HTF migration (#24)

* WIP -- Starting HTF migration * remove flatten torsions option * reinclude fix from openfe #675 (perses #1230) * HTF: simplify _add_nonbonded_force_terms * port openfe version of LambdaProtocol into feflow perses version hasn't been touched since April '22 * fixup attempt to be clever... * port tests from perses to feflow and modernise to pytest * Upgraded badges and acknowledgements * Removing non-relevant tests (protein mut., REST, etc.). Style formatting. * using gufe tests path fixture * Comments on why lists objs are needed * Start of organized module for HTF testing -- WIP * Renaming to lambda_protocol.py * Ingesting tests/utils from perses * Need openeye for testing * old positions with old system. Fix callable. * Utility function to extract HTF data from perses top proposal * Adapt HTF signature. Skipping difficult ones. * Need to pin minimum openfe version for CI * Testing convergence difficult overlap * Modular testing. Software vs science test modules. * Skip hard to converge test. * Fix proposal from perses obj * fixup lambdaprotocol tests * Migrate tests for "new" HTF features (#32) * Vsites tests * temporarily try to get CI working * Add lambda schedule tests * add basic tests for mdt and omm topology attributes * try to fix scope issues * more scope limiting * fix lambda_schedule check * missing self entry * make gufe_data_dir session scoped * fix to_openmm calls * Add gitignore and fix tests * Update ci.yaml --------- Co-authored-by: richard gowers <richardjgowers@gmail.com> Co-authored-by: Richard Gowers <richardjgowers+github@gmail.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
OpenFreeEnergy · Mar 8, 2024 · 2e300ed · 2e300ed
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -2,7 +2,6 @@ name: "CI"
 on:
   pull_request:
     branches:
-      - main
   push:
     branches:
       - main
@@ -36,6 +35,8 @@ jobs:
         include:
           - os: "macos"
             python-version: "3.11"
+    env:
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
 
     steps:
       - uses: actions/checkout@v4
@@ -66,6 +67,14 @@ jobs:
           micromamba info
           micromamba list
 
+      - name: Decrypt OpenEye license
+        shell: bash -l {0}
+        env:
+          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+          python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
+
       - name: "Run tests"
         env:
           # Set the OFE_SLOW_TESTS to True if running a Cron job

diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,171 @@
+# custom ignores
+.duecredit.p
+.xxrun
+.idea/
+.vscode/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*~
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/reference/api/generated
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# vim
+*.swp
+
+# vscode
+.vscode/
+
+# Rever
+rever/
+
diff --git a/README.md b/README.md
@@ -1,18 +1,19 @@
 FE Flow
 ==============================
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/feflow/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/feflow/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/feflow/branch/main/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/feflow/branch/main)
+[![GitHub Actions Build Status](https://github.com/choderalab/feflow/actions/workflows/ci.yaml/badge.svg)](https://github.com/choderalab/feflow/actions/workflows/ci.yaml)
+[![codecov](https://codecov.io/gh/choderalab/feflow/branch/main/graph/badge.svg)](https://codecov.io/gh/choderalab/feflow/branch/main)
 
 
-Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
+Recipes, utilities, and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
 
 ### Copyright
 
 Copyright (c) 2023, ChoderaLab
 
 
 #### Acknowledgements
-
+[Choderalab -- Perses](https://github.com/choderalab/perses)
+[Open Free energy Consortium](https://openfree.energy/)
 Project based on the 
 [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -1,18 +1,22 @@
 name: feflow-test
 channels:
   - conda-forge
+  - openeye
 dependencies:
     # Base depends
   - gufe >=0.9.5
   - numpy
-  - openfe  # TODO: Remove once we don't depend on openfe
+  - openfe >=0.15  # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - pymbar <4
   - pydantic=1  # TODO: Modify when we support pydantic 2
   - python
 
     # Testing
+  - openeye-toolkits
+  - openmoltools  # TODO: Remove once we refactor tests
+  - perses  # TODO: Remove once we don't depend on perses for tests
   - pytest
   - pytest-cov
   - pytest-xdist

diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
@@ -120,11 +120,12 @@ def _execute(self, ctx, *, state_a, state_b, mapping, settings, **inputs):
         """
         # needed imports
         import openmm
+        import numpy as np
         from openff.units.openmm import ensure_quantity
         from openmmtools.integrators import PeriodicNonequilibriumIntegrator
         from gufe.components import SmallMoleculeComponent
         from openfe.protocols.openmm_rfe import _rfe_utils
-        from feflow.utils.hybrid_topology import HybridTopologyFactoryModded as HybridTopologyFactory
+        from feflow.utils.hybrid_topology import HybridTopologyFactory
 
         # Check compatibility between states (same receptor and solvent)
         self._check_states_compatibility(state_a, state_b)

diff --git a/feflow/tests/conftest.py b/feflow/tests/conftest.py
@@ -6,9 +6,15 @@
 from gufe.mapping import LigandAtomMapping
 
 
-@pytest.fixture
-def benzene_modifications():
-    source = files("gufe.tests.data").joinpath("benzene_modifications.sdf")
+@pytest.fixture(scope='session')
+def gufe_data_dir():
+    path = files("gufe.tests.data")
+    return path
+
+
+@pytest.fixture(scope='session')
+def benzene_modifications(gufe_data_dir):
+    source = gufe_data_dir.joinpath("benzene_modifications.sdf")
     with as_file(source) as f:
         supp = Chem.SDMolSupplier(str(f), removeHs=False)
         mols = list(supp)
@@ -23,12 +29,12 @@ def solvent_comp():
     yield gufe.SolventComponent(positive_ion="Na", negative_ion="Cl")
 
 
-@pytest.fixture
+@pytest.fixture(scope='session')
 def benzene(benzene_modifications):
     return gufe.SmallMoleculeComponent(benzene_modifications["benzene"])
 
 
-@pytest.fixture
+@pytest.fixture(scope='session')
 def toluene(benzene_modifications):
     return gufe.SmallMoleculeComponent(benzene_modifications["toluene"])
 
@@ -130,7 +136,7 @@ def production_settings(short_settings):
 
 # Mappings fixtures
 
-@pytest.fixture
+@pytest.fixture(scope='session')
 def mapping_benzene_toluene(benzene, toluene):
     """Mapping from toluene to benzene"""
     mapping_toluene_to_benzene = {0: 4, 1: 5, 2: 6, 3: 7, 4: 8, 5: 9, 6: 10, 7: 11, 8: 12, 9: 13, 11: 14}