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Update Python dependencies #17157

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merged 2 commits into from
Dec 12, 2023
Merged

Update Python dependencies #17157

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65f1633
Update Python dependencies
galaxybot Dec 9, 2023
9339fb3
Fix B018 errors reported by flake8-bugbear 23.12.2
nsoranzo Dec 11, 2023
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4 changes: 2 additions & 2 deletions lib/galaxy/config_watchers.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -31,13 +31,13 @@ def reload_toolbox():
try:
# Run and wait for toolbox reload on the process that watches the config files.
# The toolbox reload will update the integrated_tool_panel_file
self.app.queue_worker.send_local_control_task("reload_toolbox", get_response=True),
self.app.queue_worker.send_local_control_task("reload_toolbox", get_response=True)
except Exception:
save_integrated_tool_panel = True
log.exception("Exception occured while reloading toolbox")
self.app.queue_worker.send_control_task(
"reload_toolbox", noop_self=True, kwargs={"save_integrated_tool_panel": save_integrated_tool_panel}
),
)

self.tool_config_watcher = get_tool_conf_watcher(
reload_callback=reload_toolbox,
Expand Down
19 changes: 9 additions & 10 deletions lib/galaxy/dependencies/dev-requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,17 +36,16 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.12"
exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12"
fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
fonttools==4.45.1 ; python_version >= "3.8" and python_version < "3.12"
fonttools==4.46.0 ; python_version >= "3.8" and python_version < "3.12"
frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
future==0.18.3 ; python_version >= "3.8" and python_version < "3.12"
galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.12"
greenlet==3.0.1 ; python_version >= "3.8" and python_version < "3.12"
h11==0.14.0 ; python_version >= "3.8" and python_version < "3.12"
httpcore==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
httpx==0.25.2 ; python_version >= "3.8" and python_version < "3.12"
idna==3.6 ; python_version >= "3.8" and python_version < "3.12"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.12"
importlib-metadata==6.9.0 ; python_version >= "3.8" and python_version < "3.12"
importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12"
importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10"
iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -73,7 +72,7 @@ msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12"
multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
nh3==0.2.14 ; python_version >= "3.8" and python_version < "3.12"
nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.12"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12"
outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -82,14 +81,14 @@ pathspec==0.11.2 ; python_version >= "3.8" and python_version < "3.12"
pillow==10.1.0 ; python_version >= "3.8" and python_version < "3.12"
pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.12"
pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.12"
platformdirs==4.0.0 ; python_version >= "3.8" and python_version < "3.12"
platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.12"
playwright==1.40.0 ; python_version >= "3.8" and python_version < "3.12"
pluggy==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.12"
prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.12"
prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12"
psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12" and sys_platform != "cygwin"
psycopg==3.1.13 ; python_version >= "3.8" and python_version < "3.12"
psycopg==3.1.14 ; python_version >= "3.8" and python_version < "3.12"
pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12"
pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.12"
pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -99,7 +98,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.12"
pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.12"
pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.12"
pytest-asyncio==0.21.1 ; python_version >= "3.8" and python_version < "3.12"
pytest-asyncio==0.23.2 ; python_version >= "3.8" and python_version < "3.12"
pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.12"
pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -131,7 +130,7 @@ schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version <
scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
scipy==1.11.4 ; python_version >= "3.9" and python_version < "3.12"
secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "linux"
selenium==4.15.2 ; python_version >= "3.8" and python_version < "3.12"
selenium==4.16.0 ; python_version >= "3.8" and python_version < "3.12"
seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -155,7 +154,7 @@ toml==0.10.2 ; python_version >= "3.8" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.12"
trio==0.23.1 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.1 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
twill==3.2.1 ; python_version >= "3.8" and python_version < "3.12"
twine==4.0.2 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -168,5 +167,5 @@ wcwidth==0.2.12 ; python_version >= "3.8" and python_version < "3.12"
werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.12"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
yarl==1.9.3 ; python_version >= "3.8" and python_version < "3.12"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12"
zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12"
4 changes: 2 additions & 2 deletions lib/galaxy/dependencies/pinned-lint-requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
attrs==23.1.0
flake8==6.1.0
flake8-bugbear==23.11.28
flake8-bugbear==23.12.2
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.1.0
ruff==0.1.6
ruff==0.1.7
31 changes: 16 additions & 15 deletions lib/galaxy/dependencies/pinned-requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
a2wsgi==1.8.0 ; python_version >= "3.8" and python_version < "3.12"
a2wsgi==1.9.0 ; python_version >= "3.8" and python_version < "3.12"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.12"
aiobotocore==2.7.0 ; python_version >= "3.8" and python_version < "3.12"
aiobotocore==2.8.0 ; python_version >= "3.8" and python_version < "3.12"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.12"
aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.12"
aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -30,7 +30,7 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.12"
boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.12"
boto==2.49.0 ; python_version >= "3.8" and python_version < "3.12"
botocore==1.31.64 ; python_version >= "3.8" and python_version < "3.12"
botocore==1.33.1 ; python_version >= "3.8" and python_version < "3.12"
bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12"
celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -51,7 +51,7 @@ conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3
cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12"
cwl-upgrader==1.2.10 ; python_version >= "3.8" and python_version < "3.12"
cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.12"
cwltool==3.1.20231114134824 ; python_version >= "3.8" and python_version < "3.12"
cwltool==3.1.20231207110929 ; python_version >= "3.8" and python_version < "3.12"
decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.12"
defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.12"
deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -69,7 +69,7 @@ fastapi==0.98.0 ; python_version >= "3.8" and python_version < "3.12"
filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12"
frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
fs==2.4.16 ; python_version >= "3.8" and python_version < "3.12"
fsspec==2023.10.0 ; python_version >= "3.8" and python_version < "3.12"
fsspec==2023.12.1 ; python_version >= "3.8" and python_version < "3.12"
future==0.18.3 ; python_version >= "3.8" and python_version < "3.12"
galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.12"
galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -86,8 +86,8 @@ h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.12"
humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.12"
idna==3.6 ; python_version >= "3.8" and python_version < "3.12"
importlib-metadata==6.9.0 ; python_version >= "3.8" and python_version < "3.12"
importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.12"
importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12"
importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.12"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12"
jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -103,10 +103,10 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.12"
markdown==3.5.1 ; python_version >= "3.8" and python_version < "3.12"
markupsafe==2.1.3 ; python_version >= "3.8" and python_version < "3.12"
mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.12"
mercurial==6.6 ; python_version >= "3.8" and python_version < "3.12"
mercurial==6.6.1 ; python_version >= "3.8" and python_version < "3.12"
mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.12"
mrcfile==1.4.3 ; python_version >= "3.8" and python_version < "3.12"
msal==1.25.0 ; python_version >= "3.8" and python_version < "3.12"
msal==1.26.0 ; python_version >= "3.8" and python_version < "3.12"
msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12"
multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -122,7 +122,7 @@ paramiko==3.3.1 ; python_version >= "3.8" and python_version < "3.12"
parsley==1.3 ; python_version >= "3.8" and python_version < "3.12"
paste==3.7.1 ; python_version >= "3.8" and python_version < "3.12"
pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.12"
pebble==5.0.4 ; python_version >= "3.8" and python_version < "3.12"
pebble==5.0.5 ; python_version >= "3.8" and python_version < "3.12"
pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
promise==2.3 ; python_version >= "3.8" and python_version < "3.12"
prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12"
Expand Down Expand Up @@ -154,9 +154,9 @@ python-multipart==0.0.6 ; python_version >= "3.8" and python_version < "3.12"
python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.12"
pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.12"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12"
pyzmq==25.1.1 ; python_version >= "3.8" and python_version < "3.12"
pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.12"
rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.12"
referencing==0.31.1 ; python_version >= "3.8" and python_version < "3.12"
referencing==0.32.0 ; python_version >= "3.8" and python_version < "3.12"
refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.12"
regex==2023.10.3 ; python_version >= "3.8" and python_version < "3.12"
repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -171,7 +171,7 @@ rpds-py==0.13.2 ; python_version >= "3.8" and python_version < "3.12"
rsa==4.9 ; python_version >= "3.8" and python_version < "3.12"
ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8"
ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12"
s3fs==2023.10.0 ; python_version >= "3.8" and python_version < "3.12"
s3fs==2023.12.1 ; python_version >= "3.8" and python_version < "3.12"
schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12"
setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12"
setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -180,6 +180,7 @@ six==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12"
sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12"
spython==0.3.11 ; python_version >= "3.8" and python_version < "3.12"
sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12"
sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12"
sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -194,7 +195,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
tornado==6.4 ; python_version >= "3.8" and python_version < "3.12"
tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.1 ; python_version >= "3.8" and python_version < "3.12"
tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12"
typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12"
Expand All @@ -210,7 +211,7 @@ webob==1.8.7 ; python_version >= "3.8" and python_version < "3.12"
whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.12"
wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
yacman==0.9.2 ; python_version >= "3.8" and python_version < "3.12"
yarl==1.9.3 ; python_version >= "3.8" and python_version < "3.12"
yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12"
zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12"
zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.12"
zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.12"
4 changes: 2 additions & 2 deletions scripts/microbes/harvest_bacteria.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,17 +79,17 @@ def get_chroms_by_project_id(
):
html_count = 0
html = None
url = f"{base_url}{org_num}"
while html_count < 500 and html is None:
html_count += 1
url = f"{base_url}{org_num}"
try:
html = requests.get(url).text
except Exception:
print("GENOME PROJECT FAILED:", html_count, "org:", org_num, url)
html = None
time.sleep(1) # Throttle Connection
if html is None:
"GENOME PROJECT COMPLETELY FAILED TO LOAD", "org:", org_num, "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=" + org_num
print("GENOME PROJECT COMPLETELY FAILED TO LOAD", "org:", org_num, url)
return None

chroms = []
Expand Down
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