fix use of deprecated functionality, enhance unit tests to check for it

easybuild/easyblocks/a/abaqus.py

@@ -35,7 +35,7 @@
 
 from easybuild.easyblocks.generic.binary import Binary
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 from distutils.version import LooseVersion
 
 

easybuild/easyblocks/a/acml.py

@@ -37,7 +37,7 @@
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd_qa
+from easybuild.tools.run import run_cmd_qa
 
 
 class EB_ACML(EasyBlock):

easybuild/easyblocks/a/aladin.py

@@ -38,9 +38,9 @@
 import easybuild.tools.toolchain as toolchain
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd, run_cmd_qa
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.run import run_cmd, run_cmd_qa
 
 
 class EB_ALADIN(EasyBlock):

easybuild/easyblocks/a/allinea.py

@@ -42,13 +42,12 @@ class EB_Allinea(Binary):
     @staticmethod
     def extra_options(extra_vars=None):
         """Define extra easyconfig parameters specific to Allinea."""
-
         orig_vars = dict(Binary.extra_options(extra_vars))
         allinea_vars = {
             'templates': [[], "List of templates.", CUSTOM],
         }
         allinea_vars.update(orig_vars)
-        return allinea_vars.items()
+        return Binary.extra_options(allinea_vars)
 
     def extract_step(self):
         """Extract Allinea installation files."""

easybuild/easyblocks/a/ant.py

@@ -33,7 +33,7 @@
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class EB_ant(EasyBlock):

easybuild/easyblocks/a/arb.py

@@ -32,7 +32,7 @@
 
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.tools.environment import setvar
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class EB_ARB(ConfigureMake):

easybuild/easyblocks/a/atlas.py

@@ -40,8 +40,8 @@
 
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd
 from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_cpu_speed
 
 

easybuild/easyblocks/b/bisearch.py

@@ -34,7 +34,7 @@
 import os
 
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.filetools import run_cmd_qa
+from easybuild.tools.run import run_cmd_qa
 
 
 class EB_BiSearch(EasyBlock):

easybuild/easyblocks/b/blacs.py

@@ -38,7 +38,7 @@
 import shutil
 
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 # also used by ScaLAPACK

easybuild/easyblocks/c/charmm.py

@@ -34,7 +34,7 @@
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 import easybuild.tools.toolchain as toolchain
 
 # Possible systemsizes for CHARMM

easybuild/easyblocks/c/clang.py

@@ -41,8 +41,9 @@
 
 from easybuild.easyblocks.generic.cmakemake import CMakeMake
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd, mkdir
+from easybuild.tools.filetools import mkdir
 from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_os_name, get_os_version
 
 # List of all possible build targets for Clang
@@ -56,13 +57,13 @@ class EB_Clang(CMakeMake):
 
     @staticmethod
     def extra_options():
-        extra_vars = [
-            ('assertions', [True, "Enable assertions.  Helps to catch bugs in Clang.", CUSTOM]),
-            ('build_targets', [["X86"], "Build targets for LLVM. Possible values: " + ', '.join(CLANG_TARGETS), CUSTOM]),
-            ('bootstrap', [True, "Bootstrap Clang using GCC", CUSTOM]),
-            ('usepolly', [False, "Build Clang with polly", CUSTOM]),
-            ('static_analyzer', [True, "Install the static analyser of Clang", CUSTOM]),
-        ]
+        extra_vars = {
+            'assertions': [True, "Enable assertions.  Helps to catch bugs in Clang.", CUSTOM],
+            'build_targets': [["X86"], "Build targets for LLVM. Possible values: " + ', '.join(CLANG_TARGETS), CUSTOM],
+            'bootstrap': [True, "Bootstrap Clang using GCC", CUSTOM],
+            'usepolly': [False, "Build Clang with polly", CUSTOM],
+            'static_analyzer': [True, "Install the static analyser of Clang", CUSTOM],
+        }
 
         return CMakeMake.extra_options(extra_vars)
 

easybuild/easyblocks/c/cp2k.py

@@ -44,8 +44,8 @@
 import easybuild.tools.toolchain as toolchain
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd
 from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_avail_core_count
 
 # CP2K needs this version of libxc

easybuild/easyblocks/c/cplex.py

@@ -39,7 +39,7 @@
 import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.binary import Binary
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd_qa
+from easybuild.tools.run import run_cmd_qa
 
 
 class EB_CPLEX(Binary):
@@ -55,10 +55,10 @@ def __init__(self, *args, **kwargs):
 
     @staticmethod
     def extra_options():
-        extra_vars = [
+        extra_vars = {
             # staged install via a tmp dir can help with the hard (potentially faulty) check on available disk space
-            ('staged_install', [False, "Should the installation should be staged via a temporary dir?", CUSTOM]),
-        ]
+            'staged_install': [False, "Should the installation should be staged via a temporary dir?", CUSTOM],
+        }
         return Binary.extra_options(extra_vars)
 
     def install_step(self):

easybuild/easyblocks/c/cuda.py

@@ -21,7 +21,8 @@
 import os
 
 from easybuild.easyblocks.generic.binary import Binary
-from easybuild.tools.filetools import patch_perl_script_autoflush, run_cmd, run_cmd_qa
+from easybuild.tools.filetools import patch_perl_script_autoflush
+from easybuild.tools.run import run_cmd, run_cmd_qa
 from distutils.version import LooseVersion
 
 

easybuild/easyblocks/d/doxygen.py

@@ -33,7 +33,7 @@
 """
 
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class EB_Doxygen(ConfigureMake):

easybuild/easyblocks/e/easybuildmeta.py

@@ -29,7 +29,9 @@
 """
 import copy
 import os
+from distutils.version import LooseVersion
 
+import easybuild.tools.environment as env
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage
 from easybuild.tools.modules import get_software_root_env_var_name
@@ -126,18 +128,23 @@ def sanity_check_step(self):
 
         # set of sanity check paths to check for EasyBuild
         custom_paths = {
-                        'files': ['bin/eb'],
-                        'dirs': [self.pylibdir] + [[x, os.path.join(self.pylibdir, x)][y] for (x, y) in eb_dirs[setup_tool]],
-                       }
+            'files': ['bin/eb'],
+            'dirs': [self.pylibdir] + [[x, os.path.join(self.pylibdir, x)][y] for (x, y) in eb_dirs[setup_tool]],
+        }
+
+        # make sure we don't trip over deprecated behavior in old EasyBuild versions
+        eb_cmd = 'eb'
+        if LooseVersion(self.version) < LooseVersion('1.16'):
+            eb_cmd = 'EASYBUILD_DEPRECATED=0.0 eb'
 
         # set of sanity check commands to run for EasyBuild
         custom_commands = [
-                           # this may spit out a wrong version, but that should be safe to ignore
-                           # occurs when the EasyBuild being used is newer than the EasyBuild being installed
-                           ('eb', '--version'),
-                           ('eb', '-a'),
-                           ('eb', '-e ConfigureMake -a')
-                          ]
+            # this may spit out a wrong version, but that should be safe to ignore
+            # occurs when the EasyBuild being used is newer than the EasyBuild being installed
+            (eb_cmd, '--version'),
+            (eb_cmd, '-a'),
+            (eb_cmd, '-e ConfigureMake -a'),
+        ]
 
         # (temporary) cleanse copy of original environment to avoid conflict with (potentially) loaded EasyBuild module
         self.orig_orig_environ = copy.deepcopy(self.orig_environ)

easybuild/easyblocks/e/epd.py

@@ -29,8 +29,8 @@
 """
 import os
 
-from easybuild.tools.filetools import run_cmd
 from easybuild.easyblocks.generic.binary import Binary
+from easybuild.tools.run import run_cmd
 
 
 class EB_EPD(Binary):

easybuild/easyblocks/e/esmf.py

@@ -34,8 +34,8 @@
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import BUILD
-from easybuild.tools.filetools import run_cmd
 from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
 
 
 class EB_ESMF(ConfigureMake):

easybuild/easyblocks/e/espresso.py

@@ -19,10 +19,10 @@
 import os
 
 import easybuild.tools.environment as env
-import easybuild.tools.toolchain   as toolchain
-from   easybuild.easyblocks.generic.configuremake import ConfigureMake
-from   easybuild.framework.easyconfig             import CUSTOM
-from   easybuild.tools.filetools                  import run_cmd
+import easybuild.tools.toolchain as toolchain
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.run import run_cmd
 
 
 class EB_ESPResSo(ConfigureMake):

easybuild/easyblocks/f/fdtd_solutions.py

@@ -28,7 +28,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.filetools import run_cmd_qa
+from easybuild.tools.run import run_cmd_qa
 
 
 class EB_FDTD_underscore_Solutions(EasyBlock):

easybuild/easyblocks/f/ferret.py

@@ -37,8 +37,8 @@
 import os,re,fileinput,sys
 import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
-from easybuild.tools.filetools import run_cmd
 from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
 
 class EB_Ferret(ConfigureMake):
     """Support for building/installing Ferret."""

easybuild/easyblocks/f/fluent.py

@@ -32,7 +32,8 @@
 import stat
 
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.filetools import adjust_permissions, run_cmd
+from easybuild.tools.filetools import adjust_permissions
+from easybuild.tools.run import run_cmd
 
 
 class EB_FLUENT(EasyBlock):

easybuild/easyblocks/f/freetype.py

@@ -33,7 +33,7 @@
 import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class EB_freetype(ConfigureMake):

easybuild/easyblocks/f/fsl.py

@@ -35,7 +35,7 @@
 
 import easybuild.tools.environment as env
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class EB_FSL(EasyBlock):

easybuild/easyblocks/g/gcc.py

@@ -44,9 +44,9 @@
 import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd
 from easybuild.tools.modules import get_software_root
-from easybuild.tools.systemtools import check_os_dependency, get_kernel_name, get_os_name, get_shared_lib_ext, get_platform_name
+from easybuild.tools.run import run_cmd
+from easybuild.tools.systemtools import check_os_dependency, get_os_name, get_os_type, get_shared_lib_ext, get_platform_name
 
 
 class EB_GCC(ConfigureMake):
@@ -488,7 +488,7 @@ def sanity_check_step(self):
         Custom sanity check for GCC
         """
 
-        kernel_name = get_kernel_name()
+        os_type = get_os_type()
         sharedlib_ext = get_shared_lib_ext()
         common_infix = os.path.join('gcc', self.platform_lib, self.version)
 
@@ -497,7 +497,7 @@ def sanity_check_step(self):
         if LooseVersion(self.version) >= LooseVersion('4.2'):
             # libgomp was added in GCC 4.2.0
             ["libgomp.%s" % sharedlib_ext, "libgomp.a"]
-        if kernel_name == 'Linux':
+        if os_type == 'Linux':
             lib_files.extend(["libgcc_s.%s" % sharedlib_ext])
             # libmudflap is replaced by asan (see release notes gcc 4.9.0)
             if self.version < LooseVersion("4.9.0"):
@@ -527,7 +527,7 @@ def sanity_check_step(self):
 
         if 'lto' in self.cfg['languages']:
             libexec_files.extend(['lto1', 'lto-wrapper'])
-            if kernel_name in ['Linux']:
+            if os_type in ['Linux']:
                 libexec_files.append('liblto_plugin.%s' % sharedlib_ext)
 
         bin_files = ["bin/%s" % x for x in bin_files]

easybuild/easyblocks/g/geant4.py

@@ -40,8 +40,8 @@
 import easybuild.tools.environment as env
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.easyblocks.generic.cmakemake import CMakeMake
-from easybuild.tools.filetools import run_cmd, run_cmd_qa
 from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd, run_cmd_qa
 from easybuild.tools.filetools import mkdir
 
 class EB_Geant4(CMakeMake):

easybuild/easyblocks/g/go.py

@@ -32,7 +32,8 @@
 import shutil
 
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
-from easybuild.tools.filetools import rmtree2, run_cmd
+from easybuild.tools.filetools import rmtree2
+from easybuild.tools.run import run_cmd
 
 class EB_Go(ConfigureMake):
     """

easybuild/easyblocks/generic/binary.py

@@ -38,7 +38,8 @@
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd, rmtree2
+from easybuild.tools.filetools import rmtree2
+from easybuild.tools.run import run_cmd
 
 
 class Binary(EasyBlock):

easybuild/easyblocks/generic/cmakemake.py

@@ -37,8 +37,8 @@
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.environment import setvar
-from easybuild.tools.filetools import run_cmd
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX
+from easybuild.tools.run import run_cmd
 
 
 class CMakeMake(ConfigureMake):

easybuild/easyblocks/generic/cmdcp.py

@@ -31,7 +31,7 @@
 
 from easybuild.easyblocks.generic.makecp import MakeCp
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class CmdCp(MakeCp):