Move all test to new folder (duartegroup#108)

* Move all test to new folder

* Test only mlptrain folder

* Add fixtures

* Remove molecules.py

.github/workflows/pytest.yml

@@ -41,7 +41,7 @@ jobs:
       run: ./install_gap.sh
 
     - name: Test basic install
-      run: pytest --cov -k "not test_openmm"
+      run: pytest --cov=mlptrain -k "not test_openmm"
 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4
@@ -83,7 +83,7 @@ jobs:
       run: ./install_ace.sh
 
     - name: Test ACE
-      run: pytest --cov -k "not test_openmm"
+      run: pytest --cov=mlptrain -k "not test_openmm"
 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4
@@ -121,7 +121,7 @@ jobs:
       run: ./install_mace.sh
 
     - name: Test MACE install
-      run: pytest --cov
+      run: pytest --cov=mlptrain
 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: check-shebang-scripts-are-executable
       - id: check-added-large-files
         args: ['--maxkb=500', '--enforce-all']
-        exclude: mlptrain/sampling/tests/data.zip
+        exclude: tests/data/data.zip
       - id: check-yaml
       - id: check-toml
 

mlptrain/sampling/tests/molecules.py → tests/conftest.py

@@ -1,8 +1,10 @@
 import mlptrain as mlt
+import pytest
 from autode.atoms import Atom
 
 
-def _h2():
+@pytest.fixture
+def h2():
     """Dihydrogen molecule"""
     atoms = [
         Atom('H', -0.80952, 2.49855, 0.0),
@@ -11,11 +13,28 @@ def _h2():
     return mlt.Molecule(atoms=atoms, charge=0, mult=1)
 
 
-def _h2o():
+@pytest.fixture
+def h2o():
     """Water molecule"""
     atoms = [
         Atom('H', 2.32670, 0.51322, 0.0),
         Atom('H', 1.03337, 0.70894, -0.89333),
         Atom('O', 1.35670, 0.51322, 0.0),
     ]
     return mlt.Molecule(atoms=atoms, charge=0, mult=1)
+
+
+@pytest.fixture
+def h2_configuration(h2):
+    system = mlt.System(h2, box=[50, 50, 50])
+    config = system.random_configuration()
+
+    return config
+
+
+@pytest.fixture
+def h2o_configuration(h2o):
+    system = mlt.System(h2o, box=[50, 50, 50])
+    config = system.random_configuration()
+
+    return config

mlptrain/sampling/tests/test_bias.py → tests/test_bias.py

@@ -4,7 +4,6 @@
 import mlptrain as mlt
 from mlptrain.utils import work_in_tmp_dir
 from .test_potential import TestPotential
-from .molecules import _h2
 
 mlt.Config.n_cores = 1
 here = os.path.abspath(os.path.dirname(__file__))
@@ -21,8 +20,8 @@ def _get_avg_dists(atoms, atom_pair_list):
 
 
 @work_in_tmp_dir()
-def test_bias():
-    system = mlt.System(_h2(), box=[50, 50, 50])
+def test_bias(h2):
+    system = mlt.System(h2, box=[50, 50, 50])
     pot = TestPotential('1D')
 
     config = system.random_configuration()

mlptrain/sampling/tests/test_md.py → tests/test_md.py

@@ -4,32 +4,17 @@
 from ase.io.trajectory import Trajectory as ASETrajectory
 from ase.constraints import Hookean
 from .test_potential import TestPotential
-from .molecules import _h2, _h2o
-from .utils import work_in_zipped_dir
+from .data.utils import work_in_zipped_dir
 
 here = os.path.abspath(os.path.dirname(__file__))
 
 
-def _h2_configuration():
-    system = mlt.System(_h2(), box=[50, 50, 50])
-    config = system.random_configuration()
-
-    return config
-
-
-def _h2o_configuration():
-    system = mlt.System(_h2o(), box=[50, 50, 50])
-    config = system.random_configuration()
-
-    return config
-
-
-@work_in_zipped_dir(os.path.join(here, 'data.zip'))
-def test_md_full_plumed_input():
+@work_in_zipped_dir(os.path.join(here, 'data/data.zip'))
+def test_md_full_plumed_input(h2o_configuration):
     bias = mlt.PlumedBias(filename='plumed_bias_nopath.dat')
 
     mlt.md.run_mlp_md(
-        configuration=_h2o_configuration(),
+        configuration=h2o_configuration,
         mlp=TestPotential('1D'),
         temp=300,
         dt=1,
@@ -43,13 +28,13 @@ def test_md_full_plumed_input():
     assert os.path.exists('HILLS.dat')
 
 
-@work_in_zipped_dir(os.path.join(here, 'data.zip'))
-def test_md_restart():
-    atoms = _h2_configuration().ase_atoms
+@work_in_zipped_dir(os.path.join(here, 'data/data.zip'))
+def test_md_restart(h2_configuration):
+    atoms = h2_configuration.ase_atoms
     initial_trajectory = ASETrajectory('md_restart.traj', 'r', atoms)
 
     mlt.md.run_mlp_md(
-        configuration=_h2_configuration(),
+        configuration=h2_configuration,
         mlp=TestPotential('1D'),
         temp=300,
         dt=1,
@@ -70,10 +55,10 @@ def test_md_restart():
     assert len(final_trajectory) == 1001 + 101 - 1
 
 
-@work_in_zipped_dir(os.path.join(here, 'data.zip'))
-def test_md_save():
+@work_in_zipped_dir(os.path.join(here, 'data/data.zip'))
+def test_md_save(h2_configuration):
     mlt.md.run_mlp_md(
-        configuration=_h2_configuration(),
+        configuration=h2_configuration,
         mlp=TestPotential('1D'),
         temp=300,
         dt=1,
@@ -96,15 +81,15 @@ def test_md_save():
     assert len(traj_200fs) == 20 + 1
 
 
-@work_in_zipped_dir(os.path.join(here, 'data.zip'))
-def test_md_traj_attachments():
+@work_in_zipped_dir(os.path.join(here, 'data/data.zip'))
+def test_md_traj_attachments(h2o_configuration):
     cv1 = mlt.PlumedAverageCV('cv1', (0, 1))
     bias = mlt.PlumedBias(cvs=cv1)
 
     hookean_constraint = Hookean(a1=1, a2=2, k=100, rt=0.5)
 
     traj = mlt.md.run_mlp_md(
-        configuration=_h2o_configuration(),
+        configuration=h2o_configuration,
         mlp=TestPotential('1D'),
         temp=300,
         dt=1,