Merge branch '5.0.x' of github.com:branfosj/easybuild-easyblocks into…

… 20240129114808_new_pr_UVhZoEOVCC

easybuild/easyblocks/a/anaconda.py

@@ -34,7 +34,7 @@
 
 from easybuild.easyblocks.generic.binary import Binary
 from easybuild.tools.filetools import adjust_permissions, remove_dir
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 class EB_Anaconda(Binary):
@@ -51,7 +51,7 @@ def install_step(self):
         # Anacondas own install instructions specify "bash [script]" despite using different shebangs
         cmd = "%s bash ./%s -p %s -b -f" % (self.cfg['preinstallopts'], install_script, self.installdir)
         self.log.info("Installing %s using command '%s'..." % (self.name, cmd))
-        run_cmd(cmd, log_all=True, simple=True)
+        run_shell_cmd(cmd)
 
     def make_module_req_guess(self):
         """

easybuild/easyblocks/b/binutils.py

@@ -38,7 +38,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import apply_regex_substitutions, copy_file
 from easybuild.tools.modules import get_software_libdir, get_software_root
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import RISCV, get_cpu_family, get_shared_lib_ext
 from easybuild.tools.utilities import nub
 
@@ -70,11 +70,11 @@ def determine_used_library_paths(self):
         compiler_cmd = os.environ.get('CC', 'gcc')
 
         # determine library search paths for GCC
-        stdout, ec = run_cmd('LC_ALL=C "%s" -print-search-dirs' % compiler_cmd, simple=False, log_all=True)
-        if ec:
+        res = run_shell_cmd('LC_ALL=C "%s" -print-search-dirs' % compiler_cmd)
+        if res.exit_code:
             raise EasyBuildError("Failed to determine library search dirs from compiler %s", compiler_cmd)
 
-        m = re.search('^libraries: *=(.*)$', stdout, re.M)
+        m = re.search('^libraries: *=(.*)$', res.output, re.M)
         paths = nub(os.path.abspath(p) for p in m.group(1).split(os.pathsep))
         self.log.debug('Unique library search paths from compiler %s: %s', compiler_cmd, paths)
 
@@ -259,14 +259,14 @@ def sanity_check_step(self):
         if any(dep['name'] == 'zlib' for dep in build_deps):
             for binary in binaries:
                 bin_path = os.path.join(self.installdir, 'bin', binary)
-                out, _ = run_cmd("file %s" % bin_path, simple=False)
-                if re.search(r'statically linked', out):
+                res = run_shell_cmd("file %s" % bin_path)
+                if re.search(r'statically linked', res.output):
                     # binary is fully statically linked, so no chance for dynamically linked libz
                     continue
 
                 # check whether libz is linked dynamically, it shouldn't be
-                out, _ = run_cmd("ldd %s" % bin_path, simple=False)
-                if re.search(r'libz\.%s' % shlib_ext, out):
-                    raise EasyBuildError("zlib is not statically linked in %s: %s", bin_path, out)
+                res = run_shell_cmd("ldd %s" % bin_path)
+                if re.search(r'libz\.%s' % shlib_ext, res.output):
+                    raise EasyBuildError("zlib is not statically linked in %s: %s", bin_path, res.output)
 
         super(EB_binutils, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

easybuild/easyblocks/b/boost.py

@@ -52,7 +52,7 @@
 from easybuild.tools.config import ERROR
 from easybuild.tools.filetools import apply_regex_substitutions, read_file, symlink, which, write_file
 from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import AARCH64, POWER, UNKNOWN
 from easybuild.tools.systemtools import get_cpu_architecture, get_glibc_version, get_shared_lib_ext
 
@@ -144,7 +144,7 @@ def configure_step(self):
 
         cmd = "%s ./bootstrap.sh --with-toolset=%s --prefix=%s %s"
         tup = (self.cfg['preconfigopts'], toolset, self.installdir, self.cfg['configopts'])
-        run_cmd(cmd % tup, log_all=True, simple=True)
+        run_shell_cmd(cmd % tup)
 
         # Use build_toolset if specified or the bootstrap toolset without the OS suffix
         self.toolset = self.cfg['build_toolset'] or re.sub('-linux$', '', toolset)
@@ -282,7 +282,7 @@ def build_step(self):
             self.paracmd,
             self.cfg['buildopts'],
         ])
-        run_cmd(cmd, log_all=True, simple=True)
+        run_shell_cmd(cmd)
 
     def install_step(self):
         """Install Boost by copying files to install dir."""
@@ -298,7 +298,7 @@ def install_step(self):
             self.paracmd,
             self.cfg['installopts'],
         ])
-        run_cmd(cmd, log_all=True, simple=True)
+        run_shell_cmd(cmd)
 
         if self.cfg['tagged_layout']:
             if LooseVersion(self.version) >= LooseVersion("1.69.0") or not self.cfg['single_threaded']:

easybuild/easyblocks/b/bzip2.py

@@ -36,7 +36,7 @@
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
 
 
@@ -70,7 +70,7 @@ def install_step(self):
         if self.cfg['with_shared_libs']:
 
             cmd = "%s make -f Makefile-libbz2_so %s" % (self.cfg['prebuildopts'], self.cfg['buildopts'])
-            run_cmd(cmd, log_all=True, simple=True)
+            run_shell_cmd(cmd)
 
             # copy shared libraries to <install dir>/lib
             shlib_ext = get_shared_lib_ext()

easybuild/easyblocks/s/scalapack.py

@@ -37,11 +37,9 @@
 from easybuild.tools import LooseVersion
 
 import easybuild.tools.toolchain as toolchain
-from easybuild.easyblocks.blacs import det_interface  # @UnresolvedImport
 from easybuild.easyblocks.generic.cmakemake import CMakeMake
 from easybuild.toolchains.linalg.acml import Acml
 from easybuild.toolchains.linalg.atlas import Atlas
-from easybuild.toolchains.linalg.blacs import Blacs
 from easybuild.toolchains.linalg.blis import Blis
 from easybuild.toolchains.linalg.flexiblas import FlexiBLAS, det_flexiblas_backend_libs
 from easybuild.toolchains.linalg.gotoblas import GotoBLAS
@@ -51,7 +49,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import copy_file, remove_file
 from easybuild.tools.modules import get_software_root
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 class EB_ScaLAPACK(CMakeMake):
@@ -90,13 +88,11 @@ def build_libscalapack_make(self):
         known_mpi_libs = [toolchain.MPICH, toolchain.MPICH2, toolchain.MVAPICH2]  # @UndefinedVariable
         known_mpi_libs += [toolchain.OPENMPI, toolchain.QLOGICMPI]  # @UndefinedVariable
         known_mpi_libs += [toolchain.INTELMPI]  # @UndefinedVariable
-        if os.getenv('MPICC') and os.getenv('MPIF77') and os.getenv('MPIF90'):
+        if os.getenv('MPICC') and os.getenv('MPIF90'):
             mpicc = os.getenv('MPICC')
-            mpif77 = os.getenv('MPIF77')
             mpif90 = os.getenv('MPIF90')
         elif self.toolchain.mpi_family() in known_mpi_libs:
             mpicc = 'mpicc'
-            mpif77 = 'mpif77'
             mpif90 = 'mpif90'
         else:
             raise EasyBuildError("Don't know which compiler commands to use.")
@@ -155,62 +151,22 @@ def build_libscalapack_make(self):
         else:
             raise EasyBuildError("Unknown LAPACK library used, no idea how to set BLASLIB/LAPACKLIB make options")
 
-        # build procedure changed in v2.0.0
-        if self.loosever < LooseVersion('2.0.0'):
-
-            blacs = get_software_root(Blacs.BLACS_MODULE_NAME[0])
-            if not blacs:
-                raise EasyBuildError("BLACS not available, yet required for ScaLAPACK version < 2.0.0")
-
-            # determine interface
-            interface = det_interface(self.log, os.path.join(blacs, 'bin'))
-
-            # set build and BLACS dir correctly
-            extra_makeopts.append('home=%s BLACSdir=%s' % (self.cfg['start_dir'], blacs))
-
-            # set BLACS libs correctly
-            blacs_libs = [
-                ('BLACSFINIT', "F77init"),
-                ('BLACSCINIT', "Cinit"),
-                ('BLACSLIB', "")
-            ]
-            for (var, lib) in blacs_libs:
-                extra_makeopts.append('%s=%s/lib/libblacs%s.a' % (var, blacs, lib))
-
-            # set compilers and options
-            noopt = ''
-            if self.toolchain.options['noopt']:
-                noopt += " -O0"
-            if self.toolchain.options['pic']:
-                noopt += " -fPIC"
-            extra_makeopts += [
-                'F77="%s"' % mpif77,
-                'CC="%s"' % mpicc,
-                'NOOPT="%s"' % noopt,
-                'CCFLAGS="-O3 %s"' % os.getenv('CFLAGS')
-            ]
-
-            # set interface
-            extra_makeopts.append("CDEFS='-D%s -DNO_IEEE $(USEMPI)'" % interface)
-
+        # determine interface
+        if self.toolchain.mpi_family() in known_mpi_libs:
+            interface = 'Add_'
         else:
+            raise EasyBuildError("Don't know which interface to pick for the MPI library being used.")
 
-            # determine interface
-            if self.toolchain.mpi_family() in known_mpi_libs:
-                interface = 'Add_'
-            else:
-                raise EasyBuildError("Don't know which interface to pick for the MPI library being used.")
-
-            # set compilers and options
-            extra_makeopts += [
-                'FC="%s"' % mpif90,
-                'CC="%s"' % mpicc,
-                'CCFLAGS="%s"' % os.getenv('CFLAGS'),
-                'FCFLAGS="%s"' % os.getenv('FFLAGS'),
-            ]
+        # set compilers and options
+        extra_makeopts += [
+            'FC="%s"' % mpif90,
+            'CC="%s"' % mpicc,
+            'CCFLAGS="%s"' % os.getenv('CFLAGS'),
+            'FCFLAGS="%s"' % os.getenv('FFLAGS'),
+        ]
 
-            # set interface
-            extra_makeopts.append('CDEFS="-D%s"' % interface)
+        # set interface
+        extra_makeopts.append('CDEFS="-D%s"' % interface)
 
         # update make opts, and build_step
         saved_buildopts = self.cfg['buildopts']
@@ -229,7 +185,7 @@ def build_libscalapack_make(self):
         cmd = "%s make %s %s" % (self.cfg['prebuildopts'], paracmd, self.cfg['buildopts'])
 
         # Ignore exit code for parallel run
-        (out, _) = run_cmd(cmd, log_ok=False, log_all=False, simple=False)
+        run_shell_cmd(cmd, fail_on_error=False)
 
         # Now prepare to remake libscalapack.a serially and the tests.
         self.cfg['buildopts'] = saved_buildopts

easybuild/easyblocks/w/wxpython.py

@@ -36,7 +36,7 @@
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_python_version
 from easybuild.tools.filetools import change_dir, symlink
 from easybuild.tools.modules import get_software_root
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
 
 
@@ -63,10 +63,10 @@ def build_step(self):
             # Do we need to build wxWidgets internally?
             if self.wxflag == '':
                 cmd = base_cmd + " build_wx"
-                run_cmd(cmd, log_all=True, simple=True)
+                run_shell_cmd(cmd)
 
             cmd = base_cmd + " %s build_py" % self.wxflag
-            run_cmd(cmd, log_all=True, simple=True)
+            run_shell_cmd(cmd)
 
     def install_step(self):
         """Custom install procedure for wxPython."""
@@ -83,7 +83,7 @@ def install_step(self):
             }
             # install fails and attempts to install in the python module. building the wheel, and then installing it
             cmd = cmd + " %s -v bdist_wheel" % self.wxflag
-            run_cmd(cmd, log_all=True, simple=True)
+            run_shell_cmd(cmd)
 
             # get whether it is 35, 36, 37, 38, etc.
             pyver = det_python_version(self.python_cmd)
@@ -106,7 +106,7 @@ def install_step(self):
             }
             cmd = cmd + " --wxpy_installdir=%s --install" % self.installdir
 
-        run_cmd(cmd, log_all=True, simple=True)
+        run_shell_cmd(cmd)
 
         # add symbolic links for libwx_*so.* files
         # (which are created automatically by 'build.py install', but not by 'pip install *.whl')

easybuild/easyblocks/x/xmipp.py

@@ -40,7 +40,7 @@
 from easybuild.tools.filetools import apply_regex_substitutions, change_dir
 from easybuild.tools.filetools import copy_file, mkdir, remove_file, symlink
 from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
 
 
@@ -112,7 +112,7 @@ def configure_step(self):
             noask,
             self.cfg['configopts'],
         ])
-        run_cmd(cmd, log_all=True, simple=True)
+        run_shell_cmd(cmd)
 
         # Parameters to be set in the config file
         params = {
@@ -237,7 +237,7 @@ def build_step(self):
                 'all',
                 self.cfg['buildopts'],
             ])
-            run_cmd(cmd, log_all=True, simple=True)
+            run_shell_cmd(cmd)
             change_dir(cwd)
             xmipp_lib = os.path.join(self.srcdir, 'xmipp', 'lib')
             mkdir(xmipp_lib)
@@ -265,7 +265,7 @@ def install_step(self):
             self.installdir,
             self.cfg['installopts'],
         ])
-        run_cmd(cmd, log_all=True, simple=True)
+        run_shell_cmd(cmd)
 
         # Remove the bash and fish files. Everything should be in the module
         remove_file(os.path.join(self.installdir, 'xmipp.bashrc'))