Merge pull request #264 from IRL2/fix/remove-lammps

Remove unmaintained lammps package

.github/workflows/conda.yml

@@ -41,7 +41,6 @@ jobs:
             python-libraries/nanover-openmm/conda \
             python-libraries/nanover-ase/conda \
             python-libraries/nanover-mdanalysis/conda \
-            python-libraries/nanover-lammps/conda \
             python-libraries/nanover-omni/conda \
             python-libraries/nanover-jupyter/conda \
             python-libraries/nanover-server/conda
@@ -78,7 +77,7 @@ jobs:
         with:
           name: conda-packages
       - name: Install NanoVer
-        run: conda install -y -c conda-forge -c ./conda-bld mpi4py nanover-server nanover-lammps
+        run: conda install -y -c conda-forge -c ./conda-bld nanover-server
       - name: Install tests dependancies
         run: python -m pip install -r python-libraries/requirements.test
       - name: Parallel tests

.github/workflows/tests.yml

@@ -41,7 +41,7 @@ jobs:
           auto-update-conda: true
           miniforge-version: latest
       - name: Install nanover dependancies
-        run: conda install -y mpi4py openmm
+        run: conda install -y openmm
       - name: Install tests dependancies
         run: python -m pip install -r python-libraries/requirements.test
       - name: Compile (mypy requires --no-edit)

.gitignore

@@ -46,5 +46,3 @@ examples/ase/neuraminidase_nanover.xml
 examples/fundamentals/.ipynb_checkpoints/
 
 examples/examples/lmp
-
-examples/examples/log\.lammps

README.md

@@ -81,7 +81,6 @@ page in our documentation for detailed instructions on installing NanoVer.
     * Activate the conda environment: `conda activate nanover-dev`
     * Install the required conda packages: `conda install -c conda-forge openmm MDAnalysis MDAnalysisTests ase`
     * Compile the protocol and install the NanoVer libraries in your conda environment: `./win_compile.ps1`.  If you do not plan on modifying the python packages, run `./win_compile.ps1 -noedit` instead. Otherwise, by default, the nanover packages will be installed in edit mode (`pip install -e`) meaning that changes in the `nanover-protocol` directory will be directly reflected in your python environment.
-* The `nanover-lammps` module and its tests require MPI to be installed. Download and install Microsoft MPI from https://docs.microsoft.com/en-us/message-passing-interface/microsoft-mpi
 
 ### Mac and Linux
 
@@ -194,11 +193,9 @@ This project has been made possible by the following open source projects. We gr
 * [gRPC](https://grpc.io/) (Apache v2) - Communication protocol.
 * [ASE](https://wiki.fysik.dtu.dk/ase/) (LGPLv3): Atomic simulation environment used for running simulations ([citation](https://iopscience.iop.org/article/10.1088/1361-648X/aa680e)).
 * [OpenMM](http://openmm.org/) (MIT, LGPLv3): GPU accelerated molecular mechanics library ([citation](https://simtk.org/plugins/publications/index.php/?group_id=161)).
-* [LAMMPS](https://lammps.sandia.gov/) (GPLv2): Molecular mechanics library ([citation](https://lammps.sandia.gov/cite.html)).
 * [MDAnalysis](https://www.mdanalysis.org/) (GPLv2): Molecular dynamics analysis library ([citations](https://www.mdanalysis.org/pages/citations/)).
 * [NGLView](https://nglviewer.org/#nglview) (MIT): IPython/Jupyter widget to interactively view structures and trajectories ([citations](http://nglviewer.org/nglview/latest/#cite)).
 * [python-osc](https://pypi.org/project/python-osc/) (Public domain) - Open sound control library.
-* [MPI4Py](https://mpi4py.readthedocs.io/en/stable/index.html) ([BSD 2-clause license](https://bitbucket.org/mpi4py/mpi4py/src/master/LICENSE.rst)): MPI library for python, used with LAMMPS ([citation](https://mpi4py.readthedocs.io/en/stable/citing.html)).
 * [Numpy](https://numpy.org/) (BSD) - Numerical computation library.
 * [Netifaces](https://pypi.org/project/netifaces/) (MIT) - Portable library for accessing network interface information.
 * [Pytest](https://docs.pytest.org/en/latest/) (MIT) - Python testing framework

compile.sh

@@ -43,16 +43,6 @@ if [[ ! -z "${edit_option}" ]]; then
 fi
 
 if [[ $with_python == true ]]; then
-	# mpi4py (required for nanover-lammps) needs MPI to be installed on the system.
-	python -c "import mpi4py" 2>&1 >/dev/null || {
-		announce "The mpi4py library is required but cannot be found."
-		announce "Because it requires a system library, it is not installed by this"
-		announce "script; you have to install it yourself."
-		announce "If you are using conda, install mpi4py by running"
-		announce "conda install -c conda-forge mpi4py"
-		exit 1
-	}
-
 	announce "Installing python requirements"
 	python -m pip install -r ./python-libraries/nanover-core/requirements.txt ${user_option}