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Towards moving to alembic [WIP] #11415

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Towards moving to alembic [WIP] #11415

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092b5dd
Pin pytest-postgresql to 2.5.2
jdavcs Feb 19, 2021
5e440cb
Pin mypy to 0.790
jdavcs Feb 19, 2021
1f572ae
Add alembic to pyproject.toml
jdavcs Feb 19, 2021
019302e
Update all dependencies
jdavcs Feb 19, 2021
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100 changes: 52 additions & 48 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
--extra-index-url https://wheels.galaxyproject.org/simple

adal==1.2.5
adal==1.2.6
aiofiles==0.6.0
alabaster==0.7.12; python_version >= "3.5"
amqp==5.0.3; python_version >= "3.6"
alembic==1.5.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
amqp==5.0.5; python_version >= "3.6"
appdirs==1.4.4; python_version >= "3.6"
argcomplete==1.12.2; python_version >= "3.6" and python_version < "4"
async-exit-stack==1.0.1; python_version >= "3.6" and python_version < "3.7"
Expand All @@ -12,34 +13,35 @@ atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" a
attmap==0.12.11
attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
babel==2.9.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
bagit==1.7.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.4.0" and python_version < "4" and python_version >= "3.6"
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==1.5.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" 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
bioblend==0.14.0; python_version >= "3.5"
bleach==3.2.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
bioblend==0.15.0; python_version >= "3.6"
bleach==3.3.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
boltons==20.2.1
boto3==1.16.57
boto3==1.16.63
boto==2.49.0
botocore==1.19.57
botocore==1.19.63
bx-python==0.8.9; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
cachetools==4.2.0; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
cachetools==4.2.1; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cffi==1.14.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
cffi==1.14.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cheetah3==3.2.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
click==7.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
cliff==3.6.0; python_version >= "3.6"
cliff==3.7.0; python_version >= "3.6"
cloudauthz==0.6.0
cloudbridge==2.1.0
cmd2==1.4.0; python_version >= "3.6"
cmd2==1.5.0; python_version >= "3.6"
colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
coloredlogs==15.0; 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"
commonmark==0.9.1
coverage==5.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cryptography==3.3.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
coverage==5.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cryptography==3.4.6; python_version >= "3.6"
cwltool==3.0.20201109103151; python_version >= "3.6" and python_version < "4"
dataclasses==0.8; python_version >= "3.6" and python_version < "3.7"
debtcollector==2.2.0; python_version >= "3.6"
Expand All @@ -50,34 +52,34 @@ deprecation==2.1.0
dictobj==0.4
docopt==0.6.2
docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
dogpile.cache==1.1.1; python_version >= "3.6"
dogpile.cache==1.1.2; python_version >= "3.6"
ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
fabric3==1.14.post1
fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
fastapi==0.63.0; python_version >= "3.6"
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")
galaxy-sequence-utils==1.1.5
google-api-core==1.25.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
google-api-core==1.26.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
google-api-python-client==1.12.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
google-auth-httplib2==0.0.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
google-auth==1.24.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
google-auth==1.27.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
googleapis-common-protos==1.52.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
gunicorn==20.0.4; python_version >= "3.4"
gxformat2==0.15.0
h11==0.12.0; python_version >= "3.6"
h5py==3.1.0; python_version >= "3.6"
httplib2==0.18.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
httplib2==0.19.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
humanfriendly==9.1; 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==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
imagesize==1.2.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5"
importlib-metadata==3.4.0; python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
importlib-resources==5.1.0; python_version < "3.7" and python_version >= "3.6"
iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
isa-rwval==0.10.9
iso8601==0.1.13; python_version >= "3.6"
iso8601==0.1.14; python_version >= "3.6"
isodate==0.6.0; python_version >= "3.6" and python_version < "4"
jinja2==2.11.2; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5"
jinja2==2.11.3; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5"
jmespath==0.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
jsonpatch==1.28; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
jsonpointer==2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
Expand All @@ -86,10 +88,10 @@ kombu==5.0.2; python_version >= "3.6"
lockfile==0.12.2; python_version >= "3.6" and python_version < "4"
lxml==4.6.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
mako==1.1.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
markdown==3.3.3; python_version >= "3.6"
markdown-it-reporter==0.0.2
markdown==3.3.3; python_version >= "3.6"
markupsafe==1.1.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
mercurial==5.6.1
mercurial==5.7
mirakuru==2.3.0; python_version >= "3.6"
mistune==0.8.4; python_version >= "3.6" and python_version < "4"
msgpack==1.0.2; python_version >= "3.6"
Expand All @@ -112,60 +114,61 @@ oslo.config==8.4.0; python_version >= "3.6"
oslo.context==3.1.1; python_version >= "3.6"
oslo.i18n==5.0.1; python_version >= "3.6"
oslo.log==4.4.0; python_version >= "3.6"
oslo.serialization==4.0.1; python_version >= "3.6"
oslo.utils==4.7.0; python_version >= "3.6"
oslo.serialization==4.1.0; python_version >= "3.6"
oslo.utils==4.8.0; python_version >= "3.6"
oyaml==1.0
packaging==20.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
packaging==20.9; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
paramiko==2.7.2
parsley==1.3
paste==3.5.0
pastedeploy==2.1.1
pastescript==3.2.0
pbr==5.5.1; python_version >= "3.6"
pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
port-for==0.4; python_version >= "3.6"
prettytable==0.7.2; python_version >= "3.6"
protobuf==3.14.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
protobuf==3.15.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
prov==1.5.1; python_version >= "3.6" and python_version < "4"
psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
pulsar-galaxy-lib==0.14.2
py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
pycryptodome==3.9.9; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
pycryptodome==3.10.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
pydot==1.4.1; 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 >= "3.4.0"
pydot==1.4.2; 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 >= "3.4.0"
pyeventsystem==0.1.0
pyfaidx==0.5.9.2
pygithub==1.54.1; python_version >= "3.6"
pygments==2.7.4; python_version >= "3.5"
pygments==2.8.0; python_version >= "3.5"
pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
pyjwt==1.7.1; python_version >= "3.6"
pykwalify==1.8.0
pynacl==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
pyperclip==1.8.1; python_version >= "3.6"
pyreadline==2.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" and sys_platform == "win32" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" and sys_platform == "win32"
pyreadline3==3.3; sys_platform == "win32" and python_version >= "3.8"
pyreadline==2.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" and sys_platform == "win32" or python_version >= "3.6" and python_version < "3.8" and python_full_version >= "3.5.0" and sys_platform == "win32"
pysam==0.16.0.1
pytest-cov==2.11.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
pytest-html==3.1.1; python_version >= "3.6"
pytest-json-report==1.2.4
pytest-metadata==1.11.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
pytest-mock==3.5.1; python_version >= "3.5"
pytest-postgresql==2.5.2; python_version >= "3.6"
pytest-pythonpath==0.7.3
pytest-shard==0.1.2; python_version >= "3.6"
pytest==6.2.1; python_version >= "3.6"
python-dateutil==2.8.1; 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 >= "3.3.0"
python-irodsclient==0.8.5
pytest-json-report==1.2.1
pytest==6.2.2; python_version >= "3.6"
python-dateutil==2.8.1; 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 >= "3.6.0"
python-editor==1.0.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
python-irodsclient==0.8.6
python-jose==3.2.0
python-keystoneclient==4.1.1; python_version >= "3.6"
python-neutronclient==7.2.1; python_version >= "3.6"
python-novaclient==17.2.1; python_version >= "3.6"
python-swiftclient==3.10.1
python3-openid==3.2.0; python_version >= "3.0"
pytz==2020.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
pytz==2021.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
pyuwsgi==2.0.19.1.post0
pyyaml==5.4.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
rdflib-jsonld==0.5.0; python_version >= "3.6" and python_version < "4"
Expand All @@ -174,17 +177,17 @@ recommonmark==0.7.1
refgenconf==0.9.3
repoze.lru==0.7
requests-oauthlib==1.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
requests-toolbelt==0.9.1; python_version >= "3.5"
requests-toolbelt==0.9.1; python_version >= "3.6"
requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
requestsexceptions==1.4.0; python_version >= "3.6"
responses==0.12.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
rfc3986==1.4.0; python_version >= "3.6"
routes==2.5.1
rsa==4.7; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
rsa==4.7.1; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
ruamel.yaml.clib==0.2.2; platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"
ruamel.yaml==0.16.5; python_version >= "3.6" and python_version < "4"
s3transfer==0.3.4
schema-salad==7.0.20201119201711; python_version >= "3.6" and python_version < "4"
schema-salad==7.0.20210124093443; python_version >= "3.6" and python_version < "4"
selenium==3.141.0
setuptools-scm==5.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
shellescape==3.4.1; python_version >= "3.6" and python_version < "4"
Expand All @@ -195,7 +198,7 @@ social-auth-core==3.3.0
sortedcontainers==2.3.0
sphinx-markdown-tables==0.0.15
sphinx-rtd-theme==0.5.1
sphinx==3.4.3; python_version >= "3.5"
sphinx==3.5.1; python_version >= "3.5"
sphinxcontrib-applehelp==1.0.2; python_version >= "3.5"
sphinxcontrib-devhelp==1.0.2; python_version >= "3.5"
sphinxcontrib-htmlhelp==1.0.3; python_version >= "3.5"
Expand All @@ -204,30 +207,31 @@ sphinxcontrib-qthelp==1.0.3; python_version >= "3.5"
sphinxcontrib-serializinghtml==1.1.4; python_version >= "3.5"
sqlalchemy-migrate==0.13.0
sqlalchemy-utils==0.36.7
sqlalchemy==1.3.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
sqlalchemy==1.3.23; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
sqlitedict==1.7.0
sqlparse==0.4.1; python_version >= "3.5"
starlette==0.13.6; python_version >= "3.6" and python_version < "4.0"
statsd==3.3.0
stevedore==3.3.0; python_version >= "3.6"
svgwrite==1.4.1; python_version >= "3.6"
tempita==0.5.2
tenacity==6.3.1
testfixtures==6.17.1
toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
tqdm==4.56.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
twill==2.0.1
tqdm==4.57.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
twill==2.0.2
typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8"
tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version < "4"
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==0.6.1
unidecode==1.1.2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.0"
unidecode==1.2.0; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.0"
uritemplate==3.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
urllib3==1.26.2; python_version >= "2.7" and python_full_version < "3.0.0" and python_version != "3.4" or python_full_version >= "3.5.0" and python_version < "4" and python_version != "3.4"
urllib3==1.26.3; python_version >= "2.7" and python_full_version < "3.0.0" and python_version != "3.4" or python_full_version >= "3.5.0" and python_version < "4" and python_version != "3.4"
uvicorn==0.13.3
vine==5.0.0; python_version >= "3.6"
watchdog==1.0.2; python_version >= "3.6"
watchdog==2.0.1; python_version >= "3.6"
wcwidth==0.2.5; python_version >= "3.6"
webencodings==0.5.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
webob==1.8.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
webob==1.8.7; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
whoosh==2.7.4
wrapt==1.12.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
xmlrunner==1.7.7
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2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/lint-requirements.txt
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flake8
flake8-bugbear
flake8-import-order
mypy
mypy==0.790
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