fix conversion of anim.py pyani_files.py to pathlib

pyani/anim.py

@@ -105,7 +105,7 @@ def get_version(nucmer_exe=pyani_config.NUCMER_DEFAULT):
 # Generate list of Job objects, one per NUCmer run
 def generate_nucmer_jobs(
     filenames,
-    outdir=".",
+    outdir=Path("."),
     nucmer_exe=pyani_config.NUCMER_DEFAULT,
     filter_exe=pyani_config.FILTER_DEFAULT,
     maxmatch=False,

pyani/pyani_files.py

@@ -74,10 +74,9 @@ def get_fasta_paths(dirname, extlist=None):
     """
     extlist = extlist or [".fna", ".fa", ".fasta", ".fas"]
     return [
-        os.path.join(dirname, fname)
-        for fname in os.listdir(dirname)
-        if os.path.isfile(os.path.join(dirname, fname))
-        and os.path.splitext(fname)[-1] in extlist
+        dirname / fname
+        for fname in dirname.iterdir()
+        if (dirname / fname).is_file() and fname.suffix in extlist
     ]
 
 
@@ -92,8 +91,8 @@ def get_fasta_and_hash_paths(dirname="."):
     infiles = get_fasta_paths(dirname)
     outfiles = []
     for infile in infiles:
-        hashfile = os.path.splitext(infile)[0] + ".md5"
-        if not os.path.isfile(hashfile):
+        hashfile = infile.with_suffix(".md5")
+        if not hashfile.is_file():
             raise IOError("Hashfile %s does not exist" % hashfile)
         outfiles.append((infile, hashfile))
     return outfiles
@@ -106,8 +105,8 @@ def get_input_files(dirname, *ext):
     :param dirname:  str, path to input directory
     :param *ext:  list of arguments describing permitted file extensions
     """
-    filelist = [f for f in os.listdir(dirname) if os.path.splitext(f)[-1] in ext]
-    return [os.path.join(dirname, f) for f in filelist]
+    filelist = [fname for fname in dirname.iterdir() if fname.suffix in ext]
+    return [dirname / fname for fname in filelist]
 
 
 # Get lengths of input sequences
@@ -124,9 +123,7 @@ def get_sequence_lengths(fastafilenames):
     """
     tot_lengths = {}
     for fname in fastafilenames:
-        tot_lengths[os.path.splitext(os.path.split(fname)[-1])[0]] = sum(
-            [len(s) for s in SeqIO.parse(fname, "fasta")]
-        )
+        tot_lengths[fname.stem] = sum([len(s) for s in SeqIO.parse(fname, "fasta")])
     return tot_lengths
 
 
@@ -195,7 +192,5 @@ def collect_existing_output(dirpath, program, args):
             suffix = ".filter"
     elif program == "blastn":
         suffix = ".blast_tab"
-    existingfiles = [
-        fname for fname in os.listdir(dirpath) if os.path.splitext(fname)[-1] == suffix
-    ]
+    existingfiles = [fname for fname in dirpath.iterdir() if fname.suffix == suffix]
     return existingfiles

tests/test_anim.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-"""test_anim.py
-
-Test anim.py module.
+"""Test anim.py module.
 
 These tests are intended to be run from the repository root using:
 
@@ -50,6 +48,8 @@
 import os
 import unittest
 
+from pathlib import Path
+
 import pandas as pd
 import pytest
 
@@ -68,6 +68,7 @@ class TestNUCmerCmdline(unittest.TestCase):
     def setUp(self):
         """Set parameters for tests."""
         # Basic NUCmer and delta-filter command-line targets
+        testdir = Path("tests")
         self.ntgt = " ".join(
             [
                 "nucmer --mum -p",
@@ -89,90 +90,90 @@ def setUp(self):
                 "tests/test_output/anim/nucmer_output/file1_vs_file2.filter",
             ]
         )
-        self.files = ["file1", "file2", "file3", "file4"]
+        self.files = [Path("file1"), Path("file2"), Path("file3"), Path("file4")]
         self.ncmdlist = [
-            "nucmer --mum -p ./nucmer_output/file1_vs_file2 file1 file2",
-            "nucmer --mum -p ./nucmer_output/file1_vs_file3 file1 file3",
-            "nucmer --mum -p ./nucmer_output/file1_vs_file4 file1 file4",
-            "nucmer --mum -p ./nucmer_output/file2_vs_file3 file2 file3",
-            "nucmer --mum -p ./nucmer_output/file2_vs_file4 file2 file4",
-            "nucmer --mum -p ./nucmer_output/file3_vs_file4 file3 file4",
+            "nucmer --mum -p nucmer_output/file1_vs_file2 file1 file2",
+            "nucmer --mum -p nucmer_output/file1_vs_file3 file1 file3",
+            "nucmer --mum -p nucmer_output/file1_vs_file4 file1 file4",
+            "nucmer --mum -p nucmer_output/file2_vs_file3 file2 file3",
+            "nucmer --mum -p nucmer_output/file2_vs_file4 file2 file4",
+            "nucmer --mum -p nucmer_output/file3_vs_file4 file3 file4",
         ]
         self.fcmdlist = [
             " ".join(
                 [
                     "delta_filter_wrapper.py delta-filter -1",
-                    "./nucmer_output/file1_vs_file2.delta",
-                    "./nucmer_output/file1_vs_file2.filter",
+                    "nucmer_output/file1_vs_file2.delta",
+                    "nucmer_output/file1_vs_file2.filter",
                 ]
             ),
             " ".join(
                 [
                     "delta_filter_wrapper.py delta-filter -1",
-                    "./nucmer_output/file1_vs_file3.delta",
-                    "./nucmer_output/file1_vs_file3.filter",
+                    "nucmer_output/file1_vs_file3.delta",
+                    "nucmer_output/file1_vs_file3.filter",
                 ]
             ),
             " ".join(
                 [
                     "delta_filter_wrapper.py delta-filter -1",
-                    "./nucmer_output/file1_vs_file4.delta",
-                    "./nucmer_output/file1_vs_file4.filter",
+                    "nucmer_output/file1_vs_file4.delta",
+                    "nucmer_output/file1_vs_file4.filter",
                 ]
             ),
             " ".join(
                 [
                     "delta_filter_wrapper.py delta-filter -1",
-                    "./nucmer_output/file2_vs_file3.delta",
-                    "./nucmer_output/file2_vs_file3.filter",
+                    "nucmer_output/file2_vs_file3.delta",
+                    "nucmer_output/file2_vs_file3.filter",
                 ]
             ),
             " ".join(
                 [
                     "delta_filter_wrapper.py delta-filter -1",
-                    "./nucmer_output/file2_vs_file4.delta",
-                    "./nucmer_output/file2_vs_file4.filter",
+                    "nucmer_output/file2_vs_file4.delta",
+                    "nucmer_output/file2_vs_file4.filter",
                 ]
             ),
             " ".join(
                 [
                     "delta_filter_wrapper.py delta-filter -1",
-                    "./nucmer_output/file3_vs_file4.delta",
-                    "./nucmer_output/file3_vs_file4.filter",
+                    "nucmer_output/file3_vs_file4.delta",
+                    "nucmer_output/file3_vs_file4.filter",
                 ]
             ),
         ]
-        self.outdir = os.path.join("tests", "test_output", "anim")
-        self.indir = os.path.join("tests", "test_input", "anim")
+        self.outdir = testdir / "test_output" / "anim"
+        self.indir = testdir / "test_input" / "anim"
 
     def test_single_cmd_generation(self):
-        """generate single abstract NUCmer/delta-filter command-line.
+        """Generate single abstract NUCmer/delta-filter command-line.
 
         Tests that a single NUCmer/delta-filter command-line pair is
         produced correctly
         """
         cmds = anim.construct_nucmer_cmdline(
-            "file1.fna", "file2.fna", outdir=self.outdir
+            Path("file1.fna"), Path("file2.fna"), outdir=self.outdir
         )
         self.assertEqual(cmds, (self.ntgt, self.ftgt))
 
     def test_maxmatch_cmd_generation(self):
-        """generate NUCmer command line with maxmatch."""
+        """Generate NUCmer command line with maxmatch."""
         ncmd, _ = anim.construct_nucmer_cmdline(
-            "file1.fna", "file2.fna", outdir=self.outdir, maxmatch=True
+            Path("file1.fna"), Path("file2.fna"), outdir=self.outdir, maxmatch=True
         )
         self.assertEqual(ncmd, self.ntgtmax)
 
     def test_multi_cmd_generation(self):
-        """generate multiple abstract NUCmer/delta-filter command-lines.
+        """Generate multiple abstract NUCmer/delta-filter command-lines.
 
         Tests that all the input files are correctly-paired
         """
         cmds = anim.generate_nucmer_commands(self.files)
         self.assertEqual(cmds, (self.ncmdlist, self.fcmdlist))
 
     def test_nucmer_job_generation(self):
-        """generate dependency tree of NUCmer/delta-filter jobs.
+        """Generate dependency tree of NUCmer/delta-filter jobs.
 
         Tests that the correct dependency graph and naming scheme is produced.
         """
@@ -188,12 +189,13 @@ def test_nucmer_job_generation(self):
 
 class TestDeltafileProcessing(unittest.TestCase):
 
-    """Class defining tests for .delta/.filter file parsing"""
+    """Class defining tests for .delta/.filter file parsing."""
 
     def setUp(self):
         """Set parameters for tests."""
-        self.indir = os.path.join("tests", "test_input", "anim")
-        self.seqdir = os.path.join("tests", "test_input", "sequences")
+        testdir = Path("tests")
+        self.indir = testdir / "test_input" / "anim"
+        self.seqdir = testdir / "test_input" / "sequences"
         self.deltafile = os.path.join(self.indir, "test.delta")
         self.deltadir = os.path.join(self.indir, "deltadir")
         self.df_pid = pd.DataFrame(
@@ -208,12 +210,12 @@ def setUp(self):
         )
 
     def test_deltafile_import(self):
-        """parses NUCmer .delta/.filter file."""
+        """Parse test NUCmer .delta/.filter file."""
         result = anim.parse_delta(self.deltafile)
         self.assertEqual(result, (4074001, 2191))
 
     def test_process_deltadir(self):
-        """processes directory of .delta files into ANIResults."""
+        """Process test directory of .delta files into ANIResults."""
         seqfiles = pyani_files.get_fasta_files(self.seqdir)
         orglengths = pyani_files.get_sequence_lengths(seqfiles)
         result = anim.process_deltadir(self.deltadir, orglengths)

tests/test_subcmd_02_index.py

@@ -1,9 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-"""test_subcmd_02_index.py
-
-Test index subcommand for pyani
+"""Test index subcommand for pyani.
 
 The test suite is intended to be run from the repository root using:
 
@@ -62,6 +60,7 @@
 import unittest
 
 from argparse import Namespace
+from pathlib import Path
 
 from pyani.scripts import subcommands
 
@@ -71,11 +70,12 @@ class TestIndexSubcommand(unittest.TestCase):
 
     def setUp(self):
         """Configure parameters for tests."""
-        self.indir = os.path.join("tests", "test_input", "subcmd_index")
-        self.outdir = os.path.join("tests", "test_output", "subcmd_index")
-        self.tgtdir = os.path.join("tests", "test_targets", "subcmd_index")
+        testdir = Path("tests")
+        self.indir = testdir / "test_input" / "subcmd_index"
+        self.outdir = testdir / "test_output" / "subcmd_index"
+        self.tgtdir = testdir / "test_targets" / "subcmd_index"
         # Remove output directory before copying input data across
-        if os.path.exists(self.outdir):
+        if self.outdir.exists():
             shutil.rmtree(self.outdir)
         shutil.copytree(self.indir, self.outdir)
 
@@ -86,14 +86,12 @@ def setUp(self):
         # Command line namespaces
         self.argsdict = {
             "index": Namespace(
-                indir=self.outdir,
-                labelfname=os.path.join("labels.txt"),
-                classfname=os.path.join("classes.txt"),
+                indir=self.outdir, labelfname="labels.txt", classfname="classes.txt"
             )
         }
 
     def test_index(self):
-        """test indexing of downloaded files"""
+        """Test indexing of downloaded files."""
         # Create index
         subcommands.subcmd_index(self.argsdict["index"], self.logger)