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Merge pull request #15435 from galaxybot/dev_auto_update_dependencies

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Update Python dependencies
This commit is contained in:
Marius van den Beek
2023-02-05 11:04:50 +01:00
committed by GitHub
parent 95056eaa54 29dff74843
commit f1f16517e6
12 changed files with 34 additions and 41 deletions
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lib/galaxy/auth/providers/ldap_ad.py
+2 -4
View File
@@ -213,8 +213,7 @@ class LDAP(AuthProvider):
if self.auto_create_roles_or_groups and self.role_search_option not in params:
raise ConfigurationError(
"Missing or mismatching LDAP parameters for %s. Make sure the %s is "
"included in the 'search-fields'." % (self.role_search_option, self.role_search_attribute)
f"Missing or mismatching LDAP parameters for {self.role_search_option}. Make sure the {self.role_search_attribute} is included in the 'search-fields'."
)
params["dn"] = dn
except Exception:
@@ -400,8 +399,7 @@ class LDAP3(LDAP):
if self.auto_create_roles_or_groups and self.role_search_option not in params:
raise ConfigurationError(
"Missing or mismatching LDAP parameters for %s. Make sure the %s is "
"included in the 'search-fields'." % (self.role_search_option, self.role_search_attribute)
f"Missing or mismatching LDAP parameters for {self.role_search_option}. Make sure the {self.role_search_attribute} is included in the 'search-fields'."
)
params["dn"] = dn
except Exception:
lib/galaxy/dependencies/dev-requirements.txt
+8 -8
View File
@@ -24,7 +24,7 @@ click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
codespell==2.2.2 ; 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 python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.12"
coverage[toml]==7.0.5 ; python_version >= "3.7" and python_version < "3.12"
coverage[toml]==7.1.0 ; python_version >= "3.7" and python_version < "3.12"
cwltest==2.3.20230108193615 ; python_version >= "3.7" and python_version < "3.12"
cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
darker==1.6.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -44,7 +44,7 @@ imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.12"
importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.10"
iniconfig==2.0.0 ; python_version >= "3.7" and python_version < "3.12"
isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12"
isort==5.11.4 ; python_version >= "3.7" and python_version < "3.12"
isort==5.11.5 ; python_version >= "3.7" and python_version < "3.12"
jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12"
kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
@@ -64,7 +64,7 @@ numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
numpy==1.24.1 ; python_version >= "3.8" and python_version < "3.12"
outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
packaging==21.3 ; python_version >= "3.7" and python_version < "3.12"
pathspec==0.10.3 ; python_version >= "3.7" and python_version < "3.12"
pathspec==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
pillow==9.4.0 ; python_version >= "3.7" and python_version < "3.12"
pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
platformdirs==2.6.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -101,12 +101,12 @@ responses==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
rfc3986[idna2008]==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.12"
schema-salad==8.4.20230201194352 ; python_version >= "3.7" and python_version < "3.12"
scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
scipy==1.10.0 ; python_version >= "3.8" and python_version < "3.12"
selenium==4.7.2 ; python_version >= "3.7" and python_version < "3.12"
selenium==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
seletools==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.12"
setuptools==67.1.0 ; python_version >= "3.7" and python_version < "3.12"
six==1.16.0 ; python_version >= "3.7" and python_version < "3.12"
sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -130,7 +130,7 @@ trio==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
twill==3.1 ; python_version >= "3.7" and python_version < "3.12"
typed-ast==1.5.4 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7"
types-toml==0.10.8.1 ; python_version >= "3.7" and python_version < "3.12"
types-toml==0.10.8.2 ; python_version >= "3.7" and python_version < "3.12"
typing-extensions==4.4.0 ; python_version >= "3.7" and python_version < "3.12"
urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.12"
urllib3[socks]==1.26.14 ; python_version >= "3.7" and python_version < "3.12"
@@ -140,4 +140,4 @@ wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.12"
wrapt==1.14.1 ; python_version >= "3.7" and python_version < "3.12"
wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
yarl==1.8.2 ; python_version >= "3.7" and python_version < "3.12"
zipp==3.11.0 ; python_version >= "3.7" and python_version < "3.10"
zipp==3.12.0 ; python_version >= "3.7" and python_version < "3.10"
lib/galaxy/dependencies/pinned-lint-requirements.txt
+2 -2
View File
@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
mccabe==0.7.0
pycodestyle==2.9.1
pyflakes==2.5.0
ruff==0.0.228
ruff==0.0.241
typing_extensions==4.4.0
zipp==3.11.0
zipp==3.12.0
lib/galaxy/dependencies/pinned-requirements.txt
+10 -10
View File
@@ -21,11 +21,11 @@ babel==2.11.0 ; python_version >= "3.7" and python_version < "3.12"
bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.12"
bcrypt==4.0.1 ; python_version >= "3.7" and python_version < "3.12"
bdbag==1.6.3 ; python_version >= "3.7" and python_version < "3.12"
bdbag==1.6.4 ; python_version >= "3.7" and python_version < "3.12"
beaker==1.11.0 ; python_version >= "3.7" and python_version < "3.12"
billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12"
bioblend==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
bleach==5.0.1 ; python_version >= "3.7" and python_version < "3.12"
bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12"
boltons==21.0.0 ; python_version >= "3.7" and python_version < "3.12"
boto==2.49.0 ; python_version >= "3.7" and python_version < "3.12"
bx-python==0.9.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -48,7 +48,7 @@ colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platfo
coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12"
cryptography==39.0.0 ; python_version >= "3.7" and python_version < "3.12"
cwl-upgrader==1.2.4 ; python_version >= "3.7" and python_version < "3.12"
cwl-utils==0.21 ; python_version >= "3.7" and python_version < "3.12"
cwl-utils==0.23 ; python_version >= "3.7" and python_version < "3.12"
cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -59,7 +59,7 @@ docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.12"
docutils==0.16 ; python_version >= "3.7" and python_version < "3.12"
ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
email-validator==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
email-validator==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
fastapi==0.89.1 ; python_version >= "3.7" and python_version < "3.12"
flupy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -70,7 +70,7 @@ future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
gravity @ git+https://github.com/galaxyproject/gravity.git@release_1.x ; python_version >= "3.7" and python_version < "3.12"
greenlet==2.0.1 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12"
greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12"
gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12"
gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.12"
h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -120,7 +120,7 @@ psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.12"
pulsar-galaxy-lib==0.15.0.dev0 ; python_version >= "3.7" and python_version < "3.12"
pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.12"
pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
pycryptodome==3.16.0 ; python_version >= "3.7" and python_version < "3.12"
pycryptodome==3.17 ; python_version >= "3.7" and python_version < "3.12"
pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12"
pydantic==1.10.4 ; python_version >= "3.7" and python_version < "3.12"
pydantic[email]==1.10.4 ; python_version >= "3.7" and python_version < "3.12"
@@ -152,15 +152,15 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
requests-toolbelt==0.10.1 ; python_version >= "3.7" and python_version < "3.12"
requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
requests==2.28.2 ; python_version >= "3.7" and python_version < "3.12"
rich==13.2.0 ; python_version >= "3.7" and python_version < "3.12"
rich==13.3.1 ; python_version >= "3.7" and python_version < "3.12"
rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.12"
routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
rsa==4.9 ; python_version >= "3.7" and python_version < "3.12"
ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
ruamel-yaml==0.17.21 ; python_version < "3.12" and python_version >= "3.7"
schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.12"
schema-salad==8.4.20230201194352 ; python_version >= "3.7" and python_version < "3.12"
setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12"
setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.12"
setuptools==67.1.0 ; python_version >= "3.7" and python_version < "3.12"
shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12"
six==1.16.0 ; python_version >= "3.7" and python_version < "3.12"
sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -195,5 +195,5 @@ webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12"
whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12"
yacman==0.8.4 ; python_version >= "3.7" and python_version < "3.12"
yarl==1.8.2 ; python_version >= "3.7" and python_version < "3.12"
zipp==3.11.0 ; python_version >= "3.7" and python_version < "3.10"
zipp==3.12.0 ; python_version >= "3.7" and python_version < "3.10"
zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12"
lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+2 -2
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@@ -5,7 +5,7 @@ mypy-extensions==0.4.3
pycparser==2.21
tomli==2.0.1
typed-ast==1.5.4
types-bleach==5.0.3.1
types-bleach==6.0.0.0
types-boto==2.49.18.5
types-contextvars==2.4.7
types-dataclasses==0.6.6
@@ -14,7 +14,7 @@ types-Markdown==3.4.2.2
types-paramiko==2.12.0.3
types-pkg-resources==0.1.3
types-python-dateutil==2.8.19.6
types-PyYAML==6.0.12.3
types-PyYAML==6.0.12.4
types-requests==2.28.11.8
types-six==1.16.21.4
types-urllib3==1.26.25.4
lib/galaxy/jobs/runners/drmaa.py
+1 -3
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@@ -70,9 +70,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
drmaa = __import__("drmaa")
except (ImportError, RuntimeError) as exc:
raise exc.__class__(
"The Python drmaa package is required to use this "
"feature, please install it or correct the "
"following error:\n%s: %s" % (exc.__class__.__name__, str(exc))
f"The Python drmaa package is required to use this feature, please install it or correct the following error:\n{exc.__class__.__name__}: {str(exc)}"
)
from pulsar.managers.util.drmaa import DrmaaSessionFactory
lib/galaxy/jobs/runners/kubernetes.py
+3 -2
View File
@@ -956,8 +956,9 @@ class KubernetesJobRunner(AsynchronousJobRunner):
jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
if len(jobs.response["items"]) > 1:
log.warning(
"More than one job matches selector: %s. Possible configuration error"
" in job id '%s'" % (jobs.response["items"], job_state.job_id)
"More than one job matches selector: %s. Possible configuration error in job id '%s'",
jobs.response["items"],
job_state.job_id,
)
elif len(jobs.response["items"]) == 0:
log.warning("No k8s job found which matches job id '%s'. Ignoring...", job_state.job_id)
lib/galaxy/model/orm/engine_factory.py
+1 -2
View File
@@ -117,8 +117,7 @@ def build_engine(
if connection_record.info["pid"] != pid:
connection_record.dbapi_connection = connection_proxy.dbapi_connection = None
raise exc.DisconnectionError(
"Connection record belongs to pid %s, "
"attempting to check out in pid %s" % (connection_record.info["pid"], pid)
f"Connection record belongs to pid {connection_record.info['pid']}, attempting to check out in pid {pid}"
)
return engine
lib/galaxy/objectstore/__init__.py
+2 -4
View File
@@ -986,12 +986,10 @@ class DistributedObjectStore(NestedObjectStore):
obj.object_store_id = random.choice(self.weighted_backend_ids)
except IndexError:
raise ObjectInvalid(
"objectstore.create, could not generate "
"obj.object_store_id: %s, kwargs: %s" % (str(obj), str(kwargs))
f"objectstore.create, could not generate obj.object_store_id: {obj}, kwargs: {kwargs}"
)
log.debug(
"Selected backend '%s' for creation of %s %s"
% (obj.object_store_id, obj.__class__.__name__, obj.id)
"Selected backend '%s' for creation of %s %s", obj.object_store_id, obj.__class__.__name__, obj.id
)
else:
log.debug(
lib/galaxy/web/framework/middleware/error.py
+1 -1
View File
@@ -461,7 +461,7 @@ def send_report(rep, exc_data, html=True):
markupsafe.escape(str(rep)), output.getvalue()
)
else:
return "Additionally an error occurred while sending the " "%s report:\n%s" % (str(rep), output.getvalue())
return f"Additionally an error occurred while sending the {rep} report:\n{output.getvalue()}"
else:
return ""
lib/galaxy/webapps/galaxy/api/job_files.py
+1 -1
View File
@@ -97,7 +97,7 @@ class JobFilesAPIController(BaseGalaxyAPIController):
)
assert file_path.startswith(
upload_store
), "Filename provided by nginx (%s) is not in correct" " directory (%s)" % (file_path, upload_store)
), f"Filename provided by nginx ({file_path}) is not in correct directory ({upload_store})"
input_file = open(file_path)
else:
input_file = payload.get("file", payload.get("__file", None)).file
lib/galaxy/webapps/util.py
+1 -2
View File
@@ -43,8 +43,7 @@ def wrap_if_allowed_or_fail(app, stack, wrap, name=None, args=None, kwargs=None)
name = name or wrap.__name__
if not stack.allowed_middleware(wrap):
raise MiddlewareWrapUnsupported(
"'%s' is enabled in your configuration but the %s application stack does not support it, this "
"middleware has been disabled" % (name, stack.name)
f"'{name}' is enabled in your configuration but the {stack.name} application stack does not support it, this middleware has been disabled"
)
args = args or []
kwargs = kwargs or {}