Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in…

…to maciej/reactivate-atom-trace

.github/workflows/black.yml → .github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Black
+name: Lint
 
 on:
   push:
@@ -16,6 +16,15 @@ jobs:
           options: "--check --verbose"
           src: "MDANSE/Src"
 
+  lint_check_ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+        with:
+          src: "./MDANSE/Src"
+          args: "check"
+
   lint-mdanse-gui:
     runs-on: ubuntu-latest
     steps:
@@ -24,3 +33,12 @@ jobs:
         with:
           options: "--check --verbose"
           src: "MDANSE_GUI/Src"
+
+  lint_check_ruff_gui:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+        with:
+          src: "./MDANSE_GUI/Src"
+          args: "check"

MDANSE/Src/MDANSE/Chemistry/Databases.py

@@ -215,7 +215,7 @@ def __getitem__(self, item: str) -> dict:
             return copy.deepcopy(self._data[item])
         except KeyError:
             raise AtomsDatabaseError(
-                "The element {} is not registered in the database.".format(item)
+                f"The element {item} is not registered in the database."
             )
 
     def _load(self, user_database: str = None, default_database: str = None) -> None:
@@ -253,7 +253,7 @@ def add_atom(self, atom: str) -> None:
 
         if atom in self._data:
             raise AtomsDatabaseError(
-                "The atom {} is already stored in the database".format(atom)
+                f"The atom {atom} is already stored in the database"
             )
 
         self._data[atom] = {}
@@ -272,11 +272,11 @@ def add_property(self, pname: str, ptype: str) -> None:
 
         if pname in self._properties:
             raise AtomsDatabaseError(
-                "The property {} is already registered in the database.".format(pname)
+                f"The property {pname} is already registered in the database."
             )
 
         if ptype not in AtomsDatabase._TYPES:
-            raise AtomsDatabaseError("The property type {} is unknown".format(ptype))
+            raise AtomsDatabaseError(f"The property type {ptype} is unknown")
 
         self._properties[pname] = ptype
         ptype = AtomsDatabase._TYPES[ptype]
@@ -307,7 +307,7 @@ def get_isotopes(self, atom: str) -> list[str]:
         """
 
         if atom not in self._data:
-            raise AtomsDatabaseError("The atom {} is unknown".format(atom))
+            raise AtomsDatabaseError(f"The atom {atom} is unknown")
 
         # The isotopes are searched according to |symbol| property
         symbol = self._data[atom]["symbol"]
@@ -340,7 +340,7 @@ def get_property(self, pname: str) -> dict[str, Union[str, int, float, list]]:
 
         if pname not in self._properties:
             raise AtomsDatabaseError(
-                "The property {} is not registered in the database".format(pname)
+                f"The property {pname} is not registered in the database"
             )
 
         ptype = AtomsDatabase._TYPES[self._properties[pname]]
@@ -365,11 +365,11 @@ def get_value(self, atom: str, pname: str) -> Union[str, int, float, list]:
         """
 
         if atom not in self._data:
-            raise AtomsDatabaseError("The atom {} is unknown".format(atom))
+            raise AtomsDatabaseError(f"The atom {atom} is unknown")
 
         if pname not in self._properties:
             raise AtomsDatabaseError(
-                "The property {} is not registered in the database".format(pname)
+                f"The property {pname} is not registered in the database"
             )
 
         ptype = self._properties[pname]
@@ -397,12 +397,12 @@ def get_values_for_multiple_atoms(
 
         if not all(atom in self._data for atom in atoms):
             raise AtomsDatabaseError(
-                "One or more of the provided atoms {} are unknown".format(atoms)
+                f"One or more of the provided atoms {atoms} are unknown"
             )
 
         if prop not in self._properties:
             raise AtomsDatabaseError(
-                "The property {} is not registered in the database".format(prop)
+                f"The property {prop} is not registered in the database"
             )
 
         values = {name: self._data[name][prop] for name in unique_atoms}
@@ -425,11 +425,11 @@ def set_value(
         """
 
         if atom not in self._data:
-            raise AtomsDatabaseError("The element {} is unknown".format(atom))
+            raise AtomsDatabaseError(f"The element {atom} is unknown")
 
         if pname not in self._properties:
             raise AtomsDatabaseError(
-                "The property {} is not registered in the database".format(pname)
+                f"The property {pname} is not registered in the database"
             )
 
         try:
@@ -438,7 +438,7 @@ def set_value(
             )
         except ValueError:
             raise AtomsDatabaseError(
-                "Can not coerce {} to {} type".format(value, self._properties[pname])
+                f"Can not coerce {value} to {self._properties[pname]} type"
             )
 
     def has_atom(self, atom: str) -> bool:
@@ -480,19 +480,18 @@ def info(self, atom: str) -> str:
 
         # A delimiter line.
         delimiter = "-" * 70
+        tab_fmt = " {:<20}{!s:>50}"
 
         info = [
             delimiter,
-            "%s" % atom.center(70),
-            "%s" % " {0:<20}{1:>50}".format("property", "value"),
+            f"{atom:^70}",
+            tab_fmt.format("property", "value"),
             delimiter,
         ]
 
         # The values for all element's properties
         for pname in sorted(self._properties):
-            info.append(
-                " {0:<20}{1:>50}".format(pname, str(self._data[atom].get(pname, None)))
-            )
+            info.append(tab_fmt.format(pname, self._data[atom].get(pname, None)))
 
         info.append(delimiter)
         info = "\n".join(info)
@@ -525,7 +524,7 @@ def match_numeric_property(
                 )
         except KeyError:
             raise AtomsDatabaseError(
-                "The property {} is not registered in the database".format(pname)
+                f"The property {pname} is not registered in the database"
             )
 
         tolerance = abs(tolerance)

MDANSE/Src/MDANSE/Core/SubclassFactory.py

@@ -90,7 +90,7 @@ def recursive_keys(parent_class: type) -> list:
     """
     try:
         results = parent_class.subclasses()
-    except:
+    except Exception:
         return []
     else:
         for child in parent_class.subclasses():
@@ -117,7 +117,7 @@ def recursive_dict(parent_class: type) -> dict:
             ckey: parent_class._registered_subclasses[ckey]
             for ckey in parent_class.subclasses()
         }
-    except:
+    except Exception:
         return {}
     else:
         for child in parent_class.subclasses():

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

@@ -37,7 +37,7 @@ def __init__(self, atm_label: str, **kwargs):
         # methods as of writing e.g. re.sub
         translation = str.maketrans("", "", ";=")
         self.atm_label = atm_label.translate(translation)
-        self.grp_label = f""
+        self.grp_label = ""
         if kwargs:
             for k, v in kwargs.items():
                 self.grp_label += f"{k}={str(v).translate(translation)};"

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

@@ -13,15 +13,31 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-import json
 import copy
+import json
 from typing import Union
+
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 from MDANSE.Framework.AtomSelector.all_selector import select_all
-from MDANSE.Framework.AtomSelector.atom_selectors import *
-from MDANSE.Framework.AtomSelector.group_selectors import *
-from MDANSE.Framework.AtomSelector.molecule_selectors import *
+from MDANSE.Framework.AtomSelector.atom_selectors import (
+    select_atom_fullname,
+    select_atom_name,
+    select_dummy,
+    select_element,
+    select_hs_on_element,
+    select_hs_on_heteroatom,
+    select_index,
+)
+from MDANSE.Framework.AtomSelector.group_selectors import (
+    select_hydroxy,
+    select_methyl,
+    select_phosphate,
+    select_primary_amine,
+    select_sulphate,
+    select_thiol,
+)
+from MDANSE.Framework.AtomSelector.molecule_selectors import select_water
 
 
 class Selector:

MDANSE/Src/MDANSE/Framework/Configurable.py

@@ -31,14 +31,14 @@ class ConfigurationError(Error):
 class Configurable(object):
     """
     This class allows any object that derives from it to be configurable within the MDANSE framework.
-    
+
     Within that framework, to be configurable, a class must:
         #. derive from this class
         #. implement the "configurators"  class attribute as a list of 3-tuple whose:
             #.. 0-value is the type of the configurator that will be used to fetch the corresponding \
             MDANSE.Framework.Configurators.IConfigurator.IConfigurator derived class from the configurators registry
             #.. 1-value is the name of the configurator that will be used as the key of the _configuration attribute.
-            #.. 2-value is the dictionary of the keywords used when initializing the configurator.  
+            #.. 2-value is the dictionary of the keywords used when initializing the configurator.
     """
 
     enabled = True
@@ -93,8 +93,8 @@ def build_configuration(self):
                     typ, name, configurable=self, **kwds
                 )
             # Any kind of error has to be caught
-            except:
-                raise ConfigurationError("Could not set %r configuration item" % name)
+            except Exception:
+                raise ConfigurationError(f"Could not set {name!r} configuration item")
 
     def set_settings(self, settings):
         self.settings = settings
@@ -228,10 +228,10 @@ def build_doc_example(cls):
         docstring += ">>> \n"
         docstring += ">>> \n"
         docstring += ">>> parameters = {}\n"
-        for k, v in list(cls.get_default_parameters().items()):
-            docstring += ">>> parameters[%r]=%r\n" % (k, v)
+        for k, v in cls.get_default_parameters().items():
+            docstring += f">>> parameters[{k!r}]={v!r}\n"
         docstring += ">>> \n"
-        docstring += ">>> job = IJob.create(%r)\n" % cls.__name__
+        docstring += f">>> job = IJob.create({cls.__name__!r})\n"
         docstring += ">>> job.setup(parameters)\n"
         docstring += ">>> job.run()\n"
         return docstring
@@ -249,53 +249,25 @@ def build_doc_texttable(cls, doclist):
             sizes[1] = max(sizes[1], len(v["Default value"]))
             # Case of Description field: has to be splitted and parsed for inserting sphinx "|" keyword for multiline
             v["Description"] = v["Description"].strip()
-            v["Description"] = v["Description"].split("\n")
+            v["Description"] = v["Description"].splitlines()
             v["Description"] = ["| " + vv.strip() for vv in v["Description"]]
-            sizes[2] = max(sizes[2], max([len(d) for d in v["Description"]]))
-
-        docstring += "+%s+%s+%s+\n" % (
-            "-" * (sizes[0] + 1),
-            "-" * (sizes[1] + 1),
-            "-" * (sizes[2] + 1),
-        )
-        docstring += "| %-*s| %-*s| %-*s|\n" % (
-            sizes[0],
-            columns[0],
-            sizes[1],
-            columns[1],
-            sizes[2],
-            columns[2],
-        )
-        docstring += "+%s+%s+%s+\n" % (
-            "=" * (sizes[0] + 1),
-            "=" * (sizes[1] + 1),
-            "=" * (sizes[2] + 1),
-        )
+            sizes[2] = max(sizes[2], max(map(len, v["Description"])))
+
+        data_line = "| " + "| ".join(f"{{}}:<{size}" for size in sizes) + "|\n"
+        sep_line = "+" + "+".join("-" * (size + 1) for size in sizes) + "+\n"
+
+        docstring += sep_line
+        docstring += data_line.format(*columns)
+        docstring += sep_line.replace("-", "=")
 
         for v in doclist:
-            docstring += "| %-*s| %-*s| %-*s|\n" % (
-                sizes[0],
-                v["Configurator"],
-                sizes[1],
-                v["Default value"],
-                sizes[2],
-                v["Description"][0],
+            docstring += data_line.format(
+                v["Configurator"], v["Default value"], v["Description"][0]
             )
             if len(v["Description"]) > 1:
                 for descr in v["Description"][1:]:
-                    docstring += "| %-*s| %-*s| %-*s|\n" % (
-                        sizes[0],
-                        "",
-                        sizes[1],
-                        "",
-                        sizes[2],
-                        descr,
-                    )
-            docstring += "+%s+%s+%s+\n" % (
-                "-" * (sizes[0] + 1),
-                "-" * (sizes[1] + 1),
-                "-" * (sizes[2] + 1),
-            )
+                    data_line.format("", "", descr)
+            docstring += sep_line
 
         docstring += "\n"
         return docstring

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

@@ -31,7 +31,7 @@ def parse(self):
 
         try:
             self._input = ASETrajectory(self["filename"])
-        except:
+        except Exception:
             self._input = iread(self["filename"], index="[:]")
             first_frame = read(self["filename"], index=0)
         else:

MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py

@@ -70,7 +70,7 @@ def configure(self, values):
         if file_format == "guess":
             file_format = None
 
-        if file_format is not None and not file_format in self._allowed_formats:
+        if file_format is not None and file_format not in self._allowed_formats:
             LOG.error(f"WRONG FORMAT in {self._name}")
             self.error_status = f"The ASE file format {file_format} is not supported"
             return
@@ -99,10 +99,10 @@ def get_information(self):
         :rtype: str
         """
         try:
-            val = self["value"]
+            self["value"]
         except KeyError:
             result = f"No VALUE in {self._name}"
             LOG.error(result)
             return result
         else:
-            return "Input file: %r\n" % self["value"]
+            return f"Input file: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -127,8 +127,8 @@ def get_information(self) -> str:
             return "Not configured yet\n"
 
         info = []
-        info.append("Number of selected atoms:%d" % self["selection_length"])
-        info.append("Selected elements:%s" % self["unique_names"])
+        info.append(f"Number of selected atoms:{self['selection_length']:d}")
+        info.append(f"Selected elements:{self['unique_names']}")
 
         return "\n".join(info) + "\n"
 

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

@@ -203,7 +203,7 @@ def get_information(self) -> str:
         if self["value"] is None:
             return "No atoms selected for transmutation\n"
 
-        return "Number of transmuted atoms:%d\n" % self._nTransmutedAtoms
+        return f"Number of transmuted atoms:{self._nTransmutedAtoms:d}\n"
 
     def get_transmuter(self) -> AtomTransmuter:
         """