Merge branch 'main' into mglob_prior

.github/workflows/test.yml

@@ -30,9 +30,9 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies with conda
       run: |
-        conda install -y python=3.11
-        conda env update --file conda/environment.yml --name base
-        conda install flake8
+        conda install --solver=classic -y python=3.11
+        conda env update --solver=classic --file conda/environment.yml --name base
+        conda install --solver=classic flake8
     - name: Run flake8 
       run: |
         # Flake8 exit on most issues
@@ -60,7 +60,7 @@ jobs:
         cd test; bash run_make_mat.sh; cd ..
 
   build-macos-conda:
-    runs-on: macos-12
+    runs-on: macos-13
 
     steps:
     - uses: actions/checkout@v4
@@ -74,11 +74,12 @@ jobs:
       with:
         python-version: '3.11'
     - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment:
     - name: Install dependencies with conda
       run: |
+        echo $CONDA/bin >> $GITHUB_PATH
         conda install -y python=3.11
         conda env update --file conda/environment.yml --name base
     - name: Run tests

CITATION.cff

@@ -14,7 +14,7 @@ authors:
 - family-names: "Camilloni"
   given-names: "Carlo"
 title: "Multi-eGO"
-version: beta.1
+version: beta.4
 date-released: 2023-10-24
 url: "https://github.com/multi-ego/multi-ego"
 preferred-citation:

README.md

@@ -1,5 +1,5 @@
 # Multi-*e*GO: a multi-ensemble Gō model
-[![Version](https://img.shields.io/badge/Version-beta.3-blue)](https://github.com/multi-ego/multi-eGO/releases)
+[![Version](https://img.shields.io/badge/Version-beta.4-blue)](https://github.com/multi-ego/multi-eGO/releases)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Multi-eGO test](https://github.com/multi-ego/multi-eGO/actions/workflows/test.yml/badge.svg)](https://github.com/multi-ego/multi-eGO/actions/workflows/test.yml)
@@ -99,7 +99,7 @@ Create a folder in which you want to run the random coil simulation. Copy the ``
 python multiego.py --system $SYSTEM_NAME --egos rc
 ```
 ```multiego.py``` will then create an output directory in ```multi-eGO/outputs/${SYSTEM_NAME}_rc``` which provides the inputs for the random coil simulation.
-The contents of the output folder are ```ffnonbonded.itp``` and ```topol_GRETA.top```. The former is the non-bonded interaction file and needs to be copied into the ```multi-ego-basic.ff/``` folder. The latter needs to be placed in the simulation root directory. We provide ```mdps``` simulation setup files tested with various multi-*e*GO setups in the ```multi-eGO/mdps``` folder. The order in which the simulations are run is as follows:
+The contents of the output folder are ```ffnonbonded.itp``` and ```topol_mego.top```. The former is the non-bonded interaction file and needs to be copied into the ```multi-ego-basic.ff/``` folder. The latter needs to be placed in the simulation root directory. We provide ```mdps``` simulation setup files tested with various multi-*e*GO setups in the ```multi-eGO/mdps``` folder. The order in which the simulations are run is as follows:
 
 ```
     1. ff_em.mdp
@@ -138,7 +138,7 @@ To setup a multi-*e*GO production simulation, you need to run ```multiego.py```
 ```
 python multiego.py --system $SYSTEM_NAME --egos production --epsilon 0.3 --train md_ensemble
 ```
-Here one sets the energy scale ε to 0.3 kJ/mol and trains the model from the ```md_ensemble``` data. The output directory will be ```multi-eGO/outputs/${SYSTEM_NAME}_production_e0.3_0.3``` and will contain the inputs for the production simulation. Again, the contents of the output directory are ```ffnonbonded.itp``` and ```topol_GRETA.top``` and need to be copied to the ```multi-ego-basic.ff/``` folder and the simulation root directory. The ```mdps``` files are the same except for the last step which is now ```ff_aa.mdp```.
+Here one sets the energy scale ε to 0.3 kJ/mol and trains the model from the ```md_ensemble``` data. The output directory will be ```multi-eGO/outputs/${SYSTEM_NAME}_production_e0.3_0.3``` and will contain the inputs for the production simulation. Again, the contents of the output directory are ```ffnonbonded.itp``` and ```topol_mego.top``` and need to be copied to the ```multi-ego-basic.ff/``` folder and the simulation root directory. The ```mdps``` files are the same except for the last step which is now ```ff_aa.mdp```.
 
 Happy simulating :)
 

conda/environment.yml

@@ -7,3 +7,5 @@ dependencies:
   - numpy
   - pandas
   - parmed
+  - gitpython
+  - pyyaml