Add pre-commit hook and lint all files.

.github/workflows/CI.yaml

@@ -34,6 +34,8 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - uses: pre-commit/action@v3.0.0
+        with:
+          extra_args: --files solvation_analysis/*
 
   test:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
@@ -91,7 +93,7 @@ jobs:
         file: ./coverage.xml
         flags: unittests
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-  
+
   test_pip_install:
     name: pip (PEP517) install on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}

.pre-commit-config.yaml

@@ -15,12 +15,6 @@ repos:
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-#- repo: https://github.com/asottile/blacken-docs
-#  rev: 1.16.0
-#  hooks:
-#  - id: blacken-docs
-#    additional_dependencies: [black]
-#    exclude: README.md
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:

solvation_analysis/__init__.py

@@ -2,14 +2,18 @@
 SolvationAnalysis
 An MDAnalysis rmodule for solvation analysis.
 """
+
+from . import _version
 from solvation_analysis.solute import Solute
 
 # Handle versioneer
 from ._version import get_versions
+
 versions = get_versions()
-__version__ = versions['version']
-__git_revision__ = versions['full-revisionid']
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
 del get_versions, versions
 
-from . import _version
-__version__ = _version.get_versions()['version']
+
+__version__ = _version.get_versions()["version"]
+__all__ = ["Solute"]

solvation_analysis/_column_names.py

@@ -8,7 +8,6 @@
 1. change the variable name in all files
 """
 
-
 # for solvation_data
 FRAME = "frame"
 SOLUTE_IX = "solute_ix"

solvation_analysis/_utils.py

@@ -7,7 +7,7 @@
 import MDAnalysis as mda
 from MDAnalysis.analysis import distances
 
-from solvation_analysis._column_names import *
+from solvation_analysis._column_names import FRAME, SOLUTE_IX, SOLVENT_IX, DISTANCE
 
 
 def verify_solute_atoms(solute_atom_group: mda.AtomGroup) -> dict[int, mda.AtomGroup]:
@@ -16,63 +16,74 @@ def verify_solute_atoms(solute_atom_group: mda.AtomGroup) -> dict[int, mda.AtomG
     # and that the residues are all the same length
     # then this should work
     all_res_len = np.array([res.atoms.n_atoms for res in solute_atom_group.residues])
-    assert np.all(all_res_len[0] == all_res_len), (
-        "All residues must be the same length."
-    )
+    assert np.all(
+        all_res_len[0] == all_res_len
+    ), "All residues must be the same length."
     res_atom_local_ix = defaultdict(list)
     res_atom_ix = defaultdict(list)
 
     for atom in solute_atom_group.atoms:
         res_atom_local_ix[atom.resindex].append(atom.ix - atom.residue.atoms[0].ix)
         res_atom_ix[atom.resindex].append(atom.index)
     res_occupancy = np.array([len(ix) for ix in res_atom_local_ix.values()])
-    assert np.all(res_occupancy[0] == res_occupancy), (
-        "All residues must have the same number of solute_atoms atoms on them."
-    )
+    assert np.all(
+        res_occupancy[0] == res_occupancy
+    ), "All residues must have the same number of solute_atoms atoms on them."
 
     res_atom_array = np.array(list(res_atom_local_ix.values()))
-    assert np.all(res_atom_array[0] == res_atom_array), (
-        "All residues must have the same solute_atoms atoms on them."
-    )
+    assert np.all(
+        res_atom_array[0] == res_atom_array
+    ), "All residues must have the same solute_atoms atoms on them."
 
     res_atom_ix_array = np.array(list(res_atom_ix.values()))
     solute_atom_group_dict = {}
     for i in range(0, res_atom_ix_array.shape[1]):
-        solute_atom_group_dict[i] = solute_atom_group.universe.atoms[res_atom_ix_array[:, i]]
+        solute_atom_group_dict[i] = solute_atom_group.universe.atoms[
+            res_atom_ix_array[:, i]
+        ]
     return solute_atom_group_dict
 
 
-def verify_solute_atoms_dict(solute_atoms_dict: dict[str, mda.AtomGroup]) -> mda.AtomGroup:
+def verify_solute_atoms_dict(
+    solute_atoms_dict: dict[str, mda.AtomGroup],
+) -> mda.AtomGroup:
     # first we verify the input format
     atom_group_lengths = []
     for solute_name, solute_atom_group in solute_atoms_dict.items():
-        assert isinstance(solute_name, str), (
-            "The keys of solutes_dict must be strings."
-        )
+        assert isinstance(solute_name, str), "The keys of solutes_dict must be strings."
         assert isinstance(solute_atom_group, mda.AtomGroup), (
             f"The values of solutes_dict must be MDAnalysis.AtomGroups. But the value"
             f"for {solute_name} is a {type(solute_atom_group)}."
         )
-        assert len(solute_atom_group) == len(solute_atom_group.residues), (
-            "The solute_atom_group must have a single atom on each residue."
-        )
+        assert len(solute_atom_group) == len(
+            solute_atom_group.residues
+        ), "The solute_atom_group must have a single atom on each residue."
         atom_group_lengths.append(len(solute_atom_group))
     assert np.all(np.array(atom_group_lengths) == atom_group_lengths[0]), (
         "AtomGroups in solutes_dict must have the same length because there should be"
         "one atom per solute residue."
     )
 
     # verify that the solute_atom_groups have no overlap
-    solute_atom_group = reduce(lambda x, y: x | y, [atoms for atoms in solute_atoms_dict.values()])
-    assert solute_atom_group.n_atoms == sum([atoms.n_atoms for atoms in solute_atoms_dict.values()]), (
-        "The solute_atom_groups must not overlap."
+    solute_atom_group = reduce(
+        lambda x, y: x | y, [atoms for atoms in solute_atoms_dict.values()]
     )
+    assert solute_atom_group.n_atoms == sum(
+        [atoms.n_atoms for atoms in solute_atoms_dict.values()]
+    ), "The solute_atom_groups must not overlap."
     verify_solute_atoms(solute_atom_group)
 
     return solute_atom_group
 
 
-def get_atom_group(selection: Union[mda.core.groups.Residue, mda.core.groups.ResidueGroup, mda.core.groups.Atom, mda.core.groups.AtomGroup]) -> mda.AtomGroup:
+def get_atom_group(
+    selection: Union[
+        mda.core.groups.Residue,
+        mda.core.groups.ResidueGroup,
+        mda.core.groups.Atom,
+        mda.core.groups.AtomGroup,
+    ],
+) -> mda.AtomGroup:
     """
     Cast an MDAnalysis.Atom, MDAnalysis.Residue, or MDAnalysis.ResidueGroup to AtomGroup.
 
@@ -103,14 +114,22 @@ def get_atom_group(selection: Union[mda.core.groups.Residue, mda.core.groups.Res
     return selection
 
 
-
 def get_closest_n_mol(
-    central_species: Union[mda.core.groups.Residue, mda.core.groups.ResidueGroup, mda.core.groups.Atom, mda.core.groups.AtomGroup],
+    central_species: Union[
+        mda.core.groups.Residue,
+        mda.core.groups.ResidueGroup,
+        mda.core.groups.Atom,
+        mda.core.groups.AtomGroup,
+    ],
     n_mol: int,
     guess_radius: Union[float, int] = 3,
     return_ordered_resix: bool = False,
     return_radii: bool = False,
-) -> Union[mda.AtomGroup, tuple[mda.AtomGroup, np.ndarray], tuple[mda.AtomGroup, np.ndarray, np.ndarray]]:
+) -> Union[
+    mda.AtomGroup,
+    tuple[mda.AtomGroup, np.ndarray],
+    tuple[mda.AtomGroup, np.ndarray, np.ndarray],
+]:
     """
     Returns the closest n molecules to the central species, an array of their resix,
     and an array of the distance of the closest atom in each molecule.
@@ -152,15 +171,15 @@ def get_closest_n_mol(
             n_mol,
             guess_radius + 1,
             return_ordered_resix=return_ordered_resix,
-            return_radii=return_radii
+            return_radii=return_radii,
         )
     radii = distances.distance_array(coords, partial_shell.positions, box=u.dimensions)[
         0
     ]
     ordering = np.argsort(radii)
     ordered_resix = shell_resix[ordering]
     closest_n_resix = np.sort(np.unique(ordered_resix, return_index=True)[1])[
-        0: n_mol + 1
+        0 : n_mol + 1
     ]
     str_resix = " ".join(str(resix) for resix in ordered_resix[closest_n_resix])
     full_shell = u.select_atoms(f"resindex {str_resix}")
@@ -179,8 +198,13 @@ def get_closest_n_mol(
 
 
 def get_radial_shell(
-    central_species: Union[mda.core.groups.Residue, mda.core.groups.ResidueGroup, mda.core.groups.Atom, mda.core.groups.AtomGroup],
-    radius: Union[float, int]
+    central_species: Union[
+        mda.core.groups.Residue,
+        mda.core.groups.ResidueGroup,
+        mda.core.groups.Atom,
+        mda.core.groups.AtomGroup,
+    ],
+    radius: Union[float, int],
 ) -> mda.AtomGroup:
     """
     Returns all molecules with atoms within the radius of the central species.