Bump ruff from 0.1.14 to 0.3.5 in /backend

dependabot[bot] commented 8 months ago

Bumps ruff from 0.1.14 to 0.3.5.

Release notes

v0.3.5

Changes

Preview features

[pylint] Implement modified-iterating-set (E4703) (#10473)

[refurb] Implement for-loop-set-mutations (FURB142) (#10583)

[refurb] Implement unnecessary-from-float (FURB164) (#10647)

[refurb] Implement verbose-decimal-constructor (FURB157) (#10533)

Rule changes

[flake8-comprehensions] Handled special case for C401 which also matches C416 (#10596)

[flake8-pyi] Mark unaliased-collections-abc-set-import fix as "safe" for more cases in stub files (PYI025) (#10547)

[numpy] Add row_stack to NumPy 2.0 migration rule (#10646)

[pycodestyle] Allow cell magics before an import (E402) (#10545)

[pycodestyle] Avoid blank line rules for the first logical line in cell (#10291)

Configuration

Respected nested namespace packages (#10541)

[flake8-boolean-trap] Add setting for user defined allowed boolean trap (#10531)

Bug fixes

Correctly handle references in __all__ definitions when renaming symbols in autofixes (#10527)

Track ranges of names inside __all__ definitions (#10525)

[flake8-bugbear] Avoid false positive for usage after continue (B031) (#10539)

[flake8-copyright] Accept commas in default copyright pattern (#9498)

[flake8-datetimez] Allow f-strings with %z for DTZ007 (#10651)

[flake8-pytest-style] Fix PT014 autofix for last item in list (#10532)

[flake8-quotes] Ignore Q000, Q001 when string is inside forward ref (#10585)

[isort] Always place non-relative imports after relative imports (#10669)

[isort] Respect Unicode characters in import sorting (#10529)

[pyflakes] Fix F821 false negatives when from __future__ import annotations is active (attempt 2) (#10524)

[pyflakes] Make unnecessary-lambda an always-unsafe fix (#10668)

[pylint] Fixed false-positive on the rule PLW1641 (eq-without-hash) (#10566)

[ruff] Fix panic in unused # noqa removal with multi-byte space (RUF100) (#10682)

Documentation

Add PR title format to CONTRIBUTING.md (#10665)

Fix list markup to include blank lines required (#10591)

Put flake8-logging next to the other flake8 plugins in registry (#10587)

[flake8-bandit] Update warning message for rule S305 to address insecure block cipher mode use (#10602)

[flake8-bugbear] Document use of anonymous assignment in useless-expression (#10551)

[flake8-datetimez] Clarify error messages and docs for DTZ rules (#10621)

[pycodestyle] Use same before vs. after numbers for space-around-operator (#10640)

[ruff] Change quadratic-list-summation docs to use iadd consistently (#10666)

... (truncated)

Changelog

Sourced from ruff's changelog.

0.3.5

Preview features

[pylint] Implement modified-iterating-set (E4703) (#10473)

[refurb] Implement for-loop-set-mutations (FURB142) (#10583)

[refurb] Implement unnecessary-from-float (FURB164) (#10647)

[refurb] Implement verbose-decimal-constructor (FURB157) (#10533)

Rule changes

[flake8-comprehensions] Handled special case for C401 which also matches C416 (#10596)

[flake8-pyi] Mark unaliased-collections-abc-set-import fix as "safe" for more cases in stub files (PYI025) (#10547)

[numpy] Add row_stack to NumPy 2.0 migration rule (#10646)

[pycodestyle] Allow cell magics before an import (E402) (#10545)

[pycodestyle] Avoid blank line rules for the first logical line in cell (#10291)

Configuration

Respected nested namespace packages (#10541)

[flake8-boolean-trap] Add setting for user defined allowed boolean trap (#10531)

Bug fixes

Correctly handle references in __all__ definitions when renaming symbols in autofixes (#10527)

Track ranges of names inside __all__ definitions (#10525)

[flake8-bugbear] Avoid false positive for usage after continue (B031) (#10539)

[flake8-copyright] Accept commas in default copyright pattern (#9498)

[flake8-datetimez] Allow f-strings with %z for DTZ007 (#10651)

[flake8-pytest-style] Fix PT014 autofix for last item in list (#10532)

[flake8-quotes] Ignore Q000, Q001 when string is inside forward ref (#10585)

[isort] Always place non-relative imports after relative imports (#10669)

[isort] Respect Unicode characters in import sorting (#10529)

[pyflakes] Fix F821 false negatives when from __future__ import annotations is active (attempt 2) (#10524)

[pyflakes] Make unnecessary-lambda an always-unsafe fix (#10668)

[pylint] Fixed false-positive on the rule PLW1641 (eq-without-hash) (#10566)

[ruff] Fix panic in unused # noqa removal with multi-byte space (RUF100) (#10682)

Documentation

Add PR title format to CONTRIBUTING.md (#10665)

Fix list markup to include blank lines required (#10591)

Put flake8-logging next to the other flake8 plugins in registry (#10587)

[flake8-bandit] Update warning message for rule S305 to address insecure block cipher mode use (#10602)

[flake8-bugbear] Document use of anonymous assignment in useless-expression (#10551)

[flake8-datetimez] Clarify error messages and docs for DTZ rules (#10621)

[pycodestyle] Use same before vs. after numbers for space-around-operator (#10640)

[ruff] Change quadratic-list-summation docs to use iadd consistently (#10666)

0.3.4

... (truncated)

Commits

200ebee Bump version to v0.3.5 (#10717)
23e8279 chore(deps): update npm development dependencies (#10716)
221b323 chore(deps): update strum to 0.26.0 (#10715)
a0e1544 chore(deps): update rust crate pep440_rs to 0.5.0 (#10703)
2740fab Renovate: group all strum dependencies together (#10714)
7042b9b fix(deps): update rust crate similar to v2.5.0 (#10711)
4047d45 chore(deps): update rust crate insta to v1.38.0 (#10701)
20d69ea chore(deps): update npm development dependencies (#10697)
d021cac chore(deps): update rust crate tracing-tree to 0.3.0 (#10709)
46369d4 chore(deps): update rust crate uuid to v1.8.0 (#10710)
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codecov[bot] commented 8 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 100.00%. Comparing base (de3ef77) to head (e049d50).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #548 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 7 7 Lines 105 105 ========================================= Hits 105 105 ``` | [Flag](https://app.codecov.io/gh/paulscherrerinstitute/alphafold-on-fire/pull/548/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulscherrerinstitute) | Coverage Δ | | |---|---|---| | [backend](https://app.codecov.io/gh/paulscherrerinstitute/alphafold-on-fire/pull/548/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulscherrerinstitute) | `100.00% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulscherrerinstitute#carryforward-flags-in-the-pull-request-comment) to find out more.

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github-actions[bot] commented 8 months ago

Overview

Image reference	`psisharedsharedchncr001.azurecr.io/alphafold:edge`	`psisharedsharedchncr001.azurecr.io/alphafold:pr-548`
- digest	`35cc0232bf90`	`a1a2f51f1a83`
- provenance	https://github.com/paulscherrerinstitute/alphafold-on-fire/commit/de3ef7709d4a18edecd940fd654063e7e3e5b6a6	https://github.com/paulscherrerinstitute/alphafold-on-fire/commit/e049d50a6eba1ed0b14ffef9e0d6335b2fd70caf
- vulnerabilities
- platform	linux/amd64	linux/amd64
- size	59 MB	67 MB (+8.4 MB)
- packages	110	110
Base Image	`python:3.10-alpine` also known as: • `3.10-alpine3.19` • `3.10.13-alpine` • `3.10.13-alpine3.19`	`python:3.10-alpine` also known as: • `3.10-alpine3.19`
- vulnerabilities

Environment Variables (5 changes)

> * `±` 5 changed > * _5 unchanged_ ```diff GPG_KEY=A035C8C19219BA821ECEA86B64E628F8D684696D LANG=C.UTF-8 PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin -PYTHON_GET_PIP_SHA256=7cfd4bdc4d475ea971f1c0710a5953bcc704d171f83c797b9529d9974502fcc6 +PYTHON_GET_PIP_SHA256=dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab9 -PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/049c52c665e8c5fd1751f942316e0a5c777d304f/public/get-pip.py +PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py PYTHON_PIP_VERSION=23.0.1 PYTHON_SETUPTOOLS_VERSION=65.5.1 -PYTHON_VERSION=3.10.13 +PYTHON_VERSION=3.10.14 -RELEASE_ID=de3ef7709d4a18edecd940fd654063e7e3e5b6a6 +RELEASE_ID=e049d50a6eba1ed0b14ffef9e0d6335b2fd70caf -VERSION=edge +VERSION=pr-548 ```

Labels (3 changes)

> * `±` 3 changed > * _5 unchanged_ ```diff -org.opencontainers.image.created=2024-01-25T08:16:19.691Z +org.opencontainers.image.created=2024-04-02T14:17:19.543Z org.opencontainers.image.description= org.opencontainers.image.licenses=GPL-3.0 -org.opencontainers.image.revision=de3ef7709d4a18edecd940fd654063e7e3e5b6a6 +org.opencontainers.image.revision=e049d50a6eba1ed0b14ffef9e0d6335b2fd70caf org.opencontainers.image.source=https://github.com/paulscherrerinstitute/alphafold-on-fire org.opencontainers.image.title=alphafold-on-fire org.opencontainers.image.url=https://github.com/paulscherrerinstitute/alphafold-on-fire -org.opencontainers.image.version=edge +org.opencontainers.image.version=pr-548 ```

Packages and Vulnerabilities (11 package changes and 5 vulnerability changes)

> * :infinity: 11 packages changed > * 99 packages unchanged > * :heavy_check_mark: 5 vulnerabilities removed

Changes for packages of type apk (8 changes)

	Package	Version `psisharedsharedchncr001.azurecr.io/alphafold:edge`	Version `psisharedsharedchncr001.azurecr.io/alphafold:pr-548`
:infinity:	.python-rundeps	`20231209.013648`	`20240325.221307`
:infinity:	expat	`2.5.0-r2`	`2.6.2-r0`

		Removed vulnerabilities (3):
:infinity:	libcrypto3	`3.1.4-r2`	`3.1.4-r5`
:infinity:	libexpat	`2.5.0-r2`	`2.6.2-r0`
:infinity:	libssl3	`3.1.4-r2`	`3.1.4-r5`
:infinity:	openssl	`3.1.4-r2`	`3.1.4-r5`

		Removed vulnerabilities (3):
:infinity:	tzdata	`2023c-r1`	`2024a-r0`
:infinity:	zlib	`1.3-r2`	`1.3.1-r0`