Autoformat and lint with ruff.

Author: lohedges

pyproject.toml

@@ -40,3 +40,9 @@ file = "src/BioSimSpace/_version.py"
 [tool.pytest.ini_options]
 # Ensure that test/Sandpit/Exscientia could have the same name as the tests in test
 addopts = "--import-mode=importlib"
+
+[tool.ruff.lint]
+ignore = ["E402"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["F841"]

src/BioSimSpace/Align/_align.py

@@ -47,7 +47,6 @@
     if _have_imported(_rdkit):
         from rdkit import Chem as _Chem
         from rdkit import RDLogger as _RDLogger
-        from rdkit.Chem import AllChem, Draw
         from rdkit.Chem import rdFMCS as _rdFMCS
 
         # Disable RDKit warnings.
@@ -265,17 +264,17 @@ def generateNetwork(
                             )
 
                     # Make sure that the ligands are in the names list.
-                    if not records[0] in names:
+                    if records[0] not in names:
                         raise ValueError(f"Ligand '{records[0]}' not in 'names' list!")
-                    if not records[1] in names:
+                    if records[1] not in names:
                         raise ValueError(f"Ligand '{records[1]}' not in 'names' list!")
 
         else:
             raise IOError(f"The links file doesn't exist: {links_file}")
 
     # Validate the number of edges parameter.
     if n_edges_forced is not None:
-        if not type(n_edges_forced) is int:
+        if type(n_edges_forced) is not int:
             raise TypeError("'n_edges_forced' must be of type 'int'")
 
         n_edges_fully_connected = int((len(molecules) ** 2 - len(molecules)) / 2) + 1
@@ -470,7 +469,7 @@ def generateNetwork(
 
                 # Update the list while checking that the inverse edge is not already in
                 # the network.
-                if not (mol1, mol0) in edges:
+                if (mol1, mol0) not in edges:
                     edges_excluded.append((mol0, mol1, score))
 
     # If the user has specified a forced number of edges, adjust the network
@@ -931,7 +930,7 @@ def _matchAtoms(
         # Strip underscores and whitespace, then convert to upper case.
         _scoring_function = scoring_function.replace("_", "").upper()
         _scoring_function = _scoring_function.replace(" ", "").upper()
-        if not _scoring_function in scoring_functions:
+        if _scoring_function not in scoring_functions:
             raise ValueError(
                 "Unsupported scoring function '%s'. Options are: %s"
                 % (scoring_function, scoring_functions)
@@ -943,7 +942,7 @@ def _matchAtoms(
             "https://pdbj.org/kcombu"
         )
 
-    if not type(matches) is int:
+    if type(matches) is not int:
         raise TypeError("'matches' must be of type 'int'")
     else:
         if matches < 0:
@@ -963,7 +962,7 @@ def _matchAtoms(
     if not isinstance(complete_rings_only, bool):
         raise TypeError("'complete_rings_only' must be of type 'bool'")
 
-    if not type(max_scoring_matches) is int:
+    if type(max_scoring_matches) is not int:
         raise TypeError("'max_scoring_matches' must be of type 'int'")
 
     if max_scoring_matches <= 0:
@@ -1437,7 +1436,6 @@ def _roiMatch(
         # In the case when we are not at the last residue of interest,
         # we need to map the atoms to the next ROI.
         if res_idx != roi[-1]:
-
             # If the next ROI residue index in the ROI list is next to
             # the current ROI index, after_roi atom index list will be empty
             # i.e. if we're currently at residue 10 and the next ROI is 11,
@@ -2266,7 +2264,7 @@ def viewMapping(
 
     if isinstance(pixels, float):
         pixels = int(pixels)
-    if not type(pixels) is int:
+    if type(pixels) is not int:
         raise TypeError("'pixels' must be of type 'int'")
     if pixels <= 0:
         raise ValueError("pixels' must be > 0!")
@@ -2716,7 +2714,7 @@ def _score_rdkit_mappings(
             }
 
             # This is a new mapping:
-            if not mapping in mappings:
+            if mapping not in mappings:
                 # Check that the mapping contains the pre-match.
                 is_valid = True
                 for idx0, idx1 in prematch.items():

src/BioSimSpace/Align/_merge.py

@@ -337,7 +337,7 @@ def merge(
 
     # lambda = 0
     for prop in props0:
-        if not prop in ignored_props:
+        if prop not in ignored_props:
             # This is a perturbable property.
             if prop in shared_props:
                 name = f"{prop}0"
@@ -357,7 +357,7 @@ def merge(
 
     # lambda = 1
     for prop in props1:
-        if not prop in ignored_props:
+        if prop not in ignored_props:
             # This is a perturbable property.
             if prop in shared_props:
                 name = f"{prop}1"

src/BioSimSpace/Convert/_convert.py

@@ -179,7 +179,7 @@ def to(obj, format="biosimspace", property_map={}, **kwargs):
     # Convert to lower case and strip whitespace.
     format = format.lower().replace(" ", "")
 
-    if not format in supportedFormats():
+    if format not in supportedFormats():
         raise ValueError(
             f"Unsupported format '{format}', options are: {', '.join(supportedFormats())}."
         )

src/BioSimSpace/FreeEnergy/_atm.py

@@ -28,9 +28,6 @@
 from .. import _is_notebook
 from ..Notebook import View as _View
 
-if _is_notebook:
-    from IPython.display import FileLink as _FileLink
-
 
 class ATMSetup:
     """
@@ -601,7 +598,6 @@ def _makeSystemFromThree(protein, ligand_bound, ligand_free, displacement):
         from ..Types import Vector as _Vector
 
         def _findTranslationVector(system, displacement, protein, ligand):
-
             import warnings as _warnings
 
             from sire.legacy.Maths import Vector
@@ -1418,8 +1414,6 @@ def getData(self, name="data", file_link=False, work_dir=None):
         import pathlib as _pathlib
         import zipfile as _zipfile
 
-        from IPython.display import FileLink as _FileLink
-
         if self._work_dir is None:
             raise ValueError("'work_dir' must be set!")
         else:
@@ -1461,6 +1455,8 @@ def getData(self, name="data", file_link=False, work_dir=None):
         # Return a link to the archive.
         if _is_notebook:
             if file_link:
+                from IPython.display import FileLink as _FileLink
+
                 # Create a FileLink to the archive.
                 f_link = _FileLink(zipname)
 
@@ -1722,7 +1718,6 @@ def __init__(self, handle, property_map={}, is_lambda1=False):
         super().__init__(handle, property_map, is_lambda1)
 
     def _create_view(self, system=None, view=None, gui=True, **kwargs):
-
         from sire.legacy import IO as _SireIO
 
         from .. import _isVerbose

src/BioSimSpace/FreeEnergy/_relative.py

@@ -454,7 +454,7 @@ def analyse(work_dir, estimator="MBAR", method="alchemlyb", **kwargs):
             if data and engine == "AMBER":
                 if method != "ALCHEMLYB":
                     raise _AnalysisError(
-                        f"AMBER can only use the 'alchemlyb' analysis method."
+                        "AMBER can only use the 'alchemlyb' analysis method."
                     )
             if data and engine == "SOMD" and estimator == "TI" and method == "native":
                 raise _AnalysisError(
@@ -463,7 +463,7 @@ def analyse(work_dir, estimator="MBAR", method="alchemlyb", **kwargs):
             if data and engine == "SOMD2":
                 if method != "ALCHEMLYB":
                     raise _AnalysisError(
-                        f"SOMD2 can only use the 'alchemlyb' analysis method."
+                        "SOMD2 can only use the 'alchemlyb' analysis method."
                     )
             if data and engine == "GROMACS" and method == "native":
                 _warnings.warn(
@@ -694,15 +694,15 @@ def _get_data(files, temperatures, engine, estimator):
         if not isinstance(engine, str):
             raise TypeError("'engine' must be of type 'str'.")
         engine = engine.replace(" ", "").upper()
-        if not engine in Relative._engines_analysis:
+        if engine not in Relative._engines_analysis:
             raise ValueError(
                 f"Unsupported engine '{engine}'. Options are: {', '.join(Relative._engines_analysis)}"
             )
 
         if not isinstance(estimator, str):
             raise TypeError("'estimator' must be of type 'str'.")
         estimator = estimator.replace(" ", "").upper()
-        if not estimator in ["MBAR", "TI"]:
+        if estimator not in ["MBAR", "TI"]:
             raise ValueError("'estimator' must be either 'MBAR' or 'TI'.")
 
         if estimator == "MBAR":
@@ -1154,7 +1154,7 @@ def _preprocess_data(data, estimator, **kwargs):
 
         if not isinstance(estimator, str):
             raise TypeError("'estimator' must be of type 'str'.")
-        if not estimator.replace(" ", "").upper() in ["MBAR", "TI"]:
+        if estimator.replace(" ", "").upper() not in ["MBAR", "TI"]:
             raise ValueError("'estimator' must be either 'MBAR' or 'TI'.")
 
         # Assign defaults in case not passed via kwargs.
@@ -1307,15 +1307,15 @@ def _analyse_internal(files, temperatures, lambdas, engine, estimator, **kwargs)
 
         if not isinstance(engine, str):
             raise TypeError("'engine' must be of type 'str'.")
-        if not engine.replace(" ", "").upper() in Relative._engines_analysis:
+        if engine.replace(" ", "").upper() not in Relative._engines_analysis:
             raise ValueError(
                 f"Unsupported engine '{engine}'. Options are: {', '.join(Relative._engines_analysis)}"
             )
 
         if not isinstance(estimator, str):
             raise TypeError("'estimator' must be of type 'str'.")
         estimator = estimator.replace(" ", "").upper()
-        if not estimator in ["MBAR", "TI"]:
+        if estimator not in ["MBAR", "TI"]:
             raise ValueError("'estimator' must be either 'MBAR' or 'TI'.")
 
         if estimator == "MBAR":
@@ -1544,7 +1544,7 @@ def _analyse_gromacs(work_dir=None, estimator="MBAR", method="alchemlyb", **kwar
 
         if not isinstance(estimator, str):
             raise TypeError("'estimator' must be of type 'str'.")
-        if not estimator.replace(" ", "").upper() in ["MBAR", "TI"]:
+        if estimator.replace(" ", "").upper() not in ["MBAR", "TI"]:
             raise ValueError("'estimator' must be either 'MBAR' or 'TI'.")
 
         if not isinstance(method, str):
@@ -1735,7 +1735,7 @@ def _analyse_somd(work_dir=None, estimator="MBAR", method="alchemlyb", **kwargs)
         if not isinstance(method, str):
             raise TypeError("'method' must be of type 'str'.")
         method = method.replace(" ", "").upper()
-        if not method in ["ALCHEMLYB", "NATIVE"]:
+        if method not in ["ALCHEMLYB", "NATIVE"]:
             raise ValueError("'method' must be either 'alchemlyb' or 'native'.")
 
         if method == "ALCHEMLYB":

src/BioSimSpace/Gateway/_node.py

@@ -34,13 +34,6 @@
 
 from .. import _is_notebook
 
-# Enable Jupyter widgets.
-if _is_notebook:
-    from IPython.display import FileLink as _FileLink
-
-    import ipywidgets as _widgets
-    import zipfile as _zipfile
-
 from ._requirements import Area as _Area
 from ._requirements import Charge as _Charge
 from ._requirements import Energy as _Energy
@@ -133,7 +126,6 @@ def __call__(self, parser, namespace, values, option_string=None):
         exe = _sys.executable
 
         # Store the absolute path of the node.
-        import __main__
 
         node = _os.path.abspath(__main__.__file__)
 
@@ -1140,7 +1132,7 @@ def addAuthor(self, name=None, email=None, affiliation=None):
             self._authors = [{"name": name, "email": email, "affiliation": affiliation}]
         else:
             author = {"name": name, "email": email, "affiliation": affiliation}
-            if not author in self._authors:
+            if author not in self._authors:
                 self._authors.append(author)
 
     def getAuthors(self):
@@ -1321,7 +1313,7 @@ def _validateInput(self):
                     if value is True:
                         self._strict_file_naming = True
                 else:
-                    if not key in ["config", "export_cwl"]:
+                    if key not in ["config", "export_cwl"]:
                         self._inputs[key].setValue(value, name=key)
 
     def validate(self, file_prefix="output"):
@@ -1346,8 +1338,6 @@ def validate(self, file_prefix="output"):
         import sys as _sys
         import zipfile as _zipfile
 
-        from IPython.display import FileLink as _FileLink
-
         from ._requirements import File as _File
         from ._requirements import FileSet as _FileSet
 
@@ -1380,6 +1370,8 @@ def validate(self, file_prefix="output"):
 
         # Create a compressed archive containing all file output for the node.
         if self._is_notebook:
+            from IPython.display import FileLink as _FileLink
+
             # There are files.
             if len(file_outputs) > 0:
                 # Create the archive name.

src/BioSimSpace/Gateway/_resources.py

@@ -99,7 +99,7 @@ def setNodes(self, nodes):
             The number of nodes.
         """
 
-        if not type(nodes) is int:
+        if type(nodes) is not int:
             raise TypeError("'nodes' must be of type 'int'.")
 
         if nodes < 0:
@@ -130,7 +130,7 @@ def setCPUs(self, cpus):
             The number of cpus.
         """
 
-        if not type(cpus) is int:
+        if type(cpus) is not int:
             raise TypeError("'cpus' must be of type 'int'.")
 
         if cpus < 0:
@@ -161,7 +161,7 @@ def setGPUs(self, gpus):
             The number of GPUs.
         """
 
-        if not type(gpus) is int:
+        if type(gpus) is not int:
             raise TypeError("'gpus' must be of type 'int'.")
 
         if gpus < 0:

src/BioSimSpace/MD/_md.py

@@ -27,7 +27,7 @@
 __all__ = ["run"]
 
 
-from .. import _amber_home, _gmx_exe
+from .. import _gmx_exe
 
 # A dictionary mapping MD engines to their executable names and GPU support.
 # engine, exe, gpu
@@ -120,7 +120,6 @@ def _find_md_engines(system, protocol, engine="AUTO", gpu_support=False):
     from sire.legacy import Base as _SireBase
 
     from .. import Protocol as _Protocol
-    from .. import _gmx_exe
     from .._Exceptions import MissingSoftwareError as _MissingSoftwareError
 
     # The input has already been validated in the run method, so no need
@@ -129,7 +128,7 @@ def _find_md_engines(system, protocol, engine="AUTO", gpu_support=False):
     fileformat = system.fileFormat()
 
     # Make sure that this format is supported.
-    if not fileformat in _file_extensions:
+    if fileformat not in _file_extensions:
         raise ValueError(
             "Cannot find an MD engine that supports format: %s" % fileformat
         )
@@ -348,7 +347,7 @@ def run(
             raise TypeError("'work_dir' must be of type 'str'")
 
     if seed is not None:
-        if not type(seed) is int:
+        if type(seed) is not int:
             raise TypeError("'seed' must be of type 'int'")
 
     if not isinstance(property_map, dict):

src/BioSimSpace/Metadynamics/CollectiveVariable/_rmsd.py

@@ -335,7 +335,7 @@ def __init__(
         # Also strip any TER records.
         self._reference_pdb = []
         for line, idx in zip(lines[1:-2], abs_atom_indices):
-            if not "TER" in line:
+            if "TER" not in line:
                 self._reference_pdb.append(line[:6] + str(idx).rjust(5) + line[11:])
         self._reference_pdb.append(lines[-1])
 
@@ -678,7 +678,7 @@ def _compute_initial_rmsd(
                     i.value(): i.value()
                     for i in align_indices[ref._sire_object.number()]
                 }
-            except Exception as e:
+            except Exception:
                 pass
 
             if len(align_mapping) > 0:
@@ -699,7 +699,7 @@ def _compute_initial_rmsd(
 
             try:
                 rmsd_mapping = {i: i for i in rmsd_indices[ref._sire_object.number()]}
-            except Exception as e:
+            except Exception:
                 pass
 
             if len(rmsd_mapping) > 0: