diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 4120de7c2bd..a36e1c17f4a 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -1587,12 +1587,12 @@ class ConnectivityTable(Tabular): if not self.header_regexp.match(line): return False else: - length = int(re.split(r"\W+", line, 1)[0]) + length = int(re.split(r"\W+", line, maxsplit=1)[0]) else: if not self.structure_regexp.match(line.upper()): return False else: - if j != int(re.split(r"\W+", line, 1)[0]): + if j != int(re.split(r"\W+", line, maxsplit=1)[0]): return False elif j == length: # Last line of first sequence has been reached return True diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 94efbf98aac..08149e289b8 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -22,14 +22,14 @@ charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -click==8.1.4 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.5 ; python_version >= "3.7" and python_version < "3.12" codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12" cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12" cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12" -darker==1.7.1 ; python_version >= "3.7" and python_version < "3.12" +darker==1.7.2 ; python_version >= "3.7" and python_version < "3.12" defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12" docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12" @@ -83,7 +83,7 @@ pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12" pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12" platformdirs==3.8.1 ; python_version >= "3.7" and python_version < "3.12" pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12" -port-for==0.7.0 ; python_version >= "3.7" and python_version < "3.12" +port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.12" prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12" prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12" psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin" @@ -96,7 +96,7 @@ pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12" pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12" -pytest-asyncio==0.21.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-asyncio==0.21.1 ; python_version >= "3.7" and python_version < "3.12" pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12" pytest-cov==4.1.0 ; python_version >= "3.7" and python_version < "3.12" pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -148,7 +148,7 @@ tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12" toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12" tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" trio-websocket==0.10.3 ; python_version >= "3.7" and python_version < "3.12" -trio==0.22.1 ; python_version >= "3.7" and python_version < "3.12" +trio==0.22.2 ; python_version >= "3.7" and python_version < "3.12" tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12" twill==3.1 ; python_version >= "3.7" and python_version < "3.12" twine==4.0.2 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index ea47ca838f1..a155a560b39 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -5,6 +5,6 @@ importlib-metadata==4.2.0 mccabe==0.7.0 pycodestyle==2.9.1 pyflakes==2.5.0 -ruff==0.0.277 +ruff==0.0.278 typing_extensions==4.7.1 zipp==3.15.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 2371ba3ab8e..4e8b4b4f67d 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -42,7 +42,7 @@ circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -click==8.1.4 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.5 ; python_version >= "3.7" and python_version < "3.12" cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12" cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index ac30ee3ce3f..372a39e9481 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -578,11 +578,7 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F default_cond = "dataset.object_store_id IS NULL" if default_quota_enabled and default_exclude_ids else "" exclude_cond = "dataset.object_store_id NOT IN :exclude_object_store_ids" if default_exclude_ids else "" use_or = " OR " if (default_cond != "" and exclude_cond != "") else "" - default_usage_dataset_condition = "{default_cond} {use_or} {exclude_cond}".format( - default_cond=default_cond, - exclude_cond=exclude_cond, - use_or=use_or, - ) + default_usage_dataset_condition = f"{default_cond} {use_or} {exclude_cond}" if default_usage_dataset_condition.strip(): default_usage_dataset_condition = f"AND ( {default_usage_dataset_condition} )" default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)