Lints with ruff (#226)

* Runs the ruff linter

* Adds ruff to the pre-commit hooks

* Runs ruff and adds it to the linting checks

* Fixes a small error on tox's use of ruff

* Fixes an erroneous import in a test

.pre-commit-config.yaml

@@ -14,3 +14,10 @@ repos:
     rev: 5.13.2
     hooks:
     -   id: isort
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.5.5
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]

examples/observers/adding_a_wandb_observer/example_logging_rdkit_qed_using_wandb.py

@@ -11,7 +11,6 @@
 import numpy as np
 from wandb_observer import WandbObserver
 
-from poli.core.problem import Problem
 from poli.objective_repository import QEDProblemFactory
 
 THIS_DIR = Path(__file__).parent.resolve()

examples/observers/adding_an_mlflow_observer/mlflow_observer.py

@@ -61,8 +61,6 @@ def initialize_observer(
             }
         )
 
-        mlflow.log_param("x0", x0)
-        mlflow.log_param("y0", y0)
         mlflow.log_param("seed", seed)
 
     def observe(self, x: np.ndarray, y: np.ndarray, context=None) -> None:

examples/the_basics/a_simple_objective_function_registration/registering_aloha.py

@@ -6,7 +6,6 @@
 """
 
 from string import ascii_uppercase
-from typing import Tuple
 
 import numpy as np
 

pyproject.toml

@@ -48,3 +48,6 @@ markers = [
 
 [tool.isort]
 profile = "black"
+
+[tool.ruff]
+exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]

src/poli/__init__.py

@@ -6,3 +6,5 @@
 # from .core import get_problems
 from .objective_factory import create
 from .objective_repository import get_problems
+
+__all__ = ["create", "get_problems", "instance_function_as_isolated_process"]

src/poli/benchmarks/__init__.py

@@ -5,3 +5,11 @@
     EmbeddedHartmann6D,
     ToyContinuousFunctionsBenchmark,
 )
+
+__all__ = [
+    "GuacaMolGoalDirectedBenchmark",
+    "PMOBenchmark",
+    "ToyContinuousFunctionsBenchmark",
+    "EmbeddedBranin2D",
+    "EmbeddedHartmann6D",
+]

src/poli/core/abstract_black_box.py

@@ -9,7 +9,6 @@
 
 from poli.core.black_box_information import BlackBoxInformation
 from poli.core.exceptions import BudgetExhaustedException
-from poli.core.problem_setup_information import ProblemSetupInformation
 from poli.core.util.abstract_observer import AbstractObserver
 from poli.core.util.alignment import is_aligned_input
 from poli.core.util.batch import batched

src/poli/core/abstract_problem_factory.py

@@ -1,10 +1,5 @@
 """This module implements the abstract problem factory."""
 
-from typing import Tuple
-
-import numpy as np
-
-from poli.core.abstract_black_box import AbstractBlackBox
 from poli.core.black_box_information import BlackBoxInformation
 from poli.core.problem import Problem
 

src/poli/core/chemistry/tdc_isolated_function.py

@@ -82,7 +82,7 @@ def __call__(self, x, context=None):
         scores : array-like
             An array of oracle scores computed for each input molecule.
         """
-        if not x.dtype.kind in ["U", "S"]:
+        if x.dtype.kind not in ["U", "S"]:
             raise ValueError(
                 f"We expect x to be an array of strings, but we got {x.dtype}"
             )

src/poli/core/multi_objective_black_box.py

@@ -10,7 +10,6 @@
 
 from poli.core.abstract_black_box import AbstractBlackBox
 from poli.core.black_box_information import BlackBoxInformation
-from poli.core.problem_setup_information import ProblemSetupInformation
 
 
 class MultiObjectiveBlackBox(AbstractBlackBox):

src/poli/core/problem_setup_information.py

@@ -2,8 +2,6 @@
 Implements the problem setup information, which contains the problem information (e.g. alphabet, sequence length...).
 """
 
-import numpy as np
-
 from poli.core.black_box_information import BlackBoxInformation
 
 

src/poli/core/proteins/foldx_isolated_function.py

@@ -1,4 +1,3 @@
-from multiprocessing import cpu_count
 from pathlib import Path
 from time import time
 from typing import List, Union
@@ -7,7 +6,6 @@
 import numpy as np
 
 from poli.core.abstract_isolated_function import AbstractIsolatedFunction
-from poli.core.problem_setup_information import ProblemSetupInformation
 from poli.core.util.proteins.foldx import FoldxInterface
 from poli.core.util.proteins.pdb_parsing import (
     parse_pdb_as_residue_strings,

src/poli/core/registry.py

@@ -5,7 +5,7 @@
 import subprocess
 import warnings
 from pathlib import Path
-from typing import Dict, List, Type, Union
+from typing import List, Type, Union
 
 from poli.core.abstract_black_box import AbstractBlackBox
 from poli.core.abstract_isolated_function import AbstractIsolatedFunction

src/poli/core/util/alignment/__init__.py

@@ -1 +1,3 @@
 from .is_aligned import is_aligned_input
+
+__all__ = ["is_aligned_input"]

src/poli/core/util/batch/__init__.py

@@ -1,3 +1,5 @@
 """Utility functions for batching data."""
 
 from .batch_input import batched
+
+__all__ = ["batched"]

src/poli/core/util/chemistry/string_to_molecule.py

@@ -40,7 +40,7 @@ def translate_smiles_to_selfies(
             selfies_strings.append(sf.encoder(smile))
         except sf.EncoderError:
             if strict:
-                raise ValueError(f"Failed to encode SMILES to SELFIES.")
+                raise ValueError("Failed to encode SMILES to SELFIES.")
             else:
                 selfies_strings.append(None)
 
@@ -78,7 +78,7 @@ def translate_selfies_to_smiles(
             smiles_strings.append(sf.decoder(selfies))
         except sf.DecoderError:
             if strict:
-                raise ValueError(f"Failed to decode SELFIES to SMILES.")
+                raise ValueError("Failed to decode SELFIES to SMILES.")
             else:
                 smiles_strings.append(None)
 

src/poli/core/util/files/__init__.py

@@ -1,3 +1,5 @@
 """Utilities for downloading files from GitHub repositories."""
 
 from .download_files_from_github import download_file_from_github_repository
+
+__all__ = ["download_file_from_github_repository"]

src/poli/core/util/inter_process_communication/process_wrapper.py

@@ -47,14 +47,14 @@ def get_connection(port: int, password: str) -> Client:
             # if we manage to establish a connection we exit the function
             return Client(address, authkey=password.encode())
         # maybe the host process isn't ready yet
-        except EOFError as e:
+        except EOFError:
             pass
-        except ConnectionRefusedError as e:
+        except ConnectionRefusedError:
             pass
         retries -= 1
     # when we get here, e must have been instantiated
     logging.fatal("Could not connect to host process.")
-    raise e
+    raise ConnectionError("Could not connect to host process.")
 
 
 class ProcessWrapper:

src/poli/core/util/isolation/external_black_box.py

@@ -93,7 +93,7 @@ def terminate(self):
             try:
                 self.observer.finish()
                 self.observer = None
-            except:
+            except Exception:
                 pass
 
     def __getattr__(self, __name: str) -> Any:

src/poli/core/util/isolation/instancing.py

@@ -233,13 +233,13 @@ def register_isolated_function_if_available(
         # Register problem
         if name == "tdc__isolated":
             logging.debug(
-                f"poli 🧪: Registered the isolated function from the repository."
+                "poli 🧪: Registered the isolated function from the repository."
             )
             __register_isolated_function_from_core(name, quiet=quiet)
             config = load_config()
         else:
             logging.debug(
-                f"poli 🧪: Registered the isolated function from the repository."
+                "poli 🧪: Registered the isolated function from the repository."
             )
             __register_isolated_function_from_repository(name, quiet=quiet)
             # Refresh the config

src/poli/core/util/objective_management/make_run_script.py

@@ -10,7 +10,6 @@
 from typing import List, Type, Union
 
 from poli import external_isolated_function_script, external_problem_factory_script
-from poli.core.abstract_black_box import AbstractBlackBox
 from poli.core.abstract_isolated_function import AbstractIsolatedFunction
 from poli.core.abstract_problem_factory import AbstractProblemFactory
 from poli.core.util import observer_wrapper

src/poli/core/util/observer_wrapper.py

@@ -7,10 +7,7 @@
 
 from poli.core.util.abstract_observer import AbstractObserver
 from poli.core.util.inter_process_communication.process_wrapper import get_connection
-from poli.external_problem_factory_script import (
-    dynamically_instantiate,
-    parse_factory_kwargs,
-)
+from poli.external_problem_factory_script import dynamically_instantiate
 
 
 def start_observer_process(observer_name, port: int, password: str):

src/poli/core/util/proteins/rasp/__init__.py

@@ -2,3 +2,5 @@
 
 from .load_models import load_cavity_and_downstream_models
 from .rasp_interface import RaspInterface
+
+__all__ = ["load_cavity_and_downstream_models", "RaspInterface"]