IMDReader removed from imdclient

.github/workflows/gh-ci.yaml

@@ -96,10 +96,6 @@ jobs:
     - name: Run IMDClient tests
       run: |
         pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdclient.py
-
-    - name: Run IMDReader tests
-      run: |
-        pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdreader.py
 
     - name: codecov
       if: github.event_name != 'schedule'

AUTHORS.md

@@ -4,7 +4,7 @@ IMDClient was created by Lawson in 2024.
 
 
 <!-- All contributing authors are listed in this file below.
-The repository history at https://github.com/becksteinlab/imdreader
+The repository history at https://github.com/becksteinlab/imdclient
 and the CHANGELOG show individual code contributions. -->
 
 ## Chronological list of authors

README.md

@@ -23,7 +23,7 @@ IMDClient
 
 Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
 
-IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
+IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdclient/blob/main/CODE_OF_CONDUCT.md).
 
 ### Installation
 
@@ -53,8 +53,8 @@ conda activate imdclient
 <!-- Install the development and documentation dependencies:
 
 ```
-conda env update --name imdreader --file devtools/conda-envs/test_env.yaml
-conda env update --name imdreader --file docs/requirements.yaml
+conda env update --name imdclient --file devtools/conda-envs/test_env.yaml
+conda env update --name imdclient --file docs/requirements.yaml
 ``` -->
 
 Build this package from source:

docs/requirements.yaml

@@ -1,4 +1,4 @@
-name: imdreader-docs
+name: imdclient-docs
 channels:
 
   - conda-forge

examples/gromacs/repo_files/client.py

@@ -1,10 +1,10 @@
 import MDAnalysis as mda
-from MDAnalysis.coordinates.IMD import IMDReader
+from imdclient.tests.minimalReader import minimalReader
 import logging
 from imdclient.tests.datafiles import GROMACS_TOP
 
 logger = logging.getLogger("imdclient.IMDClient")
-file_handler = logging.FileHandler("imdreader.log")
+file_handler = logging.FileHandler("imdclient.log")
 formatter = logging.Formatter(
     "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 )
@@ -13,8 +13,13 @@
 logger.setLevel(logging.INFO)
 
 i = 0
-u = mda.Universe(GROMACS_TOP, "imd://localhost:8888")
-for ts in u.trajectory:
-    i += 1
+u = minimalReader("imd://localhost:8888")
+
+while True:
+    try:
+        u._read_next_frame()
+        i += 1
+    except EOFError:
+        break
 
 logger.info(f"Parsed {i} frames")

examples/gromacs/slurm/README.md

@@ -1,24 +1,24 @@
 Full walkthrough
 ================
 
-Create IMDReader mamba env
+Create IMDClient mamba env
 --------------------------
 
 Assuming you're in a login node to start, get a compute node:
 ```bash
 salloc -p general
 ```
 
-From the compute node, create env with name "imdreader-test":
+From the compute node, create env with name "imdclient-test":
 ```bash
 mkdir -p workspace
 cd workspace
-git clone https://github.com/Becksteinlab/imdreader.git
+git clone https://github.com/Becksteinlab/imdclient.git
 cd imdreader
 git checkout develop
 module load mamba/latest
 mamba env create --file devtools/conda-envs/test_env.yaml
-source activate imdreader-test
+source activate imdclient-test
 pip install -e .
 ```
 

examples/gromacs/slurm/client.py

@@ -1,11 +1,11 @@
 # NOTE: chamge
 import MDAnalysis as mda
-from MDAnalysis.coordinates.IMD import IMDReader
+from imdclient.tests.minimalReader import minimalReader
 import logging
 from imdclient.tests.datafiles import GROMACS_TOP
 
 logger = logging.getLogger("imdclient.IMDClient")
-file_handler = logging.FileHandler("imdreader.log")
+file_handler = logging.FileHandler("imdclient.log")
 formatter = logging.Formatter(
     "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 )
@@ -14,8 +14,13 @@
 logger.setLevel(logging.INFO)
 
 i = 0
-u = mda.Universe(GROMACS_TOP, "imd://localhost:8888")
-for ts in u.trajectory:
-    i += 1
+u = minimalReader("imd://localhost:8888")
+
+while True:
+    try:
+        u._read_next_frame()
+        i += 1
+    except EOFError:
+        break
 
 logger.info(f"Parsed {i} frames")

examples/gromacs/slurm/imd.sh

@@ -17,7 +17,7 @@ env | grep ^SLURM | sort
 env | grep CUDA
 
 module load mamba/latest
-source activate imdreader-test
+source activate imdclient-test
 
 output_dir="output_${SLURM_JOB_ID}"
 mkdir -p $output_dir
@@ -36,7 +36,7 @@ while ! await_gmx_imd; do
     sleep 5
 done
 
-echo "GROMACS is ready. Running IMDReader"
+echo "GROMACS is ready. Running IMD-reader"
 
 python client.py
 

examples/lammps/repo_files/client.py

@@ -1,10 +1,10 @@
 import MDAnalysis as mda
-from MDAnalysis.coordinates.IMD import IMDReader
+from imdclient.tests.minimalReader import minimalReader
 import logging
 from imdclient.tests.datafiles import LAMMPS_TOPOL
 
 logger = logging.getLogger("imdclient.IMDClient")
-file_handler = logging.FileHandler("imdreader.log")
+file_handler = logging.FileHandler("imdclient.log")
 formatter = logging.Formatter(
     "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 )
@@ -13,8 +13,13 @@
 logger.setLevel(logging.INFO)
 
 i = 0
-u = mda.Universe(LAMMPS_TOPOL, "imd://localhost:8888")
-for ts in u.trajectory:
-    i += 1
+u = minimalReader("imd://localhost:8888")
+
+while True:
+    try:
+        u._read_next_frame()
+        i += 1
+    except EOFError:
+        break
 
 logger.info(f"Parsed {i} frames")

examples/namd/repo_files/client.py

@@ -1,10 +1,10 @@
 import MDAnalysis as mda
-from MDAnalysis.coordinates.IMD import IMDReader
+from imdclient.tests.minimalReader import minimalReader
 import logging
 from imdclient.tests.datafiles import NAMD_TOPOL
 
 logger = logging.getLogger("imdclient.IMDClient")
-file_handler = logging.FileHandler("imdreader.log")
+file_handler = logging.FileHandler("imdclient.log")
 formatter = logging.Formatter(
     "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 )
@@ -13,8 +13,13 @@
 logger.setLevel(logging.INFO)
 
 i = 0
-u = mda.Universe(NAMD_TOPOL, "imd://localhost:8888")
-for ts in u.trajectory:
-    i += 1
+u = minimalReader("imd://localhost:8888")
+
+while True:
+    try:
+        u._read_next_frame()
+        i += 1
+    except EOFError:
+        break
 
 logger.info(f"Parsed {i} frames")

imdclient/tests/base.py

@@ -1,4 +1,5 @@
 from imdclient.IMDClient import IMDClient
+from .minimalReader import minimalReader
 import pytest
 from pathlib import Path
 import os
@@ -127,13 +128,7 @@ def docker_client(
 
     @pytest.fixture()
     def imd_u(self, docker_client, topol, tmp_path, port):
-        u = mda.Universe((tmp_path / topol), f"imd://localhost:{port}")
-        with mda.Writer(
-            (tmp_path / "imd.trr").as_posix(), u.trajectory.n_atoms
-        ) as w:
-            for ts in u.trajectory:
-                w.write(u.atoms)
-        yield mda.Universe((tmp_path / topol), (tmp_path / "imd.trr"))
+        u = minimalReader(f"imd://localhost:{port}", process_stream=True)
 
     @pytest.fixture()
     def true_u(self, topol, traj, imd_u, tmp_path):

imdclient/tests/minimalReader.py

@@ -0,0 +1,75 @@
+import logging
+import select
+import time
+from imdclient.IMDClient import IMDClient
+from .utils import parse_host_port
+
+logger = logging.getLogger("imdclient.IMDClient")
+
+
+class minimalReader:
+    """
+    Minimal reader for testing purposes
+
+    Parameters
+    ----------
+    filename : str
+        a string of the form "host:port" where host is the hostname
+        or IP address of the listening MD engine server and port
+        is the port number.
+    n_atoms : int (optional)
+        number of atoms in the system. defaults to number of atoms
+        in the topology. don't set this unless you know what you're doing.
+    kwargs : dict (optional)
+        keyword arguments passed to the constructed :class:`IMDClient`
+    """
+
+    def __init__(self, filename, n_atoms=None, process_stream=False, **kwargs):
+
+        self.imd_frame = None
+
+        # a trajectory of imd frames
+        self.trajectory = None
+
+        self.n_atoms = n_atoms
+
+        host, port = parse_host_port(filename)
+
+        # This starts the simulation
+        self._imdclient = IMDClient(host, port, n_atoms, **kwargs)
+
+        imdsinfo = self._imdclient.get_imdsessioninfo()
+
+        self._frame = -1
+
+        if process_stream:
+            self._process_stream()
+
+    def _read_next_frame(self):
+        try:
+            imd_frame = self._imdclient.get_imdframe()
+        except EOFError:
+            raise
+
+        self._frame += 1
+        self.imd_frame = imd_frame
+
+        logger.debug(f"minimalReader: Loaded frame {self._frame}")
+
+    def _add_frame_to_trajectory(self):
+        # Add the current frame to the trajectory
+        if self.trajectory is None:
+            self.trajectory = []
+        self.trajectory.append(self.imd_frame)
+        logger.debug(
+            f"minimalReader: Added frame {self._frame} to trajectory"
+        )
+
+    def _process_stream(self):
+        # Process the stream of frames
+        while True:
+            try:
+                self._read_next_frame()
+                self._add_frame_to_trajectory()
+            except EOFError:
+                break