Remove the large adk_oplsaa.trr test file

CHANGELOG.md

@@ -45,6 +45,7 @@ The rules for this file:
 <!-- Changes in existing functionality -->
 
 - Switch to micromamba in CI (PR #88)
+- Default physical property is now 'position' for ACF widget (PR #89)
 
 ### Deprecated
 

mdadash/backend/analyses/acf.py

@@ -27,8 +27,8 @@ class ACFAnalysis(WidgetBase):
 
     The following physical properties are supported:
 
-    * velocity
     * position
+    * velocity
     * force
 
     A custom :class:`SlidingWindowACF` is used to calculate autocorrelation of chosen
@@ -48,8 +48,8 @@ class ACFAnalysis(WidgetBase):
             Default: ``serial``
 
     Physical property
-        The physical property to analyze - `velocity`, `position` or `force`
-            Default: ``velocity``
+        The physical property to analyze - `position`, `velocity` or `force`
+            Default: ``position``
 
     Selection
         The MDAnalysis selection phrase to run this analysis on
@@ -155,8 +155,8 @@ class ACFAnalysis(WidgetBase):
             "description": "Physical property to analyze",
             "type": "select",
             "items": [
-                "velocity",
                 "position",
+                "velocity",
                 "force",
             ],
         },
@@ -229,7 +229,7 @@ class ACFAnalysis(WidgetBase):
     def __init__(self):
         super().__init__()
         self.acf = None
-        self.physical_property = "velocity"
+        self.physical_property = "position"
         self.selection = "all"
         self.dim_type = "xyz"
         self.centered = False
@@ -382,7 +382,7 @@ class SlidingWindowACF:
     def __init__(
         self,
         u: mda.Universe,
-        physical_property: str = "velocity",
+        physical_property: str = "position",
         select: str = "all",
         dim_type: str = "xyz",
         centered: bool = False,
@@ -391,8 +391,8 @@ def __init__(
     ):
         self.u = u
         property_map = {
-            "velocity": "velocities",
             "position": "positions",
+            "velocity": "velocities",
             "force": "forces",
         }
         self.physical_property = property_map[physical_property]

mdadash/backend/tests/test_server.py

@@ -13,7 +13,7 @@
 from mdadash.backend.kernel.core import BufferedTrajectory
 from mdadash.backend.main import MDADash, app, sio, start_server
 from mdadash.backend.state.manager import StateManager
-from mdadash.backend.tests.data.files import TPR, TRR, XTC
+from mdadash.backend.tests.data.files import TPR, XTC
 from mdadash.backend.widgets.base import WidgetBase, WidgetManager
 
 from .utils import (
@@ -57,20 +57,6 @@ def imd_server_fixture():
     server.cleanup()
 
 
-@pytest.fixture(name="imd_server_trr")
-def imd_server_fixture_trr():
-    u = mda.Universe(TPR, TRR)
-    server = InThreadIMDServer(u.trajectory)
-    info = create_default_imdsinfo_v3()
-    info.velocities = True
-    info.forces = False
-    info.box = True
-    server.set_imdsessioninfo(info)
-    server.handshake_sequence("localhost", first_frame=True)
-    yield server
-    server.cleanup()
-
-
 def test_start_server_imd_trajectory(mocker):
     # mock the command line params
     mocker.patch.object(
@@ -109,7 +95,7 @@ def test_start_server_file_trajectory(mocker):
             "--topology",
             str(TPR),
             "--trajectory",
-            str(TRR),
+            str(XTC),
         ],
     )
     mock_uvicorn_run = mocker.patch("uvicorn.run")
@@ -1090,11 +1076,11 @@ async def test_widget_run_msd_diffusion_coefficient(_client):
     await disconnect_from_simulation()
 
 
-async def test_widget_run_vacf_serial(_client):
+async def test_widget_run_acf_serial(_client):
     uuid = await add_widget("ACF")
-    await connect_to_file_simulation(TRR, step=1, batch_size=3)
+    await connect_to_file_simulation(XTC, step=1, batch_size=3)
     inputs = [
-        ("physical_property", "velocity"),
+        ("physical_property", "position"),
         ("selection", "resid 1"),
         ("custom_title", ""),
         ("show_particle_acfs", True),
@@ -1109,11 +1095,11 @@ async def test_widget_run_vacf_serial(_client):
     await disconnect_from_simulation()
 
 
-async def test_widget_run_vacf_serial_batch(_client):
+async def test_widget_run_acf_serial_batch(_client):
     uuid = await add_widget("ACF")
-    await connect_to_file_simulation(TRR, step=1, batch_size=3)
+    await connect_to_file_simulation(XTC, step=1, batch_size=3)
     inputs = [
-        ("physical_property", "velocity"),
+        ("physical_property", "position"),
         ("selection", "resid 1"),
         ("_run_frequency", "batch"),
     ]
@@ -1124,11 +1110,11 @@ async def test_widget_run_vacf_serial_batch(_client):
     await disconnect_from_simulation()
 
 
-async def test_widget_run_vacf_parallel(_client):
+async def test_widget_run_acf_parallel(_client):
     uuid = await add_widget("ACF")
-    await connect_to_file_simulation(TRR, step=1, batch_size=3)
+    await connect_to_file_simulation(XTC, step=1, batch_size=3)
     inputs = [
-        ("physical_property", "velocity"),
+        ("physical_property", "position"),
         ("selection", "resid 1"),
         ("show_particle_acfs", True),
         ("_run_mode", "parallel"),
@@ -1140,11 +1126,11 @@ async def test_widget_run_vacf_parallel(_client):
     await disconnect_from_simulation()
 
 
-async def test_widget_run_vacf_parallel_batch(_client):
+async def test_widget_run_acf_parallel_batch(_client):
     uuid = await add_widget("ACF")
-    await connect_to_file_simulation(TRR, step=1, batch_size=3)
+    await connect_to_file_simulation(XTC, step=1, batch_size=3)
     inputs = [
-        ("physical_property", "velocity"),
+        ("physical_property", "position"),
         ("selection", "resid 1"),
         ("_run_frequency", "batch"),
         ("_run_mode", "parallel"),
@@ -1156,11 +1142,11 @@ async def test_widget_run_vacf_parallel_batch(_client):
     await disconnect_from_simulation()
 
 
-async def test_widget_run_vacf_running_integral(_client):
+async def test_widget_run_acf_running_integral(_client):
     uuid = await add_widget("ACF")
-    await connect_to_file_simulation(TRR, step=1, batch_size=2)
+    await connect_to_file_simulation(XTC, step=1, batch_size=2)
     inputs = [
-        ("physical_property", "velocity"),
+        ("physical_property", "position"),
         ("selection", "resid 1"),
         ("show_running_integral", True),
     ]
@@ -1483,7 +1469,7 @@ async def test_trajectory_file(_client):
     main.mdadash.sm.universe_configs[0].update(
         {
             "topology": str(TPR),
-            "trajectory": str(TRR),
+            "trajectory": str(XTC),
         }
     )
     handler = sio.handlers["/"]["connect_to_simulations"]