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Merge pull request #16409 from galaxybot/dev_auto_update_dependencies

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Update Python dependencies
This commit is contained in:
John Davis
2023-07-20 00:41:00 +10:00
committed by GitHub
parent b55752db9a 133a2ea42a
commit cf44aeeb3e
5 changed files with 10 additions and 14 deletions
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lib/galaxy/datatypes/tabular.py
+2 -2
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@@ -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
lib/galaxy/dependencies/dev-requirements.txt
+5 -5
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@@ -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"
lib/galaxy/dependencies/pinned-lint-requirements.txt
+1 -1
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@@ -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
lib/galaxy/dependencies/pinned-requirements.txt
+1 -1
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@@ -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"
lib/galaxy/model/__init__.py
+1 -5
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@@ -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)