Merge pull request #1 from lcbc-epfl/nsga

Nsga

.github/workflows/main.yml

@@ -0,0 +1,18 @@
+name: CI
+on:  
+  pull_request:    
+    branches:
+    - main  
+  push:
+    branches:
+    - main
+jobs:  
+  build:     
+   runs-on: ubuntu-latest
+
+   steps:    
+   - uses: actions/checkout@v1
+   - name: Build and test with Docker
+     run: |
+       docker build --tag ci -f ./DOCKERFILE .
+       docker run --rm ci

.gitignore

@@ -1,2 +1,3 @@
 *.pyc 
 *.bak
+.idea

Dockerfile

@@ -0,0 +1,55 @@
+# EVOLVE Dockerfile for CI
+
+# Github Actions does not support GPU acceleration and the parallized amber pmemd engine is not available for free via conda. 
+# The unittests regarding this are not executed
+
+
+FROM continuumio/miniconda3
+
+# Setup a spot for the code
+WORKDIR /evolve
+# Install Python dependencies
+COPY environment.yml environment.yml
+RUN conda env create -f environment.yml
+
+# Activate environment
+SHELL ["conda", "run", "-n", "evolve", "/bin/bash", "-c"]
+
+
+# Copy necessary files
+COPY share share/
+COPY unittests unittests/
+COPY main.py .
+COPY evaluators.py .
+
+# This is necessary due to a bug in Docker
+RUN true
+
+COPY src ./src/
+
+# Set Environment variables
+ENV PYTHONPATH="/evolve/:${PYTHONPATH}"
+
+ENV PATH="/opt/conda/envs/evolve/bin:$PATH"
+
+ENV CONDA_DEFAULT_ENV evolve
+
+ENV EVOLVE_GPU=FALSE
+
+SHELL ["conda", "run", "-n", "evolve", "/bin/bash", "-c"]
+
+# Chceck that openbabel is available
+RUN echo "Make sure openbabel is installed:"
+RUN python -c "from openbabel import openbabel"
+
+# Change to unittest directory
+WORKDIR /evolve/unittests
+
+
+# Execute tests
+RUN ["python", "test_gaapi.py"]
+RUN ["python", "test_openbabel.py"]
+RUN ["python", "test_StartGA_Run.py"]
+
+
+RUN ["/bin/bash"]

README.md

@@ -20,6 +20,8 @@ EVOLVE is python3 based and depends on the following packages
 ```
 pygmo
 amber18
+openmm
+openbabel
 ```
 
 ### Installing
@@ -37,8 +39,7 @@ evaluator and a detailed instructions to run the tests in the [Documentation](ht
 
 * [openbabel](http://openbabel.org/) - Openbabel
 * [Amber](https://ambermd.org/) - to build toplogies
-* [Gromacs](http://gromacs.com) - to run molecular dynamics
-* [MDAnalysis](http://mdanalysis) - to run automated analysis of MD simulations
+* [OpenMM](http://openmm.org) - to run molecular dynamics
 
 ## Contributing
 

environment.yml

@@ -0,0 +1,27 @@
+name: evolve
+channels:
+  - conda-forge
+  - omnia
+  - defaults
+dependencies:
+  - openbabel=3.1.0
+  - numpy=1.18.4=py37h8960a57_0
+  - openmm=7.4.1=py37_cuda101_rc_1
+  - openmmtools=0.19.0=py37_1
+  - pagmo=2.15.0=hec06268_1
+  - pip=20.1.1=pyh9f0ad1d_0
+  - ambertools=20.9
+  - pygmo=2.15.0=py37h2566bc3_0
+  - python=3.7.6=h8356626_5_cpython
+  - six=1.15.0=pyh9f0ad1d_0
+  - sphinx=3.0.3=py_0
+  - sphinxcontrib-applehelp=1.0.2=py_0
+  - sphinxcontrib-bibtex=1.0.0=py_0
+  - sphinxcontrib-devhelp=1.0.2=py_0
+  - sphinxcontrib-htmlhelp=1.0.3=py_0
+  - sphinxcontrib-jsmath=1.0.1=py_0
+  - sphinxcontrib-napoleon=0.7=py_0
+  - sphinxcontrib-qthelp=1.0.3=py_0
+  - sphinxcontrib-serializinghtml=1.1.4=py_0
+  - future
+