Fix server handling in tests.

tests/conftest.py

@@ -1,30 +1,32 @@
-import pytest
-import psutil
+import subprocess
 
 
-@pytest.fixture(autouse=True)
-def wrapper():
-    """
-    A wrapper function to stop the EMLE server after each test.
+def start_server(cwd, env=None):
     """
+    Start the EMLE server using the environment variables.
 
-    yield
+    Parameters
+    ----------
 
-    # Kill the EMLE server.
-    kill_server()
+    cwd : str
+        The current working directory.
 
+    env : dict
+        The environment variables.
 
-def kill_server():
-    """
-    Helper function to kill the EMLE server.
+    Returns
+    -------
+
+    process : subprocess.Popen
+        The EMLE server process object.
     """
 
-    # Kill the EMLE server. We do this manually rather than using emle-stop
-    # because there is sometimes a delay in the termination of the server,
-    # which causes the next test to fail. This only seems to happen when
-    # testing during CI.
-    for conn in psutil.net_connections(kind="inet"):
-        if conn.laddr.port == 10000:
-            process = psutil.Process(conn.pid)
-            process.terminate()
-            break
+    process = subprocess.Popen(
+        ["emle-server"],
+        cwd=cwd,
+        env=env,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+    )
+
+    return process

tests/test_delta_learning.py

@@ -4,19 +4,18 @@
 import shutil
 import subprocess
 import tempfile
-import time
 import yaml
 
+from conftest import start_server
 
-def test_delta_learning(backend="torchani,xtb"):
+
+def test_delta_learning():
     """
     Make sure that the server can run using two backends for the in vacuo
     vacuo calculation. The first is the "reference" backend, the second
     applies delta learning corrections.
     """
 
-    from conftest import kill_server
-
     with tempfile.TemporaryDirectory() as tmpdir:
         # Copy files to temporary directory.
         shutil.copyfile("tests/input/adp.parm7", tmpdir + "/adp.parm7")
@@ -30,6 +29,9 @@ def test_delta_learning(backend="torchani,xtb"):
         env["EMLE_BACKEND"] = "torchani,xtb"
         env["EMLE_ENERGY_FREQUENCY"] = "1"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_sp.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -60,10 +62,8 @@ def test_delta_learning(backend="torchani,xtb"):
                 + float(lines[-1].strip())
             )
 
-    # Kill the server. (Try twice, since there is sometimes a delay.)
-    kill_server()
-    time.sleep(1)
-    kill_server()
+        # Stop the server.
+        server.terminate()
 
     # Now swap the order of the backends.
 
@@ -80,6 +80,9 @@ def test_delta_learning(backend="torchani,xtb"):
         env["EMLE_BACKEND"] = "xtb,torchani"
         env["EMLE_ENERGY_FREQUENCY"] = "1"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_sp.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -109,5 +112,8 @@ def test_delta_learning(backend="torchani,xtb"):
                 + float(lines[-1].strip())
             )
 
+        # Stop the server.
+        server.terminate()
+
     # Make sure that the results are the same.
     assert math.isclose(result_ab, result_ba, rel_tol=1e-6)

tests/test_external.py

@@ -4,6 +4,8 @@
 import subprocess
 import tempfile
 
+from conftest import start_server
+
 
 def test_external_local_directory():
     """
@@ -25,6 +27,9 @@ def test_external_local_directory():
         env["EMLE_EXTERNAL_BACKEND"] = "external.run_external"
         env["EMLE_ENERGY_FREQUENCY"] = "1"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_sp.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -42,6 +47,9 @@ def test_external_local_directory():
         # Make sure that an energy file is written.
         assert os.path.isfile(tmpdir + "/emle_energy.txt")
 
+        # Stop the server.
+        server.terminate()
+
 
 def test_external_plugin_directory():
     """
@@ -63,6 +71,9 @@ def test_external_plugin_directory():
         env["EMLE_PLUGIN_PATH"] = os.getcwd() + "/tests/input"
         env["EMLE_ENERGY_FREQUENCY"] = "1"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_sp.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -79,3 +90,6 @@ def test_external_plugin_directory():
 
         # Make sure that an energy file is written.
         assert os.path.isfile(tmpdir + "/emle_energy.txt")
+
+        # Stop the server.
+        server.terminate()

tests/test_interpolate.py

@@ -5,6 +5,8 @@
 import subprocess
 import tempfile
 
+from conftest import start_server
+
 
 def parse_mdinfo(mdinfo_file):
     """
@@ -30,6 +32,9 @@ def test_interpolate():
         shutil.copyfile("tests/input/adp.rst7", tmpdir + "/adp.rst7")
         shutil.copyfile("tests/input/mm_sp.in", tmpdir + "/mm_sp.in")
 
+        # Start the server.
+        server = start_server(tmpdir)
+
         # Create the sander command.
         command = "sander -O -i mm_sp.in -p adp.parm7 -c adp.rst7"
 
@@ -50,6 +55,9 @@ def test_interpolate():
 
         assert math.isclose(nrg_ref, nrg_mm, rel_tol=1e-5)
 
+        # Stop the server.
+        server.terminate()
+
     # Now perform and interpolated EMLE simulation at lambda=0.
     with tempfile.TemporaryDirectory() as tmpdir:
         # Copy files to temporary directory.
@@ -74,6 +82,9 @@ def test_interpolate():
         env["EMLE_QM_INDICES"] = "adp_qm_indices.txt"
         env["EMLE_ENERGY_FREQUENCY"] = "1"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_sp.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -92,6 +103,9 @@ def test_interpolate():
 
         assert math.isclose(nrg_ref, nrg_emle, rel_tol=1e-4)
 
+        # Stop the server.
+        server.terminate()
+
 
 def test_interpolate_steps():
     """
@@ -123,6 +137,9 @@ def test_interpolate_steps():
         env["EMLE_QM_INDICES"] = "adp_qm_indices.txt"
         env["EMLE_ENERGY_FREQUENCY"] = "1"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_prod.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -147,6 +164,9 @@ def test_interpolate_steps():
                     nrg_interp = lam * data[4] + (1 - lam) * data[3]
                     assert math.isclose(nrg_lambda, nrg_interp, rel_tol=1e-5)
 
+        # Stop the server.
+        server.terminate()
+
 
 def test_interpolate_steps_config():
     """
@@ -168,6 +188,9 @@ def test_interpolate_steps_config():
         # Set environment variables.
         env["EMLE_CONFIG"] = "config.yaml"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_prod.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -191,3 +214,6 @@ def test_interpolate_steps_config():
                     nrg_lambda = data[2]
                     nrg_interp = lam * data[4] + (1 - lam) * data[3]
                     assert math.isclose(nrg_lambda, nrg_interp, rel_tol=1e-5)
+
+        # Stop the server.
+        server.terminate()

tests/test_qm_xyz.py

@@ -4,6 +4,8 @@
 import subprocess
 import tempfile
 
+from conftest import start_server
+
 
 def test_qm_xyz():
     """
@@ -22,6 +24,9 @@ def test_qm_xyz():
         # Set environment variables.
         env["EMLE_QM_XYZ_FREQUENCY"] = "2"
 
+        # Start the server.
+        server = start_server(tmpdir, env=env)
+
         # Create the sander command.
         command = "sander -O -i emle_prod.in -p adp.parm7 -c adp.rst7 -o emle.out"
 
@@ -46,3 +51,6 @@ def test_qm_xyz():
                 if line.startswith("22"):
                     num_frames += 1
         assert num_frames == 11
+
+        # Stop the server.
+        server.terminate()