From 46a8de9758c2a4590d105f669933a1ba04877f8c Mon Sep 17 00:00:00 2001 From: ljwoods2 <145226270+ljwoods2@users.noreply.github.com> Date: Thu, 31 Oct 2024 00:25:58 -0700 Subject: [PATCH 1/2] Update usage.rst --- docs/source/usage.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 556d647..ee9678c 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -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://:', the format can be explicitly selected by passing the keyword argument -'format="IMD"' to the :class:Universe. \ No newline at end of file +'format="IMD"' to the :class:`Universe`. From 2e285df9e1a407bb40f4057e4b90952a23ee2b65 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 27 Nov 2024 17:36:12 -0700 Subject: [PATCH 2/2] renamed IMDREADER to IMD - fix #36 - renamed module - changed imports in tests - changed docs and examples --- docs/source/api.rst | 2 +- docs/source/usage.rst | 2 +- examples/gromacs/repo_files/client.py | 2 +- examples/gromacs/slurm/client.py | 2 +- examples/gromacs/slurm/imd.sh | 2 +- examples/namd/repo_files/client.py | 2 +- imdclient/{IMDREADER.py => IMD.py} | 0 imdclient/tests/test_imdreader.py | 2 +- imdclient/tests/test_manual.py | 2 +- imdclient/tests/test_stream_analysis.py | 2 +- 10 files changed, 9 insertions(+), 9 deletions(-) rename imdclient/{IMDREADER.py => IMD.py} (100%) diff --git a/docs/source/api.rst b/docs/source/api.rst index 8e230bc..faede5b 100644 --- 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 \ No newline at end of file diff --git a/docs/source/usage.rst b/docs/source/usage.rst index ee9678c..62d39fb 100644 --- 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 diff --git a/examples/gromacs/repo_files/client.py b/examples/gromacs/repo_files/client.py index f0e3162..2d6ac20 100644 --- 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 index 00bddfa..0a50af5 100644 --- 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 index b125f8c..906763b 100644 --- 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 index f0e3162..2d6ac20 100644 --- 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 b/imdclient/IMD.py similarity index 100% rename from imdclient/IMDREADER.py rename to imdclient/IMD.py diff --git a/imdclient/tests/test_imdreader.py b/imdclient/tests/test_imdreader.py index a7a7f4c..18279dd 100644 --- 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 index cde3c0d..85a3180 100644 --- 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 index 9817c27..859a7b7 100644 --- 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: