added tests for all possible param parsing, fixed casing

Author: SamCox822

mdagent/tools/base_tools/simulation_tools/setup_and_run.py

@@ -1401,7 +1401,7 @@ def _parse_parameter(self, parameter, default_unit, possible_units):
             unit_part = "/" + unit_part
         elif "^-1" in parameter_str:
             parameter_str = parameter_str.replace("^-1", "")
-            match = re.match(r'^(\d+(?:\.\d+)?)([a-zA-Z]+)$', parameter_str)
+            match = re.match(r"^(\d+(?:\.\d+)?)([a-zA-Z]+)$", parameter_str)
             num_value = float(match.group(1))
             unit_part = "/" + match.group(2)
         else:
@@ -1419,8 +1419,8 @@ def _parse_parameter(self, parameter, default_unit, possible_units):
                     error_msg += f"Invalid format for parameter: '{parameter_str}'."
 
         # Convert the unit part to an OpenMM unit
-        if unit_part in possible_units:
-            return num_value * possible_units[unit_part], error_msg
+        if unit_part.lower() in possible_units:
+            return num_value * possible_units[unit_part.lower()], error_msg
         else:
             # If the unit is not recognized, raise an error
             error_msg += f"""Unknown unit '{unit_part}' for parameter.
@@ -1469,7 +1469,7 @@ def parse_pressure(self, pressure):
             "atmosphere": unit.atmospheres,
             "pascal": unit.pascals,
             "pascals": unit.pascals,
-            "Pa": unit.pascals,
+            "pa": unit.pascals,
             "poundforce/inch^2": unit.psi,
             "psi": unit.psi,
         }

tests/test_setup.py

@@ -16,19 +16,16 @@ def setupandrun(get_registry):
     return SetUpandRunFunction(get_registry)
 
 
-def test_parse_cutoff(setupandrun):
-    cutoff = unit.Quantity(1.0, unit.nanometers)
-    result = setupandrun._parse_cutoff(cutoff)
-    assert cutoff == result
-
-    cutoff = 3.0
-    result = setupandrun._parse_cutoff(cutoff)
-    expected_result = unit.Quantity(cutoff, unit.nanometers)
-    assert expected_result == result
-
-    cutoff = "2angstroms"
-    result = setupandrun._parse_cutoff(cutoff)
-    expected_result = unit.Quantity(2.0, unit.angstroms)
+@pytest.mark.parametrize(
+    "input_cutoff, expected_result",
+    [
+        (unit.Quantity(1.0, unit.nanometers), unit.Quantity(1.0, unit.nanometers)),
+        (3.0, unit.Quantity(3.0, unit.nanometers)),
+        ("2angstroms", unit.Quantity(2.0, unit.angstroms)),
+    ],
+)
+def test_parse_cutoff(setupandrun, input_cutoff, expected_result):
+    result = setupandrun._parse_cutoff(input_cutoff)
     assert expected_result == result
 
 
@@ -40,26 +37,72 @@ def test_parse_cutoff_unknown_unit(setupandrun):
 
 def test_parse_temperature(setupandrun):
     result = setupandrun.parse_temperature("300k")
+    result2 = setupandrun.parse_temperature("300kelvin")
     expected_result = unit.Quantity(300, unit.kelvin)
+    assert expected_result == result[0] == result2[0]
+
+
+@pytest.mark.parametrize(
+    "input_friction, expected_friction_result",
+    [
+        ("1/ps", unit.Quantity(1, 1 / unit.picoseconds)),
+        ("1/picosecond", unit.Quantity(1, 1 / unit.picosecond)),
+        ("1/picoseconds", unit.Quantity(1, 1 / unit.picosecond)),
+        ("1picosecond^-1", unit.Quantity(1, 1 / unit.picosecond)),
+        ("1picoseconds^-1", unit.Quantity(1, 1 / unit.picoseconds)),
+        ("1/ps^-1", unit.Quantity(1, 1 / unit.picoseconds)),
+        ("1ps^-1", unit.Quantity(1, 1 / unit.picoseconds)),
+        ("1*ps^-1", unit.Quantity(1, 1 / unit.picoseconds)),
+    ],
+)
+def test_parse_friction(setupandrun, input_friction, expected_friction_result):
+    result = setupandrun.parse_friction(input_friction)
+    assert (
+        expected_friction_result == result[0]
+    ), f"Expected {expected_friction_result} for {input_friction}, got {result[0]}"
+
+
+@pytest.mark.parametrize(
+    "input_time, expected_time_unit",
+    [
+        ("1ps", unit.picoseconds),
+        ("1picosecond", unit.picoseconds),
+        ("1picoseconds", unit.picoseconds),
+        ("1fs", unit.femtoseconds),
+        ("1femtosecond", unit.femtoseconds),
+        ("1femtoseconds", unit.femtoseconds),
+        ("1ns", unit.nanoseconds),
+        ("1nanosecond", unit.nanoseconds),
+        ("1nanoseconds", unit.nanoseconds),
+    ],
+)
+def test_parse_time(setupandrun, input_time, expected_time_unit):
+    result = setupandrun.parse_timestep(input_time)
+    expected_result = unit.Quantity(1, expected_time_unit)
     assert expected_result == result[0]
 
 
-def parse_friction(setupandrun):
-    result = setupandrun.parse_friction("1/ps")
-    expected_result = unit.Quantity(1, unit.picoseconds)
-    assert expected_result == result[0]
-
-
-def test_parse_time(setupandrun):
-    result = setupandrun.parse_timestep("1ns")
-    expected_result = unit.Quantity(1, unit.nanoseconds)
-    assert expected_result == result[0]
-
-
-def test_parse_pressure(setupandrun):
-    result = setupandrun.parse_pressure("1bar")
-    expected_result = unit.Quantity(1, unit.bar)
-    assert expected_result == result[0]
+@pytest.mark.parametrize(
+    "input_pressure, expected_pressure_unit",
+    [
+        ("1bar", unit.bar),
+        ("1atm", unit.atmospheres),
+        ("1atmosphere", unit.atmospheres),
+        ("1pascal", unit.pascals),
+        ("1pascals", unit.pascals),
+        ("1Pa", unit.pascals),
+        ("1poundforce/inch^2", unit.psi),
+        ("1psi", unit.psi),
+    ],
+)
+def test_parse_pressure(setupandrun, input_pressure, expected_pressure_unit):
+    result = setupandrun.parse_pressure(input_pressure)
+    expected_result = unit.Quantity(1, expected_pressure_unit)
+    # assert expected_result == result[0]
+    if expected_result != result[0]:
+        raise AssertionError(
+            f"Expected {expected_result} for {input_pressure}, got {result[0]}"
+        )
 
 
 def test_process_parameters(setupandrun):