andreas pushed a commit to branch master
in repository guix.
commit 6c462068657fe44a92ee9fa60eeb1c11c5921c8d
Author: David Elsing <david.els...@posteo.net>
AuthorDate: Wed Apr 30 16:27:04 2025 +0000
gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java.
* gnu/packages/maths.scm (hdf-java): Define as deprecated alias for...
(hdf5-java): ...this new variable. Update to 1.14.6.
[name]: Rename to hdf5-java.
[version]: Use the same as hdf5.
[source]: Use the same as hdf5.
[build-system]: Change to cmake-build-system.
[arguments]: Adjust #:configure-flags. Add (guix build ant-build-system)
to #:modules and #:imported-modules. Adjust 'unbundle phase. Add
'patch-trace-shebang, 'generate-flexbison, 'generate-headers and
'strip-jar-timestamps phases.
[native-inputs]: Use modify-inputs. Add java-slf4j-nop and zip.
[inputs]: Remove hdf4 and hdf5.
[synopsis, description]: Remove mention of HDF4.
[license]: Use the same as hdf5.
Change-Id: Idfceec17b9a8c432ab85e2fcc87de6bb5bd5a422
Signed-off-by: Andreas Enge <andr...@enge.fr>
---
gnu/packages/maths.scm | 119 +++++++++++++++++++++++++++----------------------
1 file changed, 66 insertions(+), 53 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0759c82ab6..04076530a5 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1973,33 +1973,24 @@ extremely large and complex data collections.")
(license (license:x11-style
"https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html";))))
-;; 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$")))))
- (build-system gnu-build-system)
+ (name "hdf5-java")
+ (version (package-version hdf5))
+ (source (package-source hdf5))
+ (build-system cmake-build-system)
(arguments
(list
#:configure-flags
- #~(list "--enable-java"
- "--disable-tools")
+ #~(list "-DHDF5_BUILD_JAVA=ON"
+ "-DHDF5_BUILD_TOOLS=OFF")
+ #:modules
+ '((guix build cmake-build-system)
+ ((guix build ant-build-system) #:prefix ant:)
+ (guix build utils))
+ #:imported-modules
+ `((guix build ant-build-system)
+ ,@%cmake-build-system-modules)
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'unbundle
@@ -2010,27 +2001,35 @@ extremely large and complex data collections.")
(api
(search-input-file
inputs
"/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar"))
+ (nop
+ (search-input-file
+ inputs
"/lib/m2/org/slf4j/slf4j-nop/1.7.25/slf4j-nop-1.7.25.jar"))
(junit
(search-input-file
inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar"))
(hamcrest
(search-input-file
inputs
"/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar")))
- (substitute* (append (find-files "java" "Makefile.am")
- (find-files "java" "Makefile.in"))
- (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar")
- simple)
- (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar")
- api)
- (("\\$\\(top_srcdir\\)/java/lib/junit.jar")
+ (substitute* "CMakeLists.txt"
+ (("(set *\\(HDF5_JAVA_LOGGING_JAR ).*" _ orig)
+ (string-append orig api ")\n"))
+ (("(set *\\(HDF5_JAVA_LOGGING_NOP_JAR ).*" _ orig)
+ (string-append orig nop ")\n"))
+ (("(set *\\(HDF5_JAVA_LOGGING_SIMPLE_JAR ).*" _ orig)
+ (string-append orig simple ")\n")))
+ ;; Do not install copies of external libraries
+ (substitute* "java/CMakeLists.txt"
+ ((".*HDF5_JAVA_LOGGING.*_JAR.*") ""))
+ (substitute* "java/test/CMakeLists.txt"
+ (("\\$\\{HDF5_JAVA_LIB_DIR\\}/junit\\.jar")
junit)
- (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar")
+ (("\\$\\{HDF5_JAVA_LIB_DIR\\}/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"
@@ -2050,30 +2049,44 @@ extremely large and complex data collections.")
(("/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 'unpack 'generate-headers
+ (lambda _
+ (invoke "perl" "bin/make_err" "src/H5err.txt")
+ (invoke "perl" "bin/make_vers" "src/H5vers.txt")
+ (invoke "perl" "bin/make_overflow" "src/H5overflow.txt")))
+ (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-nop)
+ (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.")
+ (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))))
- ;; BSD-style license:
- (license (license:x11-style
- "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
-/current/src/unpacked/COPYING.html"))))
+(define-public hdf-java
+ (deprecated-package "hdf-java" hdf5-java))
(define-public hdf-eos2
(package
