Ensure IMDServer sends EOF to client DURING test (#5443)

* Fixes #5442
* IMDServer in IMDReader tests now calls disconnect after sending frames so that the client does 
  not rely on the  (now 600s) timeout to see the end of the stream
   - Ensure IMDServer sends EOF to client DURING test
   - add disconnects to one-off tests
* update CHANGELOG
* black formatting of test_imd.py

Author: ljwoods2

package/CHANGELOG

@@ -247,6 +247,8 @@ Changes
  * 2.8.0
 
 Fixes
+ * Fix `test_imd.py` test failures after imdclient 0.2.4
+   increased default timeout by ensuring EOF sent (Issue #5442, PR #5443)
  * Allows bond/angle/dihedral connectivity to be guessed additively with
    `to_guess`, and as a replacement of existing values with `force_guess`.
    Also updates cached bond attributes when updating bonds. (Issue #4759, PR #4761)

testsuite/MDAnalysisTests/coordinates/test_imd.py

@@ -217,6 +217,8 @@ def reader(ref):
         )
         # Send the rest of the frames- small enough to all fit in socket itself
         ref.server.send_frames(1, 5)
+        # Send EOF so the client does not rely on timeout to mark the end of the stream
+        ref.server.disconnect()
 
         reader.add_auxiliary(
             "lowf",
@@ -249,6 +251,8 @@ def transformed(ref):
         )
         # Send the rest of the frames- small enough to all fit in socket itself
         ref.server.send_frames(1, 5)
+        # Send EOF so the client does not rely on timeout to mark the end of the stream
+        ref.server.disconnect()
         transformed.add_transformations(
             translate([1, 1, 1]), translate([0, 0, 0.33])
         )
@@ -436,6 +440,8 @@ def reader(self, universe, imdsinfo):
             buffer_size=1 * 1024 * 1024,
         )
         server.send_frames(1, 5)
+        # Send EOF so the client does not rely on timeout to mark the end of the stream
+        server.disconnect()
 
         yield reader
         server.cleanup()
@@ -513,6 +519,7 @@ def test_n_atoms_not_specified(universe, imdsinfo):
     server = InThreadIMDServer(universe.trajectory)
     server.set_imdsessioninfo(imdsinfo)
     server.handshake_sequence("localhost", first_frame=True)
+    # no EOF needed- client should fail before parsing frames
     with pytest.raises(
         ValueError,
         match="IMDReader: n_atoms must be specified",
@@ -535,6 +542,14 @@ def test_imd_stream_empty(universe, imdsinfo):
         IMDReader(
             f"imd://localhost:{server.port}",
             n_atoms=universe.trajectory.n_atoms,
+            # we have no opportunity to send an EOF here
+            # since IMDReader creation both establishes a connection
+            # and attempts to read the first frame, and the EOF
+            # would have to arrive between these two.
+            # rather than creating a special IMDServer method that
+            # immediately sends EOF after handshake,
+            # just use a 1s timeout passed to IMDClient
+            timeout=1,
         )
     server.cleanup()
 
@@ -549,6 +564,8 @@ def test_create_imd_universe(universe, imdsinfo):
         f"imd://localhost:{server.port}",
         n_atoms=universe.trajectory.n_atoms,
     )
+    # send EOF after handshake and first frame
+    server.disconnect()
     assert type(u_imd.trajectory).__name__ == "IMDReader"
     with pytest.raises(ValueError, match="IMDReader: Invalid IMD URL"):
         u_imd = mda.Universe(
@@ -576,7 +593,7 @@ def test_wrong_imd_protocol_version(universe, imdsinfo):
     server = InThreadIMDServer(universe.trajectory)
     server.set_imdsessioninfo(imdsinfo)
     server.handshake_sequence("localhost", first_frame=True)
-
+    # no EOF needed- client should fail before parsing frames
     with pytest.raises(
         ValueError,
         match=rf"IMDReader: Detected IMD version v{imdsinfo.version}, "