Merge branch 'move_things2utils' of github.com:OpenFreeEnergy/openfe-…

…gromacs into move_things2utils

README.md

@@ -3,6 +3,7 @@ openfe-gromacs
 [//]: # (Badges)
 [![GitHub Actions Build Status](https://github.com/OpenFreeEnergy/openfe-gromacs/workflows/CI/badge.svg)](https://github.com/OpenFreeEnergy/openfe-gromacs/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/OpenFreeEnergy/openfe-gromacs/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/openfe-gromacs/branch/main)
+[![documentation](https://readthedocs.org/projects/openfe-gromacs/badge/?version=latest)](https://openfe-gromacs.readthedocs.io/en/latest/?badge=latest)
 
 Gromacs-based protocols for Open Free Energy
 

environment.yml

@@ -9,3 +9,5 @@ dependencies:
   - pytest
   - pytest-xdist
   - pytest-cov
+  - pip:
+    - git+https://github.com/openforcefield/openff-interchange.git

openfe_gromacs/protocols/gromacs_md/md_methods.py

@@ -20,9 +20,16 @@
 from typing import Any
 
 import gufe
-from gufe import ChemicalSystem, settings
-from openfe.protocols.openmm_utils import system_validation
-from openfe.utils import log_system_probe
+import pint
+from gufe import ChemicalSystem, SmallMoleculeComponent, settings
+from openfe.protocols.openmm_utils import (
+    charge_generation,
+    system_creation,
+    system_validation,
+)
+from openfe.utils import log_system_probe, without_oechem_backend
+from openff.interchange import Interchange
+from openff.toolkit.topology import Molecule as OFFMolecule
 from openff.units import unit
 
 from openfe_gromacs.protocols.gromacs_md.md_settings import (

openfe_gromacs/tests/protocols/conftest.py

@@ -9,8 +9,6 @@
 from rdkit import Chem
 from rdkit.Geometry import Point3D
 
-import openfe_gromacs
-
 
 @pytest.fixture
 def benzene_vacuum_system(benzene_modifications):

openfe_gromacs/tests/protocols/test_create_systems.py

@@ -52,7 +52,7 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     ]
     with open(f"{tmpdir}/test.gro") as f:
         gromacs_res_numbers = [int(line[:5].strip()) for line in f.readlines()[2:-1]]
-    #    assert interchange_res_numbers == gromacs_res_numbers
+        assert interchange_res_numbers == gromacs_res_numbers
 
     # check a few atom names to ensure these are not empty sets
     for atom_name in ("HA", "CH3", "CA", "CB"):

openfe_gromacs/tests/protocols/test_gromacs_md.py

@@ -45,7 +45,8 @@ def test_serialize_protocol():
 
 def test_create_independent_repeat_ids(benzene_system):
     # if we create two dags each with 3 repeats, they should give 6 repeat_ids
-    # this allows multiple DAGs in flight for one Transformation that don't clash on gather
+    # this allows multiple DAGs in flight for one Transformation that don't
+    # clash on gather
     settings = GromacsMDProtocol.default_settings()
     # Default protocol is 1 repeat, change to 3 repeats
     settings.protocol_repeats = 3

openfe_gromacs/tests/protocols/test_md_settings.py

@@ -1,19 +1,9 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
-import json
-import pathlib
-from unittest import mock
-
-import gufe
 import pytest
 from openff.units import unit
 
-import openfe_gromacs
-from openfe_gromacs.protocols.gromacs_md.md_methods import (
-    GromacsMDProtocol,
-    GromacsMDProtocolResult,
-    GromacsMDSetupUnit,
-)
+from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
 
 
 def test_settings_pos_or_zero_error():

pyproject.toml

@@ -97,6 +97,15 @@ omit = [
 [tool.flake8]
 max-line-length = 88
 extend-ignore = ['E203',]
+per-file-ignores = [
+    '__init__.py:F401',
+]
+builtins = [
+    "nanometer",
+    "picosecond",
+    "kelvin",
+    "bar",
+]
 
 [tool.isort]
 profile = "black"