Merge branch 'develop' into 5.0.x

easybuild/easyblocks/generic/cmakemake.py

@@ -274,6 +274,11 @@ def configure_step(self, srcdir=None, builddir=None):
             # see https://github.com/Kitware/CMake/commit/3ec9226779776811240bde88a3f173c29aa935b5
             options['CMAKE_SKIP_RPATH'] = 'ON'
 
+        # make sure that newer CMAKE picks python based on location, not just the newest python
+        # Avoids issues like e.g. https://github.com/EESSI/software-layer/pull/370#issuecomment-1785594932
+        if LooseVersion(self.cmake_version) >= '3.15':
+            options['CMAKE_POLICY_DEFAULT_CMP0094'] = 'NEW'
+
         # show what CMake is doing by default
         options['CMAKE_VERBOSE_MAKEFILE'] = 'ON'
 

easybuild/easyblocks/m/mcr.py

@@ -157,8 +157,13 @@ def set_subdir(self):
         """Determine subdirectory in installation directory"""
         # no-op is self.subdir is already set
         if self.subdir is None:
-            # determine subdirectory (e.g. v84 (2014a, 2014b), v85 (2015a), ...)
-            subdirs = glob.glob(os.path.join(self.installdir, 'v[0-9][0-9]*'))
+            # determine subdirectory
+            if LooseVersion(self.version) < LooseVersion('R2022b'):
+                # (e.g. v84 (2014a, 2014b), v85 (2015a), ...)
+                subdirs = glob.glob(os.path.join(self.installdir, 'v[0-9][0-9]*'))
+            else:
+                # (e.g. R2023a, R2023b, ...)
+                subdirs = glob.glob(os.path.join(self.installdir, 'R[0-9][0-9][0-9][0-9]*'))
             if len(subdirs) == 1:
                 self.subdir = os.path.basename(subdirs[0])
             else:

easybuild/easyblocks/p/petsc.py

@@ -256,6 +256,10 @@ def configure_step(self):
                         ss_libs = ["UMFPACK", "KLU", "SPQR", "CHOLMOD", "BTF", "CCOLAMD",
                                    "COLAMD", "CXSparse", "LDL", "RBio", "SLIP_LU", "CAMD", "AMD"]
 
+                    # SLIP_LU was replaced by SPEX in SuiteSparse >= 6.0
+                    if LooseVersion(get_software_version('SuiteSparse')) >= LooseVersion("6.0"):
+                        ss_libs = [x if x != "SLIP_LU" else "SPEX" for x in ss_libs]
+
                     suitesparse_inc = os.path.join(suitesparse, "include")
                     inc_spec = "-include=[%s]" % suitesparse_inc
 
@@ -274,8 +278,9 @@ def configure_step(self):
                 self.cfg.update('configopts', ' '.join([withdep + spec for spec in ['=1', inc_spec, lib_spec]]))
 
             # set PETSC_DIR for configure (env) and build_step
-            env.setvar('PETSC_DIR', self.cfg['start_dir'])
-            self.cfg.update('buildopts', 'PETSC_DIR=%s' % self.cfg['start_dir'])
+            petsc_dir = self.cfg['start_dir'].rstrip(os.path.sep)
+            env.setvar('PETSC_DIR', petsc_dir)
+            self.cfg.update('buildopts', 'PETSC_DIR=%s' % petsc_dir)
 
             if self.cfg['sourceinstall']:
                 if self.petsc_arch:

easybuild/easyblocks/p/python.py

@@ -376,16 +376,19 @@ def configure_step(self):
             if tcltk_maj_min_ver != '.'.join(tkver.split('.')[:2]):
                 raise EasyBuildError("Tcl and Tk major/minor versions don't match: %s vs %s", tclver, tkver)
 
-            self.cfg.update('configopts', "--with-tcltk-includes='-I%s/include -I%s/include'" % (tcl, tk))
-
             tcl_libdir = os.path.join(tcl, get_software_libdir('Tcl'))
             tk_libdir = os.path.join(tk, get_software_libdir('Tk'))
             tcltk_libs = "-L%(tcl_libdir)s -L%(tk_libdir)s -ltcl%(maj_min_ver)s -ltk%(maj_min_ver)s" % {
                 'tcl_libdir': tcl_libdir,
                 'tk_libdir': tk_libdir,
                 'maj_min_ver': tcltk_maj_min_ver,
             }
-            self.cfg.update('configopts', "--with-tcltk-libs='%s'" % tcltk_libs)
+            if LooseVersion(self.version) < '3.11':
+                self.cfg.update('configopts', "--with-tcltk-includes='-I%s/include -I%s/include'" % (tcl, tk))
+                self.cfg.update('configopts', "--with-tcltk-libs='%s'" % tcltk_libs)
+            else:
+                env.setvar('TCLTK_CFLAGS', '-I%s/include -I%s/include' % (tcl, tk))
+                env.setvar('TCLTK_LIBS', tcltk_libs)
 
         # don't add user site directory to sys.path (equivalent to python -s)
         # This matters e.g. when python installs the bundled pip & setuptools (for >= 3.4)

easybuild/easyblocks/r/r.py

@@ -70,8 +70,11 @@ def configure_step(self):
         for dep in ['Tcl', 'Tk']:
             root = get_software_root(dep)
             if root:
-                dep_config = os.path.join(root, 'lib', '%sConfig.sh' % dep.lower())
-                self.cfg.update('configopts', '--with-%s-config=%s' % (dep.lower(), dep_config))
+                for libdir in ['lib', 'lib64']:
+                    dep_config = os.path.join(root, libdir, '%sConfig.sh' % dep.lower())
+                    if os.path.exists(dep_config):
+                        self.cfg.update('configopts', '--with-%s-config=%s' % (dep.lower(), dep_config))
+                        break
 
         if "--with-x=" not in self.cfg['configopts'].lower():
             if get_software_root('X11'):

easybuild/easyblocks/v/vep.py

@@ -30,6 +30,7 @@
 import easybuild.tools.environment as env
 from easybuild.easyblocks.perl import get_major_perl_version
 from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import print_warning
 from easybuild.tools.filetools import apply_regex_substitutions
 from easybuild.tools.modules import get_software_version, get_software_root
@@ -48,6 +49,15 @@ def __init__(self, *args, **kwargs):
 
         self.api_mods_subdir = os.path.join('modules', 'api')
 
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Extra easyconfig parameters specific to VEP easyblock."""
+        extra_vars = EasyBlock.extra_options(extra_vars)
+        extra_vars.update({
+            'species': ['all', "Comma-separated list of species to pass to INSTALL.pl", CUSTOM],
+        })
+        return extra_vars
+
     def configure_step(self):
         """No custom configuration procedure for VEP."""
         pass
@@ -97,8 +107,8 @@ def install_step(self):
             # l: Bio::DB::HTS, should be provided via EasyBuild
             # p: plugins
             '--AUTO af',
-            # install all species
-            '--SPECIES all',
+            # install selected species
+            '--SPECIES %s' % self.cfg['species'],
             # don't update VEP during installation
             '--NO_UPDATE',
             # location to install Perl API modules into