test: Add tests for new 'misc' module

Author: Alan Christie

.coveragerc

@@ -0,0 +1,5 @@
+[run]
+omit = tests/*,**/__init__.py
+
+[report]
+include_namespace_packages = True

.github/workflows/build.yaml

@@ -49,6 +49,7 @@ jobs:
         pip install -r package-requirements.txt
     - name: Test
       run: |
+        pytest
         pyroma .
         pylint dm_job_utilities
         mypy dm_job_utilities --install-types --non-interactive

build-requirements.txt

@@ -1,3 +1,5 @@
 pylint
 pyroma
+pytest
+pytest-cov
 mypy

dm_job_utilities/misc.py

@@ -3,36 +3,25 @@
 
 # Extracted 19th March 2024
 #
-# Includes style changes to align with the pre-existing modules.
+# Includes style changes to align with the pre-existing modules
+# and the following modifications/changes: -
+#
+# 'get_path_from_digest()' has been removed because it is obsolete.
+#
+# 'round_to_significant_number()' has been removed. Its implementation
+# was inaccurate and is easily replaced by round() from the sigfig package.
 
 import os
 import sys
 from math import log10, floor
 from typing import Any, List, Optional, Tuple
 
-DEFAULT_NUM_CHARS = 2
-DEFAULT_NUM_LEVELS = 2
-
 
 def log(*args, **kwargs) -> None:
     """Log output to STDERR"""
     print(*args, file=sys.stderr, **kwargs)
 
 
-def get_path_from_digest(
-    digest, num_chars=DEFAULT_NUM_CHARS, num_levels=DEFAULT_NUM_LEVELS
-) -> List[str]:
-    """Splits a digest string into parts"""
-    parts = []
-    start = 0
-    for _ in range(0, num_levels):
-        end = start + num_chars
-        part = digest[start:end]
-        parts.append(part)
-        start = start + num_chars
-    return parts
-
-
 def expand_path(path) -> None:
     """Create any necessary directories to ensure that the file path is valid.
     The path is a filename or directory that might or not exist.
@@ -175,15 +164,11 @@ def calc_geometric_mean(scores: List[float]) -> float:
     return total ** (1.0 / len(scores))
 
 
-def round_to_significant_number(val: float, sig: int) -> float:
-    """Round the value to the specified number of significant numbers
-    """
-    return round(val, sig - int(floor(log10(abs(val)))) - 1)
-
-
 def is_type(value, typ) -> Tuple[int, Any]:
     """Returns a tuple of the form (status, value) where status is
-    -1 if the value is not of the given type, and 0 if it is."""
+    -1 if the value cannot be of the given type, and 0 if it is. The value
+    returned is cast to the given type on success.
+    """
     if value is None:
         return 0, value
     try:

test-data/atom-block-a-in.sdf

@@ -0,0 +1,13 @@
+
+     RDKit          2D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2990    2.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.5981   -0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+M  CHG  1   4  -1
+M  END

test-data/atom-block-a-out.sdf

@@ -0,0 +1,12 @@
+
+     RDKit          2D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2990    2.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.5981   -0.0000    0.0000 O   0  5  0  0  0  1  0  0  0  0  0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+M  CHG  1   4  -1

tests/__init__.py

@@ -0,0 +1,39 @@
+
+import pathlib
+import unittest
+
+from dm_job_utilities.misc import (
+    calc_geometric_mean,
+    is_type,
+    read_delimiter,
+    update_charge_flag_in_atom_block,
+)
+
+class TestMiscMethods(unittest.TestCase):
+
+    def test_update_charge_flag_in_atom_block(self):
+        atom_block_a_in = pathlib.Path('test-data/atom-block-a-in.sdf').read_text()
+        atom_block_a_out = pathlib.Path('test-data/atom-block-a-out.sdf').read_text()
+        output = update_charge_flag_in_atom_block(atom_block_a_in)
+        self.assertEqual(output, atom_block_a_out)
+
+    def test_read_delimiter(self):
+        self.assertEqual(read_delimiter("comma"), ",")
+        self.assertEqual(read_delimiter("pipe"), "|")
+        self.assertEqual(read_delimiter("space"), None)
+        self.assertEqual(read_delimiter("tab"), "\t")
+        self.assertEqual(read_delimiter("unknown"), "unknown")
+
+    def test_calc_geometric_mean(self):
+        data = [1.0, 2.0, 3.0, 4.0, 5.0]
+        mean = calc_geometric_mean(data)
+        self.assertAlmostEqual(mean, 2.605, 3)
+
+    def test_is_type(self):
+        self.assertEqual(is_type(None, int), (0, None))
+        self.assertEqual(is_type(1, int), (1, 1))
+        self.assertEqual(is_type("1", str), (1, '1'))
+        self.assertEqual(is_type(1.0, float), (1, 1))
+        self.assertEqual(is_type(1, str), (1, '1'))
+        self.assertEqual(is_type("1", float), (1, 1.0))
+        self.assertEqual(is_type(1.0, int), (1, 1))