Applied isort pre-commit hook.

legumeinfo · Feb 16, 2023 · 5c05b65 · 5c05b65
1 parent 4b310fc
commit 5c05b65
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Showing 63 changed files with 109 additions and 79 deletions.
diff --git a/chromosome/chromosome/__main__.py b/chromosome/chromosome/__main__.py
@@ -17,7 +17,6 @@
 from chromosome.http_server import run_http_server
 from chromosome.request_handler import RequestHandler
 
-
 LOG_LEVELS = {
     "DEBUG": logging.DEBUG,
     "INFO": logging.INFO,

diff --git a/chromosome/chromosome/commands.py b/chromosome/chromosome/commands.py
@@ -21,9 +21,10 @@
 
 
 import os
+import sys
+
 import pkg_resources
 import setuptools
-import sys
 
 
 class BuildProtos(setuptools.Command):

diff --git a/chromosome/chromosome/database.py b/chromosome/chromosome/database.py
@@ -4,7 +4,6 @@
 # module
 import chromosome
 
-
 COMPATIBLE_KEY = "GCV_COMPATIBLE_SCHEMA_VERSIONS"
 
 

diff --git a/chromosome/chromosome/grpc_server.py b/chromosome/chromosome/grpc_server.py
@@ -2,18 +2,22 @@
 import grpc
 from grpc.experimental import aio
 
+# isort: split
+
 # module
+# isort: off
 # from chromosome.proto.chromosome_service.v1 import chromosome_pb2
 # from chromosome.proto.chromosome_service.v1 import chromosome_pb2_grpc
 # from chromosome.proto.track.v1 import track_pb2
 # NOTE: the following imports are a temporary workaround for a known protobuf
 # bug; the commented imports above should be used when the bug is fixed:
 # https://github.com/protocolbuffers/protobuf/issues/10075
 from chromosome import proto  # noqa: F401
-from chromosome_service.v1 import chromosome_pb2
-from chromosome_service.v1 import chromosome_pb2_grpc
+from chromosome_service.v1 import chromosome_pb2, chromosome_pb2_grpc
 from track.v1 import track_pb2
 
+# isort: on
+
 
 class Chromosome(chromosome_pb2_grpc.ChromosomeServicer):
     def __init__(self, handler):

diff --git a/chromosome/chromosome/proto/__init__.py b/chromosome/chromosome/proto/__init__.py
@@ -1,7 +1,6 @@
 import os
 import sys
 
-
 # protoc can't generate Python files with relative imports and Python 3 doesn't
 # have implicit relative imports like Python 2. This is unfortunate because we
 # don't want to add service-specific absolute import paths to .proto files

diff --git a/chromosome/setup.py b/chromosome/setup.py
@@ -7,7 +7,6 @@
 # package
 from chromosome import commands
 
-
 PACKAGE_DIRECTORIES = {
     "": ".",
 }

diff --git a/chromosome_region/chromosome_region/__main__.py b/chromosome_region/chromosome_region/__main__.py
@@ -17,7 +17,6 @@
 from chromosome_region.http_server import run_http_server
 from chromosome_region.request_handler import RequestHandler
 
-
 LOG_LEVELS = {
     "DEBUG": logging.DEBUG,
     "INFO": logging.INFO,

diff --git a/chromosome_region/chromosome_region/commands.py b/chromosome_region/chromosome_region/commands.py
@@ -21,9 +21,10 @@
 
 
 import os
+import sys
+
 import pkg_resources
 import setuptools
-import sys
 
 
 class BuildProtos(setuptools.Command):

diff --git a/chromosome_region/chromosome_region/database.py b/chromosome_region/chromosome_region/database.py
@@ -4,7 +4,6 @@
 # module
 import chromosome_region
 
-
 COMPATIBLE_KEY = "GCV_COMPATIBLE_SCHEMA_VERSIONS"
 
 

diff --git a/chromosome_region/chromosome_region/grpc_server.py b/chromosome_region/chromosome_region/grpc_server.py
@@ -2,7 +2,10 @@
 import grpc
 from grpc.experimental import aio
 
+# isort: split
+
 # module
+# isort: off
 # from chromosome_region.proto.chromosomeregion_service.v1 import chromosomeregion_pb2
 # from chromosome_region.proto.chromosomeregion_service.v1
 #   import chromosomeregion_pb2_grpc
@@ -11,10 +14,11 @@
 # bug; the commented imports above should be used when the bug is fixed:
 # https://github.com/protocolbuffers/protobuf/issues/10075
 from chromosome_region import proto  # noqa: F401
-from chromosomeregion_service.v1 import chromosomeregion_pb2
-from chromosomeregion_service.v1 import chromosomeregion_pb2_grpc
+from chromosomeregion_service.v1 import chromosomeregion_pb2, chromosomeregion_pb2_grpc
 from region.v1 import region_pb2
 
+# isort: on
+
 
 class ChromosomeRegion(chromosomeregion_pb2_grpc.ChromosomeRegionServicer):
     def __init__(self, handler):

diff --git a/chromosome_region/chromosome_region/proto/__init__.py b/chromosome_region/chromosome_region/proto/__init__.py
@@ -1,7 +1,6 @@
 import os
 import sys
 
-
 # protoc can't generate Python files with relative imports and Python 3 doesn't
 # have implicit relative imports like Python 2. This is unfortunate because we
 # don't want to add service-specific absolute import paths to .proto files

diff --git a/chromosome_region/setup.py b/chromosome_region/setup.py
@@ -7,7 +7,6 @@
 # package
 from chromosome_region import commands
 
-
 PACKAGE_DIRECTORIES = {
     "": ".",
 }

diff --git a/chromosome_search/chromosome_search/__main__.py b/chromosome_search/chromosome_search/__main__.py
@@ -17,7 +17,6 @@
 from chromosome_search.http_server import run_http_server
 from chromosome_search.request_handler import RequestHandler
 
-
 LOG_LEVELS = {
     "DEBUG": logging.DEBUG,
     "INFO": logging.INFO,

diff --git a/chromosome_search/chromosome_search/commands.py b/chromosome_search/chromosome_search/commands.py
@@ -21,9 +21,10 @@
 
 
 import os
+import sys
+
 import pkg_resources
 import setuptools
-import sys
 
 
 class BuildProtos(setuptools.Command):

diff --git a/chromosome_search/chromosome_search/database.py b/chromosome_search/chromosome_search/database.py
@@ -4,7 +4,6 @@
 # module
 import chromosome_search
 
-
 COMPATIBLE_KEY = "GCV_COMPATIBLE_SCHEMA_VERSIONS"
 
 

diff --git a/chromosome_search/chromosome_search/grpc_server.py b/chromosome_search/chromosome_search/grpc_server.py
@@ -2,7 +2,10 @@
 import grpc
 from grpc.experimental import aio
 
+# isort: split
+
 # module
+# isort: off
 # from chromosome_search.proto.chromosomesearch_service.v1 import chromosomesearch_pb2
 # from chromosome_search.proto.chromosomesearch_service.v1
 #   import chromosomesearch_pb2_grpc
@@ -11,8 +14,9 @@
 # bug; the commented imports above should be used when the bug is fixed:
 # https://github.com/protocolbuffers/protobuf/issues/10075
 from chromosome_search import proto  # noqa: F401
-from chromosomesearch_service.v1 import chromosomesearch_pb2
-from chromosomesearch_service.v1 import chromosomesearch_pb2_grpc
+from chromosomesearch_service.v1 import chromosomesearch_pb2, chromosomesearch_pb2_grpc
+
+# isort: on
 
 
 class ChromosomeSearch(chromosomesearch_pb2_grpc.ChromosomeSearchServicer):

diff --git a/chromosome_search/chromosome_search/proto/__init__.py b/chromosome_search/chromosome_search/proto/__init__.py
@@ -1,7 +1,6 @@
 import os
 import sys
 
-
 # protoc can't generate Python files with relative imports and Python 3 doesn't
 # have implicit relative imports like Python 2. This is unfortunate because we
 # don't want to add service-specific absolute import paths to .proto files

diff --git a/chromosome_search/setup.py b/chromosome_search/setup.py
@@ -7,7 +7,6 @@
 # package
 from chromosome_search import commands
 
-
 PACKAGE_DIRECTORIES = {
     "": ".",
 }

diff --git a/gene_search/gene_search/__main__.py b/gene_search/gene_search/__main__.py
@@ -17,7 +17,6 @@
 from gene_search.http_server import run_http_server
 from gene_search.request_handler import RequestHandler
 
-
 LOG_LEVELS = {
     "DEBUG": logging.DEBUG,
     "INFO": logging.INFO,

diff --git a/gene_search/gene_search/commands.py b/gene_search/gene_search/commands.py
@@ -21,9 +21,10 @@
 
 
 import os
+import sys
+
 import pkg_resources
 import setuptools
-import sys
 
 
 class BuildProtos(setuptools.Command):

diff --git a/gene_search/gene_search/database.py b/gene_search/gene_search/database.py
@@ -4,7 +4,6 @@
 # module
 import gene_search
 
-
 COMPATIBLE_KEY = "GCV_COMPATIBLE_SCHEMA_VERSIONS"
 
 

diff --git a/gene_search/gene_search/grpc_server.py b/gene_search/gene_search/grpc_server.py
@@ -2,15 +2,19 @@
 import grpc
 from grpc.experimental import aio
 
+# isort: split
+
 # module
+# isort: off
 # from gene_search.proto.genesearch_service.v1 import genesearch_pb2
 # from gene_search.proto.genesearch_service.v1 import genesearch_pb2_grpc
 # NOTE: the following imports are a temporary workaround for a known protobuf
 # bug; the commented imports above should be used when the bug is fixed:
 # https://github.com/protocolbuffers/protobuf/issues/10075
 from gene_search import proto  # noqa: F401
-from genesearch_service.v1 import genesearch_pb2
-from genesearch_service.v1 import genesearch_pb2_grpc
+from genesearch_service.v1 import genesearch_pb2, genesearch_pb2_grpc
+
+# isort: on
 
 
 class GeneSearch(genesearch_pb2_grpc.GeneSearchServicer):

diff --git a/gene_search/gene_search/proto/__init__.py b/gene_search/gene_search/proto/__init__.py
@@ -1,7 +1,6 @@
 import os
 import sys
 
-
 # protoc can't generate Python files with relative imports and Python 3 doesn't
 # have implicit relative imports like Python 2. This is unfortunate because we
 # don't want to add service-specific absolute import paths to .proto files

diff --git a/gene_search/setup.py b/gene_search/setup.py
@@ -6,7 +6,6 @@
 # package
 from gene_search import commands
 
-
 PACKAGE_DIRECTORIES = {
     "": ".",
 }

diff --git a/genes/genes/__main__.py b/genes/genes/__main__.py
@@ -17,7 +17,6 @@
 from genes.http_server import run_http_server
 from genes.request_handler import RequestHandler
 
-
 LOG_LEVELS = {
     "DEBUG": logging.DEBUG,
     "INFO": logging.INFO,

diff --git a/genes/genes/commands.py b/genes/genes/commands.py
@@ -21,9 +21,10 @@
 
 
 import os
+import sys
+
 import pkg_resources
 import setuptools
-import sys
 
 
 class BuildProtos(setuptools.Command):

diff --git a/genes/genes/database.py b/genes/genes/database.py
@@ -4,7 +4,6 @@
 # module
 import genes
 
-
 COMPATIBLE_KEY = "GCV_COMPATIBLE_SCHEMA_VERSIONS"
 
 

diff --git a/genes/genes/grpc_server.py b/genes/genes/grpc_server.py
@@ -2,18 +2,22 @@
 import grpc
 from grpc.experimental import aio
 
+# isort: split
+
 # module
+# isort: off
 # from genes.proto.genes_service.v1 import genes_pb2
 # from genes.proto.genes_service.v1 import genes_pb2_grpc
 # from genes.proto.gene.v1 import gene_pb2
 # NOTE: the following imports are a temporary workaround for a known protobuf
 # bug; the commented imports above should be used when the bug is fixed:
 # https://github.com/protocolbuffers/protobuf/issues/10075
 from genes import proto  # noqa: F401
-from genes_service.v1 import genes_pb2
-from genes_service.v1 import genes_pb2_grpc
+from genes_service.v1 import genes_pb2, genes_pb2_grpc
 from gene.v1 import gene_pb2
 
+# isort: on
+
 
 class Genes(genes_pb2_grpc.GenesServicer):
     def __init__(self, handler):

diff --git a/genes/genes/proto/__init__.py b/genes/genes/proto/__init__.py
@@ -1,7 +1,6 @@
 import os
 import sys
 
-
 # protoc can't generate Python files with relative imports and Python 3 doesn't
 # have implicit relative imports like Python 2. This is unfortunate because we
 # don't want to add service-specific absolute import paths to .proto files

diff --git a/genes/genes/request_handler.py b/genes/genes/request_handler.py
@@ -1,7 +1,7 @@
 # dependencies
 from redis.commands.search import AsyncSearch
-from redis.commands.search.document import Document
 from redis.commands.search._util import to_string
+from redis.commands.search.document import Document
 
 
 class RequestHandler:

diff --git a/genes/setup.py b/genes/setup.py
@@ -7,7 +7,6 @@
 # package
 from genes import commands
 
-
 PACKAGE_DIRECTORIES = {
     "": ".",
 }

diff --git a/linkouts/linkouts/request_handler.py b/linkouts/linkouts/request_handler.py
@@ -1,7 +1,8 @@
-import yaml
+import glob
 import logging
 import re
-import glob
+
+import yaml
 
 HREF = "href"
 METHOD = "method"

diff --git a/macro_synteny_blocks/macro_synteny_blocks/__main__.py b/macro_synteny_blocks/macro_synteny_blocks/__main__.py
@@ -17,7 +17,6 @@
 from macro_synteny_blocks.http_server import run_http_server
 from macro_synteny_blocks.request_handler import RequestHandler
 
-
 LOG_LEVELS = {
     "DEBUG": logging.DEBUG,
     "INFO": logging.INFO,

diff --git a/macro_synteny_blocks/macro_synteny_blocks/commands.py b/macro_synteny_blocks/macro_synteny_blocks/commands.py
@@ -23,9 +23,10 @@
 
 
 import os
+import sys
+
 import pkg_resources
 import setuptools
-import sys
 
 
 class BuildProtos(setuptools.Command):

diff --git a/macro_synteny_blocks/macro_synteny_blocks/database.py b/macro_synteny_blocks/macro_synteny_blocks/database.py
@@ -4,7 +4,6 @@
 # module
 import macro_synteny_blocks
 
-
 COMPATIBLE_KEY = "GCV_COMPATIBLE_SCHEMA_VERSIONS"