Hotfix for edges from master

Plus issues with isort and black

bel/Config.py

@@ -10,6 +10,7 @@
     ~/.belbio_{conf|secrets}   (dotfiles in home directory)
 """
 
+# Standard Library
 import collections
 import copy
 import functools
@@ -18,6 +19,7 @@
 import re
 from typing import Any, Mapping, MutableMapping
 
+# Third Party Imports
 import yaml
 
 log = logging.getLogger(__name__)

bel/__init__.py

@@ -2,8 +2,10 @@
 # BEL FUNCTION IMPORTS #
 ########################
 
+# Standard Library
 import logging
 
+# Local Imports
 import bel.db
 import bel.edge
 import bel.lang

bel/cli/scripts.py

@@ -1,10 +1,17 @@
+# Standard Library
 import gzip
 import json
 import logging
 import logging.config
 import re
 import sys
 
+# Third Party Imports
+import click
+import timy
+import yaml
+
+# Local Imports
 import bel.Config
 import bel.db.arangodb
 import bel.db.elasticsearch
@@ -13,9 +20,6 @@
 import bel.nanopub.files as bnf
 import bel.nanopub.nanopubs as bnn
 import bel.utils as utils
-import click
-import timy
-import yaml
 from bel.Config import config
 from bel.lang.belobj import BEL
 

bel/db/elasticsearch.py

@@ -1,11 +1,15 @@
+# Standard Library
 import logging
 import os
 
+# Third Party Imports
 import elasticsearch.helpers
 import yaml
-from bel.Config import config
 from elasticsearch import Elasticsearch
 
+# Local Imports
+from bel.Config import config
+
 log = logging.getLogger(__name__)
 
 cur_dir_name = os.path.dirname(os.path.realpath(__file__))

bel/edge/computed.py

@@ -1,11 +1,15 @@
 # Compute Edges related code
 
+# Standard Library
 import copy
 from typing import Any, List, Mapping, MutableSequence
 
-from bel.lang.ast import BELAst, Function, NSArg
+# Third Party Imports
 from structlog import get_logger
 
+# Local Imports
+from bel.lang.ast import BELAst, Function, NSArg
+
 log = get_logger()
 
 # Typings

bel/edge/edges.py

@@ -292,6 +292,7 @@ def generate_assertion_edge_info(
                 causal_edge_type = []
                 if "causal" in bo.spec["relations"]["info"][assertion["relation"]]["categories"]:
                     edge_types.append("causal")
+                    causal_edge_type = ["causal"]
 
                 edge_info = {
                     "edge_types": edge_types,

bel/lang/migrate_1_2.py

@@ -5,12 +5,16 @@
 # Migrate BEL from 1 to 2.0.0
 #
 
+# Standard Library
 import json
 
+# Third Party Imports
+import structlog
+
+# Local Imports
 import bel
 import bel.lang.ast
 import bel.lang.partialparse
-import structlog
 from bel import BEL
 from bel.Config import config
 from bel.lang.ast import BELAst, Function, NSArg, StrArg

bel/lang/partialparse.py

@@ -9,14 +9,18 @@
 
 
 """
+# Standard Library
 import copy
 import logging
 import logging.config
 import re
 from typing import Any, List, Mapping, MutableMapping, Optional, Tuple
 
-import bel.lang.bel_specification as bel_specification
+# Third Party Imports
 import structlog
+
+# Local Imports
+import bel.lang.bel_specification as bel_specification
 from bel.Config import config
 from bel.lang.ast import BELAst, Function, NSArg, StrArg
 

bel/nanopub/belscripts.py

@@ -13,6 +13,7 @@
     *
 """
 
+# Standard Library
 import collections
 import copy
 import csv
@@ -21,6 +22,7 @@
 import re
 import sys
 
+# Third Party Imports
 import structlog
 import yaml
 

bel/nanopub/validate.py

@@ -1,9 +1,13 @@
+# Standard Library
 import re
 from typing import Tuple
 
+# Third Party Imports
+import structlog
+
+# Local Imports
 import bel.db.elasticsearch
 import bel.lang.belobj
-import structlog
 from bel.Config import config
 
 log = structlog.getLogger(__name__)

bel/resources/namespace.py

@@ -1,15 +1,19 @@
+# Standard Library
 import copy
 import gzip
 import json
 from typing import IO
 
+# Third Party Imports
+import timy
+from arango import ArangoError
+from structlog import get_logger
+
+# Local Imports
 import bel.db.arangodb as arangodb
 import bel.db.elasticsearch as elasticsearch
 import bel.utils
-import timy
-from arango import ArangoError
 from bel.Config import config
-from structlog import get_logger
 
 # import structlog
 # import logging

bel/resources/ortholog.py

@@ -1,14 +1,18 @@
+# Standard Library
 import gzip
 import json
 from typing import IO
 
-import bel.db.arangodb as arangodb
-import bel.utils
+# Third Party Imports
 import timy
 from arango import ArangoError
-from bel.Config import config
 from structlog import get_logger
 
+# Local Imports
+import bel.db.arangodb as arangodb
+import bel.utils
+from bel.Config import config
+
 log = get_logger()
 
 

bel/resources/resource.py

@@ -1,15 +1,19 @@
+# Standard Library
 import copy
 import gzip
 import json
 
+# Third Party Imports
+import timy
+from structlog import get_logger
+
+# Local Imports
 import bel.db.arangodb as arangodb
 import bel.db.elasticsearch as elasticsearch
 import bel.resources.namespace
 import bel.resources.ortholog
 import bel.utils
-import timy
 from bel.Config import config
-from structlog import get_logger
 
 log = get_logger()
 

bel/scripts.py

@@ -1,10 +1,17 @@
+# Standard Library
 import gzip
 import json
 import logging
 import logging.config
 import re
 import sys
 
+# Third Party Imports
+import click
+import timy
+import yaml
+
+# Local Imports
 import bel.Config
 import bel.db.arangodb
 import bel.db.elasticsearch
@@ -13,9 +20,6 @@
 import bel.nanopub.files as bnf
 import bel.nanopub.nanopubs as bnn
 import bel.utils as utils
-import click
-import timy
-import yaml
 from bel.Config import config
 from bel.lang.belobj import BEL
 

docs/source/conf.py

@@ -18,9 +18,11 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 
+# Standard Library
 import os
 import sys
 
+# Third Party Imports
 import sphinx_rtd_theme
 
 # To get ReadTheDocs working - autodoc missing modules error

tests/edge/test_computed_edges.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.edge.computed
 import bel.lang.belobj
 from bel.Config import config

tests/edge/test_create_edges.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.edge.edges
 import pytest
 from bel.Config import config

tests/lang/test_ast.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.lang.ast
 import bel.lang.bel_utils
 import bel.lang.belobj

tests/lang/test_auto_version.py

@@ -1,3 +1,4 @@
+# Local Imports
 from bel.lang.bel_utils import _default_to_version
 
 EXAMPLE_AVAILABLE_VERSIONS = ["1.0.0", "0.0.3", "3.0.1", "2.0.1", "2.0.0", "6.1.1", "0.5.1"]

tests/lang/test_belobj.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.db.arangodb
 import bel.lang.ast
 import bel.lang.bel_utils

tests/lang/test_canonicalize.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.Config
 import bel.lang.bel_utils
 import bel.lang.belobj

tests/lang/test_orthologize.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.lang.belobj
 import pytest
 from bel.Config import config

tests/lang/test_parse.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.lang.belobj
 import pytest
 from bel.Config import config

tests/lang/test_semantic_checks.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.lang.belobj
 import pytest
 from bel.Config import config

tests/lang/test_syntax_checks.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.lang.belobj
 from bel.Config import config
 

tests/nanopub/test_nanopub_to_edge.py

@@ -1,6 +1,8 @@
+# Standard Library
 import json
 import os
 
+# Local Imports
 import bel.nanopub.nanopubs as nb
 import pytest
 

tests/nanopub/test_nanopub_validation.py

@@ -1,7 +1,9 @@
 # import bel.nanopub.nanopubs as nb
 # import yaml
+# Standard Library
 import os
 
+# Local Imports
 import pytest
 
 local_dir = os.path.dirname(__file__)

tests/nanopub/test_pubmed.py

@@ -1,6 +1,8 @@
+# Standard Library
 import json
 import time
 
+# Local Imports
 import bel.nanopub.pubmed
 
 

tests/terms/test_terms.py

@@ -1,3 +1,4 @@
+# Local Imports
 import bel.terms.terms