Merge pull request #27 from chrisjonesBSU/bonds_ibi

Add functionality to perofrm IBI on bonded parameters

Author: chrisjonesBSU

.github/workflows/build_cpu.yml

@@ -6,7 +6,7 @@ on:
     # Run when container or environment is changed
     paths:
         - 'containers/dockerfile_cpu'
-        - 'environment.yml'
+        - 'environment-cpu.yml'
   # Allows workflow to be manually triggered
   workflow_dispatch:
 

.github/workflows/pytest.yml

@@ -5,13 +5,13 @@ on:
     branches: [ master ]
     paths:
       - '.github/workflows/pytest.yml'
-      - 'environment.yml'
+      - 'environment-cpu.yml'
       - 'msibi/**'
   pull_request:
     branches: [ master ]
     paths:
       - 'msibi/**'
-      - 'environment.yml'
+      - 'environment-cpu.yml'
       - '.github/workflows/pytest.yml'
   # Allows workflow to be manually triggered
   workflow_dispatch:
@@ -27,7 +27,7 @@ jobs:
     - name: Build environment
       uses: conda-incubator/setup-miniconda@v2
       with:
-        environment-file: environment.yml
+        environment-file: environment-cpu.yml
         miniforge-variant: Mambaforge
         miniforge-version: 4.9.2-4
         use-mamba: true

containers/dockerfile_cpu

@@ -6,7 +6,7 @@ ADD . /msibi
 
 WORKDIR /msibi
 
-RUN micromamba install -y -n base -f environment.yml && \
+RUN micromamba install -y -n base -f environment-cpu.yml && \
     micromamba clean --all --yes && \
     python setup.py install
 

environment-cpu.yml

@@ -0,0 +1,20 @@
+name: msibi
+channels:
+- conda-forge
+dependencies:
+- freud=2.7.0
+- gsd=2.4.1
+- hoomd=2.9.6=*cpu*
+- mbuild=0.13.1
+- more-itertools
+- numpy=1.20.1
+- pip=21.0
+- py3Dmol=0.8.0
+- python=3.9
+- pytest
+- pytest-cov
+- jupyterlab
+- ipython
+- nodejs>=10
+- pip:
+    - git+https://github.com/cmelab/cmeutils

environment-gpu.yml

@@ -0,0 +1,20 @@
+name: msibi
+channels:
+- conda-forge
+dependencies:
+- freud=2.7.0
+- gsd=2.4.1
+- hoomd=2.9.6=gpu_py39he2a7f1f_1
+- mbuild=0.13.1
+- more-itertools
+- numpy=1.20.1
+- pip=21.0
+- py3Dmol=0.8.0
+- python=3.9
+- pytest
+- pytest-cov
+- jupyterlab
+- ipython
+- nodejs>=10
+- pip:
+    - git+https://github.com/cmelab/cmeutils

environment.yml

@@ -13,8 +13,5 @@
     "State",
     "Bond",
     "Angle",
-    # Potentials.
-    "mie",
-    "morse",
     "utils"
 ]