Apply ruff unsafe fixes

Author: ElliottKasoar

abcd/__init__.py

@@ -60,11 +60,3 @@ def from_url(cls, url, **kwargs):
     url = "mongodb://mongoadmin:secret@localhost:27017/abcd_new"
     abcd = ABCD.from_url(url)
     abcd.print_info()
-
-    # from ase.io import iread
-    # for atoms in iread('../tutorials/data/bcc_bulk_54_expanded_2_high.xyz', index=slice(1)):
-    #     # Hack to fix the representation of forces
-    #     atoms.calc.results['forces'] = atoms.arrays['force']
-    #
-    #     abcd.push(atoms)
-    #     print(atoms)

abcd/backends/atoms_http.py

@@ -1,7 +1,6 @@
 import json
 import logging
 from os import linesep
-from typing import List
 
 import ase
 import requests
@@ -45,14 +44,12 @@ def pull(self, query=None, properties=None):
     def query(self, query_string):
         pass
 
-    def search(self, query_string: str) -> List[str]:
-        results = requests.get(self.url + "/calculation").json()
-        return results
+    def search(self, query_string: str) -> list[str]:
+        return requests.get(self.url + "/calculation").json()
 
     def get_atoms(self, id: str) -> Atoms:
         data = requests.get(self.url + f"/calculation/{id}").json()
-        atoms = Atoms.from_dict(data)
-        return atoms
+        return Atoms.from_dict(data)
 
     def __repr__(self):
         return f"ABCD(type={self.__class__.__name__}, url={self.url}, ...)"

abcd/backends/atoms_pymongo.py

@@ -161,7 +161,7 @@ def __init__(
         collection_name="atoms",
         username=None,
         password=None,
-        authSource="admin",
+        auth_source="admin",
         uri_mode=False,
         **kwargs,
     ):
@@ -175,31 +175,31 @@ def __init__(
                 collection_name,
                 username,
                 password,
-                authSource,
+                auth_source,
                 kwargs,
             )
         )
 
         if uri_mode:
-            self.client = MongoClient(host=host, authSource=authSource)
+            self.client = MongoClient(host=host, authSource=auth_source)
         else:
             self.client = MongoClient(
                 host=host,
                 port=port,
                 username=username,
                 password=password,
-                authSource=authSource,
+                authSource=auth_source,
             )
 
         try:
             info = self.client.server_info()  # Forces a call.
             logger.info(f"DB info: {info}")
 
-        except pymongo.errors.OperationFailure:
-            raise abcd.errors.AuthenticationError()
+        except pymongo.errors.OperationFailure as err:
+            raise abcd.errors.AuthenticationError() from err
 
-        except pymongo.errors.ServerSelectionTimeoutError:
-            raise abcd.errors.TimeoutError()
+        except pymongo.errors.ServerSelectionTimeoutError as err:
+            raise abcd.errors.TimeoutError() from err
 
         self.db = self.client[db_name]
         self.collection = self.db[collection_name]
@@ -258,8 +258,7 @@ def upload(self, file: Path, extra_infos=None, store_calc=True):
     def get_items(self, query=None):
         # TODO: better method for aggregations
         query = parser(query)
-        for dct in self.db.atoms.find(query):
-            yield dct
+        yield from self.db.atoms.find(query)
 
     def get_atoms(self, query=None):
         query = parser(query)
@@ -320,18 +319,18 @@ def properties(self, query=None):
         return properties
 
     def get_type_of_property(self, prop, category):
-        # TODO: Probably it would be nicer to store the type info in the database from the beginning.
+        # TODO: Store the type info in the database from the beginning?
         atoms = self.db.atoms.find_one({prop: {"$exists": True}})
         data = atoms[prop]
 
         if category == "arrays":
-            if type(data[0]) == list:
+            if isinstance(data[0], list):
                 return f"array({map_types[type(data[0][0])]}, N x {len(data[0])})"
             return f"vector({map_types[type(data[0])]}, N)"
 
-        if type(data) == list:
-            if type(data[0]) == list:
-                if type(data[0][0]) == list:
+        if isinstance(data, list):
+            if isinstance(data[0], list):
+                if isinstance(data[0][0], list):
                     return "list(list(...)"
                 return f"array({map_types[type(data[0][0])]})"
             return f"vector({map_types[type(data[0])]})"
@@ -397,7 +396,8 @@ def add_property(self, data, query=None):
 
     def rename_property(self, name, new_name, query=None):
         logger.info(f"rename: query={query}, old={name}, new={new_name}")
-        # TODO name in derived.info_keys OR name in derived.arrays_keys OR name in derived.derived_keys
+        # TODO name in derived.info_keys OR name in derived.arrays_keys
+        # OR name in derived.derived_keys
         self.collection.update_many(
             parser(query), {"$push": {"derived.info_keys": new_name}}
         )
@@ -407,15 +407,6 @@ def rename_property(self, name, new_name, query=None):
             {"$pull": {"derived.info_keys": name}, "$rename": {name: new_name}},
         )
 
-        # self.collection.update_many(
-        #     parser(query + ['arrays.{}'.format(name)]),
-        #     {'$push': {'derived.arrays_keys': new_name}})
-        #
-        # self.collection.update_many(
-        #     parser(query + ['arrays.{}'.format(name)]),
-        #     {'$pull': {'derived.arrays_keys': name},
-        #      '$rename': {'arrays.{}'.format(name): 'arrays.{}'.format(new_name)}})
-
     def delete_property(self, name, query=None):
         logger.info(f"delete: query={name}, porperty={query}")
 
@@ -435,7 +426,7 @@ def exec(self, code, query=None):
         # TODO: Separate python environment with its own packages loaded
 
         for dct in self.get_items(query):
-            atoms = AtomsModel(self.collection, dct)
+            AtomsModel(self.collection, dct)
             exec(code)
 
     def __repr__(self):
@@ -483,30 +474,30 @@ def histogram(name, data, **kwargs):
             print(f"Mixed type error of the {name} property!")
             return None
 
-        if ptype == float:
+        if isinstance(data[0], float):
             bins = kwargs.get("bins", 10)
             return _hist_float(name, data, bins)
 
-        if ptype == int:
+        if isinstance(data[0], int):
             bins = kwargs.get("bins", 10)
             return _hist_int(name, data, bins)
 
-        if ptype == str:
+        if isinstance(data[0], str):
             return _hist_str(name, data, **kwargs)
 
-        if ptype == datetime:
+        if isinstance(data[0], datetime):
             bins = kwargs.get("bins", 10)
             return _hist_date(name, data, bins)
 
         print(f"{name}: Histogram for list of {type(data[0])} types are not supported!")
         logger.info(
             f"{name}: Histogram for list of {type(data[0])} types are not supported!"
         )
-
-    else:
-        logger.info(f"{name}: Histogram for {type(data)} types are not supported!")
         return None
 
+    logger.info(f"{name}: Histogram for {type(data)} types are not supported!")
+    return None
+
 
 def _hist_float(name, data, bins=10):
     data = np.array(data)
@@ -596,39 +587,7 @@ def _hist_str(name, data, bins=10, truncate=20):
 
 
 if __name__ == "__main__":
-    # import json
-    # from ase.io import iread
-    # from pprint import pprint
-    # from server.styles.myjson import JSONEncoderOld, JSONDecoderOld, JSONEncoder
-
-    print("hello")
     db = MongoDatabase(username="mongoadmin", password="secret")
     print(db.info())
     print(db.count())
-
     print(db.hist("uploaded"))
-
-    # for atoms in iread('../../tutorials/data/bcc_bulk_54_expanded_2_high.xyz', index=slice(None)):
-    #     # print(at)
-    #     atoms.calc.results['forces'] = atoms.arrays['force']
-    #     # at.arrays['force'] = None
-    #
-    #     json_data = json.dumps(atoms, cls=JSONEncoderOld)
-    #     print(json_data)
-    #
-    #     atom_dict = json.loads(json_data, cls=JSONDecoderOld)
-    #     print(atom_dict)
-    #
-    #     print(atoms == atom_dict)
-    #
-    # with JSONEncoder() as encoder:
-    #     data = encoder.encode(atoms)
-    #
-    # print(data)
-    #
-    # with DictEncoder() as encoder:
-    #     data = encoder.encode(atoms)
-    #
-    # pprint(data)
-    #
-    # db.collection.insert_one(DictEncoder().encode(atoms))

abcd/database.py

@@ -1,4 +1,5 @@
-from abc import ABCMeta, abstractmethod
+# ruff: noqa: B024, B027
+from abc import ABCMeta
 import logging
 
 logger = logging.getLogger(__name__)
@@ -7,7 +8,6 @@
 class AbstractABCD(metaclass=ABCMeta):
     """Factory method"""
 
-    @abstractmethod
     def __init__(self):
         pass
 

abcd/frontends/commandline/commands.py

@@ -218,7 +218,8 @@ def key_delete(*, db, query, yes, keys, **kwargs):
 
     if not yes:
         print(
-            f"Please use --yes for deleting keys from {db.count(query=query)} configurations"
+            f"Please use --yes for deleting keys from {db.count(query=query)} "
+            "configurations"
         )
         exit(1)
 
@@ -232,7 +233,8 @@ def key_delete(*, db, query, yes, keys, **kwargs):
 def execute(*, db, query, yes, python_code, **kwargs):
     if not yes:
         print(
-            f"Please use --yes for executing code on {db.count(query=query)} configurations"
+            f"Please use --yes for executing code on {db.count(query=query)} "
+            "configurations"
         )
         exit(1)
 
@@ -258,16 +260,14 @@ def server(*, abcd_url, url, api_only, **kwargs):
 
 
 class Formater:
-    partialBlocks = ["▏", "▎", "▍", "▌", "▋", "▊", "▉", "█"]  # char=pb
-
     def title(self, title):
         print("", title, "=" * len(title), sep=os.linesep)
 
     def describe(self, data):
         if data["type"] == "hist_float":
             print(
-                "{}  count: {} min: {:11.4e} med: {:11.4e} max: {:11.4e} std: {:11.4e} var:{"
-                ":11.4e}".format(
+                "{}  count: {} min: {:11.4e} med: {:11.4e} max: {:11.4e} std: {:11.4e} "
+                "var:{:11.4e}".format(
                     data["name"],
                     sum(data["counts"]),
                     data["min"],

abcd/frontends/commandline/config.py

@@ -32,9 +32,7 @@ def load(cls):
 
         logger.info(f"Using config file: {file}")
 
-        config = cls.from_json(file)
-
-        return config
+        return cls.from_json(file)
 
     def save(self):
         file = (

abcd/frontends/commandline/parser.py

@@ -234,20 +234,4 @@ def main(args=None):
 if __name__ == "__main__":
     main(["summary"])
     main("delete-key -q pbc pbc".split())
-    # main('upload -e cas -i ../../../tutorials/GB_alphaFe_001/tilt/00110391110_v6bxv2_tv0.4bxv0.2_d1.6z_traj.xyz'.split())
-    # main('summary -q formula~"Si2"'.split())
-    # main('upload -e cas -i ../../../tutorials/GB_alphaFe_001/tilt/00110391110_v6bxv2_tv0.4bxv0.2_d1.6z_traj.xyz'.split())
-    # main('-v login mongodb://mongoadmin:secret@localhost:27017/abcd'.split())
-    # main('-v summary'.split())
-    # main('-v summary -p energy'.split())
-    # main('-v summary -p *'.split())
-    # main('add-key -q cas selected user="cas"'.split())
     main("delete-key user".split())
-    # main(['summary', '-p', '*'])
-    # main(['summary', '-p', 'info.config_name, info.energy'])
-    # main(['summary', '-p', 'info.config_name, info.energy,info.energy;info.energy info.energy'])
-    # main(['-s', 'fancy', 'summary', '-p', '*'])
-    # main(['summary', '-p', '*'])
-    # main(['-s', 'fancy', 'summary'])
-    # main(['-v', 'summary', '-p', 'config_type', '-p', 'haha', '-p' 'sdgsdg, dsgsdg,asd fgg', '-q', 'config_type~bcc',
-    #      '-q', 'config_type~bcc'])

abcd/model.py

@@ -86,7 +86,9 @@ def __getitem__(self, key):
 
     def __setitem__(self, key, value):
         if key == "derived":
-            # raise KeyError('Please do not use "derived" as key because it is protected!')
+            # raise KeyError(
+            #     'Please do not use "derived" as key because it is protected!'
+            # )
             # Silent return to avoid raising error in pymongo package
             return
 
@@ -96,7 +98,8 @@ def __setitem__(self, key, value):
         super().__setitem__(key, value)
 
     def convert(self, value):
-        # TODO: https://api.mongodb.com/python/current/api/bson/index.html using type_registry
+        # TODO: https://api.mongodb.com/python/current/api/bson/index.html
+        # using type_registry
 
         if isinstance(value, np.int64):
             return int(value)
@@ -105,7 +108,9 @@ def convert(self, value):
 
     def update_key_category(self, key, value):
         if key == "_id":
-            # raise KeyError('Please do not use "derived" as key because it is protected!')
+            # raise KeyError(
+            #     'Please do not use "derived" as key because it is protected!'
+            # )
             return
 
         for category in ("arrays_keys", "info_keys", "results_keys", "derived_keys"):
@@ -136,8 +141,7 @@ def __delitem__(self, key):
         super().__delitem__(key)
 
     def __iter__(self):
-        for item in super().__iter__():
-            yield item
+        yield from super().__iter__()
         yield "derived"
 
     @classmethod
@@ -319,14 +323,3 @@ def pre_save(self):
 
     model = AbstractModel.from_atoms(atoms)
     print(model.to_ase())
-
-    # xyz = io.StringIO(
-    #     """
-    #     2
-    #     Properties=species:S:1:pos:R:3 s="sadf" _vtk_test="t e s t _ s t r" pbc="F F F"
-    #     Si       0.00000000       0.00000000       0.00000000
-    #     Si       0.00000000       0.00000000       0.00000000
-    #
-    #     """)
-    #
-    # atoms = read(xyz, format='extxyz', index=0)