diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index e433047..6149d52 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -69,7 +69,7 @@ jobs: - name: Run Tests shell: bash -l {0} run: | - pytest -v --cov=openff --cov-report=xml --color=yes openff/fragmenter/tests/ + pytest -v --cov=openff --cov-report=xml --color=yes openff/fragmenter/tests/ -nauto - name: CodeCov uses: codecov/codecov-action@v3 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c55f50c..743283b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,7 +17,7 @@ repos: - id: isort files: ^openff - repo: https://github.com/PyCQA/flake8 - rev: 6.0.0 + rev: 6.1.0 hooks: - id: flake8 files: ^openff diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 7049e0d..e6f02bf 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -2,19 +2,19 @@ name: openff-fragmenter-test channels: - conda-forge - - defaults - dependencies: - - # Core dependencies + # Core - python + - pydantic + - jinja2 + # OpenFF stack - openff-toolkit-base >=0.11.0 - openff-utilities >=0.1.9 + + # Optional tools - ambertools - rdkit - - pydantic - - jinja2 # Testing - pytest diff --git a/openff/fragmenter/depiction.py b/openff/fragmenter/depiction.py index 6427873..3076c50 100644 --- a/openff/fragmenter/depiction.py +++ b/openff/fragmenter/depiction.py @@ -6,8 +6,11 @@ from openff.fragmenter.fragment import BondTuple, FragmentationResult from openff.fragmenter.utils import get_map_index from openff.toolkit.topology import Molecule -from openff.utilities import MissingOptionalDependencyError, requires_oe_module -from pkg_resources import resource_filename +from openff.utilities import ( + MissingOptionalDependencyError, + get_data_file_path, + requires_oe_module, +) @requires_oe_module("oechem") @@ -341,8 +344,9 @@ def depict_fragments( for bond_tuple, fragment in fragments.items() ] - template_path = resource_filename( - "openff.fragmenter", os.path.join("data", "report-template.html") + template_path = get_data_file_path( + os.path.join("data", "report-template.html"), + "openff.fragmenter", ) with open(template_path) as file: diff --git a/openff/fragmenter/tests/test_utils.py b/openff/fragmenter/tests/test_utils.py index 0690781..89f9a24 100644 --- a/openff/fragmenter/tests/test_utils.py +++ b/openff/fragmenter/tests/test_utils.py @@ -69,7 +69,7 @@ def from_smiles(self, *args, **kwargs): assert isinstance(Molecule.from_smiles("C"), Molecule) assert all( - type(original) == type(current) + type(original) is type(current) for original, current in zip( original_toolkits, GLOBAL_TOOLKIT_REGISTRY.registered_toolkits ) diff --git a/openff/fragmenter/utils.py b/openff/fragmenter/utils.py index 9b7253a..8b29879 100644 --- a/openff/fragmenter/utils.py +++ b/openff/fragmenter/utils.py @@ -9,7 +9,7 @@ ToolkitRegistry, ToolkitWrapper, ) -from pkg_resources import resource_filename +from openff.utilities import get_data_file_path def default_functional_groups() -> Dict[str, str]: @@ -28,8 +28,9 @@ def default_functional_groups() -> Dict[str, str]: the corresponding SMARTS pattern. """ - file_name = resource_filename( - "openff.fragmenter", os.path.join("data", "default-functional-groups.json") + file_name = get_data_file_path( + os.path.join("data", "default-functional-groups.json"), + "openff.fragmenter", ) with open(file_name, "r") as file: