test: correct tests and add them to CI/CD

.github/workflows/release.yml

@@ -27,6 +27,7 @@ jobs:
         CIBW_ARCHS: aarch64
         CIBW_BUILD: ${{ matrix.python-tag }}
         CIBW_BEFORE_BUILD: pip install cython
+        CIBW_TEST_COMMAND: python -m unittest mDeepFRI.tests -vv
         CIBW_BUILD_VERBOSITY: 2
         CIBW_TEST_REQUIRES: importlib-resources
       with:
@@ -52,6 +53,7 @@ jobs:
         CIBW_ARCHS: x86_64
         CIBW_BUILD: ${{ matrix.python-tag }}
         CIBW_BEFORE_BUILD: pip install cython
+        CIBW_TEST_COMMAND: python -m unittest mDeepFRI.tests -vv
         CIBW_BUILD_VERBOSITY: 2
         CIBW_TEST_REQUIRES: importlib-resources
       with:
@@ -129,6 +131,8 @@ jobs:
       with:
         name: wheels
         path: dist/*
+    - name: Run tests without coverage
+      run: python -m unittest
 
   test-sdist:
     runs-on: ubuntu-latest
@@ -149,8 +153,8 @@ jobs:
       run: python -m pip install -U pip setuptools wheel
     - name: Install built wheel
       run: python -m pip install --no-binary mDeepFRI --find-links=dist mDeepFRI
-    # - name: Run tests without coverage
-      # run: python -m unittest mDeepFRI.tests -vv
+    - name: Run tests without coverage
+      run: python -m unittest mDeepFRI.tests -vv
 
   upload:
     environment: PyPI

mDeepFRI/bio_utils.py

@@ -223,7 +223,7 @@ def get_residues_coordinates(structure: np.ndarray, chain: str = "A"):
     protein_chain = structure[structure.chain_id == chain]
     # extract CA atoms coordinates
     ca_atoms = protein_chain[(protein_chain.atom_name == "CA")
-                             & (protein_chain.hetero is False)]
+                             & (protein_chain.hetero is not False)]
 
     residues = str(
         ProteinSequence(

mDeepFRI/tests/__init__.py

@@ -0,0 +1,13 @@
+from . import (test_alignment, test_bio_utils, test_install, test_mmseqs,
+               test_pdb, test_predict, test_utils)
+
+
+def load_tests(loader, suite, pattern):
+    suite.addTests(loader.loadTestsFromModule(test_alignment))
+    suite.addTests(loader.loadTestsFromModule(test_bio_utils))
+    suite.addTests(loader.loadTestsFromModule(test_install))
+    suite.addTests(loader.loadTestsFromModule(test_mmseqs))
+    suite.addTests(loader.loadTestsFromModule(test_pdb))
+    suite.addTests(loader.loadTestsFromModule(test_predict))
+    suite.addTests(loader.loadTestsFromModule(test_utils))
+    return suite

mDeepFRI/tests/test_alignment.py

@@ -2,7 +2,7 @@
 
 import pyopal
 
-from mDeepFRI.alignment import align_pairwise, best_hit_database
+from mDeepFRI.alignment import align_pairwise, best_hit_database, insert_gaps
 
 
 class TestAlignment(unittest.TestCase):
@@ -26,7 +26,20 @@ def test_best_hit_database(self):
         self.assertEqual(best_hit, "seq3")
 
     def test_align_pairwise(self):
-        alignment = align_pairwise(self.queries["query_seq"],
-                                   self.targets["seq3"])
+        alignment, iden, coverage = align_pairwise(self.queries["query_seq"],
+                                                   self.targets["seq3"])
         self.assertEqual(alignment,
                          "MMMMMMMMMXMMMMMMMMMMMMMMMMMMMMMMXMMMMMMMMMMX")
+        self.assertAlmostEqual(iden, 0.93, places=2)
+        self.assertAlmostEqual(coverage, 1.0, places=2)
+
+
+class TestInsertGaps(unittest.TestCase):
+    def test_deletion(self):
+        self.assertEqual(insert_gaps('AACT', 'AAT', 'MMDM'), ('AACT', 'AA-T'))
+
+    def test_insertion(self):
+        self.assertEqual(insert_gaps('AAT', 'AATC', 'MMMI'), ('AAT-', 'AATC'))
+
+    def test_unaligned(self):
+        self.assertEqual(insert_gaps('AAT', 'FGTC', 'XXMI'), ('AAT-', 'FGTC'))

mDeepFRI/tests/test_bio_utils.py

@@ -3,21 +3,10 @@
 import numpy as np
 from biotite.structure.io.pdb import PDBFile
 
-from mDeepFRI.bio_utils import get_residues_coordinates, insert_gaps
+from mDeepFRI.bio_utils import get_residues_coordinates
 from mDeepFRI.contact_map_utils import pairwise_sqeuclidean
 
 
-class TestInsertGaps(unittest.TestCase):
-    def test_deletion(self):
-        self.assertEqual(insert_gaps('AACT', 'AAT', 'MMDM'), ('AACT', 'AA-T'))
-
-    def test_insertion(self):
-        self.assertEqual(insert_gaps('AAT', 'AATC', 'MMMI'), ('AAT-', 'AATC'))
-
-    def test_unaligned(self):
-        self.assertEqual(insert_gaps('AAT', 'FGTC', 'XXMI'), ('AAT-', 'FGTC'))
-
-
 class TestPairwiseSqeuclidean(unittest.TestCase):
     def test_pairwise_sqeuclidean(self):
         np.random.seed(42)

mDeepFRI/tests/test_conctact_map.py

@@ -0,0 +1,46 @@
+import unittest
+
+import numpy as np
+
+from mDeepFRI.contact_map import CAlphaCoordinates
+
+
+class TestCAlphaCoords(unittest.TestCase):
+    def test_init_valid_coords(self):
+        coords = np.array([[1, 2, 3], [4, 5, 6]])
+        alpha_coords = CAlphaCoordinates(coords)
+        assert np.array_equal(alpha_coords.coords, coords)
+
+    def test_init_invalid_dims(self):
+        coords = np.array([[1, 2], [3, 4]])
+        with self.assertRaisesRegex(ValueError, "Coordinates are not 3D."):
+            CAlphaCoordinates(coords)
+
+    def test_init_negative_coords(self):
+        coords = np.array([[-1, 2, 3], [4, 5, 6]])
+        with self.assertRaisesRegex(ValueError,
+                                    "Coordinates contain negative values."):
+            CAlphaCoordinates(coords)
+
+    def test_calculate_distance_map(self):
+        coords = np.array([[0, 0, 0], [1, 1, 1]])
+        alpha_coords = CAlphaCoordinates(coords)
+        distance_map = alpha_coords.calculate_distance_map(
+            distance="sqeuclidean")
+        expected_distances = np.array([[0, 3], [3, 0]], dtype=np.float32)
+        assert np.allclose(np.sqrt(distance_map.distance_map),
+                           expected_distances)
+
+    def test_calculate_distance_map_invalid_function(self):
+        coords = np.array([[0, 0, 0], [1, 1, 1]])
+        alpha_coords = CAlphaCoordinates(coords)
+        with self.assertRaisesRegex(NotImplementedError,
+                                    "Distance metric not implemented."):
+            alpha_coords.calculate_distance_map(distance="euclidean")
+
+    def test_calculate_contact_map(self):
+        coords = np.array([[0, 0, 0], [5, 0, 0], [10, 0, 0]])
+        alpha_coords = CAlphaCoordinates(coords)
+        contact_map = alpha_coords.calculate_contact_map(threshold=6.0)
+        expected_contact_map = np.array([[1, 1, 0], [1, 1, 1], [0, 1, 1]])
+        assert np.array_equal(contact_map.cmap, expected_contact_map)

mDeepFRI/utils.py

@@ -32,17 +32,25 @@ def run_command(command):
                                shell=True,
                                universal_newlines=True)
 
+    stdout = []
     while True:
         line = process.stdout.readline()
+
         if not line:
             break
+        stdout.append(line)
         print(line, end='')
 
     process.wait()
     if process.returncode != 0:
         raise RuntimeError(
             f"Command {command} failed with exit code {process.returncode}")
 
+    # close file
+    process.stdout.close()
+
+    return "".join(stdout)
+
 
 def download_file(url, path):
     """