Merge branch 'develop' into docker

Becksteinlab · Nov 28, 2024 · 4157b46 · 4157b46
2 parents 922d00a + 6b4b626
commit 4157b46
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diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,5 +1,5 @@
 API Documentation
 =================
 
-.. automodule:: imdclient.IMDREADER
+.. automodule:: imdclient.IMD
 .. automodule:: imdclient.IMDClient
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -42,7 +42,7 @@ Using IMDClient with MDAnalysis
 Once the simulation is ready for a client connection, setup your MDAnalysis :class:`Universe`
 like this: ::
 
-    from IMDClient.IMDREADER import IMDReader
+    from IMDClient.IMD import IMDReader
     import MDAnalysis as mda
     # Pass host and port of the listening simulation
     # engine as the trajectory argument
@@ -55,4 +55,4 @@ like this: ::
 While this package allows the IMDReader to be automatically selected
 based on the trajectory URL matching the pattern 'imd://<host>:<port>',
 the format can be explicitly selected by passing the keyword argument
-'format="IMD"' to the :class:Universe.
+'format="IMD"' to the :class:`Universe`.
diff --git a/examples/gromacs/repo_files/client.py b/examples/gromacs/repo_files/client.py
@@ -1,4 +1,4 @@
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 import MDAnalysis as mda
 import logging
 from imdclient.tests.datafiles import NAMD_TOPOL

diff --git a/examples/gromacs/slurm/client.py b/examples/gromacs/slurm/client.py
@@ -1,5 +1,5 @@
 # NOTE: chamge
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 import MDAnalysis as mda
 import logging
 

diff --git a/examples/gromacs/slurm/imd.sh b/examples/gromacs/slurm/imd.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-#SBATCH -J GMX_IMDREADER
+#SBATCH -J GMX_IMD
 #SBATCH -N 1
 #SBATCH -n 16
 #SBATCH --gres=gpu:1

diff --git a/examples/namd/repo_files/client.py b/examples/namd/repo_files/client.py
@@ -1,4 +1,4 @@
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 import MDAnalysis as mda
 import logging
 from imdclient.tests.datafiles import NAMD_TOPOL

diff --git a/imdclient/IMDREADER.py → imdclient/IMD.py b/imdclient/IMDREADER.py → imdclient/IMD.py
diff --git a/imdclient/tests/test_imdreader.py b/imdclient/tests/test_imdreader.py
@@ -31,7 +31,7 @@
 from MDAnalysis.transformations import translate
 import pickle
 
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 
 logger = logging.getLogger("imdclient.IMDClient")
 file_handler = logging.FileHandler("test.log")

diff --git a/imdclient/tests/test_manual.py b/imdclient/tests/test_manual.py
@@ -1,4 +1,4 @@
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 import pytest
 import MDAnalysis as mda
 from MDAnalysisTests.coordinates.base import assert_timestep_almost_equal

diff --git a/imdclient/tests/test_stream_analysis.py b/imdclient/tests/test_stream_analysis.py
@@ -15,7 +15,7 @@
 )
 import numpy as np
 import pytest
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 
 
 class TestStreamAnalysis: