Python 3.8 as minimum #16954
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Python 3.8 as minimum #16954
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It looks like that https://github.com/messense/nh3 can be used, but it's not urgent, I think. |
nsoranzo
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Nov 1, 2023
nsoranzo
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Fixes: galaxyproject#16394 Also upgrade code to Python 3.8 syntax with: ``` ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|lib/tool_shed_client/schema/trs.*.py\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs pyupgrade --py38-plus ```
Fixed by running: ``` ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs auto-walrus make format ``` Note that the directories for the packages listed in `packages/packages_for_pulsar_by_dep_dag.txt` were explictly excluded.
"Unpack is already enabled by default" in version 1.7.0
twill 3.2 replaced `requests` with `httpx`, and `httpx` has a default
timeout of 5 s on a request, while `requests` didn't enforce a timeout by
default.
Fix errors like the following in ToolShed tests, where resetting
repository metadata takes longer than 5 s:
```
self = <tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures object at 0x7f28f99197c0>
def test_0090_verify_repository_metadata(self):
"""Verify that resetting the metadata does not change it."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
> self.verify_unchanged_repository_metadata(repository)
lib/tool_shed/test/functional/test_0000_basic_repository_features.py:264:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/tool_shed/test/base/twilltestcase.py:2073: in verify_unchanged_repository_metadata
self.reset_repository_metadata(repository)
lib/tool_shed/test/base/twilltestcase.py:1774: in reset_repository_metadata
self.visit_url("/repository/reset_all_metadata", params=params)
lib/tool_shed/test/base/twilltestcase.py:845: in visit_url
return self._browser.visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/twillbrowser.py:35: in visit_url
return visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/twillbrowser.py:20: in visit_url
new_url = tc.go(url)
.venv/lib/python3.8/site-packages/twill/commands.py:120: in go
browser.go(url)
.venv/lib/python3.8/site-packages/twill/browser.py:192: in go
self._journey("open", try_url)
.venv/lib/python3.8/site-packages/twill/browser.py:677: in _journey
result = self._client.get(url)
.venv/lib/python3.8/site-packages/httpx/_client.py:1041: in get
return self.request(
.venv/lib/python3.8/site-packages/httpx/_client.py:814: in request
return self.send(request, auth=auth, follow_redirects=follow_redirects)
.venv/lib/python3.8/site-packages/httpx/_client.py:901: in send
response = self._send_handling_auth(
.venv/lib/python3.8/site-packages/httpx/_client.py:929: in _send_handling_auth
response = self._send_handling_redirects(
.venv/lib/python3.8/site-packages/httpx/_client.py:966: in _send_handling_redirects
response = self._send_single_request(request)
.venv/lib/python3.8/site-packages/httpx/_client.py:1002: in _send_single_request
response = transport.handle_request(request)
.venv/lib/python3.8/site-packages/httpx/_transports/default.py:228: in handle_request
resp = self._pool.handle_request(req)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/contextlib.py:131: in __exit__
self.gen.throw(type, value, traceback)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
@contextlib.contextmanager
def map_httpcore_exceptions() -> typing.Iterator[None]:
try:
yield
except Exception as exc:
mapped_exc = None
for from_exc, to_exc in HTTPCORE_EXC_MAP.items():
if not isinstance(exc, from_exc):
continue
# We want to map to the most specific exception we can find.
# Eg if `exc` is an `httpcore.ReadTimeout`, we want to map to
# `httpx.ReadTimeout`, not just `httpx.TimeoutException`.
if mapped_exc is None or issubclass(to_exc, mapped_exc):
mapped_exc = to_exc
if mapped_exc is None: # pragma: no cover
raise
message = str(exc)
> raise mapped_exc(message) from exc
E httpx.ReadTimeout: timed out
.venv/lib/python3.8/site-packages/httpx/_transports/default.py:83: ReadTimeout
```
Add type hints + fixes
with `make update-requirements`
nsoranzo
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Thanks a lot @mr-c ! |
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Fixes: #16394
Major or minor packages bumps now that Python 3.8 is the minimum
idsecondaryFilesfix for containersQEMU_LD_PREFIXby defaultResourceRequirementfields can return floats in CWL v1.2+Lint
Dev
Typecheck
If any of the above release have desired features, we should document their new minimum versions (which will also speed up future
poetryruns).How to test the changes?
(Select all options that apply)
I've included appropriate automated tests.License