Merge branch 'protos' into chi/documentation-cleanup

.github/workflows/lint.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: psf/black@stable
+      - uses: astral-sh/ruff-action@v3
         with:
-          options: "--check --verbose"
-          src: "MDANSE/Src"
+          src: "./MDANSE/Src"
+          args: "format --check"
 
   lint_check_ruff:
     runs-on: ubuntu-latest
@@ -25,14 +25,14 @@ jobs:
           src: "./MDANSE/Src"
           args: "check"
 
-  lint-mdanse-gui:
+  lint_format_ruff_gui:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: psf/black@stable
+      - uses: astral-sh/ruff-action@v3
         with:
-          options: "--check --verbose"
-          src: "MDANSE_GUI/Src"
+          src: "./MDANSE_GUI/Src"
+          args: "format --check"
 
   lint_check_ruff_gui:
     runs-on: ubuntu-latest

MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py

@@ -28,7 +28,6 @@
 
 
 class ChemicalSystem:
-
     def __init__(self, name: str = "", trajectory=None):
         """
 

MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py

@@ -21,7 +21,6 @@
 
 
 class AtomLabel:
-
     def __init__(self, atm_label: str, **kwargs):
         """Creates an atom label object which is used for atom mapping
         and atom type guessing.

MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py

@@ -202,7 +202,6 @@ def get_idxs(self) -> set[int]:
         idxs = set([])
 
         for k, v in self.settings.items():
-
             if isinstance(v, dict):
                 args = [{self._kwarg_keys[k]: i} for i in v.keys()]
                 switches = v.values()
@@ -234,7 +233,6 @@ def update_with_idxs(self, idxs: set[int]) -> None:
 
         added = set([])
         for k, v in self.settings.items():
-
             if k == "index":
                 continue
 
@@ -338,7 +336,6 @@ def check_valid_setting(self, settings: dict[str, Union[bool, dict]]) -> bool:
         setting_keys = self._default.keys()
         dict_setting_keys = self._kwarg_keys.keys()
         for k0, v0 in settings.items():
-
             if k0 not in setting_keys:
                 return False
 

MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py

@@ -28,7 +28,6 @@ class ASEFileConfigurator(FileWithAtomDataConfigurator):
     """
 
     def parse(self):
-
         try:
             self._input = ASETrajectory(self["filename"])
         except Exception:

MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -142,7 +142,6 @@ def configure(self, value: str):
 
         self._nTransmutedAtoms = 0
         for idx, element in value.items():
-
             try:
                 idx = int(idx)
             except ValueError:

MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py

@@ -29,7 +29,6 @@ class LAMMPSConfigFileError(Error):
 
 
 def parse_unit_cell(inputs):
-
     unit_cell = np.zeros(9)
 
     xlo, xhi, xy = inputs[0], inputs[1], inputs[2]
@@ -53,7 +52,6 @@ def parse_unit_cell(inputs):
 
 
 class ConfigFileConfigurator(FileWithAtomDataConfigurator):
-
     def parse(self):
         self._filename = self["filename"]
 

MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py

@@ -19,7 +19,6 @@
 
 
 class CorrelationFramesConfigurator(FramesConfigurator):
-
     def configure(self, value: tuple[int, int, int, int]):
         """Configure the correlation and set the number of correlation
         frames to use.
@@ -50,8 +49,7 @@ def configure(self, value: tuple[int, int, int, int]):
 
         if c_frames < 2:
             self.error_status = (
-                "Number of frames used for the correlation "
-                "should be greater then zero."
+                "Number of frames used for the correlation should be greater then zero."
             )
             return
 

MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py

@@ -6,7 +6,6 @@
 
 
 class DistHistCutoffConfigurator(RangeConfigurator):
-
     def __init__(self, name, **kwargs):
         super().__init__(name, **kwargs)
         self._max_value = kwargs.get("max_value", True)

MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py

@@ -22,7 +22,6 @@
 
 
 class FileWithAtomDataConfigurator(InputFileConfigurator):
-
     def configure(self, filepath: str) -> None:
         """
         Parameters

MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py

@@ -90,7 +90,7 @@ def configure(self, value):
                 ):
                     indices.append(cluster)
                     elements.append([chemical_system.atom_list[x] for x in cluster])
-                    names.append(f"{mol_name}_mol{mol_number+1}")
+                    names.append(f"{mol_name}_mol{mol_number + 1}")
                     masses.append([mass_lookup[x] for x in cluster])
         elif value == "group":
             for group_name, group_indices in chemical_system._labels.items():

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py

@@ -22,7 +22,6 @@
 
 
 class MDAnalysisCoordinateFileConfigurator(MultiInputFileConfigurator):
-
     _default = ("", "AUTO")
 
     def __init__(self, name, wildcard="All files (*)", **kwargs):

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py

@@ -19,7 +19,6 @@
 
 
 class MDAnalysisTimeStepConfigurator(FloatConfigurator):
-
     _default = 0.0
 
     def configure(self, value):

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py

@@ -22,7 +22,6 @@
 
 
 class MDAnalysisTopologyFileConfigurator(FileWithAtomDataConfigurator):
-
     _default = ("", "AUTO")
 
     def configure(self, setting: str) -> None:

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py

@@ -19,7 +19,6 @@
 
 
 class MDTrajTimeStepConfigurator(FloatConfigurator):
-
     _default = 0.0
 
     def configure(self, value):

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py

@@ -25,7 +25,6 @@
 
 
 class MDTrajTopologyFileConfigurator(FileWithAtomDataConfigurator):
-
     def configure(self, value: Optional[str]):
         """
         Parameters

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py

@@ -21,7 +21,6 @@
 
 
 class MDTrajTrajectoryFileConfigurator(MultiInputFileConfigurator):
-
     def configure(self, value):
         super().configure(value)
 

MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py

@@ -21,7 +21,6 @@
 
 
 class MultiInputFileConfigurator(IConfigurator):
-
     _default = ""
 
     def __init__(self, name, wildcard="All files (*)", **kwargs):

MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py

@@ -211,7 +211,6 @@ def get_information(self):
         """
 
         if self._valid:
-
             info = f"{self['number']:d} values from {self['first']} to {self['last']}"
 
             if self._includeLast:

MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py

@@ -74,7 +74,6 @@ def check_trajectory(filename: str):
 
 
 class XDATCARFileConfigurator(FileWithAtomDataConfigurator):
-
     def parse(self):
         filename = self["filename"]
         with open(filename, "r") as source:
@@ -107,7 +106,6 @@ def parse(self):
         self._coordinates = np.empty((self["n_atoms"], 3))
 
     def read_step(self, step):
-
         if step > 0 and not self._has_fixed_cell:
             unit_cell, atoms, atom_numbers, system_name = read_modern_header(
                 self["instance"]

MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py

@@ -33,7 +33,6 @@
 
 
 class XTDFileConfigurator(FileWithAtomDataConfigurator):
-
     def __init__(self, name, **kwargs):
         super().__init__(name, **kwargs)
         self._atoms = None

MDANSE/Src/MDANSE/Framework/Converters/CP2K.py

@@ -184,7 +184,7 @@ def initialize(self):
         self._cellFile = CellFile(self.configuration["cell_file"]["filename"])
 
         if abs(self._cellFile["time_step"] - self._xyzFile["time_step"]) > 1.0e-09:
-            LOG.error(f'{self._cellFile["time_step"]}, {self._xyzFile["time_step"]}')
+            LOG.error(f"{self._cellFile['time_step']}, {self._xyzFile['time_step']}")
             raise CP2KConverterError(
                 "Inconsistent time step between pos and cell files"
             )

MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py

@@ -37,7 +37,6 @@ class DL_POLYConverterError(Error):
 
 
 class HistoryFile(dict):
-
     def __init__(self, filename):
         super().__init__()
         self._dist_conversion = measure(1.0, "ang").toval("nm")

MDANSE/Src/MDANSE/Framework/Converters/Forcite.py

@@ -55,7 +55,7 @@ def parse_header(self):
         rec = "!i"
         recSize = struct.calcsize(rec)
         (NTRJTI,) = struct.unpack(rec, trjfile.read(recSize))
-        rec = f"!{80*NTRJTI}s8x"
+        rec = f"!{80 * NTRJTI}s8x"
         recSize = struct.calcsize(rec)
         self["title"] = struct.unpack(rec, trjfile.read(recSize))
         self["title"] = "\n".join([t.decode("utf-8") for t in self["title"]])
@@ -82,7 +82,7 @@ def parse_header(self):
         recSize = struct.calcsize(rec)
         NFLUSD = struct.unpack(rec, trjfile.read(recSize))[0]
 
-        rec = f"!{NFLUSD}i{NFLUSD}i{8*NFLUSD}s8x"
+        rec = f"!{NFLUSD}i{NFLUSD}i{8 * NFLUSD}s8x"
         recSize = struct.calcsize(rec)
         trjfile.read(recSize)
 

MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py

@@ -102,9 +102,10 @@ def initialize(self):
                     )
 
             # The TRRTrajectoryFile object returns ints for these values, so turn them into bools
-            self._read_velocities, self._read_forces = bool(
-                self._read_velocities
-            ), bool(self._read_forces)
+            self._read_velocities, self._read_forces = (
+                bool(self._read_velocities),
+                bool(self._read_forces),
+            )
 
             if self._read_velocities:
                 data_to_be_written.append("velocities")

MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py

@@ -40,7 +40,6 @@ class LAMMPSTrajectoryFileError(Error):
 
 
 class LAMMPSReader:
-
     def __init__(self, *args, **kwargs):
         self._units = kwargs.get("lammps_units", "real")
         self._timestep = kwargs.get("timestep", 1.0)
@@ -116,7 +115,6 @@ def set_units(self, lammps_units):
 
 
 class LAMMPScustom(LAMMPSReader):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
@@ -135,7 +133,6 @@ def open_file(self, filename: str):
         self._start = 0
 
     def parse_first_step(self, aliases, config):
-
         self._itemsPosition = collections.OrderedDict()
 
         comp = -1
@@ -387,7 +384,6 @@ def run_step(self, index):
 
 
 class LAMMPSxyz(LAMMPSReader):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._full_cell = None
@@ -406,7 +402,6 @@ def open_file(self, filename: str):
         self._file = open(filename, "r")
 
     def read_any_step(self):
-
         line = self._file.readline()
         number_of_atoms = int(line)
         line = self._file.readline()
@@ -416,7 +411,6 @@ def read_any_step(self):
         atom_types = np.empty(number_of_atoms, dtype=int)
 
         for at_num in range(number_of_atoms):
-
             line = self._file.readline()
 
             if not line:
@@ -433,7 +427,6 @@ def read_any_step(self):
         return timestep, atom_types, positions
 
     def parse_first_step(self, aliases, config):
-
         _, atom_types, positions = self.read_any_step()
 
         self._nAtoms = len(atom_types)
@@ -527,7 +520,6 @@ def run_step(self, index):
 
 
 class LAMMPSh5md(LAMMPSReader):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._charges_fixed = None
@@ -544,7 +536,6 @@ def open_file(self, filename: str):
         self._file = h5py.File(filename, "r")
 
     def parse_first_step(self, aliases, config):
-
         try:
             atom_types = self._file["/particles/all/species/value"][0]
         except KeyError:

MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py

@@ -108,7 +108,7 @@ def initialize(self):
                 *coord_files,
                 continuous=self.configuration["continuous"]["value"],
                 format=coord_format,
-                topology_format=self.configuration["topology_file"]["format"]
+                topology_format=self.configuration["topology_file"]["format"],
             )
         else:
             coord_files = [(i, coord_format) for i in coord_files]
@@ -176,7 +176,7 @@ def initialize(self):
             self.configuration["output_files"]["file"],
             self._chemical_system,
             self.numberOfSteps,
-            **kwargs
+            **kwargs,
         )
         super().initialize()
 

MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py

@@ -156,7 +156,7 @@ def initialize(self):
             self.configuration["output_files"]["file"],
             self._chemical_system,
             self.numberOfSteps,
-            **kwargs
+            **kwargs,
         )
         super().initialize()
 

MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -98,8 +98,7 @@ def initialize(self):
         )
         if self._nMolecules == 0:
             raise AreaPerMoleculeError(
-                "No molecule matches "
-                f"{self.configuration['molecule_name']['value']!r} name."
+                f"No molecule matches {self.configuration['molecule_name']['value']!r} name."
             )
 
         self._outputData.add(