switch to run_shell_cmd in easybuild/tools/container

easybuild/tools/containers/apptainer.py

@@ -35,7 +35,7 @@
 from easybuild.tools.config import CONT_IMAGE_FORMAT_SIF, CONT_IMAGE_FORMAT_SQUASHFS
 from easybuild.tools.config import build_option, container_path
 from easybuild.tools.filetools import remove_file, which
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 class ApptainerContainer(SingularityContainer):
@@ -48,15 +48,15 @@ class ApptainerContainer(SingularityContainer):
     def apptainer_version():
         """Get Apptainer version."""
         version_cmd = "apptainer --version"
-        out, ec = run_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
-        if ec:
-            raise EasyBuildError("Error running '%s': %s for tool {1} with output: {2}" % (version_cmd, out))
+        res = run_shell_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
+        if res.exit_code:
+            raise EasyBuildError(f"Error running '{version_cmd}': {res.output}")
 
-        res = re.search(r"\d+\.\d+(\.\d+)?", out.strip())
-        if not res:
-            raise EasyBuildError("Error parsing Apptainer version: %s" % out)
+        regex_res = re.search(r"\d+\.\d+(\.\d+)?", res.output.strip())
+        if not regex_res:
+            raise EasyBuildError(f"Error parsing Apptainer version: {res.output}")
 
-        return res.group(0)
+        return regex_res.group(0)
 
     def build_image(self, recipe_path):
         """Build container image by calling out to 'sudo apptainer build'."""
@@ -108,5 +108,5 @@ def build_image(self, recipe_path):
 
         cmd = ' '.join(['sudo', cmd_env, apptainer, 'build', cmd_opts, img_path, recipe_path])
         print_msg("Running '%s', you may need to enter your 'sudo' password..." % cmd)
-        run_cmd(cmd, stream_output=True)
+        run_shell_cmd(cmd, stream_output=True)
         print_msg("Apptainer image created at %s" % img_path, log=self.log)

easybuild/tools/containers/docker.py

@@ -36,7 +36,7 @@
 from easybuild.tools.containers.utils import det_os_deps
 from easybuild.tools.filetools import remove_dir
 from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 DOCKER_TMPL_HEADER = """\
@@ -164,7 +164,7 @@ def build_image(self, dockerfile):
         docker_cmd = ' '.join(['sudo', 'docker', 'build', '-f', dockerfile, '-t', container_name, '.'])
 
         print_msg("Running '%s', you may need to enter your 'sudo' password..." % docker_cmd)
-        run_cmd(docker_cmd, path=tempdir, stream_output=True)
+        run_shell_cmd(docker_cmd, work_dir=tempdir, stream_output=True)
         print_msg("Docker image created at %s" % container_name, log=self.log)
 
         remove_dir(tempdir)

easybuild/tools/containers/singularity.py

@@ -40,7 +40,7 @@
 from easybuild.tools.config import build_option, container_path
 from easybuild.tools.containers.base import ContainerGenerator
 from easybuild.tools.filetools import read_file, remove_file, which
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 ARCH = 'arch'  # Arch Linux
@@ -162,15 +162,15 @@ class SingularityContainer(ContainerGenerator):
     def singularity_version():
         """Get Singularity version."""
         version_cmd = "singularity --version"
-        out, ec = run_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
-        if ec:
-            raise EasyBuildError("Error running '%s': %s for tool {1} with output: {2}" % (version_cmd, out))
+        res = run_shell_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
+        if res.exit_code:
+            raise EasyBuildError(f"Error running '{version_cmd}': {res.output}")
 
-        res = re.search(r"\d+\.\d+(\.\d+)?", out.strip())
-        if not res:
-            raise EasyBuildError("Error parsing Singularity version: %s" % out)
+        regex_res = re.search(r"\d+\.\d+(\.\d+)?", res.output.strip())
+        if not regex_res:
+            raise EasyBuildError(f"Error parsing Singularity version: {res.output}")
 
-        return res.group(0)
+        return regex_res.group(0)
 
     def resolve_template(self):
         """Return template container recipe."""
@@ -403,5 +403,5 @@ def build_image(self, recipe_path):
 
         cmd = ' '.join(['sudo', cmd_env, singularity, 'build', cmd_opts, img_path, recipe_path])
         print_msg("Running '%s', you may need to enter your 'sudo' password..." % cmd)
-        run_cmd(cmd, stream_output=True)
+        run_shell_cmd(cmd, stream_output=True)
         print_msg("Singularity image created at %s" % img_path, log=self.log)

easybuild/tools/containers/utils.py

@@ -36,7 +36,7 @@
 from easybuild.tools import LooseVersion
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.filetools import which
-from easybuild.tools.run import run_cmd
+from easybuild.tools.run import run_shell_cmd
 
 
 def det_os_deps(easyconfigs):
@@ -70,20 +70,23 @@ def check_tool(tool_name, min_tool_version=None):
     if not tool_path:
         return False
 
-    print_msg("{0} tool found at {1}".format(tool_name, tool_path))
+    print_msg(f"{tool_name} tool found at {tool_path}")
 
     if not min_tool_version:
         return True
 
-    version_cmd = "{0} --version".format(tool_name)
-    out, ec = run_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
-    if ec:
-        raise EasyBuildError("Error running '{0}' for tool {1} with output: {2}".format(version_cmd, tool_name, out))
-    res = re.search(r"\d+\.\d+(\.\d+)?", out.strip())
-    if not res:
-        raise EasyBuildError("Error parsing version for tool {0}".format(tool_name))
-    tool_version = res.group(0)
+    version_cmd = f"{tool_name} --version")
+    res = run_shell_cmd(version_cmd, hidden=True, in_dry_run=True)
+    if res.exit_code:
+        raise EasyBuildError(f"Error running '{version_cmd}' for tool {tool_name} with output: {res.output}")
+
+    regex_res = re.search(r"\d+\.\d+(\.\d+)?", res.output.strip())
+    if not regex_res:
+        raise EasyBuildError(f"Error parsing version for tool {tool_name}")
+
+    tool_version = regex_res.group(0)
     version_ok = LooseVersion(str(min_tool_version)) <= LooseVersion(tool_version)
     if version_ok:
-        print_msg("{0} version '{1}' is {2} or higher ... OK".format(tool_name, tool_version, min_tool_version))
+        print_msg(f"{tool_name} version '{tool_version}' is {min_tool_version} or higher ... OK")
+
     return version_ok