Add GAFF test (and GAFF skips) to CI (#847)

* see if this is enough to test the removal of gaff

* see if now we get the right error message

* rerun ci

* rerun ci

* see what happens if we the solver do its thing

* add omff version to matrix

* Added note about how to use gaff

* depending on the ommff version, we make sure the test does what we expect

* add an osx arm test since we should be able to do that now

* see if we can install missing stubs

* add missing stubs directly

* we return a sampler and not a system for the rfe

* Apply suggestions from code review

Co-authored-by: Hannah Baumann <[email protected]>

* added link to give some context

* testing on python 3.12 now

* unpin numpy

* no openeye toolkits for 3.12

---------

Co-authored-by: Hannah Baumann <[email protected]>

.github/workflows/ci.yaml

@@ -37,13 +37,14 @@ jobs:
         os: ["ubuntu-latest"]
         pydantic-version: [">1"]
         python-version:
-          - "3.9"
           - "3.10"
           - "3.11"
+          - "3.12"
         openeye: ["no"]
+        ommff-version: ["0.13"]
         include:
           - os: "macos-12"
-            python-version: "3.11"
+            python-version: "3.12"
             pydantic-version: ">1"
           - os: "ubuntu-latest"
             python-version: "3.11"
@@ -52,6 +53,11 @@ jobs:
             python-version: "3.11"
             pydantic-version: ">1"
             openeye: "yes"
+          - os: "ubuntu-latest"
+            python-version: "3.10"
+            pydantic-version: ">1"
+            openeye: "no"
+            ommff-version: "<0.13"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -77,6 +83,7 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pydantic=${{ matrix.pydantic-version }}
+            openmmforcefields=${{ matrix.ommff-version }}
           init-shell: bash
 
       - name: "Install OpenEye"

.github/workflows/mypy.yaml

@@ -43,6 +43,7 @@ jobs:
         run: |
           python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
           python -m pip install mypy
+          python -m pip install types-pkg_resources
           python -m pip install --no-deps -e .
 
       - name: "Environment Information"

docs/installation.rst

@@ -20,6 +20,12 @@ If you already have a Mamba installation, you can install ``openfe`` with:
 
 Note that you must run the latter line in each shell session where you want to use ``openfe``. OpenFE recommends the Mamba package manager for most users as it is orders of magnitude faster than the default Conda package manager. Mamba is a drop in replacement for Conda.
 
+.. note::
+   If you plan on using GAFF to parametrize your system, you **must** install ``openmmforcefields`` version ``0.12.0``.
+   This will create an environment with python 3.10 and the correct version of Ambertools.
+
+   ``mamba create -c conda-forge -n openfe_env openfe=1 openmmforcefields=0.12.0``
+
 Installation with ``miniforge`` (recommended)
 ----------------------------------------------
 

environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - duecredit
   - kartograf>=1.0.0
   - lomap2>=3.0.0
-  - numpy<1.24
+  - numpy
   - networkx
   - rdkit
   - pip
@@ -28,7 +28,7 @@ dependencies:
   - typing-extensions
   - lomap2>=2.3.0
   - openmmtools
-  - openmmforcefields>=0.11.2
+  - openmmforcefields
   - perses
   - pooch
   - py3dmol

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py

@@ -245,8 +245,31 @@ def test_dry_run_gaff_vacuum(benzene_vacuum_system, toluene_vacuum_system,
     )
     unit = list(dag.protocol_units)[0]
 
-    with tmpdir.as_cwd():
-        sampler = unit.run(dry=True)['debug']['sampler']
+    # If we do a lot of GAFF testing, this should be refactored so we don't
+    # have to copy it all over the place.
+    # https://github.com/OpenFreeEnergy/openfe/pull/847#issuecomment-2096810453
+
+
+    import openmmforcefields
+    from pkg_resources import packaging
+
+    ommff_version = openmmforcefields.__version__
+
+    gaff_should_fail = packaging.version.parse(
+        ommff_version
+    ) >= packaging.version.parse("0.13.0")
+
+    if gaff_should_fail:
+        from openmmforcefields.generators.template_generators import (
+            GAFFNotSupportedError,
+        )
+
+        with pytest.raises(GAFFNotSupportedError):
+            with tmpdir.as_cwd():
+                sampler = unit.run(dry=True)["debug"]["sampler"]
+    else:
+        with tmpdir.as_cwd():
+            sampler = unit.run(dry=True)["debug"]["sampler"]
 
 
 @pytest.mark.slow

openfe/tests/protocols/test_openmm_plain_md_protocols.py

@@ -177,8 +177,30 @@ def test_dry_run_gaff_vacuum(benzene_vacuum_system, tmpdir):
     )
     unit = list(dag.protocol_units)[0]
 
-    with tmpdir.as_cwd():
-        system = unit.run(dry=True)['debug']['system']
+    # If we do a lot of GAFF testing, this should be refactored so we don't
+    # have to copy it all over the place.
+    # https://github.com/OpenFreeEnergy/openfe/pull/847#issuecomment-2096810453
+
+    import openmmforcefields
+    from pkg_resources import packaging
+
+    ommff_version = openmmforcefields.__version__
+
+    gaff_should_fail = packaging.version.parse(
+        ommff_version
+    ) >= packaging.version.parse("0.13.0")
+
+    if gaff_should_fail:
+        from openmmforcefields.generators.template_generators import (
+            GAFFNotSupportedError,
+        )
+
+        with pytest.raises(GAFFNotSupportedError):
+            with tmpdir.as_cwd():
+                system = unit.run(dry=True)["debug"]["system"]
+    else:
+        with tmpdir.as_cwd():
+            system = unit.run(dry=True)["debug"]["system"]
 
 
 @pytest.mark.parametrize('method, backend, ref_key', [