update fixtures

Author: atravitz

environment.yml

@@ -53,7 +53,7 @@ dependencies:
   # Control blas/openmp threads
   - threadpoolctl
   - pip:
-    - git+https://github.com/OpenFreeEnergy/gufe@parse_gzipped_pdbs
+    - git+https://github.com/OpenFreeEnergy/gufe@main
   - run_constrained:
     # drop this pin when handled upstream in espaloma-feedstock
     - smirnoff99frosst>=1.1.0.1  #https://github.com/openforcefield/smirnoff99Frosst/issues/109

src/openfe/tests/conftest.py

@@ -297,8 +297,7 @@ def a2a_protein_membrane_pdb():
 
 @pytest.fixture(scope="session")
 def a2a_protein_membrane_component(a2a_protein_membrane_pdb) -> openfe.ProteinMembraneComponent:
-    with gzip.open(a2a_protein_membrane_pdb, "rb") as f:
-        yield openfe.ProteinMembraneComponent.from_pdb_file(f, name="a2a")
+    yield openfe.ProteinMembraneComponent.from_pdb_file(a2a_protein_membrane_pdb, name="a2a")
 
 
 @pytest.fixture(scope="session")

src/openfecli/parameters/protein.py

@@ -55,7 +55,6 @@ def _load_protein_membrane_file(user_input, context):
 
     from gufe import ProteinMembraneComponent
 
-    # TODO: upstream gufe work may make this change for the better
     try:
         return ProteinMembraneComponent.from_pdb_file(user_input)
     except ValueError:

src/openfecli/tests/commands/test_plan_rbfe_network.py

@@ -7,7 +7,6 @@
 from click.testing import CliRunner
 from gufe import (
     AlchemicalNetwork,
-    ProteinComponent,
     SmallMoleculeComponent,
     SolventComponent,
 )
@@ -20,7 +19,7 @@
     ligand_network_planning,
     lomap_scorers,
 )
-from openfe.tests.conftest import T4_protein_component_pdb
+from openfe.tests.conftest import T4_protein_component, T4_protein_component_pdb
 from openfecli.commands.plan_rbfe_network import plan_rbfe_network, plan_rbfe_network_main
 
 from ..utils import assert_click_success
@@ -430,10 +429,7 @@ def custom_yaml_radial():
 """
 
 
-@pytest.mark.skipif(
-    not HAS_NAGL,
-    reason="needs NAGL",
-)
+@pytest.mark.skipif(not HAS_NAGL, reason="needs NAGL")
 @pytest.mark.skipif(
     HAS_OPENEYE, reason="cannot use NAGL with rdkit backend when OpenEye is installed"
 )