[R] Bump flake8 to 7.1.1 (#6511)

requirements.all.txt

@@ -30,7 +30,7 @@ elasticsearch==7.17.12
 elasticsearch-dsl==7.4.1
 et_xmlfile==2.0.0
 fastavro==1.9.7
-flake8==5.0.4
+flake8==7.1.1
 flask==3.0.3
 flask-cors==5.0.0
 flask-login==0.6.3
@@ -94,9 +94,9 @@ psutil==6.1.0
 py-partiql-parser==0.5.6
 pyasn1==0.6.1
 pyasn1_modules==0.4.1
-pycodestyle==2.9.1
+pycodestyle==2.12.1
 pycparser==2.22
-pyflakes==2.5.0
+pyflakes==3.2.0
 pygithub==2.4.0
 pyjwt==2.9.0
 pynacl==1.5.0

requirements.dev.trans.txt

@@ -35,8 +35,8 @@ openapi-schema-validator==0.6.2
 pathable==0.4.3
 psutil==6.1.0
 py-partiql-parser==0.5.6
-pycodestyle==2.9.1
-pyflakes==2.5.0
+pycodestyle==2.12.1
+pyflakes==3.2.0
 pyjwt==2.9.0
 pynacl==1.5.0
 pyparsing==3.2.0

requirements.dev.txt

@@ -3,7 +3,7 @@ awscli==1.35.14
 boto3-stubs[s3,sqs,lambda,dynamodb,iam,ecr,stepfunctions,kms]==1.35.48  # match this with the version of the `boto3` runtime dependency
 coverage==7.6.4
 docker==7.1.0
-flake8==5.0.4
+flake8==7.1.1
 gevent==24.10.2
 git+https://github.com/DataBiosphere/[email protected]+12#egg=chalice
 git+https://github.com/hannes-ucsc/[email protected]+1#egg=requirements-parser

src/azul/plugins/metadata/hca/indexer/aggregate.py

@@ -49,7 +49,6 @@ class HCAAggregate(Aggregate):
 
     @cached_property
     def cell_count(self) -> int:
-        cs: JSON
         return sum(cs['total_estimated_cells']
                    for cs in self.contents['cell_suspensions']
                    if cs['total_estimated_cells'] is not None)