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Replace pandas with numpy.testing

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Addresses https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429104797
This commit is contained in:
Nathan Baker
2020-05-23 08:40:17 -07:00
parent 0b4241cce6
commit 73f0ce47af
4 changed files with 12 additions and 14 deletions
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2
requirements.txt
View File

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

2
setup.py
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@@ -57,6 +57,6 @@ See http://propka.org/ for the PROPKA web server.
}, },
zip_safe=True, zip_safe=True,
python_requires='>=3.5', python_requires='>=3.5',
tests_require=["pandas", "pytest"], tests_require=["pandas", "numpy"],
test_suite="tests", test_suite="tests",
) )

3
tests/README.md
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@@ -1,6 +1,7 @@
# Testing PROPKA # 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 If you are running in a virtual environment and want to make changes to your
code, module installation accomplished by code, module installation accomplished by
``` ```

19
tests/test_basic_regression.py
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@@ -4,7 +4,7 @@ import os
import re import re
from pathlib import Path from pathlib import Path
import pytest import pytest
import pandas as pd from numpy.testing import assert_almost_equal
import propka.lib import propka.lib
import propka.molecular_container import propka.molecular_container
@@ -12,9 +12,10 @@ import propka.molecular_container
_LOGGER = logging.getLogger(__name__) _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 # This directory
@@ -102,13 +103,9 @@ def compare_output(pdb, tmp_path, ref_path):
m = re.search(r'([0-9]+\.[0-9]+)', line) m = re.search(r'([0-9]+\.[0-9]+)', line)
value = float(m.group(0)) value = float(m.group(0))
test_data.append(value) 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", [ @pytest.mark.parametrize("pdb, options", [