Merge pull request #2 from Jhsmit/refactor_tests

refactor tests and add CI testing

.github/workflows/pytest.yaml

@@ -0,0 +1,35 @@
+name: Run Tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install .
+        pip install pytest
+
+    - name: Run tests
+      run: pytest

tests/test_hdxrate.py

@@ -8,63 +8,146 @@
 from itertools import combinations
 from operator import add
 
+import pytest
+
 pth = Path(__file__).parent
 
-class TestHDXrate(object):
-    """Tests for `hdxrate` package."""
-
-    @classmethod
-    def setup_class(cls):
-        cls.seq1 = list('AAAWADEAA')
-
-        k_reference = {'D': 3.87, 'E': 4.33, 'H': 7.0}  # DH
-        dict = get_side_chain_dictionary(278, 8, k_reference)
-        one_letter = [k for k in dict.keys() if len(k) == 1]
-        cls.seq2 = reduce(add, [a + b for a, b in combinations(one_letter, 2)])
-
-        cls.seq2 = np.genfromtxt(pth / 'sequence.txt', dtype='U')
-
-    def test_seq1(self):
-        # HD rates
-        pH_read = 6.6
-        temp = 279
-        rates = k_int_from_sequence(self.seq1, temp, pH_read, reference='poly', wildcard='X') * 60
-        # Reference rates obtained from Englander group xls sheet
-        ref_rates = np.array([np.inf, 1.29939811E+03, 3.11703908E+01, 1.21266892E+01, 2.41959255E+01, 3.95805093E+01,
-                              1.63948783E+01, 2.25232682E+01, 4.94028674E-01])
-        assert np.allclose(rates, ref_rates)
-
-        # DH rates
-        pH_read = 7.0
-        temp = 278
-        rates = k_int_from_sequence(self.seq1, temp, pH_read, exchange_type='DH', reference='poly') * 60
-        # Reference rates obtained from Englander group xls sheet
-        ref_rates = np.array([np.inf, 5.831286065E+03, 1.398828104E+02, 5.442072826E+01, 1.085836280E+02,
-                              1.764790873E+02, 7.219785837E+01, 9.955072660E+01, 2.216999376E+00])
-        assert np.allclose(rates, ref_rates)
-
-        #HH rates
-        pH_read = 7.0
-        temp = 278
-        rates = k_int_from_sequence(self.seq1, temp, pH_read, exchange_type='HH', reference='poly', wildcard='X') * 60
-        # Reference rates obtained from Englander group xls sheet
-        ref_rates = np.array([np.inf, 7.01071144E+03, 1.68175255E+02, 6.54277663E+01, 1.30545556E+02, 2.12183978E+02,
-                              8.68187188E+01, 1.19715146E+02, 2.66540425E+00])
-        assert np.allclose(rates, ref_rates)
-
-    def test_seq2(self):
-        reference_rates = np.genfromtxt(pth / 'exchange_rates_xls.txt', skip_header=2,
-                                        delimiter='\t', filling_values=0.)
-
-        reference_rates[0][:] = np.inf
-
-        #HD exchange
-        rates = k_int_from_sequence(self.seq2, 279, 7 - 0.4, exchange_type='HD') * 60
-        assert np.allclose(rates, reference_rates[:, 0], rtol=0.1, equal_nan=True)
-
-        #
-        rates = k_int_from_sequence(self.seq2, 279, 7, exchange_type='DH') * 60
-        assert np.allclose(rates, reference_rates[:, 1], rtol=0.1, equal_nan=True)
-
-        rates = k_int_from_sequence(self.seq2, 279, 7, exchange_type='HH') * 60
-        assert np.allclose(rates, reference_rates[:, 2], rtol=0.1, equal_nan=True)
+
+@pytest.fixture()
+def seq1():
+    return list("AAAWADEAA")
+
+
+@pytest.fixture()
+def seq2():
+    """sequence two a sequence of the pairwise combination of all side chains"""
+    k_reference = {"D": 3.87, "E": 4.33, "H": 7.0}  # DH
+    chains_dict = get_side_chain_dictionary(278, 8, k_reference)
+    one_letter = [k for k in chains_dict.keys() if len(k) == 1]
+    seq2 = reduce(add, [a + b for a, b in combinations(one_letter, 2)])
+
+    return list(seq2)
+
+
+def test_seq1_HD(seq1):
+    # HD rates
+    pH_read = 6.6
+    temp = 279
+    rates = (
+        k_int_from_sequence(seq1, temp, pH_read, reference="poly", wildcard="X") * 60
+    )
+    # Reference rates obtained from Englander group xls sheet
+    ref_rates = np.array(
+        [
+            np.inf,
+            1.29939811e03,
+            3.11703908e01,
+            1.21266892e01,
+            2.41959255e01,
+            3.95805093e01,
+            1.63948783e01,
+            2.25232682e01,
+            4.94028674e-01,
+        ]
+    )
+    assert np.allclose(rates, ref_rates)
+
+
+def test_seq1_DH(seq1):
+    # DH rates
+    pH_read = 7.0
+    temp = 278
+    rates = (
+        k_int_from_sequence(seq1, temp, pH_read, exchange_type="DH", reference="poly")
+        * 60
+    )
+    # check repeated calls give the same result
+    rep_rates = (
+        k_int_from_sequence(seq1, temp, pH_read, exchange_type="DH", reference="poly")
+        * 60
+    )
+    # Reference rates obtained from Englander group xls sheet
+    ref_rates = np.array(
+        [
+            np.inf,
+            5.831286065e03,
+            1.398828104e02,
+            5.442072826e01,
+            1.085836280e02,
+            1.764790873e02,
+            7.219785837e01,
+            9.955072660e01,
+            2.216999376e00,
+        ]
+    )
+    assert np.allclose(rates, ref_rates)
+    assert np.allclose(rates, rep_rates)
+
+
+def test_seq1_HH(seq1):
+    # HH rates
+    pH_read = 7.0
+    temp = 278
+    rates = (
+        k_int_from_sequence(
+            seq1,
+            temp,
+            pH_read,
+            exchange_type="HH",
+            reference="poly",
+            wildcard="X",
+        )
+        * 60
+    )
+
+    rep_rates = (
+        k_int_from_sequence(
+            seq1,
+            temp,
+            pH_read,
+            exchange_type="HH",
+            reference="poly",
+            wildcard="X",
+        )
+        * 60
+    )
+
+    # Reference rates obtained from Englander group xls sheet
+    ref_rates = np.array(
+        [
+            np.inf,
+            7.01071144e03,
+            1.68175255e02,
+            6.54277663e01,
+            1.30545556e02,
+            2.12183978e02,
+            8.68187188e01,
+            1.19715146e02,
+            2.66540425e00,
+        ]
+    )
+    assert np.allclose(rates, ref_rates)
+    assert np.allclose(rates, rep_rates)
+
+
+def test_seq2(seq2):
+    reference_rates = np.genfromtxt(
+        pth / "exchange_rates_xls.txt",
+        skip_header=2,
+        delimiter="\t",
+        filling_values=0.0,
+    )
+
+    reference_rates[0][:] = np.inf
+
+    # HD exchange
+    rates = k_int_from_sequence(seq2, 279, 7 - 0.4, exchange_type="HD") * 60
+    assert np.allclose(rates, reference_rates[:, 0], rtol=0.1, equal_nan=True)
+
+    # DH exchange
+    rates = k_int_from_sequence(seq2, 279, 7, exchange_type="DH") * 60
+    assert np.allclose(rates, reference_rates[:, 1], rtol=0.1, equal_nan=True)
+
+    # HH exchange
+    rates = k_int_from_sequence(seq2, 279, 7, exchange_type="HH") * 60
+    assert np.allclose(rates, reference_rates[:, 2], rtol=0.1, equal_nan=True)