switch to run_shell_cmd where possible in easybuild.* modules

easybuild/framework/extension.py

@@ -42,7 +42,7 @@
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP, template_constant_dict
 from easybuild.tools.build_log import EasyBuildError, raise_nosupport
 from easybuild.tools.filetools import change_dir
-from easybuild.tools.run import check_async_cmd, run_cmd
+from easybuild.tools.run import check_async_cmd, run_cmd, run_shell_cmd
 
 
 def resolve_exts_filter_template(exts_filter, ext):
@@ -274,14 +274,14 @@ def sanity_check_step(self):
         elif exts_filter:
             cmd, stdin = resolve_exts_filter_template(exts_filter, self)
             # set log_ok to False so we can catch the error instead of run_cmd
-            (output, ec) = run_cmd(cmd, log_ok=False, simple=False, regexp=False, inp=stdin)
+            cmd_res = run_shell_cmd(cmd, fail_on_error=False, stdin=stdin)
 
-            if ec:
+            if cmd_res.exit_code:
                 if stdin:
                     fail_msg = 'command "%s" (stdin: "%s") failed' % (cmd, stdin)
                 else:
                     fail_msg = 'command "%s" failed' % cmd
-                fail_msg += "; output:\n%s" % output.strip()
+                fail_msg += "; output:\n%s" % cmd_res.output.strip()
                 self.log.warning("Sanity check for '%s' extension failed: %s", self.name, fail_msg)
                 res = (False, fail_msg)
                 # keep track of all reasons of failure

easybuild/toolchains/linalg/flexiblas.py

@@ -34,7 +34,7 @@
 
 from easybuild.tools.toolchain.linalg import LinAlg
 
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
 
 
@@ -48,11 +48,11 @@ def det_flexiblas_backend_libs():
     # System-wide (config directory):
     #  OPENBLAS
     #    library = libflexiblas_openblas.so
-    out, _ = run_cmd("flexiblas list", simple=False, trace=False)
+    res = run_shell_cmd("flexiblas list", hidden=True)
 
     shlib_ext = get_shared_lib_ext()
     flexiblas_lib_regex = re.compile(r'library = (?P<lib>lib.*\.%s)' % shlib_ext, re.M)
-    flexiblas_libs = flexiblas_lib_regex.findall(out)
+    flexiblas_libs = flexiblas_lib_regex.findall(res.output)
 
     backend_libs = []
     for flexiblas_lib in flexiblas_libs:

easybuild/tools/job/slurm.py

@@ -37,7 +37,7 @@
 from easybuild.tools.config import JOB_DEPS_TYPE_ABORT_ON_ERROR, JOB_DEPS_TYPE_ALWAYS_RUN, build_option
 from easybuild.tools.job.backend import JobBackend
 from easybuild.tools.filetools import which
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 _log = fancylogger.getLogger('slurm', fname=False)
@@ -78,8 +78,8 @@ def __init__(self, *args, **kwargs):
 
     def _check_version(self):
         """Check whether version of Slurm complies with required version."""
-        (out, _) = run_cmd("sbatch --version", trace=False)
-        slurm_ver = out.strip().split(' ')[-1]
+        res = run_shell_cmd("sbatch --version", hidden=True)
+        slurm_ver = res.output.strip().split(' ')[-1]
         self.log.info("Found Slurm version %s", slurm_ver)
 
         if LooseVersion(slurm_ver) < LooseVersion(self.REQ_VERSION):
@@ -116,16 +116,16 @@ def queue(self, job, dependencies=frozenset()):
             else:
                 submit_cmd += ' --%s "%s"' % (key, job.job_specs[key])
 
-        (out, _) = run_cmd(submit_cmd, trace=False)
+        cmd_res = run_shell_cmd(submit_cmd, hidden=True)
 
         jobid_regex = re.compile("^Submitted batch job (?P<jobid>[0-9]+)")
 
-        res = jobid_regex.search(out)
-        if res:
-            job.jobid = res.group('jobid')
+        regex_res = jobid_regex.search(cmd_res.output)
+        if regex_res:
+            job.jobid = regex_res.group('jobid')
             self.log.info("Job submitted, got job ID %s", job.jobid)
         else:
-            raise EasyBuildError("Failed to determine job ID from output of submission command: %s", out)
+            raise EasyBuildError("Failed to determine job ID from output of submission command: %s", cmd_res.output)
 
         self._submitted.append(job)
 
@@ -142,7 +142,7 @@ def complete(self):
                 job_ids.append(job.jobid)
 
         if job_ids:
-            run_cmd("scontrol release %s" % ' '.join(job_ids), trace=False)
+            run_shell_cmd("scontrol release %s" % ' '.join(job_ids), hidden=True)
 
         submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
         print_msg("List of submitted jobs (%d): %s" % (len(self._submitted), submitted_jobs), log=self.log)

easybuild/tools/options.py

@@ -98,7 +98,7 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.modules import Lmod
 from easybuild.tools.robot import det_robot_path
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.package.utilities import avail_package_naming_schemes
 from easybuild.tools.toolchain.compiler import DEFAULT_OPT_LEVEL, OPTARCH_MAP_CHAR, OPTARCH_SEP, Compiler
 from easybuild.tools.toolchain.toolchain import SYSTEM_TOOLCHAIN_NAME
@@ -1893,8 +1893,9 @@ def set_tmpdir(tmpdir=None, raise_error=False):
             fd, tmptest_file = tempfile.mkstemp()
             os.close(fd)
             os.chmod(tmptest_file, 0o700)
-            if not run_cmd(tmptest_file, simple=True, log_ok=False, regexp=False, force_in_dry_run=True, trace=False,
-                           stream_output=False, with_hooks=False):
+            res = run_shell_cmd(tmptest_file, fail_on_error=False, in_dry_run=True, hidden=True, stream_output=False,
+                                with_hooks=False)
+            if res.exit_code:
                 msg = "The temporary directory (%s) does not allow to execute files. " % tempfile.gettempdir()
                 msg += "This can cause problems in the build process, consider using --tmpdir."
                 if raise_error:

easybuild/tools/package/utilities.py

@@ -45,7 +45,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import change_dir, which
 from easybuild.tools.package.package_naming_scheme.pns import PackageNamingScheme
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.utilities import get_subclasses, import_available_modules
 
 
@@ -145,7 +145,7 @@ def package_with_fpm(easyblock):
     ])
     cmd = ' '.join(cmdlist)
     _log.debug("The flattened cmdlist looks like: %s", cmd)
-    run_cmd(cmdlist, log_all=True, simple=True, shell=False)
+    run_shell_cmd(cmdlist, use_bash=False)
 
     _log.info("Created %s package(s) in %s", pkgtype, workdir)