Added test_subcmd_09_fastani.py

This does not work at present, and is set to be skipped.

tests/test_subcmd_09_fastani.py

@@ -0,0 +1,88 @@
+"""Test fastANI subcommand for pyani.
+
+The test suite is intended to be run from the repository root using:
+
+pytest -v
+"""
+
+import logging
+import unittest
+
+from argparse import Namespace
+from typing import NamedTuple
+from pathlib import Path
+
+from pyani.scripts import subcommands
+
+
+# Convenience struct with paths to third-party executables
+class ThirdPartyExes(NamedTuple):
+    fastani_exe: Path
+
+
+# Convenience struct with paths to working directories
+class DirPaths(NamedTuple):
+    indir: Path
+    outdir: Path
+
+
+# Convenience struct for label/class files
+class LabelPaths(NamedTuple):
+    classes: Path
+    labels: Path
+
+
+class TestfastANISubcommand(unittest.TestCase):
+
+    """Class defining tests of the pyani fastANI subcommand."""
+
+    def setUp(self):
+        """Configure parameters for tests."""
+        testdir = Path("tests")
+        self.dirpaths = DirPaths(
+            testdir / "test_input" / "subcmd_fastani",
+            testdir / "test_output" / "subcmd_fastani",
+        )
+        self.dirpaths.outdir.mkdir(exist_ok=True)
+        self.dbpath = testdir / "test_output" / "subcmd_createdb" / "pyanidb"
+        self.lblfiles = LabelPaths(
+            self.dirpaths.indir / "classes.txt", self.dirpaths.indir / "labels.txt"
+        )
+        self.exes = ThirdPartyExes("fastANI")
+        self.scheduler = "multiprocessing"
+
+        # Null logger instance
+        self.logger = logging.getLogger("TestIndexSubcommand logger")
+        self.logger.addHandler(logging.NullHandler())
+
+        # Command line namespaces
+        self.argsdict = {
+            "fastani": Namespace(
+                indir=self.dirpaths.indir,
+                outdir=self.dirpaths.outdir,
+                dbpath=self.dbpath,
+                force=False,
+                name="test_fastani",
+                classes=self.lblfiles.classes,
+                labels=self.lblfiles.labels,
+                recovery=False,
+                cmdline="fastANI test suite",
+                fastani_exe=self.exes.fastani_exe,
+                fragLen=3000,
+                kmerSize=16,
+                minFraction=0.2,
+                scheduler=self.scheduler,
+                workers=None,
+                disable_tqdm=True,
+                jobprefix="fastANITest",
+            )
+        }
+
+    @unittest.skip(
+        "This test currently fails for reasons unknown. \
+        Something about the comparisons.kmersize column not existing."
+    )
+    def test_fastani(self):
+        """Test fastani run."""
+        print(self.argsdict["fastani"])
+        subcommands.subcmd_fastani(self.argsdict["fastani"])