) ;julia-patch #:use-module (gnu packages libedit) #:use-module (gnu packages libffi) #:use-module (gnu packages lua) @@ -2100,126 +2099,20 @@ LLVM.")))) (define-public llvm-julia (package - (inherit llvm-11) - (name "llvm-julia") - (properties `((hidden? . #t) - ,@(package-properties llvm-11))) - (source (origin - (inherit (package-source llvm-11)) - ;; Those patches are inside the Julia source repo. - ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm) - ;; but they are required to build Julia. - ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628 - (patches - (map (match-lambda - ((name hash) - (julia-patch name hash))) - (list - '("llvm-D27629-AArch64-large_model_6.0.1" - "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") - '("llvm8-D34078-vectorize-fdiv" - "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602") - '("llvm-7.0-D44650" - "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir") - '("llvm7-symver-jlprefix" - "00ng32x6xhm9czczirn5r1q1mc1myad44fqhi061hwh1vb46dwgm") - '("llvm-6.0-DISABLE_ABI_CHECKS" - "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") - '("llvm9-D50010-VNCoercion-ni" - "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx") - '("llvm7-revert-D44485" - "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n") - '("llvm-11-D75072-SCEV-add-type" - "176xi1lnbnv2rcs05ywhyb7pd0xgmibayvwzksksg44wg2dh8mbx") - '("llvm-julia-tsan-custom-as" - "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s") - '("llvm-D80101" - "1gsdwmgmpbignvqyxcnlprj899259p3dvdznlncd84ss445qgq3j") - '("llvm-D84031" - "0nks9sbk7p0r5gyr0idrmm93a5fmdai8kihz9532dx4zhcvvqbjc") - '("llvm-10-D85553" - "1zjq7j9q2qp56hwkc8yc8f0z7kvam3j7hj8sb7qyd77r255ff78l") - '("llvm-10-unique_function_clang-sa" - "1jys9w2zqk3dasnxqh0qz5ij7rxi6mkgq9pqjsclmamr5169zyan") - ;'("llvm-D88630-clang-cmake" - ; "0rs6s71nqnjkny7i69gqazhqj5jqfdr0bkxs2v5a55sfx8fa1k54") - '("llvm-11-D85313-debuginfo-empty-arange" - "1f672d5385xpgb8yrim8d3b7wg2z1l81agnshm1q61kdvjixqx32") - '("llvm-11-D90722-rtdyld-absolute-relocs" - "0kmnai229yyxkmpk9lxd180mcnhk2i8d87k2sg89gc8as18w10r6") - '("llvm-invalid-addrspacecast-sink" - "1n1b7j4s80vj7x5377aj9vyphmxx1q6bm0chhkxp6zsy3mx3g2ry") - '("llvm-11-D92906-ppc-setjmp" - "0cmd4dsblp7a8m03j16dqxws0ijh55zf4jzzxmj341qxa1gamdp9") - '("llvm-11-PR48458-X86ISelDAGToDAG" - "0vwzvlhsdazhxg4gj8g2f00a4f8qc5cgac23w575xk3pgba1jh6y") - '("llvm-11-D93092-ppc-knownbits" - "1748bypsc7c9lbs3fnkv0kwvch6bn85kj98j4jdaz254ig0wa6xj") - '("llvm-11-D93154-globalisel-as" - "1k5wd4z3pa7zj0gyjkif7viqj906dhqlbb7dc95gig40nbxv6zpj") - '("llvm-11-ppc-half-ctr" - "0piywisfz6cmw3133kz7vzhiqflq2y7igakqxlym0gi8pqylv7w9") - '("llvm-11-ppc-sp-from-bp" - "1wmg3485cx5f9pbykyl3jibk1wwv4w1x30hl4jyfndzr2yh8azf9") - '("llvm-rGb498303066a6-gcc11-header-fix" - "0hkd4rwhvh8g2yh13g29wiwnjpv2yd1hdyiv1ryw8izl25bz9c67") - '("llvm-11-D94813-mergeicmps" - "0cmy0ywkgyrdcvr9bd6pd912lyd4gcsrib4z0v05dwgcdxhk7y29") - '("llvm-11-D94980-CTR-half" - "1yf8cxib3z8hz7zi9n6v2g2c6vpfr4slq9hpx8m8yq8f1jbyw3fw") - '("llvm-11-D94058-sext-atomic-ops" - "1x6p6k6q651z5jcqxx8vj17cxnv196mka7mwn7dpp6c23lwgfdpb") - '("llvm-11-D96283-dagcombine-half" - "0lv4iq2f8qrcz1xyxfic3bcr5p0aqam3a7c6pp6fnw3riixm096k")))) - (patch-flags '("-p1")))) + (inherit llvm-13) (arguments - (substitute-keyword-arguments (package-arguments llvm-11) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'patch-round-two - ;; We have to do the patching in two rounds because we can't - ;; pass '-p1' and '-p2' in the source field. - (lambda* (#:key inputs #:allow-other-keys) - (map (lambda (patchname) - (invoke "patch" patchname "-p2")) - (list "llvm-11-AArch64-FastIsel-bug" - "llvm-11-D97435-AArch64-movaddrreg" - "llvm-11-D97571-AArch64-loh" - "llvm-11-aarch64-addrspace")))))) - ((#:build-type _) "Release") - ((#:configure-flags flags) - `(list - ;; Build a native compiler and the NVPTX backend (NVIDIA) since - ;; Julia insists on it, nothing more. This reduces build times and - ;; disk usage. - ,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target)) - "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX" - - "-DLLVM_INSTALL_UTILS=ON" - "-DLLVM_BUILD_TESTS=ON" - "-DLLVM_ENABLE_FFI=ON" - "-DLLVM_ENABLE_RTTI=ON" - ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}" - ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" - ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" - "-DLLVM_ENABLE_DUMP=ON" - "-DLLVM_LINK_LLVM_DYLIB=ON" - "-DLLVM_VERSION_SUFFIX:STRING=jl")))) - (inputs - (append - (package-inputs llvm-11) - `(("llvm-11-AArch64-FastIsel-bug" - ,(julia-patch "llvm-11-AArch64-FastIsel-bug" - "1m2vddj1mw4kbij8hbrx82piyy6bvr2x7wwdnlxfaqcm72ipzyh9")) - ("llvm-11-D97435-AArch64-movaddrreg" - ,(julia-patch "llvm-11-D97435-AArch64-movaddrreg" - "10jnavq9ljkj7j2gqj2zd1pwqpqb5zs3zp9h96pmz0djbmxwa86y")) - ("llvm-11-D97571-AArch64-loh" - ,(julia-patch "llvm-11-D97571-AArch64-loh" - "128zcbg1w1j7hngsf7z1a7alc6lig6l2rqgjp6i8nk3k3f842v6n")) - ("llvm-11-aarch64-addrspace" - ,(julia-patch "llvm-11-aarch64-addrspace" - "0ckbzgfirxrf2d5bpinpngp7gnilbjrk0cbdfyl3h6f5v6i6xj6m"))))))) + (substitute-keyword-arguments (package-arguments llvm-13) + ((#:configure-flags flags ''()) + #~(cons* "-DLLVM_BUILD_LLVM_DYLIB=ON" + "-DLLVM_LINK_LLVM_DYLIB=ON" + ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX" + "-DLLVM_VERSION_SUFFIX:STRING=jl" ; Perhaps not needed. + #$(string-append "-DLLVM_TARGETS_TO_BUILD=" + (system->llvm-target)) + (delete "-DBUILD_SHARED_LIBS:BOOL=TRUE" #$flags))) + ((#:build-type _) "Release"))) + (properties `((hidden? . #t) + ,@(package-properties llvm-13))))) (define %cling-version "0.9") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e2236f0f70..27b8eaf60d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4853,7 +4853,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (define-public openlibm (package (name "openlibm") - (version "0.7.4") + (version "0.8.1") (source (origin (method git-fetch) @@ -4862,7 +4862,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i")))) + (base32 "1xsrcr49z0wdqpwd98jmw2xh18myzsa9xman0kp1h2i89x8mic5b")))) (build-system gnu-build-system) (arguments `(#:make-flags diff --git a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch index b60f284923..c6ca48fff0 100644 --- a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch +++ b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch @@ -8,15 +8,16 @@ Patch by Nicoló Balzarotti . --- a/base/loading.jl +++ b/base/loading.jl -@@ -807,7 +807,10 @@ - path = normpath(joinpath(dirname(prev), _path)) +@@ -1131,7 +1131,10 @@ function _include_dependency(mod::Module, _path::AbstractString) end if _track_dependencies[] + @lock require_lock begin - push!(_require_dependencies, (mod, path, mtime(path))) + push!(_require_dependencies, + (mod, path, + haskey(ENV, "SOURCE_DATE_EPOCH") ? + parse(Float64, ENV["SOURCE_DATE_EPOCH"]) : mtime(path))) + end end return path, prev end diff --git a/gnu/packages/patches/julia-allow-parallel-build.patch b/gnu/packages/patches/julia-allow-parallel-build.patch deleted file mode 100644 index cc1d42fee4..0000000000 --- a/gnu/packages/patches/julia-allow-parallel-build.patch +++ /dev/null @@ -1,32 +0,0 @@ -Allow parallel tests with isolated environment. - -See https://github.com/JuliaLang/julia/issues/43205 and -https://github.com/JuliaLang/julia/pull/43211. - -diff --git a/test/runtests.jl b/test/runtests.jl -index 2f9cd058bb..150395e78c 100644 ---- a/test/runtests.jl -+++ b/test/runtests.jl -@@ -4,7 +4,7 @@ using Test - using Distributed - using Dates - import REPL --using Printf: @sprintf -+using Printf: @sprintf, @printf - using Base: Experimental - - include("choosetests.jl") -@@ -83,11 +83,12 @@ prepend!(tests, linalg_tests) - import LinearAlgebra - cd(@__DIR__) do - n = 1 -- if net_on -+ if net_on || haskey(ENV, "JULIA_CPU_THREADS") - n = min(Sys.CPU_THREADS, length(tests)) - n > 1 && addprocs_with_testenv(n) - LinearAlgebra.BLAS.set_num_threads(1) - end -+ @printf("Number of threads: %i\n", n) - skipped = 0 - - @everywhere include("testdefs.jl") diff --git a/gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch b/gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch deleted file mode 100644 index 8ef4b111e4..0000000000 --- a/gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch +++ /dev/null @@ -1,40 +0,0 @@ -Fix compilation with -fno-common. - -Borrowed from upstream 29e17d8d2ccbca07c423e3089a6d5ae8a1c9cb6e. -Author: Yichao Yu -AuthorDate: Tue Mar 31 00:43:32 2020 -0400 -Commit: Dave Watson -CommitDate: Tue Mar 31 08:06:29 2020 -0700 - -diff --git a/src/x86/Ginit.c b/src/x86/Ginit.c -index f6b8dc2..9550efa 100644 ---- a/src/x86/Ginit.c -+++ b/src/x86/Ginit.c -@@ -54,13 +54,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) - - # endif /* UNW_LOCAL_ONLY */ - --HIDDEN unw_dyn_info_list_t _U_dyn_info_list; -- --/* XXX fix me: there is currently no way to locate the dyn-info list -- by a remote unwinder. On ia64, this is done via a special -- unwind-table entry. Perhaps something similar can be done with -- DWARF2 unwind info. */ -- - static void - put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) - { -@@ -71,7 +64,12 @@ static int - get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, - void *arg) - { -- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; -+#ifndef UNW_LOCAL_ONLY -+# pragma weak _U_dyn_info_list_addr -+ if (!_U_dyn_info_list_addr) -+ return -UNW_ENOINFO; -+#endif -+ *dyn_info_list_addr = _U_dyn_info_list_addr (); - return 0; - } - diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 2264e3ccb6..151add964e 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -210,11 +210,11 @@ normalization, case-folding, and other operations for data in the UTF-8 encoding, supporting Unicode version 9.0.0.") (license license:expat))) -(define-public utf8proc-2.6.1 +(define-public utf8proc-2.7.0 (package (inherit utf8proc) (name "utf8proc") - (version "2.6.1") + (version "2.7.0") (source (origin (method git-fetch) @@ -223,7 +223,7 @@ encoding, supporting Unicode version 9.0.0.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1zqc6airkzkssbjxanx5v8blfk90180gc9id0dx8ncs54f1ib8w7")))) + (base32 "1wrsmnaigal94gc3xbzdrrm080zjhihjfdla5admllq2w5dladjj")))) (arguments (substitute-keyword-arguments (package-arguments utf8proc) ((#:phases phases) @@ -239,14 +239,14 @@ encoding, supporting Unicode version 9.0.0.") (native-inputs (append (package-native-inputs utf8proc) - (let ((UNICODE_VERSION "13.0.0")) + (let ((UNICODE_VERSION "14.0.0")) `(("DerivedCoreProperties.txt" ,(origin (method url-fetch) (uri (string-append "https://www.unicode.org/Public/" UNICODE_VERSION "/ucd/DerivedCoreProperties.txt")) (sha256 - (base32 "0j12x112cd8fpgazkc8izxnhhpia44p1m36ff8yapslxndcmzm55")))) + (base32 "1g77s8g9443dd92f82pbkim7rk51s7xdwa3mxpzb1lcw8ryxvvg3")))) ;; For tests ("ruby" ,ruby))))))) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index f1e844b608..1f40537b6a 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -1002,25 +1002,16 @@ number generator") (name "mbedtls-apache") ;; XXX Check whether ‘-Wformat-signedness’ still breaks mbedtls-for-hiawatha ;; when updating. - (version "2.26.0") + (version "2.28.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ARMmbed/mbedtls") (commit (string-append "mbedtls-" version)))) - (sha256 - (base32 "0scwpmrgvg6q7rvqkc352d2fqlsx0aylcbyibcp1f1rsn8iiif2m")) (file-name (git-file-name name version)) - (modules '((guix build utils))) - (snippet - '(begin - ;; Can be removed with the next version. - ;; Reduce level of format truncation warnings due to false positives. - ;; https://github.com/ARMmbed/mbedtls/commit/2065a8d8af27c6cb1e40c9462b5933336dca7434 - (substitute* "CMakeLists.txt" - (("Wformat-truncation=2") "Wformat-truncation")) - #t)))) + (sha256 + (base32 "0s37dsi29v7146fi9k4frvx5rz2snxdm6c3rwq2fvnca2r80hfjl")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -1030,8 +1021,7 @@ number generator") (modify-phases %standard-phases (add-after 'unpack 'make-source-writable (lambda _ - (for-each make-file-writable (find-files ".")) - #t))))) + (for-each make-file-writable (find-files "."))))))) (native-inputs (list perl python)) (synopsis "Small TLS library") @@ -1048,6 +1038,26 @@ coding footprint.") (hidden-package (package (inherit mbedtls-apache) + (name "mbedtls-apache") + (version "2.26.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ARMmbed/mbedtls") + (commit (string-append "mbedtls-" version)))) + (sha256 + (base32 "0scwpmrgvg6q7rvqkc352d2fqlsx0aylcbyibcp1f1rsn8iiif2m")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(begin + ;; Can be removed with the next version. + ;; Reduce level of format truncation warnings due to false positives. + ;; https://github.com/ARMmbed/mbedtls/commit/2065a8d8af27c6cb1e40c9462b5933336dca7434 + (substitute* "CMakeLists.txt" + (("Wformat-truncation=2") "Wformat-truncation")) + #t)))) (arguments (substitute-keyword-arguments (package-arguments mbedtls-apache) ((#:phases phases) -- cgit 1.4.1 From 2d989ad59793e10c6fef94d9eaa51be91469318a Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 12 Oct 2022 16:49:17 +0530 Subject: gnu: python-seaborn: Update to 0.12.0. * gnu/packages/python-xyz.scm (python-seaborn): Update to 0.12.0. [source]: Remove patches. [arguments]: Import (ice-9 match) module. Remove patch-more-tests and start-xserver phases. Replace build and install phases. Fix pytest command in check phase. [native-inputs]: Add python-flit-core and python-pypa-build. Remove xorg-server-for-tests. * gnu/packages/patches/python-seaborn-2690.patch, gnu/packages/patches/python-seaborn-kde-test.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Unregister them. --- gnu/local.mk | 2 - gnu/packages/patches/python-seaborn-2690.patch | 268 --------------------- gnu/packages/patches/python-seaborn-kde-test.patch | 36 --- gnu/packages/python-xyz.scm | 51 ++-- 4 files changed, 24 insertions(+), 333 deletions(-) delete mode 100644 gnu/packages/patches/python-seaborn-2690.patch delete mode 100644 gnu/packages/patches/python-seaborn-kde-test.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index af570125bd..6e12f9cdb1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1759,8 +1759,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-robotframework-atest.patch \ %D%/packages/patches/python-robotframework-source-date-epoch.patch \ %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \ - %D%/packages/patches/python-seaborn-kde-test.patch \ - %D%/packages/patches/python-seaborn-2690.patch \ %D%/packages/patches/python-unittest2-python3-compat.patch \ %D%/packages/patches/python-unittest2-remove-argparse.patch \ %D%/packages/patches/python-versioneer-guix-support.patch \ diff --git a/gnu/packages/patches/python-seaborn-2690.patch b/gnu/packages/patches/python-seaborn-2690.patch deleted file mode 100644 index 4662d19c2d..0000000000 --- a/gnu/packages/patches/python-seaborn-2690.patch +++ /dev/null @@ -1,268 +0,0 @@ -This patch was adapted from the upstream pull request 2690. - -From ebd6812d48f5b8ed1ebb7d79bda0b2a7b9ae2812 Mon Sep 17 00:00:00 2001 -From: Michael Waskom -Date: Sun, 31 Oct 2021 15:09:27 -0400 -Subject: [PATCH 1/4] Update boxplot tests for mpl3.5 compatability - ---- - seaborn/tests/test_categorical.py | 30 +++++++++++++++++++----------- - 1 file changed, 19 insertions(+), 11 deletions(-) - -diff --git a/seaborn/tests/test_categorical.py b/seaborn/tests/test_categorical.py -index d4e09b703..488fad2d6 100644 ---- a/seaborn/tests/test_categorical.py -+++ b/seaborn/tests/test_categorical.py -@@ -110,6 +110,11 @@ class CategoricalFixture: - df = pd.DataFrame(dict(y=y, g=g, h=h, u=u)) - x_df["W"] = g - -+ def get_box_artists(self, ax): -+ -+ # Exclude labeled patches, which are for the legend -+ return [p for p in ax.patches if not p.get_label()] -+ - - class TestCategoricalPlotter(CategoricalFixture): - -@@ -855,12 +863,12 @@ def test_hue_offsets(self): - def test_axes_data(self): - - ax = cat.boxplot(x="g", y="y", data=self.df) -- assert len(ax.artists) == 3 -+ assert len(self.get_box_artists(ax)) == 3 - - plt.close("all") - - ax = cat.boxplot(x="g", y="y", hue="h", data=self.df) -- assert len(ax.artists) == 6 -+ assert len(self.get_box_artists(ax)) == 6 - - plt.close("all") - -@@ -868,14 +876,14 @@ def test_box_colors(self): - - ax = cat.boxplot(x="g", y="y", data=self.df, saturation=1) - pal = palettes.color_palette(n_colors=3) -- for patch, color in zip(ax.artists, pal): -+ for patch, color in zip(self.get_box_artists(ax), pal): - assert patch.get_facecolor()[:3] == color - - plt.close("all") - - ax = cat.boxplot(x="g", y="y", hue="h", data=self.df, saturation=1) - pal = palettes.color_palette(n_colors=2) -- for patch, color in zip(ax.artists, pal * 2): -+ for patch, color in zip(self.get_box_artists(ax), pal * 2): - assert patch.get_facecolor()[:3] == color - - plt.close("all") -@@ -884,7 +892,7 @@ def test_draw_missing_boxes(self): - - ax = cat.boxplot(x="g", y="y", data=self.df, - order=["a", "b", "c", "d"]) -- assert len(ax.artists) == 3 -+ assert len(self.get_box_artists(ax)) == 3 - - def test_missing_data(self): - -@@ -894,13 +902,13 @@ def test_missing_data(self): - y[-2:] = np.nan - - ax = cat.boxplot(x=x, y=y) -- assert len(ax.artists) == 3 -+ assert len(self.get_box_artists(ax)) == 3 - - plt.close("all") - - y[-1] = 0 - ax = cat.boxplot(x=x, y=y, hue=h) -- assert len(ax.artists) == 7 -+ assert len(self.get_box_artists(ax)) == 7 - - plt.close("all") - -@@ -2766,11 +2774,11 @@ def test_plot_elements(self): - - g = cat.catplot(x="g", y="y", data=self.df, kind="box") - want_artists = self.g.unique().size -- assert len(g.ax.artists) == want_artists -+ assert len(self.get_box_artists(g.ax)) == want_artists - - g = cat.catplot(x="g", y="y", hue="h", data=self.df, kind="box") - want_artists = self.g.unique().size * self.h.unique().size -- assert len(g.ax.artists) == want_artists -+ assert len(self.get_box_artists(g.ax)) == want_artists - - g = cat.catplot(x="g", y="y", data=self.df, - kind="violin", inner=None) -@@ -3137,14 +3145,14 @@ def test_box_colors(self): - - ax = cat.boxenplot(x="g", y="y", data=self.df, saturation=1) - pal = palettes.color_palette(n_colors=3) -- for patch, color in zip(ax.artists, pal): -+ for patch, color in zip(self.get_box_artists(ax), pal): - assert patch.get_facecolor()[:3] == color - - plt.close("all") - - ax = cat.boxenplot(x="g", y="y", hue="h", data=self.df, saturation=1) - pal = palettes.color_palette(n_colors=2) -- for patch, color in zip(ax.artists, pal * 2): -+ for patch, color in zip(self.get_box_artists(ax), pal * 2): - assert patch.get_facecolor()[:3] == color - - plt.close("all") - -From ff78ed38817a346e760194ab3b03b28d7ea3ba1b Mon Sep 17 00:00:00 2001 -From: Michael Waskom -Date: Sun, 31 Oct 2021 15:50:54 -0400 -Subject: [PATCH 2/4] Update kdeplot tests for mpl3.5 compatability - ---- - seaborn/tests/test_distributions.py | 53 ++++++++++++++++++++--------- - 1 file changed, 37 insertions(+), 16 deletions(-) - -diff --git a/seaborn/tests/test_distributions.py b/seaborn/tests/test_distributions.py -index d241fd978..466efb69e 100644 ---- a/seaborn/tests/test_distributions.py -+++ b/seaborn/tests/test_distributions.py -@@ -39,6 +39,27 @@ - ) - - -+def get_contour_coords(c): -+ """Provide compatability for change in contour artist type in mpl3.5.""" -+ # See https://github.com/matplotlib/matplotlib/issues/20906 -+ if isinstance(c, mpl.collections.LineCollection): -+ return c.get_segments() -+ elif isinstance(c, mpl.collections.PathCollection): -+ return [p.vertices[:np.argmax(p.codes) + 1] for p in c.get_paths()] -+ -+ -+def get_contour_color(c): -+ """Provide compatability for change in contour artist type in mpl3.5.""" -+ # See https://github.com/matplotlib/matplotlib/issues/20906 -+ if isinstance(c, mpl.collections.LineCollection): -+ return c.get_color() -+ elif isinstance(c, mpl.collections.PathCollection): -+ if c.get_facecolor().size: -+ return c.get_facecolor() -+ else: -+ return c.get_edgecolor() -+ -+ - class TestDistPlot(object): - - rs = np.random.RandomState(0) -@@ -902,7 +923,7 @@ def test_fill_artists(self, long_df): - f, ax = plt.subplots() - kdeplot(data=long_df, x="x", y="y", hue="c", fill=fill) - for c in ax.collections: -- if fill: -+ if fill or Version(mpl.__version__) >= Version("3.5.0b0"): - assert isinstance(c, mpl.collections.PathCollection) - else: - assert isinstance(c, mpl.collections.LineCollection) -@@ -918,8 +939,8 @@ def test_common_norm(self, rng): - kdeplot(x=x, y=y, hue=hue, common_norm=True, ax=ax1) - kdeplot(x=x, y=y, hue=hue, common_norm=False, ax=ax2) - -- n_seg_1 = sum([len(c.get_segments()) > 0 for c in ax1.collections]) -- n_seg_2 = sum([len(c.get_segments()) > 0 for c in ax2.collections]) -+ n_seg_1 = sum([len(get_contour_coords(c)) > 0 for c in ax1.collections]) -+ n_seg_2 = sum([len(get_contour_coords(c)) > 0 for c in ax2.collections]) - assert n_seg_2 > n_seg_1 - - def test_log_scale(self, rng): -@@ -946,7 +967,7 @@ def test_log_scale(self, rng): - ax2.contour(10 ** xx, yy, density, levels=levels) - - for c1, c2 in zip(ax1.collections, ax2.collections): -- assert_array_equal(c1.get_segments(), c2.get_segments()) -+ assert_array_equal(get_contour_coords(c1), get_contour_coords(c2)) - - def test_bandwidth(self, rng): - -@@ -959,7 +980,7 @@ def test_bandwidth(self, rng): - kdeplot(x=x, y=y, bw_adjust=2, ax=ax2) - - for c1, c2 in zip(ax1.collections, ax2.collections): -- seg1, seg2 = c1.get_segments(), c2.get_segments() -+ seg1, seg2 = get_contour_coords(c1), get_contour_coords(c2) - if seg1 + seg2: - x1 = seg1[0][:, 0] - x2 = seg2[0][:, 0] -@@ -980,9 +1001,9 @@ def test_weights(self, rng): - kdeplot(x=x, y=y, hue=hue, weights=weights, ax=ax2) - - for c1, c2 in zip(ax1.collections, ax2.collections): -- if c1.get_segments() and c2.get_segments(): -- seg1 = np.concatenate(c1.get_segments(), axis=0) -- seg2 = np.concatenate(c2.get_segments(), axis=0) -+ if get_contour_coords(c1) and get_contour_coords(c2): -+ seg1 = np.concatenate(get_contour_coords(c1), axis=0) -+ seg2 = np.concatenate(get_contour_coords(c2), axis=0) - assert not np.array_equal(seg1, seg2) - - def test_hue_ignores_cmap(self, long_df): -@@ -1030,7 +1051,7 @@ def test_levels_and_thresh(self, long_df): - kdeplot(**plot_kws, levels=np.linspace(thresh, 1, n), ax=ax2) - - for c1, c2 in zip(ax1.collections, ax2.collections): -- assert_array_equal(c1.get_segments(), c2.get_segments()) -+ assert_array_equal(get_contour_coords(c1), get_contour_coords(c2)) - - with pytest.raises(ValueError): - kdeplot(**plot_kws, levels=[0, 1, 2]) -@@ -1042,7 +1063,7 @@ def test_levels_and_thresh(self, long_df): - kdeplot(**plot_kws, levels=n, thresh=0, ax=ax2) - - for c1, c2 in zip(ax1.collections, ax2.collections): -- assert_array_equal(c1.get_segments(), c2.get_segments()) -+ assert_array_equal(get_contour_coords(c1), get_contour_coords(c2)) - for c1, c2 in zip(ax1.collections, ax2.collections): - assert_array_equal(c1.get_facecolors(), c2.get_facecolors()) - -@@ -2322,13 +2343,13 @@ def test_bivariate_kde_norm(self, rng): - z = [0] * 80 + [1] * 20 - - g = displot(x=x, y=y, col=z, kind="kde", levels=10) -- l1 = sum(bool(c.get_segments()) for c in g.axes.flat[0].collections) -- l2 = sum(bool(c.get_segments()) for c in g.axes.flat[1].collections) -+ l1 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[0].collections) -+ l2 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[1].collections) - assert l1 > l2 - - g = displot(x=x, y=y, col=z, kind="kde", levels=10, common_norm=False) -- l1 = sum(bool(c.get_segments()) for c in g.axes.flat[0].collections) -- l2 = sum(bool(c.get_segments()) for c in g.axes.flat[1].collections) -+ l1 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[0].collections) -+ l2 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[1].collections) - assert l1 == l2 - - def test_bivariate_hist_norm(self, rng): - -From a20ce3fabeb23c97b5827d9fb0c6a96ac109ea64 Mon Sep 17 00:00:00 2001 -From: Michael Waskom -Date: Sun, 31 Oct 2021 16:10:47 -0400 -Subject: [PATCH 3/4] Update legend tests for mpl3.5 compatability - ---- - seaborn/tests/test_distributions.py | 5 ++++- - 1 file changed, 4 insertions(+), 1 deletion(-) - -diff --git a/seaborn/tests/test_distributions.py b/seaborn/tests/test_distributions.py -index 466efb69e..024fe7541 100644 ---- a/seaborn/tests/test_distributions.py -+++ b/seaborn/tests/test_distributions.py -@@ -872,7 +872,7 @@ def test_legend(self, long_df): - for label, level in zip(legend_labels, order): - assert label.get_text() == level - -- legend_artists = ax.legend_.findobj(mpl.lines.Line2D)[::2] -+ legend_artists = ax.legend_.findobj(mpl.lines.Line2D) - palette = color_palette() - for artist, color in zip(legend_artists, palette): - assert_colors_equal(artist.get_color(), color) - diff --git a/gnu/packages/patches/python-seaborn-kde-test.patch b/gnu/packages/patches/python-seaborn-kde-test.patch deleted file mode 100644 index f300dffc6f..0000000000 --- a/gnu/packages/patches/python-seaborn-kde-test.patch +++ /dev/null @@ -1,36 +0,0 @@ -This patch is an excerpt of this upstream commit: - - commit 0a24478a550132f1882e5be5f5dbc0fc446a8a6c - Author: Michael Waskom - Date: Mon Dec 21 18:44:58 2020 -0500 - - Raise minimal supported Python to 3.7 and bump requirements (#2396) - -It fixes the failure of 'test_weights'. - ---- a/seaborn/tests/test_distributions.py -+++ b/seaborn/tests/test_distributions.py -@@ -709,21 +708,17 @@ class TestKDEPlotUnivariate: - integral = integrate.trapz(ydata, np.log10(xdata)) - assert integral == pytest.approx(1) - -- @pytest.mark.skipif( -- LooseVersion(scipy.__version__) < "1.2.0", -- reason="Weights require scipy >= 1.2.0" -- ) - def test_weights(self): - - x = [1, 2] - weights = [2, 1] - -- ax = kdeplot(x=x, weights=weights) -+ ax = kdeplot(x=x, weights=weights, bw_method=.1) - - xdata, ydata = ax.lines[0].get_xydata().T - -- y1 = ydata[np.argwhere(np.abs(xdata - 1).min())] -- y2 = ydata[np.argwhere(np.abs(xdata - 2).min())] -+ y1 = ydata[np.abs(xdata - 1).argmin()] -+ y2 = ydata[np.abs(xdata - 2).argmin()] - - assert y1 == pytest.approx(2 * y2) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b830ade9ca..a9b123d4c2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10280,40 +10280,37 @@ SVG, EPS, PNG and terminal output.") (define-public python-seaborn (package (name "python-seaborn") - (version "0.11.2") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "seaborn" version)) (sha256 (base32 - "1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg")) - (patches (search-patches "python-seaborn-kde-test.patch" - "python-seaborn-2690.patch")))) - (build-system python-build-system) - (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-more-tests - (lambda _ - (substitute* "seaborn/tests/test_distributions.py" - (("get_contour_color\\(ax\\.collections\\[0\\]\\)") - "get_contour_color(ax.collections[0])") - (("c\\.get_color\\(\\)") "get_contour_color(c)") - (("def test_hue_ignores_cmap") - "def skip_test_hue_ignores_cmap") - (("def test_fill_artists") - "def skip_test_fill_artists") - (("def test_with_rug") "def skip_test_with_rug")))) - (add-before 'check 'start-xserver - (lambda _ - (system "Xvfb :1 &") - (setenv "DISPLAY" ":1"))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "seaborn"))))))) + "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9")))) + (build-system python-build-system) + (arguments + (list #:modules '((guix build python-build-system) + (guix build utils) + (ice-9 match)) + #:phases #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "python" "-m" "build" "--wheel" + "--no-isolation" "."))) + (replace 'install + (lambda _ + (match (find-files "dist" "\\.whl$") + ((wheel _ ...) + (invoke "python" "-m" "pip" "install" + (string-append "--prefix=" #$output) + wheel))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) (propagated-inputs (list python-pandas python-matplotlib python-numpy python-scipy)) - (native-inputs (list python-pytest xorg-server-for-tests)) + (native-inputs (list python-flit-core python-pypa-build python-pytest)) (home-page "https://seaborn.pydata.org/") (synopsis "Statistical data visualization") (description -- cgit 1.4.1