Merge pull request #36 from Electrostatics/nathan/tests

Add pytest-based testing to PROPKA

README.md

@@ -45,7 +45,7 @@ from within a virtual environment (e.g., via [virtualenv](https://pypi.org/proje
 
 ## Requirements
 
-* Python 3.1 or higher 
+* Python 3.5 or higher 
 
 ## Getting started
 

propka/lib.py

@@ -215,7 +215,7 @@ def build_parser(parser=None):
     group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true",
                        help="Keep protons in input file", default=False)
     group.add_argument("-q", "--quiet", action="store_const", const="WARNING",
-                       dest="log_level", help="supress non-warning messages")
+                       dest="log_level", help="suppress non-warning messages")
     group.add_argument("--protonate-all", dest="protonate_all", action="store_true",
                        help="Protonate all atoms (will not influence pKa calculation)",
                        default=False)
@@ -328,4 +328,3 @@ def debug(*args):
 def warning(*args):
     """Log a WARN message"""
     logger.warning(_args_to_str(args))
-

requirements.txt

@@ -1 +1,2 @@
-pytest
+pytest
+numpy

setup.py

@@ -56,6 +56,7 @@ See http://propka.org/ for the PROPKA web server.
             ],
         },
       zip_safe=True,
-      python_requires='>=3',
+      python_requires='>=3.5',
+      tests_require=["pandas", "numpy"],
       test_suite="tests",
 )

tests/README.md

@@ -1,6 +1,7 @@
 # Testing PROPKA
 
-These tests assume that PROPKA is installed as a module on your system.
+These tests assume that PROPKA is installed as a module on your system the 
+dependencies in `../requirements.txt` are satisfied.
 If you are running in a virtual environment and want to make changes to your
 code, module installation accomplished by
 ```

tests/test_basic_regression.py

@@ -4,7 +4,7 @@ import os
 import re
 from pathlib import Path
 import pytest
-import pandas as pd
+from numpy.testing import assert_almost_equal
 import propka.lib
 import propka.molecular_container
 
@@ -12,9 +12,10 @@ import propka.molecular_container
 _LOGGER = logging.getLogger(__name__)
 
 
-# Maximum error set by number of decimal places in pKa output as well as need
+# Number of decimal places for maximum tolerable error.  Set by number of
-# to make unmodified code work on WSL Ubuntu 18.04
+# decimal places in pKa output as well as need to make unmodified code work
-MAX_ERR = 0.01
+# on WSL Ubuntu 18.04
+MAX_ERR_DECIMALS = 2
 
 
 # This directory
@@ -69,8 +70,6 @@ def run_propka(options, pdb_path, tmp_path):
         molecule = propka.molecular_container.Molecular_container(str(pdb_path), args)
         molecule.calculate_pka()
         molecule.write_pka()
-    except Exception as err:
-        raise err
     finally:
         os.chdir(cwd)
 
@@ -104,13 +103,9 @@ def compare_output(pdb, tmp_path, ref_path):
                 m = re.search(r'([0-9]+\.[0-9]+)', line)
                 value = float(m.group(0))
                 test_data.append(value)
-
+    errstr = "Error exceeds maximum allowed value (%d decimal places)" % MAX_ERR_DECIMALS
-    df = pd.DataFrame({"reference": ref_data, "test": test_data})
+    assert_almost_equal(test_data, ref_data, decimal=MAX_ERR_DECIMALS,
-    df["difference"] = df["reference"] - df["test"]
+                        err_msg=errstr, verbose=True)
-    max_err = df["difference"].abs().max()
-    if max_err > MAX_ERR:
-        errstr = "Error in test (%g) exceeds maximum (%g)" % (max_err, MAX_ERR)
-        raise ValueError(errstr)
 
 
 @pytest.mark.parametrize("pdb, options", [