From e2e1c4a6d209833f8a705adcbee29af63c90fb8e Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 16 Apr 2022 03:21:15 +0000 Subject: [PATCH 1/2] Update Python dependencies --- lib/galaxy/dependencies/dev-requirements.txt | 20 +++++++++---------- .../dependencies/pinned-lint-requirements.txt | 20 +++++++++---------- .../dependencies/pinned-requirements.txt | 11 +++++----- 3 files changed, 26 insertions(+), 25 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 0b90449cd11..e74b97d2158 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -20,7 +20,7 @@ babel==2.9.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (py bagit-profile==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" bagit==1.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" bcrypt==3.2.0; python_version >= "3.6" -bdbag==1.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") +bdbag==1.6.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") beaker==1.11.0 billiard==3.6.4.0; python_version >= "3.7" bioblend==0.16.0; python_version >= "3.6" @@ -65,7 +65,7 @@ fabric3==1.14.post1 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0" fastapi==0.75.1; python_full_version >= "3.6.1" fluent-logger==0.10.0; python_version >= "3.5" -fonttools==4.31.2; python_version >= "3.7" +fonttools==4.32.0; python_version >= "3.7" fs==2.4.15 funcsigs==1.0.2 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0") @@ -82,7 +82,7 @@ humanfriendly==10.0; python_version >= "3.6" and python_full_version < "3.0.0" a idna==3.3 imagesize==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" importlib-metadata==4.11.3; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") and python_full_version >= "3.6.2" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") -importlib-resources==5.6.0; python_version >= "3.7" +importlib-resources==5.7.0; python_version >= "3.7" iniconfig==1.1.1; python_version >= "3.7" isa-rwval==0.10.10 isodate==0.6.1; python_version >= "3.7" and python_version < "4" @@ -115,7 +115,7 @@ numpy==1.21.1; python_version >= "3.7" oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" outcome==1.1.0; python_version >= "3.7" and python_version < "4.0" oyaml==1.0 -packaging==21.3; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7" +packaging==21.3; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" paramiko==2.10.3 parsley==1.3 paste==3.5.0 @@ -146,7 +146,7 @@ pykwalify==1.8.0 pylibmagic==0.2.0; python_version >= "3.7" pynacl==1.5.0; python_version >= "3.6" pyopenssl==22.0.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7" -pyparsing==3.0.7; python_version >= "3.6" +pyparsing==3.0.8; python_full_version >= "3.6.8" pyreadline3==3.4.1; sys_platform == "win32" and python_version >= "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0") pyreadline==2.1; sys_platform == "win32" and python_version < "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0") pyrsistent==0.18.1; python_version >= "3.7" @@ -186,9 +186,9 @@ rsa==4.8; python_version >= "3.6" and python_version < "4" ruamel.yaml.clib==0.2.6; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.6" ruamel.yaml==0.17.17; python_version >= "3.7" and python_version < "4" schema-salad==8.2.20220204150214; python_version >= "3.7" and python_version < "4" -scipy==1.7.3; python_version >= "3.7" +scipy==1.6.1; python_version >= "3.7" selenium==4.1.3; python_version >= "3.7" and python_version < "4.0" -setuptools-scm==5.0.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" +setuptools-scm==6.4.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" shellescape==3.8.1; python_version >= "3.6" and python_version < "4" six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.3.0" and python_version >= "3.7" and python_version < "4" sniffio==1.2.0; python_version >= "3.7" and python_full_version >= "3.6.2" and python_version < "4.0" @@ -219,15 +219,15 @@ testfixtures==6.18.5 tifffile==2021.11.2; python_version >= "3.7" tinydb==4.7.0; python_version >= "3.6" and python_version < "4.0" toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6" -tomli==2.0.1; python_version < "3.11" and python_full_version >= "3.6.2" and python_version >= "3.7" +tomli==2.0.1; python_version < "3.11" and python_full_version >= "3.6.2" and python_version >= "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7") tornado==6.1; python_version >= "3.5" tqdm==4.64.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" trio-websocket==0.9.2; python_version >= "3.7" and python_version < "4.0" trio==0.20.0; python_version >= "3.7" and python_version < "4.0" tuspy==0.2.5 tuswsgi==0.5.4 -twill==3.0.1 -typed-ast==1.5.2; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.6" +twill==3.0.2 +typed-ast==1.5.3; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.6" typing-extensions==4.1.1; python_version >= "3.6" tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" ubiquerg==0.6.2 diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 20c852fb1ed..42b20b584c3 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -8,20 +8,20 @@ mypy-extensions==0.4.3 pycodestyle==2.8.0 pyflakes==2.4.0 tomli==2.0.1 -typed-ast==1.5.2 -types-bleach==4.1.5 -types-boto==2.49.11 +typed-ast==1.5.3 +types-bleach==5.0.1 +types-boto==2.49.12 types-contextvars==2.4.4 types-cryptography==3.3.19 types-dataclasses==0.6.4 -types-docutils==0.18.0 +types-docutils==0.18.1 types-Markdown==3.3.12 -types-paramiko==2.8.17 +types-paramiko==2.8.18 types-pkg-resources==0.1.3 -types-python-dateutil==2.8.10 -types-PyYAML==6.0.5 -types-requests==2.27.16 -types-six==1.16.12 -types-urllib3==1.26.11 +types-python-dateutil==2.8.11 +types-PyYAML==6.0.6 +types-requests==2.27.17 +types-six==1.16.15 +types-urllib3==1.26.12 typing_extensions==4.1.1 zipp==3.8.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 9423e9222d5..0d3936f1db6 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -16,7 +16,7 @@ babel==2.9.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (py bagit-profile==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" bagit==1.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" bcrypt==3.2.0; python_version >= "3.6" -bdbag==1.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") +bdbag==1.6.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") beaker==1.11.0 billiard==3.6.4.0; python_version >= "3.7" bioblend==0.16.0; python_version >= "3.6" @@ -67,7 +67,7 @@ h5py==3.6.0; python_version >= "3.7" humanfriendly==10.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" idna==3.3; python_full_version >= "3.6.2" and python_version >= "3.7" and python_version < "4" importlib-metadata==4.11.3; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") -importlib-resources==5.6.0; python_version >= "3.7" +importlib-resources==5.7.0; python_version >= "3.7" isa-rwval==0.10.10 isodate==0.6.1; python_version >= "3.7" and python_version < "4" jsonref==0.2; python_version >= "3.6" @@ -90,7 +90,7 @@ nose==1.3.7 numpy==1.21.1; python_version >= "3.7" oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" oyaml==1.0 -packaging==21.3; python_version >= "3.6" +packaging==21.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" paramiko==2.10.3 parsley==1.3 paste==3.5.0 @@ -113,7 +113,7 @@ pyjwt==2.3.0; python_version >= "3.6" pykwalify==1.8.0 pylibmagic==0.2.0; python_version >= "3.7" pynacl==1.5.0; python_version >= "3.6" -pyparsing==3.0.7; python_version >= "3.6" +pyparsing==3.0.8; python_full_version >= "3.6.8" pyreadline3==3.4.1; sys_platform == "win32" and python_version >= "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0") pyreadline==2.1; sys_platform == "win32" and python_version < "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0") pyrsistent==0.18.1; python_version >= "3.7" @@ -138,7 +138,7 @@ rsa==4.8; python_version >= "3.6" and python_version < "4" ruamel.yaml.clib==0.2.6; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.6" ruamel.yaml==0.17.17; python_version >= "3.7" and python_version < "4" schema-salad==8.2.20220204150214; python_version >= "3.7" and python_version < "4" -setuptools-scm==5.0.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" +setuptools-scm==6.4.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" shellescape==3.8.1; python_version >= "3.6" and python_version < "4" six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.3.0" and python_version >= "3.7" and python_version < "4" sniffio==1.2.0; python_version >= "3.7" and python_full_version >= "3.6.2" @@ -155,6 +155,7 @@ svgwrite==1.4.2; python_version >= "3.6" tempita==0.5.2 tenacity==8.0.1; python_version >= "3.6" tifffile==2021.11.2; python_version >= "3.7" +tomli==2.0.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" tornado==6.1; python_version >= "3.5" tqdm==4.64.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" tuswsgi==0.5.4 From faeba22f30e70bd13253d966b207cc17555ad143 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 19 Apr 2022 12:30:02 +0100 Subject: [PATCH 2/2] Stricter maximum Python version to appease numpy and scipy xref.: https://github.com/scipy/scipy/pull/12862 --- lib/galaxy/dependencies/dev-requirements.txt | 24 +++++++++---------- .../dependencies/pinned-lint-requirements.txt | 20 ++++++++-------- .../dependencies/pinned-requirements.txt | 17 +++++++------ pyproject.toml | 2 +- 4 files changed, 31 insertions(+), 32 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index e74b97d2158..4b5403d53c3 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -5,7 +5,7 @@ adal==1.2.7 aiofiles==0.8.0; python_version >= "3.6" and python_version < "4.0" alabaster==0.7.12; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" alembic==1.7.7; python_version >= "3.6" -amqp==5.1.0; python_version >= "3.7" +amqp==5.1.1; python_version >= "3.7" anyio==3.5.0; python_version >= "3.7" and python_full_version >= "3.6.2" apispec==5.1.1; python_version >= "3.6" appdirs==1.4.4 @@ -20,7 +20,7 @@ babel==2.9.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (py bagit-profile==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" bagit==1.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" bcrypt==3.2.0; python_version >= "3.6" -bdbag==1.6.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") +bdbag==1.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") beaker==1.11.0 billiard==3.6.4.0; python_version >= "3.7" bioblend==0.16.0; python_version >= "3.6" @@ -63,7 +63,7 @@ ecdsa==0.17.0; python_version >= "2.6" and python_full_version < "3.0.0" or pyth edam-ontology==1.25.2 fabric3==1.14.post1 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0" -fastapi==0.75.1; python_full_version >= "3.6.1" +fastapi==0.75.2; python_full_version >= "3.6.1" fluent-logger==0.10.0; python_version >= "3.5" fonttools==4.32.0; python_version >= "3.7" fs==2.4.15 @@ -82,7 +82,7 @@ humanfriendly==10.0; python_version >= "3.6" and python_full_version < "3.0.0" a idna==3.3 imagesize==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" importlib-metadata==4.11.3; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") and python_full_version >= "3.6.2" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") -importlib-resources==5.7.0; python_version >= "3.7" +importlib-resources==5.7.1; python_version >= "3.7" iniconfig==1.1.1; python_version >= "3.7" isa-rwval==0.10.10 isodate==0.6.1; python_version >= "3.7" and python_version < "4" @@ -111,11 +111,11 @@ networkx==2.5; python_version >= "3.6" and python_version < "4" nodeenv==1.6.0 nose==1.3.7 nosehtml==0.4.6 -numpy==1.21.1; python_version >= "3.7" +numpy==1.21.6; python_version >= "3.7" and python_version < "3.11" oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" outcome==1.1.0; python_version >= "3.7" and python_version < "4.0" oyaml==1.0 -packaging==21.3; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" +packaging==21.3; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7" paramiko==2.10.3 parsley==1.3 paste==3.5.0 @@ -123,7 +123,7 @@ pastedeploy==2.1.1 pathspec==0.9.0; python_full_version >= "3.6.2" and python_version >= "3.6" pbr==5.8.1; python_version >= "2.6" pillow==9.1.0; python_version >= "3.7" -platformdirs==2.5.1; python_version >= "3.7" and python_full_version >= "3.6.2" +platformdirs==2.5.2; python_version >= "3.7" and python_full_version >= "3.6.2" pluggy==1.0.0; python_version >= "3.7" port-for==0.6.2; python_version >= "3.7" prettytable==3.2.0; python_version >= "3.7" @@ -157,7 +157,7 @@ pytest-celery==0.0.0 pytest-cov==3.0.0; python_version >= "3.6" pytest-html==3.1.1; python_version >= "3.6" pytest-json-report==1.5.0 -pytest-metadata==2.0.0; python_version >= "3.7" and python_version < "4.0" +pytest-metadata==2.0.1; python_full_version >= "3.7.0" and python_full_version < "3.11.0" and python_version >= "3.6" pytest-mock==3.7.0; python_version >= "3.7" pytest-postgresql==4.1.1; python_version >= "3.7" pytest-shard==0.1.2; python_version >= "3.6" @@ -186,9 +186,9 @@ rsa==4.8; python_version >= "3.6" and python_version < "4" ruamel.yaml.clib==0.2.6; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.6" ruamel.yaml==0.17.17; python_version >= "3.7" and python_version < "4" schema-salad==8.2.20220204150214; python_version >= "3.7" and python_version < "4" -scipy==1.6.1; python_version >= "3.7" +scipy==1.7.3; python_version >= "3.7" and python_version < "3.11" selenium==4.1.3; python_version >= "3.7" and python_version < "4.0" -setuptools-scm==6.4.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" +setuptools-scm==5.0.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" shellescape==3.8.1; python_version >= "3.6" and python_version < "4" six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.3.0" and python_version >= "3.7" and python_version < "4" sniffio==1.2.0; python_version >= "3.7" and python_full_version >= "3.6.2" and python_version < "4.0" @@ -219,7 +219,7 @@ testfixtures==6.18.5 tifffile==2021.11.2; python_version >= "3.7" tinydb==4.7.0; python_version >= "3.6" and python_version < "4.0" toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6" -tomli==2.0.1; python_version < "3.11" and python_full_version >= "3.6.2" and python_version >= "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7") +tomli==2.0.1; python_version < "3.11" and python_full_version >= "3.6.2" and python_version >= "3.7" tornado==6.1; python_version >= "3.5" tqdm==4.64.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" trio-websocket==0.9.2; python_version >= "3.7" and python_version < "4.0" @@ -228,7 +228,7 @@ tuspy==0.2.5 tuswsgi==0.5.4 twill==3.0.2 typed-ast==1.5.3; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.6" -typing-extensions==4.1.1; python_version >= "3.6" +typing-extensions==4.2.0; python_version >= "3.7" tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" ubiquerg==0.6.2 urllib3==1.26.9; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 42b20b584c3..177c3e8c6d1 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -10,18 +10,18 @@ pyflakes==2.4.0 tomli==2.0.1 typed-ast==1.5.3 types-bleach==5.0.1 -types-boto==2.49.12 -types-contextvars==2.4.4 -types-cryptography==3.3.19 -types-dataclasses==0.6.4 -types-docutils==0.18.1 -types-Markdown==3.3.12 -types-paramiko==2.8.18 +types-boto==2.49.13 +types-contextvars==2.4.5 +types-cryptography==3.3.20 +types-dataclasses==0.6.5 +types-docutils==0.18.2 +types-Markdown==3.3.13 +types-paramiko==2.8.19 types-pkg-resources==0.1.3 types-python-dateutil==2.8.11 types-PyYAML==6.0.6 -types-requests==2.27.17 +types-requests==2.27.19 types-six==1.16.15 -types-urllib3==1.26.12 -typing_extensions==4.1.1 +types-urllib3==1.26.13 +typing_extensions==4.2.0 zipp==3.8.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 0d3936f1db6..fcf95edbbdc 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -4,7 +4,7 @@ a2wsgi==1.4.1; python_full_version >= "3.6.2" adal==1.2.7 aiofiles==0.8.0; python_version >= "3.6" and python_version < "4.0" alembic==1.7.7; python_version >= "3.6" -amqp==5.1.0; python_version >= "3.7" +amqp==5.1.1; python_version >= "3.7" anyio==3.5.0; python_version >= "3.7" and python_full_version >= "3.6.2" apispec==5.1.1; python_version >= "3.6" appdirs==1.4.4 @@ -16,7 +16,7 @@ babel==2.9.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (py bagit-profile==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" bagit==1.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" bcrypt==3.2.0; python_version >= "3.6" -bdbag==1.6.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") +bdbag==1.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4") beaker==1.11.0 billiard==3.6.4.0; python_version >= "3.7" bioblend==0.16.0; python_version >= "3.6" @@ -53,7 +53,7 @@ ecdsa==0.17.0; python_version >= "2.6" and python_full_version < "3.0.0" or pyth edam-ontology==1.25.2 fabric3==1.14.post1 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0" -fastapi==0.75.1; python_full_version >= "3.6.1" +fastapi==0.75.2; python_full_version >= "3.6.1" fs==2.4.15 funcsigs==1.0.2 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0") @@ -67,7 +67,7 @@ h5py==3.6.0; python_version >= "3.7" humanfriendly==10.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" idna==3.3; python_full_version >= "3.6.2" and python_version >= "3.7" and python_version < "4" importlib-metadata==4.11.3; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") -importlib-resources==5.7.0; python_version >= "3.7" +importlib-resources==5.7.1; python_version >= "3.7" isa-rwval==0.10.10 isodate==0.6.1; python_version >= "3.7" and python_version < "4" jsonref==0.2; python_version >= "3.6" @@ -87,10 +87,10 @@ mypy-extensions==0.4.3; python_version >= "3.6" and python_version < "4" networkx==2.5; python_version >= "3.6" and python_version < "4" nodeenv==1.6.0 nose==1.3.7 -numpy==1.21.1; python_version >= "3.7" +numpy==1.21.6; python_version >= "3.7" and python_version < "3.11" oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" oyaml==1.0 -packaging==21.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" +packaging==21.3; python_version >= "3.6" paramiko==2.10.3 parsley==1.3 paste==3.5.0 @@ -138,7 +138,7 @@ rsa==4.8; python_version >= "3.6" and python_version < "4" ruamel.yaml.clib==0.2.6; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.6" ruamel.yaml==0.17.17; python_version >= "3.7" and python_version < "4" schema-salad==8.2.20220204150214; python_version >= "3.7" and python_version < "4" -setuptools-scm==6.4.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6" +setuptools-scm==5.0.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" shellescape==3.8.1; python_version >= "3.6" and python_version < "4" six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.3.0" and python_version >= "3.7" and python_version < "4" sniffio==1.2.0; python_version >= "3.7" and python_full_version >= "3.6.2" @@ -155,11 +155,10 @@ svgwrite==1.4.2; python_version >= "3.6" tempita==0.5.2 tenacity==8.0.1; python_version >= "3.6" tifffile==2021.11.2; python_version >= "3.7" -tomli==2.0.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" tornado==6.1; python_version >= "3.5" tqdm==4.64.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" tuswsgi==0.5.4 -typing-extensions==4.1.1; python_version >= "3.6" +typing-extensions==4.2.0; python_version >= "3.7" tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" ubiquerg==0.6.2 urllib3==1.26.9; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6" diff --git a/pyproject.toml b/pyproject.toml index caf6f7f34fe..e5ec281fc4e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -83,7 +83,7 @@ pykwalify = "*" pylibmagic = "*" pyparsing = "*" pysam = "*" -python = ">=3.7,<4" +python = ">=3.7,<3.11" # Keep maximum version strict to appease numpy and scipy python-dateutil = "*" python-magic = "*" python-multipart = "*" # required to support form parsing in FastAPI/Starlette