MAINT: Linting

src/caosadvancedtools/scifolder/analysis_cfood.py

@@ -41,6 +41,9 @@ class AnalysisCFood(AbstractFileCFood, WithREADME):
     def __init__(self,  *args, **kwargs):
         super().__init__(*args, **kwargs)
         WithREADME.__init__(self)
+        self.analysis = None
+        self.people = None
+        self.project = None
 
     def collect_information(self):
         self.find_referenced_files([RESULTS, SOURCES, SCRIPTS])

src/caosadvancedtools/scifolder/simulation_cfood.py

@@ -16,17 +16,14 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-import os
-from itertools import chain
-
 import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
+from caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_has_property,
-                                     assure_object_is_in_list, get_entity)
-from caosadvancedtools.read_md_header import get_header
+                                     assure_object_is_in_list,
+                                     )
 
 from .generic_pattern import full_pattern
-from .utils import (get_files_referenced_by_field, parse_responsibles,
+from .utils import (parse_responsibles,
                     reference_records_corresponding_to_files)
 from .withreadme import DATAMODEL as dm
 from .withreadme import (RESULTS, REVISIONOF, SCRIPTS, SOURCES, WithREADME,
@@ -42,6 +39,9 @@ class SimulationCFood(AbstractFileCFood, WithREADME):
     def __init__(self,  *args, **kwargs):
         super().__init__(*args, **kwargs)
         WithREADME.__init__(self)
+        self.people = None
+        self.project = None
+        self.simulation = None
 
     def collect_information(self):
         self.find_referenced_files([RESULTS, SOURCES, SCRIPTS])

src/caosadvancedtools/scifolder/software_cfood.py

@@ -17,20 +17,16 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-import os
-from itertools import chain
-
 import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_parent,
+from caosadvancedtools.cfood import (AbstractFileCFood,
                                      assure_has_property, assure_name_is,
-                                     assure_object_is_in_list, get_entity)
+                                     assure_object_is_in_list,
+                                     )
 from caosadvancedtools.guard import global_guard as guard
-from caosadvancedtools.read_md_header import get_header
 
 from .generic_pattern import full_pattern
-from .utils import get_files_referenced_by_field, parse_responsibles
+from .utils import parse_responsibles
 from .withreadme import BINARIES
-from .withreadme import DATAMODEL as dm
 from .withreadme import SOURCECODE, WithREADME
 
 

src/caosadvancedtools/scifolder/utils.py

@@ -26,7 +26,6 @@ import pandas as pd
 from caosadvancedtools.cfood import assure_object_is_in_list, fileguide
 from caosadvancedtools.utils import (find_records_that_reference_ids,
                                      read_field_as_list,
-                                     return_field_or_property,
                                      string_to_person)
 
 logger = logging.getLogger("caosadvancedtools")

src/caosadvancedtools/scifolder/withreadme.py

@@ -26,8 +26,7 @@ import caosdb as db
 from caosadvancedtools.cfood import (assure_has_description, assure_has_parent,
                                      assure_object_is_in_list, fileguide)
 from caosadvancedtools.read_md_header import get_header as get_md_header
-from caosadvancedtools.table_importer import (win_path_converter,
-                                              win_path_list_converter)
+from caosadvancedtools.table_importer import (win_path_converter)
 from caosadvancedtools.utils import return_field_or_property
 
 from .utils import (get_entity_ids_from_include_file,
@@ -236,7 +235,7 @@ class WithREADME(object):
                     generic_references,
                     record,
                     prop_name,
-                    to_be_updated=self.to_be_updated,
+                    to_be_updated=self.to_be_updated,  # pylint: disable=no-member
                     datatype=db.LIST(db.REFERENCE),
                 )
 

src/caosadvancedtools/serverside/helper.py

@@ -223,6 +223,7 @@ def init_data_model(entities):
                         "be a {}.".format(e.role, local_role))
                 raise DataModelError(e.name, info)
     except db.exceptions.EntityDoesNotExistError:
+        # pylint: disable=raise-missing-from
         raise DataModelError(e.name, "This entity does not exist.")
 
     return True
@@ -246,7 +247,7 @@ def get_data(filename, default=None):
         Data from the given file.
     """
     result = default.copy() if default is not None else {}
-    with open(filename, 'r') as fi:
+    with open(filename, mode="r", encoding="utf-8") as fi:
         data = json.load(fi)
     result.update(data)
 

src/caosadvancedtools/table_json_conversion/table_generator.py

@@ -269,8 +269,8 @@ class TableTemplateGenerator(ABC):
 class XLSXTemplateGenerator(TableTemplateGenerator):
     """Class for generating XLSX tables from json schema definitions."""
 
-    def __init__(self):
-        pass
+    # def __init__(self):
+    #     super().__init__()
 
     def generate(self, schema: dict, foreign_keys: dict, filepath: str) -> None:
         """Generate a sheet definition from a given JSON schema.