Fixing dependencies for alchemy CI workflows

.github/workflows/dataviz.yaml

@@ -72,7 +72,7 @@ jobs:
         micromamba install -n dataviz --file devtools/conda-envs/${{ matrix.os }}/simulation.yaml
         micromamba install -n dataviz --file devtools/conda-envs/${{ matrix.os }}/modeling.yaml
         micromamba install -n dataviz --file devtools/conda-envs/${{ matrix.os }}/spectrum.yaml
-        
+
         python -m pip install -e ./drugforge-data --no-deps
         python -m pip install -e ./drugforge-modeling --no-deps
         python -m pip install -e ./drugforge-cli --no-deps
@@ -81,7 +81,7 @@ jobs:
         python -m pip install -e ./drugforge-simulation --no-deps
         python -m pip install -e ./drugforge-spectrum --no-deps
         micromamba list
-    
+
     - name: Test OE License & Write License to File
       env:
         OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}

README.md

@@ -16,9 +16,9 @@ This fork is now developed and maintained independently by the [Chodera Lab](htt
 
 ## Intro
 
-All pandemics are global health threats. Our best defense is a healthy global antiviral discovery community with a robust pipeline of open discovery tools. 
+All pandemics are global health threats. Our best defense is a healthy global antiviral discovery community with a robust pipeline of open discovery tools.
 
-The toolkit in this repo is a batteries-included drug discovery pipeline being actively developed in a transparent open-source way, with a focus on computational chemistry and informatics support for medicinal chemistry. 
+The toolkit in this repo is a batteries-included drug discovery pipeline being actively developed in a transparent open-source way, with a focus on computational chemistry and informatics support for medicinal chemistry.
 
 
 ## Getting Started
@@ -27,7 +27,7 @@ Install the `drugforge` subpackages and begin to explore! The drugforge [documen
 
 There are a range of workflows and tooling to use split into several namespace subpackages by theme.
 
-**Warning:** The implementation of drugforge-ML is still in the works and will be available in the next release. If you want to use ML scoring please refer to the original version of this code under [asapdiscovery](https://github.com/asapdiscovery/asapdiscovery). 
+**Warning:** The implementation of drugforge-ML is still in the works and will be available in the next release. If you want to use ML scoring please refer to the original version of this code under [asapdiscovery](https://github.com/asapdiscovery/asapdiscovery).
 
 `drugforge-alchemy`: Free energy calculations using [OpenFE](https://openfree.energy/) and [Alchemiscale](https://docs.alchemiscale.org/en/latest/). See [tutorial](https://drugforge.readthedocs.io/en/latest/tutorials/running_alchemical_free_energy_calculations.html) and CLI [guide](https://asapdiscovery.readthedocs.io/en/latest/guides/using_asap_alchemy_cli.html)
 

devtools/conda-envs/macos-latest/alchemy.yaml

@@ -5,15 +5,16 @@ channels:
 dependencies:
   - alchemiscale-client
   - bokeh
-  - cinnabar
+  - cinnabar ~=0.5.0
   - click
-  - gufe
+  - gufe ~=1.6.0
+  - importlib_resources  # manually added. More info at https://github.com/conda-forge/openmmforcefields-feedstock/pull/26
   - kartograf
   - lomap2
   - networkx
   - numpy
   - openeye-toolkits
-  - openfe ~=1.0
+  - openfe ~=1.4
   - openff-toolkit
   - openff-models
   - openff-qcsubmit

devtools/conda-envs/macos-latest/cli.yaml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
 dependencies:
   - click
-  - pytest
+  - pytest

devtools/conda-envs/ubuntu-latest/alchemy.yaml

@@ -5,15 +5,16 @@ channels:
 dependencies:
   - alchemiscale-client
   - bokeh
-  - cinnabar
+  - cinnabar ~=0.5.0
   - click
-  - gufe
+  - gufe ~=1.6.0
+  - importlib_resources  # manually added. More info at https://github.com/conda-forge/openmmforcefields-feedstock/pull/26
   - kartograf
   - lomap2
   - networkx
   - numpy
   - openeye-toolkits
-  - openfe ~=1.0
+  - openfe ~=1.4
   - openff-toolkit
   - openff-models
   - openff-qcsubmit

devtools/conda-envs/ubuntu-latest/cli.yaml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
 dependencies:
   - click
-  - pytest
+  - pytest

devtools/conda-envs/ubuntu-latest/simulation.yaml

@@ -71,4 +71,4 @@ dependencies:
   - multimethod
 
   # ML
-  - mtenn >=0.6.3
+  - mtenn >=0.6.3

devtools/conda-envs/ubuntu-latest/spectrum.yaml

@@ -64,4 +64,3 @@ dependencies:
   - moto
   - boto3
   - multimethod
-

devtools/conda-envs/ubuntu-latest/workflows.yaml

@@ -6,4 +6,4 @@ dependencies:
   # drugforge {all the other packages}
   click
   pydantic
-  unittest
+  unittest

devtools/detect_imports.py

@@ -14,15 +14,15 @@
 from pathlib import Path
 
 
-def get_imports_from_file(file_path: str) -> Set[Tuple[str, str]]:
+def get_imports_from_file(file_path: str) -> set[tuple[str, str]]:
     """
     Extract import names and their submodules from a Python file.
     Returns set of tuples (package, submodule).
     """
     imports = set()
 
     try:
-        with open(file_path, 'r', encoding='utf-8') as f:
+        with open(file_path, encoding='utf-8') as f:
             tree = ast.parse(f.read())
 
         for node in ast.walk(tree):
@@ -49,7 +49,7 @@ def get_imports_from_file(file_path: str) -> Set[Tuple[str, str]]:
     return imports
 
 
-def find_all_imports_with_files(directory: str) -> Dict[str, Dict[str, Set[str]]]:
+def find_all_imports_with_files(directory: str) -> dict[str, dict[str, set[str]]]:
     """
     Find all unique imports and their submodules in Python files.
 
@@ -132,4 +132,4 @@ def main(directory: str, output: str, packages_only: bool):
 
 
 if __name__ == "__main__":
-    main()
+    main()

docs/README.md

@@ -1,12 +1,12 @@
 # Compiling drugforge's Documentation
 
-For the docs to compile properly, you will need to have the full drugforge environment installed. 
+For the docs to compile properly, you will need to have the full drugforge environment installed.
 
 The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/).
 To install the needed dependencies, you can run:
 
 ```bash
- mamba env update -f docs/requirements.yaml -n YOUR_DRUGFORGE_ENVIRONMENT_NAME 
+ mamba env update -f docs/requirements.yaml -n YOUR_DRUGFORGE_ENVIRONMENT_NAME
 ```
 
 You can then build the docs with:

docs/index.md

@@ -2,7 +2,7 @@ Welcome to drugforge's documentation!
 =========================================
 <img src="_static/drugforge_logo.png" width="200">
 
-All pandemics are global health threats. Our best defense is a healthy global antiviral discovery community with a robust pipeline of open discovery tools. 
+All pandemics are global health threats. Our best defense is a healthy global antiviral discovery community with a robust pipeline of open discovery tools.
 
 The toolkit in this repo is a batteries-included drug discovery pipeline being actively developed in a transparent open-source way, with a focus on computational chemistry and informatics support for medicinal chemistry.
 
@@ -15,7 +15,7 @@ drugforge is not designed as a one size fits all solution for drug discovery, ra
 ```
 
 ```{warning}
-The implementation of drugforge-ML is still in the works and will be available in the next release. If you want to use ML scoring please refer to the original version of this code under [asapdiscovery](https://github.com/asapdiscovery/asapdiscovery). 
+The implementation of drugforge-ML is still in the works and will be available in the next release. If you want to use ML scoring please refer to the original version of this code under [asapdiscovery](https://github.com/asapdiscovery/asapdiscovery).
 ```
 
 The `drugforge` toolkit is focused around the following core competencies, organised into submodules:

docs/installation.md

@@ -53,7 +53,7 @@ Note that the Docker image assumes that your OpenEye license is located at `~/.O
 Developer installation from source
 ----------------------------------
 
-To install `drugforge` from source, you will need to clone the repository, create a compatible base environment with mamba (or conda), we recommend using only the dependencies for `drugforge` for this step. 
+To install `drugforge` from source, you will need to clone the repository, create a compatible base environment with mamba (or conda), we recommend using only the dependencies for `drugforge` for this step.
 Install the development dependencies/utils (such as openeye-toolkits, pytest, ipython, etc.).
 And finally, install all the subpackages with `pip` using an editable install (so changes get automatically updated). This needs a for loop and compatibility config mode.
 You can do this using the following commands:

drugforge-alchemy/drugforge/alchemy/cli/prep.py

@@ -301,11 +301,7 @@ def run(
 
     import pandas
     import rich
-    from drugforge.alchemy.cli.utils import (
-        get_cpus,
-        print_header,
-        pull_from_postera,
-    )
+    from drugforge.alchemy.cli.utils import get_cpus, print_header, pull_from_postera
     from drugforge.alchemy.schema.prep_workflow import AlchemyPrepWorkflow
     from drugforge.data.readers.molfile import MolFileFactory
     from drugforge.modeling.schema import PreppedComplex

drugforge-alchemy/drugforge/alchemy/cli/utils.py

@@ -5,9 +5,9 @@
 import rich
 
 if TYPE_CHECKING:
+    from cinnabar import FEMap
     from drugforge.alchemy.schema.fec import FreeEnergyCalculationNetwork
     from drugforge.data.schema.ligand import Ligand
-    from cinnabar import FEMap
 
 
 def print_header(console: "rich.Console"):
@@ -68,8 +68,8 @@ def upload_to_postera(
     from drugforge.data.services.postera.manifold_data_validation import (
         rename_output_columns_for_manifold,
     )
-    from drugforge.workflows.postera.postera_uploader import PosteraUploader
     from drugforge.data.services.services_config import PosteraSettings
+    from drugforge.workflows.postera.postera_uploader import PosteraUploader
 
     # mock an enum to specify which columns are allowed
     class AlchemyResults(str, Enum):

drugforge-alchemy/drugforge/alchemy/predict.py

@@ -10,9 +10,9 @@
 import pandas as pd
 import panel
 import plotmol
-from drugforge.data.schema.ligand import Ligand
 from bokeh.models import Band, ColumnDataSource, Range1d, Whisker
 from cinnabar import stats
+from drugforge.data.schema.ligand import Ligand
 from openff.units import unit
 from rdkit import Chem
 from rdkit.Chem import Draw

drugforge-alchemy/drugforge/alchemy/schema/_util.py

@@ -1,7 +1,8 @@
 from collections import Counter
 from typing import TYPE_CHECKING
-from gufe.serialization.json import JSONCodec
+
 from alchemiscale import ScopedKey
+from gufe.serialization.json import JSONCodec
 
 if TYPE_CHECKING:
     from drugforge.data.schema.ligand import Ligand

drugforge-alchemy/drugforge/alchemy/schema/base.py

@@ -17,6 +17,7 @@ def to_file(self, filename: str):
         Write the model to JSON file.
         """
         from gufe.tokenization import JSON_HANDLER
+
         from ._util import SCOPEDKEY_CODEC
 
         JSON_HANDLER.add_codec(SCOPEDKEY_CODEC)
@@ -30,6 +31,7 @@ def from_file(cls, filename: str):
         Load the model from a JSON file
         """
         from gufe.tokenization import JSON_HANDLER
+
         from ._util import SCOPEDKEY_CODEC
 
         JSON_HANDLER.add_codec(SCOPEDKEY_CODEC)

drugforge-alchemy/drugforge/alchemy/schema/fec.py

@@ -1,5 +1,5 @@
 import warnings
-from typing import TYPE_CHECKING, Any, Literal, Optional, Union, Dict
+from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union
 
 import gufe
 import openfe
@@ -300,7 +300,7 @@ class AlchemiscaleResults(_BaseResults):
     )
 
     @validator("network_key", pre=True)
-    def convert_to_scoped_key(cls, value: Union[Dict, ScopedKey]) -> ScopedKey:
+    def convert_to_scoped_key(cls, value: Union[dict, ScopedKey]) -> ScopedKey:
         # if we have a dict convert it to a ScopedKey
         if isinstance(value, dict):
             return ScopedKey(**value)

drugforge-alchemy/drugforge/alchemy/schema/prep_workflow.py

@@ -9,15 +9,13 @@
     ProtomerExpander,
 )
 from drugforge.data.operators.state_expanders.stereo_expander import StereoExpander
-from drugforge.data.operators.state_expanders.tautomer_expander import (
-    TautomerExpander,
-)
-from drugforge.modeling.schema import PreppedComplex
+from drugforge.data.operators.state_expanders.tautomer_expander import TautomerExpander
 from drugforge.data.schema.ligand import Ligand
 from drugforge.docking.schema.pose_generation import (
     OpenEyeConstrainedPoseGenerator,
     RDKitConstrainedPoseGenerator,
 )
+from drugforge.modeling.schema import PreppedComplex
 from pydantic.v1 import Field
 from rich import pretty
 from rich.padding import Padding

drugforge-alchemy/drugforge/alchemy/tests/conftest.py

@@ -7,10 +7,10 @@
 from drugforge.alchemy.schema.prep_workflow import AlchemyPrepWorkflow
 from drugforge.alchemy.utils import AlchemiscaleHelper
 from drugforge.data.readers.molfile import MolFileFactory
-from drugforge.modeling.schema import PreppedComplex
 from drugforge.data.schema.ligand import Ligand, write_ligands_to_multi_sdf
 from drugforge.data.testing.test_resources import fetch_test_file
 from drugforge.docking.schema.pose_generation import OpenEyeConstrainedPoseGenerator
+from drugforge.modeling.schema import PreppedComplex
 from gufe.protocols import Context, ProtocolUnit, ProtocolUnitFailure
 
 

drugforge-alchemy/drugforge/alchemy/tests/test_cli.py

@@ -8,18 +8,15 @@
 import rich
 from alchemiscale import AlchemiscaleClient
 from alchemiscale.models import ScopedKey
+from click.testing import CliRunner
 from drugforge.alchemy.cli.cli import alchemy
 from drugforge.alchemy.schema.fec import (
     FreeEnergyCalculationFactory,
     FreeEnergyCalculationNetwork,
 )
-from drugforge.alchemy.schema.prep_workflow import (
-    AlchemyDataSet,
-    AlchemyPrepWorkflow,
-)
+from drugforge.alchemy.schema.prep_workflow import AlchemyDataSet, AlchemyPrepWorkflow
 from drugforge.data.services.cdd.cdd_api import CDDAPI
 from drugforge.data.testing.test_resources import fetch_test_file
-from click.testing import CliRunner
 from openfe.setup import LigandNetwork
 from rdkit import Chem
 

drugforge-alchemy/drugforge/alchemy/tests/test_utils.py

@@ -378,9 +378,7 @@ def get_cdd_data(protocol_name: str):
         ]
         return pandas.DataFrame(data)
 
-    monkeypatch.setattr(
-        drugforge.alchemy.predict, "download_cdd_data", get_cdd_data
-    )
+    monkeypatch.setattr(drugforge.alchemy.predict, "download_cdd_data", get_cdd_data)
 
     molecules = get_cdd_molecules(
         protocol_name="my-protocol",
@@ -410,9 +408,7 @@ def get_cdd_data(protocol_name: str):
         ]
         return pandas.DataFrame(data)
 
-    monkeypatch.setattr(
-        drugforge.alchemy.predict, "download_cdd_data", get_cdd_data
-    )
+    monkeypatch.setattr(drugforge.alchemy.predict, "download_cdd_data", get_cdd_data)
 
     molecules = get_cdd_molecules(
         protocol_name="my-protocol",

drugforge-alchemy/drugforge/alchemy/utils.py

@@ -12,11 +12,10 @@
 from drugforge.alchemy.schema.forcefield import ForceFieldParams
 from openmm.app import ForceField, Modeller, PDBFile
 
-
 if TYPE_CHECKING:
-    from drugforge.modeling.schema import PreppedComplex, PreppedTarget
     from drugforge.data.schema.ligand import Ligand
     from drugforge.data.schema.target import PreppedTarget
+    from drugforge.modeling.schema import PreppedComplex, PreppedTarget
 
 
 def create_protein_only_system(input_pdb_path: str, ff_params: ForceFieldParams):

drugforge-cli/drugforge/cli/cli.py

@@ -5,9 +5,7 @@
 def cli(help="Command-line interface for drugforge"): ...
 
 
-from drugforge.workflows.docking_workflows.cli import (  # noqa: F401, E402, F811
-    docking,
-)
+from drugforge.workflows.docking_workflows.cli import docking  # noqa: F401, E402, F811
 
 cli.add_command(docking)
 

drugforge-cli/drugforge/cli/tests/test_meta_cli.py

@@ -1,8 +1,8 @@
 import traceback
 
 import pytest
-from drugforge.cli.cli import cli
 from click.testing import CliRunner
+from drugforge.cli.cli import cli
 
 
 def click_success(result):

drugforge-data/drugforge/data/backend/openeye.py

@@ -4,6 +4,7 @@
 from typing import Any, Dict, List, Optional, Union  # noqa: F401
 from warnings import warn
 
+from drugforge.data.schema.schema_base import MoleculeFilter
 from openeye import (  # noqa: F401
     oechem,
     oedepict,
@@ -17,7 +18,6 @@
     oespruce,
     oeszybki,
 )
-from drugforge.data.schema.schema_base import MoleculeFilter
 
 # exec on module import