Merge pull request easybuilders#20106 from lexming/20240313114329_new…

…_pr_ResistanceGA425 strip Suppressor out of ResistanceGA
bedroge · Nov 20, 2024 · 30c6885 · 30c6885
2 parents dd036b4 + ac70aac
commit 30c6885
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Showing 5 changed files with 37 additions and 28 deletions.
diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb
@@ -403,6 +403,10 @@ exts_list = [
     }),
 ]
 
-sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"]
+_julia_env = "%(installdir)s/environments/v" + '.'.join(_julia_ver.split('.')[:2])
+
+sanity_check_commands = [
+    """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % _julia_env,
+]
 
 moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb
@@ -16,8 +16,6 @@ dependencies = [
     ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM),
 ]
 
-preinstallopts = "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && "
-
 exts_default_options = {
     'source_tmpl': 'v%(version)s.tar.gz',
 }
@@ -224,17 +222,15 @@ exts_list = [
     }),
 ]
 
-sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"%(name)s\")'"]
+local_julia_env = "%(installdir)s/environments/v" + '.'.join(local_juliaver.split('.')[:2])
+
+sanity_check_commands = [
+    """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % local_julia_env,
+]
 
 sanity_check_paths = {
     'files': [],
     'dirs': ['packages/%(name)s'],
 }
 
-# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly
-# This is a workaround to make Julia find the correct libraries
-modluafooter = """
-prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia")
-"""
-
 moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb
@@ -14,8 +14,9 @@ toolchain = {'name': 'foss', 'version': '2022a'}
 dependencies = [
     ('R', '4.2.1'),
     ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM),
+    ('RCall', '0.13.17', versionsuffix),  # order matters! RCall must be loaded before Circuitscape (#19281)
     ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM),
-    ('RCall', '0.13.17', versionsuffix),
+    ('Suppressor', '0.2.4', '-Julia-%s' % local_juliaver, SYSTEM),
 ]
 
 exts_defaultclass = 'RPackage'
@@ -31,14 +32,6 @@ exts_default_options = {
 }
 
 exts_list = [
-    ('Suppressor', '0.2.4', {
-        'easyblock': 'JuliaPackage',
-        'exts_filter': ("julia -e 'using %(ext_name)s'", ''),
-        'preinstallopts': "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && ",
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/JuliaIO/Suppressor.jl/archive/'],
-        'checksums': ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'],
-    }),
     ('GA', '3.2.2', {
         'checksums': ['6245c634a11b8414bde7ed326b8c615512645489b19969619484c865e900bf8c'],
     }),
@@ -73,12 +66,6 @@ modextrapaths = {
     'R_LIBS_SITE': '',
 }
 
-# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly
-# This is a workaround to make Julia find the correct libraries
-modluafooter = """
-prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia")
-"""
-
 sanity_check_paths = {
     'files': [],
     'dirs': ['%(name)s'],

diff --git a/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb
@@ -0,0 +1,22 @@
+easyblock = 'JuliaPackage'
+
+name = 'Suppressor'
+version = '0.2.4'
+_julia_ver = '1.9.2'
+versionsuffix = "-Julia-%s" % _julia_ver
+
+homepage = 'https://github.com/JuliaIO/Suppressor.jl'
+description = """Julia macros for suppressing and/or capturing output (STDOUT),
+warnings (STDERR) or both streams at the same time."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/JuliaIO/Suppressor.jl/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4']
+
+dependencies = [
+    ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM),
+]
+
+moduleclass = 'lib'
diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
@@ -1212,12 +1212,12 @@ def test_pr_sanity_check_paths(self):
         """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock."""
 
         # some generic easyblocks already have a decent customised sanity_check_paths,
-        # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle,
+        # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle & JuliaPackage, PerlBundle,
         #           PythonBundle & PythonPackage;
         # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check.
         whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage',
-                     'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC',
-                     'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain']
+                     'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'JuliaPackage',
+                     'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain']
         # Bundles of dependencies without files of their own
         # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore,
         # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co,