Merge pull request easybuilders#19840 from t1mk1k/new_pr_wsclean_dp3_…

…foss_2023b

{astro,lib}[foss/2023b] DP3-6.0, WSClean 3.4 and deps

easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb

@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'AOFlagger'
+version = '3.4.0'
+
+homepage = 'https://aoflagger.readthedocs.io/'
+description = """The AOFlagger is a tool that can find and remove radio-frequency interference (RFI)
+in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible,
+and the tools are applicable to a wide set of telescopes."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [
+    {
+        'source_urls': [
+            'https://gitlab.com/aroffringa/%(namelower)s/-/package_files/96704214/'
+        ],
+        'filename': '%(namelower)s-v%(version)s.tar.bz2',
+        'download_filename': 'download'
+    },
+]
+checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+dependencies = [
+    ('casacore', '3.5.0'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
+    ('GSL', '2.7'),
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('Lua', '5.4.6'),
+    ('libpng', '1.6.40'),
+    ('libxml2', '2.11.5'),
+]
+
+sanity_check_paths = {
+    'files': ['include/%(namelower)s.h', 'bin/%(namelower)s'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = [('%(namelower)s', '-v')]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb

@@ -0,0 +1,24 @@
+name = 'Armadillo'
+version = '12.8.0'
+
+homepage = 'https://arma.sourceforge.net/'
+description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
+ a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
+ as well as a subset of trigonometric and statistics functions."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = ['https://sourceforge.net/projects/arma/files']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['a89bb6fece5ce9fdd1d01a4bc145cf7cc0b939c5777cca46de69c2f5e3412cf0']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+dependencies = [
+    ('Boost', '1.83.0'),
+    ('arpack-ng', '3.9.0'),
+]
+
+
+moduleclass = 'numlib'

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb

@@ -0,0 +1,37 @@
+# Author:    Robert Mijakovic <[email protected]>
+
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.9.0'
+
+homepage = 'https://github.com/opencollab/arpack-ng'
+description = "ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+github_account = 'opencollab'
+
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('pkgconf', '2.0.3'),
+]
+dependencies = [
+    ('Eigen', '3.4.0'),
+]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT,
+              'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-13.2.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.Python'
+version = '1.83.0'
+
+homepage = 'https://boostorg.github.io/python'
+description = """Boost.Python is a C++ library which enables seamless interoperability between C++
+ and the Python programming language."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_1_83_0.tar.gz']
+checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628']
+
+dependencies = [
+    ('Boost', '1.83.0'),
+    ('Python', '3.11.5'),
+]
+
+only_python_bindings = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb

@@ -0,0 +1,43 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'ConfigureMake'
+
+name = 'CFITSIO'
+version = '4.3.1'
+
+homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/'
+description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
+FITS (Flexible Image Transport System) data format."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-3.48_install_test_data.patch']
+checksums = [
+    {SOURCELOWER_TAR_GZ: '47a7c8ee05687be1e1d8eeeb94fb88f060fbf3cd8a4df52ccb88d5eb0f5062be'},
+    {'%(name)s-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+# curl for HTTPs support
+dependencies = [
+    ('cURL', '8.3.0'),
+]
+
+# make would create just static libcfitsio.a.
+# Let's create dynamic lib and testprog too.
+buildopts = "&& make shared && make testprog"
+
+
+sanity_check_paths = {
+    'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ['cd %(installdir)s/share && testprog']
+
+moduleclass = 'lib'

easybuild/easyconfigs/c/casacore/casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch

@@ -0,0 +1,21 @@
+From 68e43f489abd3d4f1e2fe54a42695396703aa81a Mon Sep 17 00:00:00 2001
+From: Chris Broekema <[email protected]>
+Date: Tue, 9 May 2023 12:43:34 +0200
+Subject: [PATCH] add C-style header to fix GCC 13.1 compile error on uint16_t
+ not being a valid type (#1309)
+
+---
+ tables/Dysco/bytepacker.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/tables/Dysco/bytepacker.h b/tables/Dysco/bytepacker.h
+index d62754046..cb1193b41 100644
+--- a/tables/Dysco/bytepacker.h
++++ b/tables/Dysco/bytepacker.h
+@@ -2,6 +2,7 @@
+ #define DYSCO_BYTE_PACKER_H
+
+ #include <stdexcept>
++#include <cstdint>
+
+ namespace dyscostman {

easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb

@@ -0,0 +1,62 @@
+easyblock = 'CMakeMake'
+
+name = 'casacore'
+version = '3.5.0'
+
+homepage = 'https://github.com/casacore/casacore'
+description = """A suite of C++ libraries for radio astronomy data processing.
+The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime.
+Thus user's can update them.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/archive']
+sources = ['v%(version)s.tar.gz']
+patches = ['casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch']
+checksums = [
+    '63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91',  # casacore-3.5.0.tar.gz
+    '7b35d21cd654a7a215d604310f5372319ad21b6261f4a7ae038912b97ef22983',  # add-C-style-header-for-GCC-13.1.patch
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('wget', '1.21.4'),
+]
+dependencies = [
+    ('CFITSIO', '4.3.1'),
+    ('WCSLIB', '7.11'),
+    ('HDF5', '1.14.3'),
+    ('GSL', '2.7'),
+    ('Boost.Python', '1.83.0'),
+    ('SciPy-bundle', '2023.11'),
+    ('ncurses', '6.4'),
+]
+
+configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" '
+configopts += '-DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON '
+configopts += '-DUSE_MPI=ON '
+
+local_download_cmd = 'wget --retry-connrefused ftp://[email protected]/outgoing/Measures/WSRT_Measures.ztar '
+local_download_cmd += '-O /tmp/WSRT_Measures.ztar '
+
+# Install casacore data
+postinstallcmds = [
+    local_download_cmd,
+    "tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data",
+]
+
+sanity_check_paths = {
+    'files': [
+        'lib/libcasa_casa.%s' % SHLIB_EXT,
+        'lib/libcasa_mirlib.%s' % SHLIB_EXT,
+        'lib/libcasa_ms.%s' % SHLIB_EXT,
+    ],
+    'dirs': ['bin', 'include/%(name)s'],
+}
+
+sanity_check_commands = [('measuresdata', '')]
+
+moduleclass = 'lib'

easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb

@@ -0,0 +1,57 @@
+easyblock = 'CMakeMake'
+
+name = 'DP3'
+version = '6.0'
+
+homepage = 'https://dp3.readthedocs.io/'
+description = "DP3: streaming processing pipeline for radio interferometric data."
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [
+    {
+        'filename': '%(name)s-v%(version)s.tar.gz',
+        # Repo uses git submodules, which are not included in the release tarballs.
+        # Thus, we let EasyBuild download directly from the git repository.
+        'git_config': {
+            'url': 'https://git.astron.nl/RD',
+            'repo_name': '%(name)s',
+            'tag': 'v%(version)s',
+            'clone_into': '%(name)s',
+            'recursive': True
+        }
+    },
+]
+patches = ['DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch']
+checksums = [
+    None,  # checksum for git clone source is non-deterministic
+    # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch
+    '7f5069388846c9c715013d5a3a267a6d8e266520445a6427e63e9d52d3046c9d',
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+dependencies = [
+    ('casacore', '3.5.0'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
+    ('WCSLIB', '7.11'),
+    ('GSL', '2.7'),
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('EveryBeam', '0.5.2'),
+    ('Armadillo', '12.8.0'),
+    ('AOFlagger', '3.4.0'),
+    ('IDG', '1.2.0'),
+]
+
+
+sanity_check_paths = {
+    'files': ['include/include/%(namelower)s/base/%(name)s.h', 'bin/%(name)s'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = [('%(name)s', '--version')]
+
+moduleclass = 'astro'

easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch

@@ -0,0 +1,19 @@
+# Fix for XSIMD build error on Neoverse V1
+# See: https://github.com/xtensor-stack/xsimd/issues/1005 and https://github.com/xtensor-stack/xsimd/commit/1d8536b
+# Mar 11th 2024 by T. Kok (SURF)
+--- DP3.orig/external/aocommon/CMake/FetchXTensor.cmake	2024-03-11 11:20:32.024804259 +0100
++++ DP3/external/aocommon/CMake/FetchXTensor.cmake	2024-03-11 11:21:32.851493709 +0100
+@@ -6,7 +6,7 @@
+   set(xtl_GIT_TAG b3d0091a77af52f1b479b5b768260be4873aa8a7)
+ endif()
+ if (NOT xsimd_GIT_TAG)
+-  set(xsimd_GIT_TAG 2f5eddf8912c7e2527f0c50895c7560b964d29af)
++  set(xsimd_GIT_TAG 1d8536b393171b899031f01b7c2d63858b05665c)
+ endif()
+ if (NOT xtensor_GIT_TAG)
+   set(xtensor_GIT_TAG 0.24.2)
+@@ -65,3 +65,4 @@
+   endif()
+
+ endforeach()
++

easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb

@@ -0,0 +1,49 @@
+easyblock = 'CMakeMake'
+
+name = 'EveryBeam'
+version = '0.5.2'
+
+homepage = 'https://everybeam.readthedocs.io/'
+description = """Library that provides the antenna response pattern for several instruments,
+such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [
+    {
+        'filename': '%(name)s-v%(version)s.tar.gz',
+        # Repo uses git submodules, which are not included in the release tarballs.
+        # Thus, we let EasyBuild download directly from the git repository.
+        'git_config': {
+            'url': 'https://git.astron.nl/RD',
+            'repo_name': '%(name)s',
+            'tag': 'v%(version)s',
+            'clone_into': '%(name)s',
+            'recursive': True
+        }
+    },
+]
+checksums = [None]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('wget', '1.21.4'),
+]
+dependencies = [
+    ('casacore', '3.5.0'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
+    ('WCSLIB', '7.11'),
+    ('GSL', '2.7'),
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('libxml2', '2.11.5'),
+]
+
+
+sanity_check_paths = {
+    'files': ['include/%(name)s/beamformer.h', 'lib/libeverybeam.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'