Merge branch 'main' into add-complex-testing

OpenFreeEnergy · Aug 14, 2024 · dc5bd81 · dc5bd81
2 parents ccbdaf6 + 842f1ae
commit dc5bd81
Show file tree

Hide file tree

Showing 6 changed files with 10 additions and 12 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -23,11 +23,12 @@ defaults:
 jobs:
  tests:
  runs-on: ${{ matrix.os }}-latest
- name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }}"
+ name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} - pydantic ${{matrix.pydantic}}"
  strategy:
  fail-fast: false
  matrix:
  os: ["ubuntu"]
+ pydantic: ["1", "2"]
  python-version:
  - "3.10"
  - "3.11"
@@ -52,6 +53,7 @@ jobs:
  cache-downloads: true
  create-args: >-
  python=${{ matrix.python-version }}
+ pydantic=${{ matrix.pydantic }}
  init-shell: bash
 
  - name: "Install"
@@ -80,7 +82,7 @@ jobs:
  # Set the OFE_SLOW_TESTS to True if running a Cron job
  OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
  run: |
- pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
+  pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
 
  - name: codecov
  if: ${{ github.repository == 'choderalab/feflow'

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -11,7 +11,7 @@ dependencies:
  - openmm
  - openmmforcefields >=0.14.1 # TODO: remove when upstream deps fix this
  - pymbar <4
- - pydantic=1 # TODO: Modify when we support pydantic 2
+ - pydantic >=1.10.17
  - python
 
  # Testing (optional deps)

diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
@@ -450,7 +450,7 @@ def extract_positions(context, initial_atom_indices, final_atom_indices):
  ----------
  context: openmm.Context
  Current simulation context where from extract positions.
- hybrid_topology_factory: perses.annihilation.relative.HybridTopologyFactory
+ hybrid_topology_factory: HybridTopologyFactory
  Hybrid topology factory where to extract positions and mapping information
 
  Returns
@@ -508,7 +508,7 @@ def _execute(self, ctx, *, protocol, setup, **inputs):
 
  # Setting up logging to file in shared filesystem
  file_logger = logging.getLogger("neq-cycling")
- output_log_path = ctx.shared / "perses-neq-cycling.log"
+ output_log_path = ctx.shared / "feflow-neq-cycling.log"
  file_handler = logging.FileHandler(output_log_path, mode="w")
  file_handler.setLevel(logging.DEBUG) # TODO: Set to INFO in production
  log_formatter = logging.Formatter(

diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
@@ -6,10 +6,7 @@
 for the specific integrator settings.
 """
 
-try:
- from pydantic.v1 import validator
-except ImportError:
- from pydantic import validator # type: ignore[assignment]
+from pydantic.v1 import validator
 
 from openff.units import unit
 from openff.models.types import FloatQuantity

diff --git a/feflow/settings/nonequilibrium_cycling.py b/feflow/settings/nonequilibrium_cycling.py
@@ -10,7 +10,7 @@
 )
 
 from gufe.settings import Settings
-from pydantic import root_validator
+from pydantic.v1 import root_validator
 from openfe.protocols.openmm_utils.omm_settings import (
  OpenMMSolvationSettings,
  OpenMMEngineSettings,

diff --git a/feflow/utils/hybrid_topology.py b/feflow/utils/hybrid_topology.py
@@ -2551,8 +2551,7 @@ def _compute_hybrid_positions(self):
  The positions are assigned by first copying all the mapped positions
  from the old system in, then copying the
  mapped positions from the new system. This means that there is an
- assumption that the positions common to old and new are the same
- (which is the case for perses as-is).
+ assumption that the positions common to old and new are the same.
 
  Returns
  -------