{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0, PyVO v1.7. RMextract v0.5.1, SAGECal v0.8.4, toil-cwl v8.2.0

easybuild/easyconfigs/c/cwltool/cwltool-3.1.20250110105449-foss-2023b.eb

@@ -0,0 +1,88 @@
+easyblock = 'PythonBundle'
+
+name = 'cwltool'
+version = '3.1.20250110105449'
+
+homepage = "https://cwltool.readthedocs.io/"
+
+description = """
+This is the reference implementation of the Common Workflow Language open
+standards. It is intended to be feature complete and provide comprehensive
+validation of CWL files as well as provide other tools related to working with
+CWL.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('hatchling', '1.18.0')
+]
+
+# Based on https://github.com/common-workflow-language/cwltool/blob/3.1.20250110105449/pyproject.toml
+dependencies = [
+    ('nodejs', '20.9.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('ruamel.yaml', '0.18.6'),
+    ('RDFlib', '7.1.4'),
+    ('lxml', '4.9.3'),
+    ('networkx', '3.2.1'),
+    ('pydot', '2.0.0'),
+]
+
+exts_list = [
+    ('mistune', '3.0.2', {
+        'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'],
+    }),
+    ('mypy-extensions', '1.1.0', {
+        'patches': ['mypy-extensions-1.1.0_license.patch'],
+        'source_tmpl': 'mypy_extensions-%(version)s.tar.gz',
+        'checksums': [
+            {'mypy_extensions-1.1.0.tar.gz': '52e68efc3284861e772bbcd66823fde5ae21fd2fdb51c62a211403730b916558'},
+            {'mypy-extensions-1.1.0_license.patch': 'ad6f0666755104f94fc33f5da56dbf218517312d2be5bdc2877e3bfd879d20af'},
+        ],
+    }),
+    ('schema-salad', '8.9.20250408123006', {
+        'modulename': 'schema_salad',
+        'source_tmpl': 'schema_salad-%(version)s.tar.gz',
+        'checksums': ['7b95bf6ab6960b4b60605e4a908cd56f1a30ec7c16901af6e46a98e152b9f069'],
+    }),
+    ('prov', '1.5.1', {
+        'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'],
+    }),
+    ('humanfriendly', '10.0', {
+        'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
+    }),
+    ('coloredlogs', '15.0.1', {
+        'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
+    }),
+    ('argcomplete', '3.6.2', {
+        'checksums': ['d0519b1bc867f5f4f4713c41ad0aba73a4a5f007449716b16f385f2166dc6adf'],
+    }),
+    ('cwl-upgrader', '1.2.12', {
+        'source_tmpl': 'cwl_upgrader-%(version)s.tar.gz',
+        'modulename': 'cwlupgrader',
+        'checksums': ['0d4e514d32d96b60c5300de9baa30a583b09066c9aa78dd6aa7744164d72dc5c'],
+    }),
+    ('spython', '0.3.14', {
+        'checksums': ['8ad53ef034395cfa2d8a710cc1c3638e4475e5bbc6a2842d317db8013c2e4188'],
+    }),
+    ('rich-argparse', '1.7.1', {
+        'patches': ['rich-argparse-1.7.1_unkown_classifier.patch'],
+        'source_tmpl': 'rich_argparse-%(version)s.tar.gz',
+        'checksums': [
+            {'rich_argparse-1.7.1.tar.gz': 'd7a493cde94043e41ea68fb43a74405fa178de981bf7b800f7a3bd02ac5c27be'},
+            {'rich-argparse-1.7.1_unkown_classifier.patch':
+             '63e62dba328b2b857425798986af180b1baf228be5f8fd63e5b3cc43e546f972'},
+        ],
+    }),
+    ('cwl-utils', '0.38', {
+        'source_tmpl': 'cwl_utils-%(version)s.tar.gz',
+        'checksums': ['1122e1f4cc8f48f9f51ddcb8114fa9e3862d717fd4aacb00f4428008f19e9fec'],
+    }),
+    (name, version, {
+        'checksums': ['91d3a5946a2afd3e8c4d7e38a53690ad06e3dd88c1d1e1afa368caa41ec3038f'],
+    }),
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/c/cwltool/mypy-extensions-1.1.0_license.patch

@@ -0,0 +1,19 @@
+# Author: Caspar van Leeuwen
+# Company: SURF
+# Without this patch, we get an error
+# flit_core.config.ConfigError: license field should be <class 'dict'>, not <class 'str'>
+# because PEP 621 says the license must be a dict, if it is not just a file
+# Probably, this happens only with sufficiently new versions of e.g. flit_core, which is
+# probably why it wasn't an issue for upstream
+diff -Nru mypy_extensions-1.1.0.orig/pyproject.toml mypy_extensions-1.1.0/pyproject.toml
+--- mypy_extensions-1.1.0.orig/pyproject.toml	2025-06-16 16:16:04.395222990 +0200
++++ mypy_extensions-1.1.0/pyproject.toml	2025-06-16 16:24:51.865105381 +0200
+@@ -10,7 +10,7 @@
+ authors     = [
+     {name = "The mypy developers", email = "jukka.lehtosalo@iki.fi"}
+ ]
+-license     = "MIT"
++license     = {text = "MIT"}
+ classifiers = [
+     "Development Status :: 5 - Production/Stable",
+     "Environment :: Console",

easybuild/easyconfigs/c/cwltool/rich-argparse-1.7.1_unkown_classifier.patch

@@ -0,0 +1,16 @@
+# Author: Caspar van Leeuwen
+# Company: SURF
+# Python 3.14 is not an officially recognized classifier yet, even if the rich-argparse
+# already claims to support it. As a result, hatchling refuses to build it
+# Can be fixed by removing the classifier from the pyproject.toml
+diff -Nru rich_argparse-1.7.1.orig/pyproject.toml rich_argparse-1.7.1/pyproject.toml
+--- rich_argparse-1.7.1.orig/pyproject.toml	2025-06-16 16:56:11.057910803 +0200
++++ rich_argparse-1.7.1/pyproject.toml	2025-06-16 16:56:19.326904158 +0200
+@@ -23,7 +23,6 @@
+   "Programming Language :: Python :: 3.11",
+   "Programming Language :: Python :: 3.12",
+   "Programming Language :: Python :: 3.13",
+-  "Programming Language :: Python :: 3.14",
+   "Topic :: Software Development :: User Interfaces",
+ ]
+ keywords = ["argparse", "rich", "help-formatter", "optparse"]

easybuild/easyconfigs/d/dysco/dysco-1.3-foss-2023b.eb

@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'dysco'
+version = '1.3'
+
+homepage = 'https://github.com/aroffringa/dysco'
+description = """
+The Dysco compression technique is explained in the article "Compression of
+interferometric radio-astronomical data", A. R. Offringa (2016;
+http://arxiv.org/abs/1609.02019). If you use this software, please cite the
+paper.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['02cb53cc0a95a17a04fbaa6063b39641725b81f279b08e85761b01e8f186609f']
+github_account = 'aroffringa'
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('HDF5', '1.14.3'),
+    ('casacore', '3.5.0'),
+]
+
+sanity_check_paths = {
+    'files': [f'lib/libdyscostman.{SHLIB_EXT}', 'bin/dscompress'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'astro'

easybuild/easyconfigs/l/LINC/LINC-5.0-foss-2023b.eb

@@ -0,0 +1,116 @@
+easyblock = 'PythonBundle'
+
+name = 'LINC'
+version = '5.0'
+
+homepage = "https://linc.readthedocs.io/en/latest/"
+
+description = """
+LINC is a pipeline to correct for various instrumental and ionospheric effects in both LOFAR HBA and LOFAR LBA
+observations.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('scikit-build', '0.17.6'),
+    ('wget', '1.21.4'),  # Needed for the test step
+]
+
+# Based on https://git.astron.nl/RD/LINC/-/tree/releases/v5.0?ref_type=heads#software-requirements
+dependencies = [
+    ('Boost', '1.83.0'),
+    ('Boost.Python-NumPy', '1.83.0'),  # Boost_numpy is required for bdsf
+    ('DP3', '6.2'),
+    ('LoSoTo', '2.5.0'),
+    ('LSMTool', '1.7.0'),
+    ('EveryBeam', '0.6.1'),  # Should be 0.6.2 or newer according to the docs?
+    ('SAGECal', '0.8.4'),
+    ('RMextract', '0.5.1'),
+    ('AOFlagger', '3.4.0'),
+    ('WSClean', '3.5'),
+    ('IDG', '1.2.0',),
+    ('LofarStMan', '1.0'),
+    ('dysco', '1.3'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('python-casacore', '3.5.2'),
+    ('astropy', '7.0.0'),
+    ('h5py', '3.11.0'),
+    ('cwltool', '3.1.20250110105449'),
+    ('toil-cwl', '8.2.0'),
+]
+
+# Get data needed to run the test
+local_pretestopts = 'mkdir -p data && '
+local_pretestopts += 'wget -nv https://support.astron.nl/software/ci_data/linc/test_data.tar.gz '
+local_pretestopts += '-O test_data.tar.gz && '
+local_pretestopts += 'wget -nv https://support.astron.nl/software/ci_data/linc/results_calibrator.tar.gz '
+local_pretestopts += '-O results_calibrator.tar.gz && tar xfz test_data.tar.gz -C data && '
+local_pretestopts += 'tar xfz results_calibrator.tar.gz -C data && '
+
+# Patch the workflow file so that it looks for the skymodels within the LINC (temporary) install dir
+local_pretestopts += 'sed -i -e "s|\"/usr/local/share/linc/skymodels/A-Team_Midres.skymodel\"|'
+local_pretestopts += '\"${EB_PYTHONPACKAGE_TEST_INSTALLDIR}/share/linc/skymodels/A-Team_Midres.skymodel\"|" '
+local_pretestopts += '-e "s|\"/usr/local/share/linc/skymodels\"|'
+local_pretestopts += '\"${EB_PYTHONPACKAGE_TEST_INSTALLDIR}/share/linc/skymodels\"|" test_jobs/HBA_target.json && '
+
+# Ensure SLURM env vars are emptied, otherwise OpenMPI may complain that OMPI wasn't build with SLURMs PMI support
+local_pretestopts += 'for i in $(env | grep SLURM); do unset "${i%=*}"; done && '
+
+# Disable OpenMP parallelism, to avoid BLAS error with DP3 and hang in clocktek
+# LINC uses its own threading, which seems to clash with a multithreaded BLAS
+local_pretestopts += 'export OMP_NUM_THREADS=1 && export OPENBLAS_NUM_THREADS=1 && '
+
+# Set the LINC_DATA_ROOT and make sure to include the python scripts (which are in /bin for some reason)
+# to the PYTHONPATH
+local_pretestopts += 'export LINC_DATA_ROOT=$EB_PYTHONPACKAGE_TEST_INSTALLDIR/share/linc && '
+local_pretestopts += 'export PYTHONPATH=$PYTHONPATH:$EB_PYTHONPACKAGE_TEST_INSTALLDIR/bin && '
+local_testopts = '--no-container --preserve-entire-environment --outdir results --leave-tmpdir '
+local_testopts += '--tmpdir-prefix run_hba_calibrator '
+local_testopts += '$EB_PYTHONPACKAGE_TEST_INSTALLDIR/share/linc/workflows/HBA_target.cwl '
+local_testopts += 'test_jobs/HBA_target.json'
+
+exts_list = [
+    ('pyregion', '2.3.0', {
+        'checksums': ['e8498711421173239689de523bb465245f5551a18a181cb4956d87f9c7464925'],
+    }),
+    ('backports.shutil_get_terminal_size', '1.0.0', {
+        'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'],
+    }),
+    ('bdsf', '1.13.0.post2', {
+        'checksums': ['2a91647fcdb1f6574958312d85decd4529a10e710926f11300a2388f4c9e25cd'],
+        'preinstallopts': 'export CMAKE_ARGS="-DF2PY_EXECUTABLE=$EBROOTSCIPYMINBUNDLE/bin/f2py" && ',
+    }),
+    (name, version, {
+        'modulename': False,
+        'sources': [{
+            'filename': '%(name)s-v%(version)s.tar.xz',
+            'git_config': {
+                'url': 'https://git.astron.nl/RD/',
+                'repo_name': 'LINC',
+                'commit': 'v%(version)s',
+                'recursive': True,
+                'keep_git_dir': True
+            },
+        }],
+        # We cannot get a reproducible checksum, because we need to do keep_git_dir for
+        # setuptools_scm to determine the version
+        'checksums': [None],
+        'testinstall': True,
+        'pretestopts': local_pretestopts,
+        'runtest': 'cwltool',
+        'testopts': local_testopts,
+    }),
+]
+
+modloadmsg = """
+Certain components of LINC (e.g. DP3) do not support a multithreaded BLAS. You may need to set OMP_NUM_THREADS=1 and
+OPENBLAS_NUM_THREADS=1. If you're running the pipeline within a SLURM environment, you may need to clear all SLURM
+environment variables from your environment (e.g. using 'for i in $(env | grep SLURM); do unset "${i%=*}"; done').
+"""
+
+moduleclass = 'astro'

easybuild/easyconfigs/l/LSMTool/LSMTool-1.7.0-foss-2023b.eb

@@ -0,0 +1,35 @@
+easyblock = 'PythonBundle'
+
+name = 'LSMTool'
+version = '1.7.0'
+
+homepage = "https://lsmtool.readthedocs.io/en/latest/"
+
+description = """
+LSMTool is a Python package which allows for the manipulation of LOFAR sky models in the makesourcedb format.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('scikit-build-core', '0.9.3'),
+]
+
+# Based on https://git.astron.nl/RD/LSMTool/-/tree/v1.7.0?ref_type=tags#dependencies
+dependencies = [
+    ('EveryBeam', '0.6.1'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('astropy', '7.0.0'),
+    ('python-casacore', '3.5.2'),
+    ('PyVO', '1.7'),  # optional
+]
+
+exts_list = [
+    ('lsmtool', version, {
+        'checksums': ['88cacd79020f60d8dda0e16fe570aede6cee7a93099ae8a86f9d5e7c2e831448'],
+    }),
+]
+
+moduleclass = 'astro'

easybuild/easyconfigs/l/LoSoTo/LoSoTo-2.5.0-foss-2023b.eb

@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'LoSoTo'
+version = '2.5.0'
+
+homepage = "https://revoltek.github.io/losoto/"
+
+description = """
+LoSoTo: LOFAR solutions tool
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('Cython', '3.0.10'),
+]
+
+dependencies = [
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('PyTables', '3.9.2'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('python-casacore', '3.5.2'),
+]
+
+github_account = 'revoltek'
+
+exts_list = [
+    ('configparser', '7.2.0', {
+        'checksums': ['b629cc8ae916e3afbd36d1b3d093f34193d851e11998920fdcfc4552218b7b70'],
+    }),
+    (name, version, {
+        # Note that this still works for 2.5.0, but current master uses setuptools_scm
+        # So in the future this will have to be replaced by a 'git_config' with 'keep_git_dir': 'True'
+        # The checksum will then also need to be removed
+        # See LINC-5.0-foss-2023b.eb as an example
+        'source_urls': [GITHUB_LOWER_SOURCE],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['e475e04af9561e5581ac11e9359bd08b1b71b28c59b62cf73976addb93ce3c81'],
+    }),
+]
+
+moduleclass = 'astro'

easybuild/easyconfigs/l/LofarStMan/LofarStMan-1.0-foss-2023b.eb

@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'LofarStMan'
+version = '1.0'
+
+homepage = 'https://github.com/lofar-astron/LofarStMan'
+description = """
+This package provides a casacore storage manager to read raw correlator output of the LOFAR telescope.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['25d33c51f8ce9059c2c95424526c1eae8838f0163a9a0e05cf9db0715ebd022a']
+github_account = 'lofar-astron'
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('casacore', '3.5.0'),
+]
+
+sanity_check_paths = {
+    'files': [f'lib/liblofarstman.{SHLIB_EXT}'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'astro'