cleanups, docs, & make format

Author: mr-c

cwltool/singularity.py

@@ -29,15 +29,6 @@
 # Can be singularity, singularity-ce or apptainer
 _SINGULARITY_FLAVOR: str = ""
 
-def reset_singularity_version_cache():
-    """
-    Needed for resetting the cache for testing.
-    """
-    global _SINGULARITY_VERSION  # pylint: disable=global-statement
-    global _SINGULARITY_FLAVOR  # pylint: disable=global-statement
-    _SINGULARITY_VERSION = None
-    _SINGULARITY_FLAVOR = ""
-
 
 def get_version() -> Tuple[List[int], str]:
     """
@@ -74,7 +65,7 @@ def get_version() -> Tuple[List[int], str]:
 
 def is_apptainer_1_or_newer() -> bool:
     """
-    Is this the apptainer singularity distribution in version 1.0 or higher?
+    Check if apptainer singularity distribution is version 1.0 or higher.
 
     Apptainer v1.0.0 is compatible with SingularityCE 3.9.5.
     See: https://github.com/apptainer/apptainer/releases
@@ -87,7 +78,7 @@ def is_apptainer_1_or_newer() -> bool:
 
 def is_version_2_6() -> bool:
     """
-    Is this exactly version 2.6?
+    Check if this singularity version is exactly version 2.6.
 
     Also returns False if the flavor is not singularity or singularity-ce.
     """
@@ -98,13 +89,15 @@ def is_version_2_6() -> bool:
 
 
 def is_version_3_or_newer() -> bool:
+    """Check if this version is singularity version 3 or newer or equivalent."""
     if is_apptainer_1_or_newer():
         return True  # this is equivalent to singularity-ce > 3.9.5
     v = get_version()
     return v[0][0] >= 3
 
 
 def is_version_3_1_or_newer() -> bool:
+    """Check if this version is singularity version 3.1 or newer or equivalent."""
     if is_apptainer_1_or_newer():
         return True  # this is equivalent to singularity-ce > 3.9.5
     v = get_version()

tests/test_environment.py

@@ -131,10 +131,10 @@ def PWD(v: str, env: Env) -> bool:
         }
 
         # Singularity variables appear to be in flux somewhat.
-        version = get_version().split(".")
-        vmajor = int(version[0])
+        version = get_version()[0]
+        vmajor = version[0]
         assert vmajor == 3, "Tests only work for Singularity 3"
-        vminor = int(version[1])
+        vminor = version[1]
         sing_vars: EnvChecks = {
             "SINGULARITY_CONTAINER": None,
             "SINGULARITY_NAME": None,

tests/test_singularity_versions.py

@@ -1,27 +1,49 @@
+"""Test singularity{,-ce} & apptainer versions."""
 import cwltool.singularity
-from cwltool.singularity import (reset_singularity_version_cache,
-                                 get_version,
-                                 is_apptainer_1_or_newer,
-                                 is_version_2_6,
-                                 is_version_3_or_newer,
-                                 is_version_3_1_or_newer,
-                                 is_version_3_4_or_newer)
+from cwltool.singularity import (
+    get_version,
+    is_apptainer_1_or_newer,
+    is_version_2_6,
+    is_version_3_or_newer,
+    is_version_3_1_or_newer,
+    is_version_3_4_or_newer,
+)
 
+from subprocess import check_output  # nosec
 
-def set_dummy_check_output(name, version):
-    cwltool.singularity.check_output = lambda c, universal_newlines: name + " version " + version
 
+def reset_singularity_version_cache() -> None:
+    """Reset the cache for testing."""
+    cwltool.singularity._SINGULARITY_VERSION = None
+    cwltool.singularity._SINGULARITY_FLAVOR = ""
 
 
-def test_get_version():
+def set_dummy_check_output(name: str, version: str) -> None:
+    """Mock out subprocess.check_output."""
+    cwltool.singularity.check_output = (  # type: ignore[attr-defined]
+        lambda c, universal_newlines: name + " version " + version
+    )
+
+
+def restore_check_output() -> None:
+    """Undo the mock of subprocess.check_output."""
+    cwltool.singularity.check_output = check_output  # type: ignore[attr-defined]
+
+
+def test_get_version() -> None:
+    """Confirm expected types of singularity.get_version()."""
     set_dummy_check_output("apptainer", "1.0.1")
     reset_singularity_version_cache()
     v = get_version()
     assert isinstance(v, tuple)
     assert isinstance(v[0], list)
     assert isinstance(v[1], str)
-    assert cwltool.singularity._SINGULARITY_VERSION is not None  # pylint: disable=protected-access
-    assert len(cwltool.singularity._SINGULARITY_FLAVOR) > 0  # pylint: disable=protected-access
+    assert (
+        cwltool.singularity._SINGULARITY_VERSION is not None
+    )  # pylint: disable=protected-access
+    assert (
+        len(cwltool.singularity._SINGULARITY_FLAVOR) > 0
+    )  # pylint: disable=protected-access
     v_cached = get_version()
     assert v == v_cached
 
@@ -38,9 +60,11 @@ def test_get_version():
     assert v[0][1] == 8
     assert v[0][2] == 5
     assert v[1] == "singularity"
+    restore_check_output()
 
 
-def test_version_checks():
+def test_version_checks() -> None:
+    """Confirm logic in the various singularity version checks."""
     set_dummy_check_output("apptainer", "1.0.1")
     reset_singularity_version_cache()
     assert is_apptainer_1_or_newer()
@@ -112,3 +136,4 @@ def test_version_checks():
     assert is_version_3_or_newer()
     assert is_version_3_1_or_newer()
     assert is_version_3_4_or_newer()
+    restore_check_output()