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Update Python dependencies #16577

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merged 4 commits into from
Sep 21, 2023
Merged

Update Python dependencies #16577

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39e5c11
Prevent downgrade of isa-rwval
nsoranzo Sep 19, 2023
9a0fc5f
Update Python dependencies
galaxybot Sep 16, 2023
d258e57
Fix new E721 errors from ruff 0.0.290
nsoranzo Sep 20, 2023
585e07c
Pin sphinx-rtd-theme to <2 to revert update to pre-release version
nsoranzo Sep 20, 2023
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4 changes: 2 additions & 2 deletions lib/galaxy/config/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ def resolve(key):
for key in self.schema.paths_to_resolve:
value = getattr(self, key)
# Check if value is a list or should be listified; if so, listify and resolve each item separately.
if type(value) is list or (self.listify_options and key in self.listify_options):
if isinstance(value, list) or (self.listify_options and key in self.listify_options):
saved_values = listify(getattr(self, key), do_strip=True) # listify and save original value
setattr(self, key, "_") # replace value with temporary placeholder
resolve(key) # resolve temporary value (`_` becomes `parent-path/_`)
Expand Down Expand Up @@ -546,7 +546,7 @@ def get_path(current_path, initial_path):
return current_path

current_value = getattr(self, key) # resolved path or list of resolved paths
if type(current_value) is list:
if isinstance(current_value, list):
initial_paths = listify(self._raw_config[key], do_strip=True) # initial unresolved paths
updated_paths = []
# check and, if needed, update each path in the list
Expand Down
35 changes: 18 additions & 17 deletions lib/galaxy/dependencies/dev-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12"
billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12"
black==23.3.0 ; python_version >= "3.7" and python_version < "3.12"
bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12"
build==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
build==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12"
cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -22,24 +22,24 @@ 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==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
click==8.1.7 ; 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==41.0.3 ; 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"
cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12"
cwltest==2.3.20230825125225 ; python_version >= "3.7" and python_version < "3.12"
cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
darker==1.7.2 ; 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"
exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.12"
exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.12"
filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12"
frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
galaxy-release-util==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
galaxy-release-util==0.1.5 ; python_version >= "3.7" and python_version < "3.12"
h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.12"
httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -55,14 +55,15 @@ jeepney==0.8.0 ; python_version >= "3.7" and python_version < "3.12" and sys_pla
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"
keyring==24.1.1 ; python_version >= "3.7" and python_version < "3.12"
kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
kiwisolver==1.4.5 ; python_version >= "3.7" and python_version < "3.12"
kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12"
lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12"
markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.12"
markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.8"
matplotlib==3.7.2 ; python_version >= "3.8" and python_version < "3.12"
matplotlib==3.7.3 ; python_version >= "3.8" and python_version < "3.9"
matplotlib==3.8.0 ; python_version >= "3.9" and python_version < "3.12"
mdit-py-plugins==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
mirakuru==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -74,7 +75,7 @@ mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.25.2 ; python_version >= "3.9" and python_version < "3.12"
numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12"
outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
pathspec==0.11.2 ; python_version >= "3.7" and python_version < "3.12"
Expand Down Expand Up @@ -106,10 +107,10 @@ pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12"
pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12"
pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
pytest==7.4.0 ; python_version >= "3.7" and python_version < "3.12"
pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.12"
python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12"
pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12"
pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12"
pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32"
pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -118,13 +119,13 @@ requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
responses==0.23.3 ; python_version >= "3.7" and python_version < "3.12"
rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.12"
rich==13.5.2 ; python_version >= "3.7" and python_version < "3.12"
rich==13.5.3 ; 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==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12"
scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.11.1 ; python_version >= "3.9" and python_version < "3.12"
scipy==1.11.2 ; python_version >= "3.9" and python_version < "3.12"
secretstorage==3.3.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
selenium==4.11.2 ; python_version >= "3.7" and python_version < "3.12"
seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -133,7 +134,7 @@ 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"
sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12"
sphinx-rtd-theme==1.2.2 ; python_version >= "3.7" and python_version < "3.12"
sphinx-rtd-theme==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.12"
sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -143,11 +144,11 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.7" and python_version < "3.12
sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12"
testfixtures==7.1.0 ; python_version >= "3.7" and python_version < "3.12"
testfixtures==7.2.0 ; python_version >= "3.7" and python_version < "3.12"
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"
tomli==2.0.1 ; python_version >= "3.7" and python_full_version <= "3.11.0a6"
trio-websocket==0.10.4 ; 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"
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pinned-lint-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,6 @@ importlib-metadata==4.2.0
mccabe==0.7.0
pycodestyle==2.9.1
pyflakes==2.5.0
ruff==0.0.284
ruff==0.0.290
typing_extensions==4.7.1
zipp==3.15.0
37 changes: 18 additions & 19 deletions lib/galaxy/dependencies/pinned-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,19 +1,17 @@
--extra-index-url https://wheels.galaxyproject.org/simple
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Was that intentional ?

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Not sure what changed, but it was removed automatically when doing poetry export ... . I don't think it matters as we explicitly pass the --extra-index-url option to pip in scripts/common_startup.sh (and all tests still pass).


a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12"
adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12"
aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12"
aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12"
aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12"
aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
alembic==1.11.2 ; python_version >= "3.7" and python_version < "3.12"
alembic==1.12.0 ; python_version >= "3.7" and python_version < "3.12"
amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12"
apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
argcomplete==3.1.1 ; python_version >= "3.7" and python_version < "3.12"
argcomplete==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12"
asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8"
attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12"
Expand Down Expand Up @@ -43,17 +41,17 @@ 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==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
click==8.1.7 ; 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"
cloudbridge==3.2.0 ; 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"
coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12"
conda-package-streaming==0.9.0 ; python_version >= "3.7" and python_version < "3.12"
cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12"
cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12"
cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12"
cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12"
cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
cython==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
cython==3.0.2 ; 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"
deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -65,7 +63,7 @@ dparse==0.6.3 ; 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==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12"
exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.11"
exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.11"
fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
fastapi==0.98.0 ; python_version >= "3.7" and python_version < "3.12"
filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -76,7 +74,7 @@ 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==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "win32" or platform_machine == "WIN32" or platform_machine == "AMD64" or platform_machine == "amd64" or platform_machine == "x86_64" or platform_machine == "ppc64le" or platform_machine == "aarch64") 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==21.2.0 ; python_version >= "3.7" and python_version < "3.12"
gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -100,20 +98,20 @@ markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
markdown==3.4.4 ; python_version >= "3.7" and python_version < "3.12"
markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
mercurial==6.5.1 ; python_version >= "3.7" and python_version < "3.12"
mercurial==6.5.2 ; python_version >= "3.7" and python_version < "3.12"
mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12"
mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
msal==1.23.0 ; python_version >= "3.7" and python_version < "3.12"
msal==1.24.0 ; python_version >= "3.7" and python_version < "3.12"
msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.12"
multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12"
mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
networkx==2.5 ; python_version >= "3.7" and python_version < "3.12"
nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.25.2 ; python_version >= "3.9" and python_version < "3.12"
numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12"
oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
orjson==3.9.4 ; python_version >= "3.7" and python_version < "3.12"
orjson==3.9.7 ; python_version >= "3.7" and python_version < "3.12"
oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -125,10 +123,10 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9
prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12"
prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12"
pulsar-galaxy-lib==0.15.3 ; python_version >= "3.7" and python_version < "3.12"
pulsar-galaxy-lib==0.15.5 ; python_version >= "3.7" and python_version < "3.12"
pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.12"
pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
pycryptodome==3.18.0 ; python_version >= "3.7" and python_version < "3.12"
pycryptodome==3.19.0 ; python_version >= "3.7" and python_version < "3.12"
pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12"
pydantic==1.10.12 ; python_version >= "3.7" and python_version < "3.12"
pydantic[email]==1.10.12 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -151,7 +149,7 @@ python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12"
python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12"
python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12"
pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12"
pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12"
rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
Expand All @@ -162,7 +160,7 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
rich==13.5.2 ; python_version >= "3.7" and python_version < "3.12"
rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12"
rocrate==0.8.0 ; 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"
Expand All @@ -184,9 +182,10 @@ starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12"
supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
tenacity==8.2.2 ; python_version >= "3.7" and python_version < "3.12"
tenacity==8.2.3 ; python_version >= "3.7" and python_version < "3.12"
tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12"
tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
tornado==6.2 ; python_version >= "3.7" and python_version < "3.12"
tqdm==4.66.1 ; python_version >= "3.7" and python_version < "3.12"
tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
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