hdf5: Add HDF5 to thirdparty/hdfgroup/hdf5

Currently v1.8.13. Required for HDS version 5.

.gitmodules

@@ -163,3 +163,6 @@
 [submodule "thirdparty/erfa/erfa"]
 	path = thirdparty/erfa/erfa
 	url = git://github.com/liberfa/erfa.git
+[submodule "thirdparty/hdfgroup/hdf5/hdf5"]
+	path = thirdparty/hdfgroup/hdf5/hdf5
+	url = https://github.com/Starlink/hdf5.git

Makefile.dependencies

@@ -1138,6 +1138,10 @@ $(MANIFESTS)/gwm: \
 	cd libraries/gwm \
 	  && $(MAKE_CPT)
 
+$(MANIFESTS)/hdf5:
+	cd thirdparty/hdfgroup/hdf5 \
+	  && $(MAKE_CPT)
+
 $(MANIFESTS)/hds: \
 		$(MANIFESTS)/chr \
 		$(MANIFESTS)/cnf \

componentset.xml

@@ -6732,6 +6732,24 @@ Ultrix and for SunOS and may still work for them.
   <bugreports>starlink@jiscmail.ac.uk</bugreports>
 </component>
 
+<component id="hdf5" support="U">
+  <version>1.8.13</version>
+  <path>thirdparty/hdfgroup/hdf5</path>
+  <description>Hierarchical Data Format version 5</description>
+  <dependencies >
+
+  </dependencies>
+  <developers>
+    <person>
+      <name>Tim Jenness</name>
+      <uname>timj</uname>
+      <email>stardev@jiscmail.ac.uk</email>
+      <role>owner</role>
+    </person>
+  </developers>
+  <bugreports>starlink@jiscmail.ac.uk</bugreports>
+</component>
+
 <component id="cfitsio" support="U">
   <version>3.37</version>
   <path>thirdparty/heasarc/cfitsio</path>

thirdparty/hdfgroup/Makefile.am

@@ -0,0 +1,3 @@
+## Process this file with automake to produce Makefile.in
+
+SUBDIRS = @subdirs@

thirdparty/hdfgroup/bootstrap

@@ -0,0 +1,49 @@
+#! /bin/sh -
+# This is not a starconf component bootstrap file; it should be maintained
+# as a copy of buildsupport/starconf/bootstrap.bridging:
+#   $Source: /cvs/buildsupport/starconf/bootstrap.bridging,v $
+#   $Revision: 1.1 $
+# (check this in to CVS using -ko to preserve above RCS info).
+#
+# Instead, it is a bootstrap script used for `bridging' directories,
+# such as applications/ and libraries/, which group together related
+# components and, when they are bootstrapped, bridge between the parent
+# and the various children listed in the AC_CONFIG_SUBDIRS macro in the
+# configure.ac in this directory.  That is, it is for directories which
+# are traversed by the top-level bootstrap, but which are not components.
+
+
+# If STAR_SUPPRESS_AUTORECONF is true in the environment, then we
+# suppress the call of `autoreconf', and simply invoke ./bootstrap in
+# the children.  This is here _only_ so that the top-level bootstrap
+# file can suppress multiple calls of this in bootstrap scripts in its
+# children, and as an optimisation.  As such, it makes sense ONLY when
+# invoked from a top-level bootstrap.  This mechanism must not be used
+# by users, as it is liable to change without warning.
+: ${STAR_SUPPRESS_AUTORECONF=false}
+
+if $STAR_SUPPRESS_AUTORECONF; then
+    echo "Suppressing autoreconf"
+
+    thisdir=`basename $PWD`
+    for d in `autoconf --trace=AC_CONFIG_SUBDIRS:$% configure.ac` DUMMY
+    do
+        if test -n "$d" -a -d "$d"; then
+            echo "Bootstrapping $thisdir/$d..."
+            (cd $d && ./bootstrap)
+        fi
+    done
+
+else
+
+    echo "autoreconf --install --symlink" || exit 1
+    autoreconf --install --symlink
+
+    if test ! -f configure; then
+        echo "Ooooh dear, autoreconf didn't work -- I can't find ./configure"
+        exit 1
+    fi
+
+fi
+
+exit 0

thirdparty/hdfgroup/configure.ac

@@ -0,0 +1,21 @@
+dnl    Process this file with autoconf to produce a configure script
+
+dnl    This is not a package, so the first two arguments are fake.
+AC_INIT(star-thirdparty-hdfgroup, 1.0, starlink@jiscmail.ac.uk)
+AM_INIT_AUTOMAKE(1.8.2-starlink)
+
+dnl    Following sanity-check isn't terribly helpful...
+AC_CONFIG_SRCDIR(bootstrap)
+
+STAR_DEFAULTS
+
+AC_PROG_MAKE_SET
+
+dnl    The following list must be kept up-to-date by hand.
+dnl    The list is available as the substitution variable @subdirs@.
+dnl    (must be kept on one line). 
+AC_CONFIG_SUBDIRS([hdf5])
+
+AC_CONFIG_FILES([Makefile])
+
+AC_OUTPUT

thirdparty/hdfgroup/hdf5/Makefile.am

@@ -0,0 +1,24 @@
+## Process this file with automake to produce Makefile.in
+
+@SET_MAKE@
+
+RECURSIVE_TARGETS = all check
+
+$(RECURSIVE_TARGETS):
+	( cd hdf5; $(MAKE) $@; )
+
+##  Automake really requires local versions for these targets.
+distclean-local:
+	( cd hdf5; $(MAKE) distclean )
+
+clean-local:
+	( cd hdf5; $(MAKE) clean )
+
+EXTRA_DIST = hdf5
+
+##  Before distributing subdirectories we need to clean up and remove any
+##  softlinks.
+dist-hook:
+	rm -rf `find $(distdir) -type l`
+	(cd $(distdir)/hdf5; make distclean)
+

thirdparty/hdfgroup/hdf5/bootstrap

@@ -0,0 +1,134 @@
+#! /bin/sh -
+# original bootstrap file, installed by starconf 1.3, rnum=1003000
+# If you _need_ to change this file, delete `original' in the line above,
+# or else starconf may overwrite it with an updated version.
+#
+# bootstrap.installed.  Generated from bootstrap.installed.in by configure.
+#
+# Bootstrap a checked-out component of the Starlink software tree.
+# Run this script in a freshly checked-out directory to bring the
+# system to the point where you can just type ./configure;make
+#
+# Usage:
+#     ./bootstrap
+
+
+# This script should be installed, by starconf, in all `component
+# directories'.  A `component directory' is a directory which has a
+# component.xml.in file in it.  All component directories will have a
+# manifest file created and installed in .../manifests; non-component
+# directories will not have manifest files.  Everything that's
+# installed should be installed as part of some component
+# or other.
+#
+# The ./bootstrap scripts will stop recursing when they find a
+# component.xml.in file.  They'll warn if they find a component.xml.in
+# file in any AC_CONFIG_SUBDIRS directory, but ignore it, and exit
+# with an error if they do not find a component.xml.in file and there
+# are no AC_CONFIG_SUBDIRS directories in which to search further.
+# That is, the tree of directories which the top-level bootstrap
+# traverses should have component.xml.in files at or above all its
+# leaves.
+
+
+# The starconf below might update bootstrap, if a newer version is
+# available.  Unfortunately, this confuses sh, which appears _not_ to
+# keep open the script it's reading, but to reopen it afresh, or reseek
+# within the file, for each line (or something like that!?).
+# So rewrite this script to a temporary file and exec it.
+tempfile="${TMP-/tmp}/$0-$$.tmp"
+rm -f $tempfile
+echo "trap 'rm -f $tempfile' 0" >$tempfile   # remove temporary at exit
+sed '1,/^--TRAMPOLINE--/d' $0 >>$tempfile    # strip out the trampoline
+exec /bin/sh $tempfile                       # exec the temporary
+--TRAMPOLINE--
+
+
+echo "Bootstrapping `pwd` ..."
+
+if test ! -f configure.ac; then
+    echo "bootstrap: No configure.ac in directory `pwd`" >&2
+    exit 1
+fi
+
+subdirs=`autoconf --trace=AC_CONFIG_SUBDIRS:$% configure.ac`
+
+if test -f component.xml.in; then
+
+    if starconf --show buildsupport >/dev/null 2>&1; then
+
+        # starconf is in the path
+        echo "...using starconf in " `starconf --show buildsupport`
+        starconf || exit 1
+
+    else
+
+        # The temptation here is to use ./starconf.status to find the
+        # starconf that it came from and invoke that explicitly.  Don't do
+        # this, however: we don't want to be too clever, and it's better
+        # to be consistent with the way the autotools behave (the first
+        # one in your path is the one that works, and they don't have this
+        # sort of `phone home' cleverness in them).
+
+        echo "bootstrap error: The starconf application is not in your path"
+
+        # This doesn't stop us being helpful, however.
+        if test -f ./starconf.status; then
+            starconf_home=`./starconf.status --show buildsupport`
+            echo "This directory was last bootstrapped with $starconf_home/bin/starconf"
+        fi
+
+        exit 1
+    fi
+
+    # Check that there are no component.xml.in files in any subdirectories
+    if test -n "$subdirs"; then
+        for d in $subdirs
+        do
+            if test -d "$d" && test -f "$d/component.xml.in"; then
+                echo "bootstrap: warning: ignoring child $d/component.xml.in" >&2
+            fi
+        done
+    fi
+
+    # If STAR_SUPPRESS_AUTORECONF is true in the environment, then we
+    # suppress the call of `autoreconf'.  This is here _only_ so that
+    # the top-level bootstrap file can suppress multiple calls of this
+    # in bootstrap scripts in its children.  This mechanism must not
+    # be used by users, as it is likely to change without warning. 
+    if ${STAR_SUPPRESS_AUTORECONF-false}; then
+        echo "Suppressing autoreconf in" `pwd`
+    else
+        echo autoreconf --install --symlink
+        autoreconf --install --symlink || exit 1
+    fi
+
+else
+
+    # This is not a component directory, so simply recurse into the children.
+
+    # ...if there are any, that is.
+    if test -z "$subdirs"; then
+        echo "bootstrap: error: non-component directory `pwd` has no subdirs" >&2
+        exit 1
+    fi
+
+    # Bootstrap the child directories mentioned in AC_CONFIG_SUBDIRS.
+    # These bootstrap files must exist.
+    for d in $subdirs
+    do
+        if test -d "$d"; then
+            echo "Bootstrapping $d..."
+            if test -f $d/bootstrap; then
+                # good...
+                (cd $d; /bin/sh ./bootstrap)
+            else
+                echo "bootstrap: no file $d/bootstrap" >&2
+                exit 1
+            fi
+        fi
+    done
+
+fi
+
+exit 0

thirdparty/hdfgroup/hdf5/component.xml

@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<!DOCTYPE component SYSTEM "componentinfo.dtd">
+<!-- component.xml.  Generated from component.xml.in by configure. -->
+
+<component id="hdf5" support="U">
+  <version>1.8.13</version>
+  <path>thirdparty/hdfgroup/hdf5</path>
+  <description>Hierarchical Data Format version 5</description>
+  <!-- <abstract><p></p></abstract> -->
+  <dependencies >
+
+  </dependencies>
+  <developers>
+    <!-- FFTW is maintained by hdfgroup.org, but we take the call first-->
+    <person>
+      <name>Tim Jenness</name>
+      <uname>timj</uname>
+      <email>stardev@jiscmail.ac.uk</email>
+      <role>owner</role>
+    </person>
+  </developers>
+  <!-- <documentation></documentation> -->
+  <bugreports>starlink@jiscmail.ac.uk</bugreports>
+  <!-- <notes><p></p></notes> -->
+</component>

thirdparty/hdfgroup/hdf5/component.xml.in

@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<!DOCTYPE component SYSTEM "componentinfo.dtd">
+<!-- @configure_input@ -->
+
+<component id="@PACKAGE@" support="U">
+  <version>@PACKAGE_VERSION@</version>
+  <path>thirdparty/hdfgroup/hdf5</path>
+  <description>Hierarchical Data Format version 5</description>
+  <!-- <abstract><p></p></abstract> -->
+  <dependencies @STAR_DEPENDENCIES_ATTRIBUTES@>
+    @STAR_DEPENDENCIES_CHILDREN@
+  </dependencies>
+  <developers>
+    <!-- FFTW is maintained by hdfgroup.org, but we take the call first-->
+    <person>
+      <name>Tim Jenness</name>
+      <uname>timj</uname>
+      <email>stardev@jiscmail.ac.uk</email>
+      <role>owner</role>
+    </person>
+  </developers>
+  <!-- <documentation>@STAR_DOCUMENTATION@</documentation> -->
+  <bugreports>@PACKAGE_BUGREPORT@</bugreports>
+  <!-- <notes><p></p></notes> -->
+</component>

thirdparty/hdfgroup/hdf5/configure.ac

@@ -0,0 +1,43 @@
+dnl    Process this file with autoconf to produce a configure script
+
+dnl    Initialisation: package name and version number
+AC_INIT([hdf5],[1.8.13],[starlink@jiscmail.ac.uk])
+AC_CONFIG_AUX_DIR([.])
+
+dnl    Require autoconf-2.50 at least
+AC_PREREQ([2.69])
+dnl    Require Starlink automake
+AM_INIT_AUTOMAKE(1.8.2-starlink)
+
+dnl    Sanity-check: name a file in the source directory -- if this
+dnl    isn't found then configure will complain
+AC_CONFIG_SRCDIR([configure.ac])
+
+dnl    Include defaults for Starlink configurations
+STAR_DEFAULTS
+
+dnl    To configure HDF5 proper we just run ./configure in the
+dnl    hdf5 sub-directory. Do not invoke AC_CONFIG_SUBDIRS,
+dnl    since that prompts autoreconf to try to reconfigure that directory, and
+dnl    automake to assume it's allowed to play there, too.
+(
+    cd hdf5
+    ./configure --prefix=$prefix
+)
+
+dnl    Find required versions of the programs we need for configuration
+LT_INIT
+AC_PROG_MAKE_SET
+
+dnl    Install using a staging area to get all files listed in
+dnl    in the manifest. Also install "starperl" script.
+STAR_SPECIAL_INSTALL_COMMAND([
+   ( cd hdf5; $(MAKE) DESTDIR=$$DESTDIR install );
+])
+
+dnl    If you wish to configure extra files, you can add them to this
+dnl    declaration.
+AC_CONFIG_FILES([Makefile component.xml])
+
+dnl    This is the bit that does the actual work
+AC_OUTPUT