Issue# 405: New test case for previously missed code in fastani

pyani/fastani.py

@@ -86,15 +86,25 @@ def get_version(fastani_exe: Path = pyani_config.FASTANI_DEFAULT) -> str:
 
     The following circumstances are explicitly reported as strings:
 
+    - a value of None given for the executable
     - no executable at passed path
     - non-executable file at passed path (this includes cases where the user doesn't have execute permissions on the file)
     - no version info returned
     """
     try:
-        fastani_path = Path(shutil.which(fastani_exe))  # type:ignore
+        # Returns a TypeError if `fastani_exe` is None
+        try:
+            fastani_path = shutil.which(fastani_exe)  # type:ignore
+        except TypeError:
+            return f"expected path to fastANI executable; received {fastani_exe}"
+        # Returns a TypeError if `fastani_path` is not on the PATH
+        fastani_path = Path(fastani_path)
     except TypeError:
         return f"{fastani_exe} is not found in $PATH"
 
+    # If a string that is not an executable is passed to
+    # shutil.which(), the return value will be None, so
+    # this check is still needed
     if fastani_path is None:
         return f"{fastani_exe} is not found in $PATH"
 

tests/test_fastani.py

@@ -91,33 +91,44 @@ def test_get_version_nonetype():
     """Test behaviour when no location for the executable is given."""
     test_file_0 = None
 
-    assert fastani.get_version(test_file_0) == f"{test_file_0} is not found in $PATH"
+    assert (
+        fastani.get_version(test_file_0)
+        == f"expected path to fastANI executable; received {test_file_0}"
+    )
+
+
+# Test case 1: no such file exists
+def test_get_version_random_string():
+    """Test behaviour when the given 'file' is not one."""
+    test_file_1 = "string"
 
+    assert fastani.get_version(test_file_1) == f"{test_file_1} is not found in $PATH"
 
-# Test case 1: there is no executable
+
+# Test case 2: there is no executable
 def test_get_version_no_exe(executable_missing, monkeypatch):
     """Test behaviour when there is no file at the specified executable location."""
-    test_file_1 = Path("/non/existent/blastn")
-    assert fastani.get_version(test_file_1) == f"No fastANI executable at {test_file_1}"
+    test_file_2 = Path("/non/existent/fastani")
+    assert fastani.get_version(test_file_2) == f"No fastANI executable at {test_file_2}"
 
 
-# Test case 2: there is a file, but it is not executable
+# Test case 3: there is a file, but it is not executable
 def test_get_version_exe_not_executable(executable_not_executable, monkeypatch):
     """Test behaviour when the file at the executable location is not executable."""
-    test_file_2 = Path("/non/executable/blastn")
+    test_file_3 = Path("/non/executable/fastani")
     assert (
-        fastani.get_version(test_file_2)
-        == f"fastANI exists at {test_file_2} but not executable"
+        fastani.get_version(test_file_3)
+        == f"fastANI exists at {test_file_3} but not executable"
     )
 
 
-# Test case 3: there is an executable file, but the version can't be retrieved
+# Test case 4: there is an executable file, but the version can't be retrieved
 def test_get_version_exe_no_version(executable_without_version, monkeypatch):
     """Test behaviour when the version for the executable can not be retrieved."""
-    test_file_3 = Path("/missing/version/blastn")
+    test_file_4 = Path("/missing/version/fastani")
     assert (
-        fastani.get_version(test_file_3)
-        == f"fastANI exists at {test_file_3} but could not retrieve version"
+        fastani.get_version(test_file_4)
+        == f"fastANI exists at {test_file_4} but could not retrieve version"
     )
 
 

tests/test_subcmd_09_fastani.py

@@ -52,7 +52,7 @@ def setUp(self):
         self.scheduler = "multiprocessing"
 
         # Null logger instance
-        self.logger = logging.getLogger("TestIndexSubcommand logger")
+        self.logger = logging.getLogger("TestfastANISubcommand logger")
         self.logger.addHandler(logging.NullHandler())
 
         # Command line namespaces