MAINT: Linting

src/caosadvancedtools/converter/labfolder_export.py

@@ -22,17 +22,7 @@
 """ Imports labfolder exports """
 
 import os
-import re
-import shutil
-import subprocess
-import sys
-import tempfile
-import time
-import warnings
-from io import BytesIO, StringIO
-
-import requests
-import yaml
+
 from bs4 import BeautifulSoup
 
 import caosdb as db
@@ -73,8 +63,8 @@ def get_author_from_entry(entry):
 def val_or_none(stuff):
     if len(stuff) == 0:
         return None
-    else:
-        return stuff[0].getText()
+
+    return stuff[0].getText()
 
 
 def add_property_from_data_element(dbrecord, element):

src/caosadvancedtools/scifolder/experiment_cfood.py

@@ -17,15 +17,15 @@
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
 import caosdb as db
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
-                                     assure_has_parent, assure_has_property,
-                                     assure_object_is_in_list, get_entity)
-from caosadvancedtools.read_md_header import get_header
+from caosadvancedtools.cfood import (AbstractFileCFood,
+                                     assure_has_property,
+                                     assure_object_is_in_list,
+                                     )
 
 from .generic_pattern import full_pattern
 from .utils import parse_responsibles, reference_records_corresponding_to_files
 from .withreadme import DATAMODEL as dm
-from .withreadme import RESULTS, REVISIONOF, SCRIPTS, WithREADME, get_glob
+from .withreadme import RESULTS, REVISIONOF, WithREADME, get_glob
 
 
 class ExperimentCFood(AbstractFileCFood, WithREADME):
@@ -42,7 +42,10 @@ class ExperimentCFood(AbstractFileCFood, WithREADME):
         super().__init__(*args, **kwargs)
         WithREADME.__init__(self)
 
-        self.name_map = {},
+        self.name_map = ({}, )
+        self.experiment = None
+        self.people = None
+        self.project = None
 
     @staticmethod
     def get_re():

src/caosadvancedtools/scifolder/publication_cfood.py

@@ -16,18 +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_object_is_in_list, fileguide,
-                                     get_entity)
+                                     )
 from caosadvancedtools.read_md_header import get_header
-from caosadvancedtools.utils import find_records_that_reference_ids
 
 from .generic_pattern import date_suffix_pattern, readme_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,
@@ -37,16 +33,15 @@ from .withreadme import (RESULTS, REVISIONOF, SCRIPTS, SOURCES, WithREADME,
 def folder_to_type(name):
     if name == "Theses":
         return "Thesis"
-    elif name == "Articles":
+    if name == "Articles":
         return "Article"
-    elif name == "Posters":
+    if name == "Posters":
         return "Poster"
-    elif name == "Presentations":
+    if name == "Presentations":
         return "Presentation"
-    elif name == "Reports":
+    if name == "Reports":
         return "Report"
-    else:
-        raise ValueError()
+    raise ValueError()
 
 
 class PublicationCFood(AbstractFileCFood, WithREADME):
@@ -58,6 +53,8 @@ class PublicationCFood(AbstractFileCFood, WithREADME):
     def __init__(self,  *args, **kwargs):
         super().__init__(*args, **kwargs)
         WithREADME.__init__(self)
+        self.people = None
+        self.publication = None
 
     def collect_information(self):
         self.find_referenced_files([RESULTS, SOURCES, SCRIPTS])

src/caosadvancedtools/scifolder/result_table_cfood.py

@@ -20,17 +20,12 @@ import re
 
 import caosdb as db
 import pandas as pd
-from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
-                                     assure_has_parent, assure_has_property,
-                                     assure_object_is_in_list, get_entity)
-from caosadvancedtools.read_md_header import get_header
+from caosadvancedtools.cfood import (AbstractFileCFood,
+                                     )
 
 from ..cfood import assure_property_is, fileguide
 from .experiment_cfood import ExperimentCFood
 from .generic_pattern import date_pattern, date_suffix_pattern, project_pattern
-from .utils import parse_responsibles, reference_records_corresponding_to_files
-from .withreadme import DATAMODEL as dm
-from .withreadme import RESULTS, REVISIONOF, SCRIPTS, WithREADME, get_glob
 
 
 # TODO similarities with TableCrawler
@@ -49,6 +44,9 @@ class ResultTableCFood(AbstractFileCFood):
     def __init__(self,  *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.table = pd.read_csv(fileguide.access(self.crawled_path))
+        self.recs = []
+        self.experiment = None
+        self.project = None
 
     @staticmethod
     def get_re():
@@ -60,7 +58,7 @@ class ResultTableCFood(AbstractFileCFood):
         self.experiment, self.project = (
             ExperimentCFood.create_identifiable_experiment(self.match))
 
-        for idx, row in self.table.iterrows():
+        for _, row in self.table.iterrows():
             rec = db.Record()
             rec.add_parent(self.match.group("recordtype"))
 
@@ -77,10 +75,11 @@ class ResultTableCFood(AbstractFileCFood):
         self.identifiables.extend([self.project, self.experiment])
 
     def update_identifiables(self):
-        for ii, (idx, row) in enumerate(self.table.iterrows()):
+        for ii, (_, row) in enumerate(self.table.iterrows()):
             for col in row.index:
                 match = re.match(ResultTableCFood.property_name_re, col)
-                assure_property_is(self.recs[ii], match.group("pname"), row.loc[col], to_be_updated=self.to_be_updated)
+                assure_property_is(self.recs[ii], match.group("pname"), row.loc[col],
+                                   to_be_updated=self.to_be_updated)
         assure_property_is(self.experiment, self.match.group("recordtype"),
                            self.recs, to_be_updated=self.to_be_updated,
                            datatype=db.LIST(self.match.group("recordtype")))

src/caosadvancedtools/scifolder/software_cfood.py

@@ -40,6 +40,9 @@ class SoftwareCFood(AbstractFileCFood, WithREADME):
     def __init__(self,  *args, **kwargs):
         super().__init__(*args, **kwargs)
         WithREADME.__init__(self)
+        self.people = None
+        self.software = None
+        self.softwareversion = None
 
     def collect_information(self):
         self.find_referenced_files([BINARIES, SOURCECODE])