Fix the tests such that it no longer require the working directory to…

… be the root directory (#28)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>

tests/Sandpit/Exscientia/Align/test_decouple.py

@@ -6,6 +6,7 @@
 
 from BioSimSpace.Sandpit.Exscientia.Align._decouple import decouple
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Store the tutorial URL.
 url = BSS.tutorialUrl()
@@ -14,7 +15,9 @@
 @pytest.fixture(scope="session")
 def mol():
     # Alanin-dipeptide.
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])[0]
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )[0]
 
 
 def test_sanity(mol):

tests/Sandpit/Exscientia/Align/test_make_ml.py

@@ -2,14 +2,17 @@
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Align import make_ml
+from tests.conftest import root_fp
 
 # Store the tutorial URL.
 url = BSS.tutorialUrl()
 
 
 @pytest.fixture
 def mol():
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])[0]
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )[0]
 
 
 @pytest.fixture

tests/Sandpit/Exscientia/Align/test_squash.py

@@ -7,6 +7,7 @@
 from sire.maths import Vector
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Make sure AMBER is installed.
 if BSS._amber_home is not None:
@@ -60,7 +61,7 @@ def dual_topology_system():
 @pytest.fixture
 def perturbed_tripeptide():
     return pickle.load(
-        open("tests/Sandpit/Exscientia/input/merged_tripeptide.pickle", "rb")
+        open(f"{root_fp}/Sandpit/Exscientia/input/merged_tripeptide.pickle", "rb")
     )
 
 

tests/Sandpit/Exscientia/Convert/test_convert.py

@@ -3,11 +3,14 @@
 from sire.legacy import Mol as SireMol
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
-    return BSS.IO.readMolecules(["tests/input/ala.crd", "tests/input/ala.top"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"]
+    )
 
 
 def test_system(system):

tests/Sandpit/Exscientia/FreeEnergy/test_alchemical_free_energy.py

@@ -14,6 +14,7 @@
     has_gromacs,
     url,
 )
+from tests.conftest import root_fp
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Protocol import FreeEnergyEquilibration
@@ -133,7 +134,9 @@ class TestAnalysePARQUET:
     @pytest.fixture(scope="class")
     def data(tmp_path_factory):
         outdir = tmp_path_factory.mktemp("out")
-        shutil.copytree("tests/Sandpit/Exscientia/input/parquet", outdir / "parquet")
+        shutil.copytree(
+            f"{root_fp}/Sandpit/Exscientia/input/parquet", outdir / "parquet"
+        )
         return str(outdir / "parquet")
 
     def test_analyse(self, data):
@@ -153,7 +156,9 @@ class Test_gmx_ABFE:
     @staticmethod
     @pytest.fixture(scope="class")
     def freenrg():
-        m = BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])[0]
+        m = BSS.IO.readMolecules(
+            [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+        )[0]
         decouple_m = decouple(m)
         solvated = BSS.Solvent.tip3p(
             molecule=decouple_m, box=3 * [3 * BSS.Units.Length.nanometer]

tests/Sandpit/Exscientia/Gateway/test_file.py

@@ -1,6 +1,7 @@
 import pytest
 
 from BioSimSpace.Sandpit.Exscientia.Gateway import File
+from tests.conftest import root_fp
 
 
 def test_no_arguments():
@@ -10,7 +11,9 @@ def test_no_arguments():
         f = File()
 
 
-@pytest.mark.parametrize("value", ["tests/input/ala.crd", "tests/input/ala.top"])
+@pytest.mark.parametrize(
+    "value", [f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"]
+)
 def test_value(value):
     """Test whether object is initialised correctly and value is set."""
 

tests/Sandpit/Exscientia/Gateway/test_fileset.py

@@ -1,6 +1,7 @@
 import pytest
 
 from BioSimSpace.Sandpit.Exscientia.Gateway import FileSet
+from tests.conftest import root_fp
 
 
 def test_no_arguments():
@@ -13,11 +14,11 @@ def test_no_arguments():
 @pytest.mark.parametrize(
     "value",
     [
-        ["tests/input/ala.crd", "tests/input/ala.top"],
+        [f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"],
         [
-            "tests/input/alanin.pdb",
-            "tests/input/alanin.psf",
-            "tests/input/alanin.params",
+            f"{root_fp}/input/alanin.pdb",
+            f"{root_fp}/input/alanin.psf",
+            f"{root_fp}/input/alanin.params",
         ],
     ],
 )
@@ -58,7 +59,7 @@ def test_missing_files():
     # One file missing.
     with pytest.raises(IOError):
         f = FileSet(help="Help!")
-        f.setValue(["tests/input/amber/ala/ala.crd", "missing2.txt"])
+        f.setValue([f"{root_fp}/input/amber/ala/ala.crd", "missing2.txt"])
 
 
 @pytest.mark.parametrize("optional", [True, False])

tests/Sandpit/Exscientia/Gateway/test_node.py

@@ -4,9 +4,10 @@
 import sys
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Store the name of the test script.
-script_name = "tests/Gateway/node.py"
+script_name = f"{root_fp}/Gateway/node.py"
 
 # Store the name of the python interpreter.
 exe = sys.executable

tests/Sandpit/Exscientia/IO/test_file_cache.py

@@ -6,6 +6,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import has_amber, has_openff
+from tests.conftest import root_fp
 
 
 def test_file_cache():
@@ -18,7 +19,7 @@ def test_file_cache():
     BSS.IO._file_cache._cache = BSS.IO._file_cache._FixedSizeOrderedDict()
 
     # Load the molecular system.
-    s = BSS.IO.readMolecules(["tests/input/ala.crd", "tests/input/ala.top"])
+    s = BSS.IO.readMolecules([f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"])
 
     # Create a temporary working directory.
     tmp_dir = tempfile.TemporaryDirectory()

tests/Sandpit/Exscientia/IO/test_tuple.py

@@ -1,6 +1,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 def test_tuple():
     """Check that we can read from a tuple of files."""
-    BSS.IO.readMolecules(("tests/input/ala.crd", "tests/input/ala.top"))
+    BSS.IO.readMolecules((f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"))

tests/Sandpit/Exscientia/MD/test_md.py

@@ -3,6 +3,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_gromacs, has_namd
+from tests.conftest import root_fp
 
 
 @pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.")
@@ -13,7 +14,9 @@ def test_amber():
     protocol = BSS.Protocol.Minimisation(steps=100)
 
     # Load the molecular system.
-    system = BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    system = BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
     # Initialise the AMBER process.
     process = BSS.MD.run(system, protocol, name="test")
@@ -55,9 +58,9 @@ def test_namd():
     # Load the molecular system.
     system = BSS.IO.readMolecules(
         [
-            "tests/input/alanin.psf",
-            "tests/input/alanin.pdb",
-            "tests/input/alanin.params",
+            f"{root_fp}/input/alanin.psf",
+            f"{root_fp}/input/alanin.pdb",
+            f"{root_fp}/input/alanin.params",
         ]
     )
 

tests/Sandpit/Exscientia/Process/test_amber.py

@@ -10,12 +10,15 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_pyarrow
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.skipif(
@@ -280,9 +283,9 @@ def test_parse_fep_output(system, protocol):
 
     # Assign the path to the output file.
     if isinstance(protocol, BSS.Protocol.FreeEnergy):
-        out_file = "tests/Sandpit/Exscientia/output/amber_fep.out"
+        out_file = f"{root_fp}/Sandpit/Exscientia/output/amber_fep.out"
     else:
-        out_file = "tests/Sandpit/Exscientia/output/amber_fep_min.out"
+        out_file = f"{root_fp}/Sandpit/Exscientia/output/amber_fep_min.out"
 
     # Copy the existing output file into the working directory.
     shutil.copyfile(out_file, process.workDir() + "/amber.out")
@@ -320,7 +323,6 @@ def test_parse_fep_output(system, protocol):
         assert len(records_sc1) != 0
 
 
-
 class TestsaveMetric:
     @staticmethod
     @pytest.fixture()
@@ -334,7 +336,6 @@ def alchemical_system(system):
         system_copy.updateMolecule(0, mol)
         return system_copy
 
-
     @staticmethod
     @pytest.fixture()
     def setup(alchemical_system):
@@ -344,7 +345,7 @@ def setup(alchemical_system):
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         shutil.copyfile(
-            "tests/Sandpit/Exscientia/output/amber_fep.out",
+            f"{root_fp}/Sandpit/Exscientia/output/amber_fep.out",
             process.workDir() + "/amber.out",
         )
         process.saveMetric()
@@ -357,10 +358,9 @@ def test_error_alchemlyb_extract(self, alchemical_system):
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         process.wait()
-        with open(process.workDir() + '/amber.err', 'r') as f:
+        with open(process.workDir() + "/amber.err", "r") as f:
             text = f.read()
-            assert 'Exception Information' in text
-
+            assert "Exception Information" in text
 
     def test_metric_parquet_exist(self, setup):
         assert Path(f"{setup.workDir()}/metric.parquet").exists()

tests/Sandpit/Exscientia/Process/test_dummy_protocol.py

@@ -1,6 +1,7 @@
 import pytest
 
 from tests.Sandpit.Exscientia.conftest import has_amber, has_gromacs
+from tests.conftest import root_fp
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Process._process import Process
@@ -9,7 +10,9 @@
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.skipif(

tests/Sandpit/Exscientia/Process/test_gromacs.py

@@ -27,12 +27,15 @@
     has_openff,
     has_pyarrow,
 )
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.fixture(scope="session")
@@ -254,7 +257,7 @@ def setup(perturbable_system):
         )
         process = BSS.Process.Gromacs(perturbable_system, protocol)
         shutil.copyfile(
-            "tests/Sandpit/Exscientia/output/gromacs.edr",
+            f"{root_fp}/Sandpit/Exscientia/output/gromacs.edr",
             process.workDir() + "/gromacs.edr",
         )
         shutil.copyfile(
@@ -343,17 +346,18 @@ def test_u_nk_parquet(self, setup):
 
     def test_error_alchemlyb_extract(self, perturbable_system, monkeypatch):
         def extract(*args):
-            raise ValueError('alchemlyb.parsing.gmx.extract failed.')
-        monkeypatch.setattr('alchemlyb.parsing.gmx.extract', extract)
+            raise ValueError("alchemlyb.parsing.gmx.extract failed.")
+
+        monkeypatch.setattr("alchemlyb.parsing.gmx.extract", extract)
         # Create a process using any system and the protocol.
         process = BSS.Process.Gromacs(
             perturbable_system,
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         process.wait()
-        with open(process.workDir() + '/gromacs.err', 'r') as f:
+        with open(process.workDir() + "/gromacs.err", "r") as f:
             text = f.read()
-            assert 'Exception Information' in text
+            assert "Exception Information" in text
 
 
 @pytest.mark.skipif(

tests/Sandpit/Exscientia/Process/test_namd.py

@@ -3,16 +3,17 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_namd
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
     return BSS.IO.readMolecules(
         [
-            "tests/input/alanin.psf",
-            f"tests/input/alanin.pdb",
-            f"tests/input/alanin.params",
+            f"{root_fp}/input/alanin.psf",
+            f"{root_fp}/input/alanin.pdb",
+            f"{root_fp}/input/alanin.params",
         ]
     )
 

tests/Sandpit/Exscientia/Process/test_openmm.py

@@ -4,12 +4,15 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_gromacs, has_openff
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.parametrize("restraint", ["backbone", "heavy", "all", "none"])