From patchwork Mon Apr 7 14:24:40 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41402 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 E7AC627BC4B; Mon, 7 Apr 2025 15:26:21 +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 6E0E127BC49 for ; Mon, 7 Apr 2025 15:26:20 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u1nQU-0003kd-TJ; Mon, 07 Apr 2025 10:26:15 -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 1u1nQJ-0003iJ-UR for guix-patches@gnu.org; Mon, 07 Apr 2025 10:26:04 -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 1u1nQJ-0006cK-K6 for guix-patches@gnu.org; Mon, 07 Apr 2025 10:26:03 -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=aGwYmFWH9aGwNJvLRgJy2r6XUrMHRhc6lMbf+QjlylY=; b=fiS6Jakf0aK5Nv5EpqGnhZ9sRUlGbWrLrwn+es3XAj0m9qX35JYkGhNJv5gnetEnQ5EDP6NkdKpFwbdEpYnYe+7MDVtxQG/7iuAOiaMDwo6hRfJMPycW6mXt7rCPly9gZuYLZDLGmT+FxnNXtlZ3omPCinnxFUCcMaVeMrnzProSrQ/JAKzZ+HqZxp+1lU+0DUMH+7fniZ/jddkrXq7H9eucVlY263g8DAPXM2/+U2mtZpm2FBD/PZdSbHDKhh7LURmW3a9ZS7RaNcvGkr+f4/wAKpHEdLBRmCgWTthAHcJ4y/gARC80Z0dq5QpDLeA4E2cUiUR3bhmv35dkfY7aLw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u1nQJ-00081O-Em for guix-patches@gnu.org; Mon, 07 Apr 2025 10:26:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v2 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: Mon, 07 Apr 2025 14:26:03 +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=B77590.174403592230659 (code B ref 77590); Mon, 07 Apr 2025 14:26:03 +0000 Received: (at 77590) by debbugs.gnu.org; 7 Apr 2025 14:25:22 +0000 Received: from localhost ([127.0.0.1]:56105 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1nPd-0007yJ-LK for submit@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:22 -0400 Received: from mout02.posteo.de ([185.67.36.66]:60399) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1nPT-0007rO-VZ for 77590@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:13 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 9A308240101 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 16:25:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744035905; bh=szfkX1Fnf8TtARo2EJtsEM4mYkSZC3B4MeiPMfIgHyo=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=csLw6Q11v2tSggc6fmgX5yoWNolHzqOQU96/rU6Pg93/FdkXd2a9XkHtmgST+CZIY p5salb9UklEu2K82BAI3x6sScrwHQmgr3xVSVANvpbCqXCAlP/a5Rc4rzJEILVnQhU 6GfGyXuzDvXv7fOYyUFtQ4rnG6G7Ji3LwPitLua4Xc6p6Y6LYALxbFdtE7S84szALZ vnn+vYXqyrBfpdsJKyEWEnyT1T4Pj0L4brE/FECmnKv1J+Lw9VLZ1hX5Z1B0QyBx1u iU3UvPz+DS+oXrjwuXsQWvPX8hdu1DFKqj9jFMqRFGo14khT+lUHP7WYH1nGS2m5tI vmOp6JgiPo21w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWWh11cwTz9rxG; Mon, 7 Apr 2025 16:25:05 +0200 (CEST) From: David Elsing Date: Mon, 7 Apr 2025 14:24:40 +0000 Message-ID: <86f2e3cc89d54d9e9635b6baa731cb6b4cf537ba.1744035216.git.david.elsing@posteo.net> 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]: Add (guix build ant-build-system) to #:modules and #:imported-modules. Adjust 'unbundle phase. Add 'patch-trace-shebang, 'generate-flexbison and 'strip-jar-timestamps phases. [native-inputs]: Use modify-inputs. Add zip. [inputs]: Remove hdf4 and hdf5. [synopsis, description]: Remove mention of HDF4. [license]: Use the same as hdf5. --- gnu/packages/maths.scm | 85 ++++++++++++++++++++---------------------- 1 file changed, 40 insertions(+), 45 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6d7466774d..511cd1c94b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2030,33 +2030,24 @@ (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$"))))) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) (build-system gnu-build-system) (arguments (list #:configure-flags #~(list "--enable-java" "--disable-tools") + #:modules + '((guix build gnu-build-system) + ((guix build ant-build-system) #:prefix ant:) + (guix build utils)) + #:imported-modules + `((guix build ant-build-system) + ,@%default-gnu-imported-modules) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'unbundle @@ -2073,8 +2064,7 @@ (define-public hdf-java (hamcrest (search-input-file inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) - (substitute* (append (find-files "java" "Makefile.am") - (find-files "java" "Makefile.in")) + (substitute* (find-files "java" "Makefile.am") (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar") simple) (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar") @@ -2084,10 +2074,10 @@ (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" @@ -2107,30 +2097,35 @@ (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"))) + (add-after 'install 'strip-jar-timestamps + (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) (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) + (prepend (@ (gnu packages compression) zip)) + (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