Fixed linting, import sorting and unrelated mypy error (due to deprec…

…ated method)
galaxyproject · Oct 6, 2023 · d4a405e · d4a405e
1 parent a6d746a
commit d4a405e
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Showing 5 changed files with 12 additions and 6 deletions.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -664,7 +664,7 @@ def get_chunk(self, trans, dataset: HasFileName, offset: int = 0, ck_size: Optio
                             break
 
                         offset = bamfile.tell()
-                        bamline = alignment.tostring(bamfile)
+                        bamline = alignment.to_string()
                         # With multiple tags, Galaxy would display each as a separate column
                         # because the 'tostring()' function uses tabs also between tags.
                         # Below code will turn these extra tabs into spaces.

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -147,11 +147,11 @@
 from galaxy.util import (
     directory_hash_id,
     enum_values,
+    hex_to_lowercase_alphanum,
     listify,
     ready_name_for_url,
     unicodify,
     unique_id,
-    hex_to_lowercase_alphanum,
 )
 from galaxy.util.dictifiable import (
     dict_for,

diff --git a/...igrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py b/...igrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py
@@ -5,7 +5,11 @@
 Create Date: 2023-10-05 02:09:32.888292
 
 """
-from sqlalchemy import Column, Text, Boolean
+from sqlalchemy import (
+    Boolean,
+    Column,
+    Text,
+)
 
 from galaxy.model.migrations.util import (
     add_column,

diff --git a/lib/galaxy/security/idencoding.py b/lib/galaxy/security/idencoding.py
@@ -11,10 +11,10 @@
 
 import galaxy.exceptions
 from galaxy.util import (
-    smart_str,
-    unicodify,
     hex_to_lowercase_alphanum,
     lowercase_alphanum_to_hex,
+    smart_str,
+    unicodify,
 )
 
 log = logging.getLogger(__name__)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
@@ -1890,6 +1890,7 @@ def hex_to_lowercase_alphanum(hex_string: str) -> str:
     characters a-z and 0-9
     """
     import numpy as np
+
     return np.base_repr(int(hex_string, 16), 36).lower()
 
 
@@ -1899,4 +1900,5 @@ def lowercase_alphanum_to_hex(lowercase_alphanum: str) -> str:
     hexadecimal string
     """
     import numpy as np
-    return np.base_repr(int(lowercase_alphanum, 36), 16).lower()
+
+    return np.base_repr(int(lowercase_alphanum, 36), 16).lower()