make cleanup

cwltool/singularity.py

@@ -158,20 +158,22 @@ def get_image(
             cache_folder = os.environ["SINGULARITY_PULLFOLDER"]
 
         if "dockerFile" in dockerRequirement:
-            if cache_folder is None: # if environment variables were not set
+            if cache_folder is None:  # if environment variables were not set
                 cache_folder = create_tmp_dir(tmp_outdir_prefix)
 
-            image_path = os.path.join(cache_folder,str(dockerRequirement["dockerImageId"]))
+            image_path = os.path.join(cache_folder, str(dockerRequirement["dockerImageId"]))
             if not os.path.exists(image_path):
-                # otherwise will prompt user if want to continue if exists 
+                # otherwise will prompt user if want to continue if exists
                 absolute_path = os.path.abspath(cache_folder)
                 dockerfile_path = os.path.join(absolute_path, "Dockerfile")
-                singularityfile_path = dockerfile_path+'.def'
+                singularityfile_path = dockerfile_path + ".def"
                 custom_env = os.environ.copy()
-                custom_env['APPTAINER_TMPDIR'] = absolute_path
+                custom_env["APPTAINER_TMPDIR"] = absolute_path
                 # if you do not set APPTAINER_TMPDIR will crash
-                # WARNING: 'nodev' mount option set on /tmp, it could be a source of failure during build process
-                # FATAL:   Unable to create build: 'noexec' mount option set on /tmp, temporary root filesystem won't be usable at this location
+                # WARNING: 'nodev' mount option set on /tmp, it could be a
+                #          source of failure during build process
+                # FATAL:   Unable to create build: 'noexec' mount option set on
+                #          /tmp, temporary root filesystem won't be usable at this location
                 with open(dockerfile_path, "w") as dfile:
                     dfile.write(dockerRequirement["dockerFile"])
                 cmd = [

tests/test_tmpdir.py

@@ -1,8 +1,8 @@
 """Test that all temporary directories respect the --tmpdir-prefix and --tmp-outdir-prefix options."""
 import re
+import shutil
 import subprocess
 import sys
-import shutil
 from pathlib import Path
 from typing import List, cast
 
@@ -15,10 +15,10 @@
 from cwltool.command_line_tool import CommandLineTool
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.docker import DockerCommandLineJob
-from cwltool.singularity import SingularityCommandLineJob
 from cwltool.job import JobBase
 from cwltool.main import main
 from cwltool.pathmapper import MapperEnt
+from cwltool.singularity import SingularityCommandLineJob
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION, ORIGINAL_CWLVERSION
 from cwltool.utils import create_tmp_dir
@@ -170,7 +170,7 @@ def test_dockerfile_tmpdir_prefix(tmp_path: Path, monkeypatch: pytest.MonkeyPatc
 def test_dockerfile_singularity_build(monkeypatch: pytest.MonkeyPatch) -> None:
     """Test that SingularityCommandLineJob.get_image builds a Dockerfile with Singularity."""
     # cannot use /tmp for the variable APPTAINER_TMPDIR unless have root permissions
-    # FATAL:   Unable to create build: 'noexec' mount option set on /tmp, temporary root filesystem 
+    # FATAL:   Unable to create build: 'noexec' mount option set on /tmp, temporary root filesystem
     # won't be usable at this location
     # Will use current working directory instead
     tmp_path = Path.cwd()