From patchwork Sun Apr 6 23:26:42 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41383 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 5B23A27BC4B; Mon, 7 Apr 2025 00:28:48 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A4ACF27BC49 for ; Mon, 7 Apr 2025 00:28:47 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u1ZPl-0000EZ-Rg; Sun, 06 Apr 2025 19:28:33 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u1ZPH-0008Uc-Kx for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:04 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u1ZPH-000353-C6 for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=/u0i8uaotw0BjQ5r3ns0pq5FZfTGB5KWkfgqUCBxq5I=; b=mdxuLRH7Yeg3QGve3P73gOjqSz4MjL1UB7p84Mf66CraE54HA4g32SvOk8oMLbI++O8CuteoYk6flvA766m1pEoOgttgCgMMI5VnH0LxAJmSS1BrRmqIZdHo3f6Ljt50uuuXMnBldg3wz0gaT8XdrFQYYiknYz37nN0Rg8ct6TqGD2e4LF5k3HLbR90ddubBWaeeLhyx9+rHhx4s/vUq2xHAL/fWdkcq+GNox4Jr100Wz4eWbjnuMYQ8SXatPBcQEoKWlheP1O29/q+C+YgRihblJjgY5N0J7n4GF96/IXmsAjkm/ivkQCCXd9sLzhXO21N8OSer0fQGoOVxnExEOg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u1ZPH-00050O-5n for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH 3/3] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Apr 2025 23:28:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77590 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77590@debbugs.gnu.org Cc: David Elsing Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174398204319088 (code B ref 77590); Sun, 06 Apr 2025 23:28:03 +0000 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:23 +0000 Received: from localhost ([127.0.0.1]:50118 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOc-0004xl-Hv for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:23 -0400 Received: from mout01.posteo.de ([185.67.36.65]:36241) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZOP-0004wB-00 for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id A3A64240027 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:27:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982022; bh=O+FFWU1AyPT98cyPgtQdEmcP+b4+wBOQaUQR9VSXpqM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=I888tmwHPm3ZkVeO94T20UT18cRQp+/sMR4MBW3tyaGC4/c+RFB7fSnyPh3tnlKZp Bl0tcUu8PgpWLP1/HDlf0XWGPuZElc7hjQpDfN/7n3FTcvfBMILqQVcJ2244uFYl/M H6jKcf0JsDPJIxfUNKsxvqRP0byAvXmVKTp5HjiX/UxVsx0170q8tG35optoFTrKaQ s+NVz7fGTSz77dAIo7oNmoYy099lheusQp2Dynisg16JUgPEYzcP3BOSYOudMy+toh V6uXDgtvuKMaZjgYrYpS5XJPUEW0Wa5Djkd8t13UB4ohbDM6kuaegtDesGhxhxJlE8 IigKcjaLi56sQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lp2Hdvz6tlh; Mon, 7 Apr 2025 01:27:02 +0200 (CEST) From: David Elsing Date: Sun, 6 Apr 2025 23:26:42 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/maths.scm (hdf-java): Update to 1.14.6. [name]: Rename to hdf5-java. [version]: Use the same as hdf5. [source]: Use the same as hdf5. [arguments]: Adjust 'unbundle phase. Add 'patch-trace-shebang and 'generate-flexbison phases. [native-inputs]: Use modify-inputs. [inputs]: Remove hdf4 and hdf5. [synopsis, description]: Remove mention of HDF4. [license]: Use the same as hdf5. --- gnu/packages/maths.scm | 75 +++++++++++++++++------------------------- 1 file changed, 30 insertions(+), 45 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 15e4ae6c86..251d1d8481 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2031,27 +2031,11 @@ (define-public hdf5-examples (inputs (list hdf5 zlib)) (native-inputs (list autoconf-2.71 automake gfortran)))) -;; Keep this in sync with the current hdf5 package. -(define-public hdf-java +(define-public hdf5-java (package - (name "hdf-java") - (version "1.14.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/HDFGroup/hdf5") - (commit (string-append "hdf5-" - (string-map - (lambda (c) (if (char=? c #\.) #\_ c)) - version))))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0lw9f62zxyjiv7vx9nvnashjj39i44j8d626i7b788zkxw58csvs")) - (modules '((guix build utils))) - (snippet ; Make sure we don't use the bundled sources and binaries. - '(for-each delete-file - (find-files "java/lib" "\\.jar$"))))) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) (build-system gnu-build-system) (arguments (list @@ -2074,8 +2058,7 @@ (define-public hdf-java (hamcrest (search-input-file inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) - (substitute* (append (find-files "java" "Makefile.am") - (find-files "java" "Makefile.in")) + (substitute* (find-files "java" "Makefile.am") (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar") simple) (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar") @@ -2085,10 +2068,10 @@ (define-public hdf-java (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar") hamcrest)) (substitute* '("java/test/junit.sh.in" - "java/examples/datatypes/JavaDatatypeExample.sh.in" - "java/examples/datasets/JavaDatasetExample.sh.in" - "java/examples/intro/JavaIntroExample.sh.in" - "java/examples/groups/JavaGroupExample.sh.in") + "HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in" + "HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in" + "HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in" + "HDF5Examples/JAVA/TUTR/runExample.sh.in") (("^LIST_JAR_TESTFILES=\"" m) (string-append m hamcrest "\n" junit "\n" @@ -2108,30 +2091,32 @@ (define-public hdf-java (("/usr/bin/uname") (search-input-file inputs "/bin/uname"))) (substitute* (find-files "java/test/testfiles/" ".*\\.txt$") - (("JUnit version 4.11") - "JUnit version 4.12-SNAPSHOT")))))))) + (("JUnit version 4.13.2") + "JUnit version 4.12-SNAPSHOT"))))) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each patch-shebang + (find-files "bin" (lambda (file stat) + (executable-file? file)))))) + (add-after 'unpack 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src")))))) (native-inputs - (list `(,icedtea "jdk") - ;; For tests: - java-hamcrest-core - java-junit - java-slf4j-simple)) + (modify-inputs (package-native-inputs hdf5) + (prepend `(,icedtea "jdk")) + (prepend java-hamcrest-core) + (prepend java-junit) + (prepend java-slf4j-simple) + (delete "gfortran"))) (inputs - (list hdf4 - hdf5 - java-slf4j-api + (list java-slf4j-api libjpeg-turbo zlib)) (home-page "https://www.hdfgroup.org") - (synopsis "Java interface for the HDF4 and HDF5 libraries") - (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use -the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are -implemented in C.") - - ;; BSD-style license: - (license (license:x11-style - "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ -/current/src/unpacked/COPYING.html")))) + (synopsis "Java interface for the HDF5 library") + (description "The Java HDF5 Interface (JHI5) uses the Java Native +Interface to wrap the HDF5 library, which is implemented in C.") + (license (package-license hdf5)))) (define-public hdf-eos2 (package