Merge branch 'develop' of https://github.com/a-ws-m/MDPOW into develop

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Autoformat all files using `black`
+8f061e7da99eb78353e9392d6929673da5b352a3

.github/workflows/black.yaml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.gitignore

@@ -15,3 +15,11 @@ coverage.xml
 *.lock
 *.npz
 dir.csv
+
+# Files for the Martini example that can be downloaded at runtime
+doc/examples/martini/*
+!doc/examples/martini/*.mdp
+!doc/examples/martini/*.ipynb
+!doc/examples/martini/water.gro
+!doc/examples/martini/octanol.gro
+!doc/examples/martini/benzene.pdb

.readthedocs.yaml

@@ -17,5 +17,4 @@ formats:
 python:
    version: 3.8
    install:
-   - requirements: doc/requirements.txt
-   system_packages: true
+   - requirements: doc/requirements.txt

.vscode/extensions.json

@@ -0,0 +1,6 @@
+{
+    "recommendations": [
+        "ms-python.black-formatter",
+        "ms-python.python"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+    "[python]": {
+        "editor.formatOnSave": true
+    },
+    "python.testing.pytestArgs": [
+        "mdpow"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

AUTHORS

@@ -39,3 +39,7 @@ their first commit. GitHub handle is optional.
 
 - Cade Duckworth (cadeduckworth)
 
+2023
+----
+
+- Alexander Moriarty (@a-ws-m)

CHANGES

@@ -6,7 +6,7 @@ Add summary of changes for each release. Use ISO 8061 dates. Reference
 GitHub issues numbers and PR numbers.
 
 2023-??-??    0.9.0
-cadeduckworth, orbeckst, VOD555
+cadeduckworth, orbeckst, VOD555, a-ws-m
 
 Changes
 
@@ -24,6 +24,18 @@ Changes
 * _prepare_universe and _conclude_universe removed from 
   EnsembleAnalysis.run() method, no longer needed (per comments, #199)
 * internal log_banner() now uses logger as argument (PR #247)
+* use `black` formatter for codebase (#271)
+* implemented `forcefields.Forcefield` class (#267)
+  - facilitates users using non-default forcefields without changing package code
+  - `equil.Simulation` has new `ff_class` argument
+  - each `Forcefield` has unique `default_water_model`, replacing global `DEFAULT_WATER_MODEL`
+  - `get_solvent_model()` and `get_solvent_identifier()` take either `str` or `Forcefield` type for the `forcefield` argument
+  - both functions also use the `Forcefield`-specific `default_water_model` (fixes #112)
+* `forcefields.DEFAULT_WATER_MODEL` removed (#267)
+* changed `system.top` and `system_octwet.top` to act as templates and added `.template` suffix (#267)
+* removed `forcefields.get_ff_paths()` (#267)
+* changed `forcefields.get_solvent_identifier()`: will raise `ValueError` instead of returning `None` (#267)
+
 
 Enhancements
 

README.rst

@@ -2,7 +2,7 @@
  README for MDPOW
 ===================
 
-|build| |cov| |docs| |zenodo|
+|build| |cov| |docs| |black| |zenodo|
 
 .. |P_ow| replace:: *P*\ :sub:`OW`
 .. |P_cw| replace:: *P*\ :sub:`CW`
@@ -74,9 +74,14 @@ Source code
 *MDPOW* is open source and published under the `GNU General Public License
 v3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .
 
+We use `black`_ for uniform code formatting.
+
 .. _`GNU General Public License v3`:
    http://www.gnu.org/licenses/gpl-3.0.html
 
+.. _`black`: https://github.com/psf/black
+
+
 Footnotes
 ---------
 
@@ -99,6 +104,8 @@ Footnotes
    :target: https://zenodo.org/badge/latestdoi/44999898
    :alt: Zenodo
 
-
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :target: https://github.com/psf/black	 
+   :alt: black   
 
 .. _INSTALL: INSTALL.rst

doc/examples/benzene/session.py

@@ -1,31 +1,39 @@
 import mdpow.equil
+
 S = mdpow.equil.WaterSimulation(molecule="BNZ")
 S.topology("benzene.itp")
 S.solvate(struct="benzene.pdb")
 S.energy_minimize()
-S.MD_relaxed(runtime=5)   # should be at least 1e3 ps for production not just 5 ps
+S.MD_relaxed(runtime=5)  # should be at least 1e3 ps for production not just 5 ps
 
 # run simulation externally or use MDrunner
 # (see docs for using mpi etc)
 import gromacs
-r = gromacs.run.MDrunner(dirname=S.dirs['MD_relaxed'], deffnm="md", c="md.pdb", cpi=True, append=True, v=True)
-r.run()   # runs mdrun in the python shell
+
+r = gromacs.run.MDrunner(
+    dirname=S.dirs["MD_relaxed"], deffnm="md", c="md.pdb", cpi=True, append=True, v=True
+)
+r.run()  # runs mdrun in the python shell
 
 
-S.MD(runtime=10, qscript=['local.sh'])  # should be at least 10e3 ps for production, not just 10 ps
+S.MD(
+    runtime=10, qscript=["local.sh"]
+)  # should be at least 10e3 ps for production, not just 10 ps
 # run simulation
-r = gromacs.run.MDrunner(dirname=S.dirs['MD_NPT'], deffnm="md", c="md.pdb", cpi=True, append=True, v=True)
-r.run()   # runs mdrun in the python shell
+r = gromacs.run.MDrunner(
+    dirname=S.dirs["MD_NPT"], deffnm="md", c="md.pdb", cpi=True, append=True, v=True
+)
+r.run()  # runs mdrun in the python shell
 
 
 import mdpow.fep
+
 gwat = mdpow.fep.Ghyd(simulation=S, runtime=10)
 gwat.setup()
 
 # run multiple simulations on cluster
 
 
-
 O = mdpow.equil.OctanolSimulation(molecule="BNZ")
 O.topology("benzene.itp")
 O.solvate(struct="benzene.pdb")

doc/examples/martini/benzene.pdb

@@ -0,0 +1,13 @@
+REMARK    GENERATED BY TRJCONV
+TITLE     This is an auto generated system
+REMARK    THIS IS A SIMULATION BOX
+CRYST1  150.000  150.000  180.000  90.00  90.00  90.00 P 1           1
+MODEL        1
+ATOM      1  R1  BENZ    1      30.920   6.600  24.160  1.00  0.00            
+ATOM      2  R2  BENZ    1      28.820   5.000  23.610  1.00  0.00            
+ATOM      3  R3  BENZ    1      29.860   6.580  21.680  1.00  0.00            
+TER
+ENDMDL
+CONECT    1    2
+CONECT    2    3
+CONECT    1    3

doc/examples/martini/em.mdp

@@ -0,0 +1,17 @@
+include          =  
+integrator       =  steep
+dt               =  0.02
+nsteps           =  1000
+nstxout          =  0
+nstvout          =  0
+nstlog           =  100 
+nstxtcout        =  100
+xtc-precision    =  1000
+rlist            =  1.0
+coulombtype      =  Reaction-Field
+rcoulomb         =  1.0
+epsilon_r        =  15
+vdw-type         =  cutoff
+vdw-modifier     =  Potential-shift-verlet
+rvdw             =  1.0
+constraints = none

doc/examples/martini/eq.mdp

@@ -0,0 +1,24 @@
+include          =  
+dt               =  0.005 
+nsteps           =  25000
+nstxout          =  0 
+nstvout          =  0
+nstlog           =  1000
+nstxout-compressed  = 1000
+cutoff-scheme    =  Verlet
+coulombtype      =  Reaction-Field
+rcoulomb         =  1.1
+epsilon_r        =  15 
+vdw-type         =  cutoff
+vdw-modifier     =  Potential-shift-verlet 
+rvdw             =  1.1 
+tcoupl           =  v-rescale 
+tc-grps          =  System
+tau-t            =  1.0
+ref-t            =  300
+Pcoupl           =  c-rescale
+Pcoupltype       =  isotropic
+tau-p            =  3.0
+compressibility  =  3e-4
+ref-p            =  1.0
+refcoord_scaling =  all