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Merge main branch into the docs branch #1167

Merged
merged 40 commits into from
Aug 7, 2024
Merged

Merge main branch into the docs branch #1167

merged 40 commits into from
Aug 7, 2024

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hogo6002
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@hogo6002 hogo6002 commented Aug 7, 2024

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cuixq and others added 30 commits July 11, 2024 11:28
#989

For the purpose of overriding dependency requirements, we may need to
add new dependencies or even dependency management section to pom.xml.
This PR:
 - moves the patch generation from suggester to updater
 - before writing patches, prepare dependency and property patches
- when updating dependencies, if a dependency is not from the base
project, we should add a new section
- when updating a project, if dependency management is not updated and
there are patches from dependency management, add a new dependency
management section
 - marks the parent dependency patch to have type "pom"

TODOs:
- need to find a way to differentiate patches for guided remediation or
general updates, since we should not add new sections for general
updates (using `OrigRequire` seems reasonable)
- make the indentation for the new sections configuration, now defaults
to a white space
There's nothing too major here though we do get to remove a bunch of
config for deprecated linters that have finally been removed; the more
exciting thing is when we move to Go v1.22 as there's a few linters
that'll start running like for cleaning up our looping variables
Currently, the newly added dependency management is not written
correctly - `dependency` tags are missing.
This PR fixes this by specifying `dependency` in the struct.
We should merge active profiles before merging parent data. Currently,
we only merge default profiles by passing empty JDK and OS information
(this could be a TODO for the future).

Some known issue or improvement:
- Inactive profiles may not be interpolated but we probably want them to
be updated as well
- Now default profiles are merged but we may consider leveraging JDK and
OS information to activate accurate profiles
Currently, the write test is a bit flaky because the dependencies to be
added are not sorted and their order in pom.xml is not guaranteed.

This PR adds sorting of dependencies before they are going to be
written.
Start on a new 'override' remediation strategy for guided remediation
for maven, intending to remediate by forcing the use of non-vulnerable
versions by `dependencyManagement`.

This is just the logic to identify possible override patches by
searching for the first non-vulnerable version of an affected package.
- Improved the runtime of DiffVulnerabilityResults
- Precomputed the existence of Sources, Packages, and Vulnerabilities,
which brings the time complexity down from O(n^2) to O(n).
Update the documentation that the current Maven resolver does not handle
test dependencies.
Previously, `origRequire` is not set in patches from suggest, however we
plan to use this field to differentiate patches from override, this PR
sets `origRequire` for patches from suggest so that `manifest.Write()`
is able to only add dependencies from patches generated by override.
Remove the patch version as we always want the latest patch version.

Fixes #1123 

We just need to keep in mind that the library code should be compatible
with the previous go release.
https://docs.github.com/en/actions/managing-issues-and-pull-requests/closing-inactive-issues

Manage issues and PRs that are unassigned, and/or don't have the
'good-first-issue' label (for issues).

60 days for a warning, and closure two weeks later.
[![Mend
Renovate](https://app.renovatebot.com/images/banner.svg)](https://renovatebot.com)

This PR contains the following updates:

| Package | Type | Update | Change |
|---|---|---|---|
| [actions/setup-go](https://togithub.com/actions/setup-go) | action |
patch | `v5.0.1` -> `v5.0.2` |
| [actions/setup-python](https://togithub.com/actions/setup-python) |
action | patch | `v5.1.0` -> `v5.1.1` |
| [github/codeql-action](https://togithub.com/github/codeql-action) |
action | patch | `v3.25.11` -> `v3.25.13` |
| [ruby/setup-ruby](https://togithub.com/ruby/setup-ruby) | action |
minor | `v1.185.0` -> `v1.187.0` |
| [shivammathur/setup-php](https://togithub.com/shivammathur/setup-php)
| action | patch | `2.31.0` -> `2.31.1` |

---

### Release Notes

<details>
<summary>actions/setup-go (actions/setup-go)</summary>

###
[`v5.0.2`](https://togithub.com/actions/setup-go/compare/v5.0.1...v5.0.2)

[Compare
Source](https://togithub.com/actions/setup-go/compare/v5.0.1...v5.0.2)

</details>

<details>
<summary>actions/setup-python (actions/setup-python)</summary>

###
[`v5.1.1`](https://togithub.com/actions/setup-python/releases/tag/v5.1.1)

[Compare
Source](https://togithub.com/actions/setup-python/compare/v5.1.0...v5.1.1)

##### What's Changed

##### Bug fixes:

- fix(ci): update all failing workflows by
[@&#8203;mayeut](https://togithub.com/mayeut) in
[https://github.com/actions/setup-python/pull/863](https://togithub.com/actions/setup-python/pull/863)
This update ensures compatibility and optimal performance of workflows
on the latest macOS version.

##### Documentation changes:

- Documentation update for cache by
[@&#8203;gowridurgad](https://togithub.com/gowridurgad) in
[https://github.com/actions/setup-python/pull/873](https://togithub.com/actions/setup-python/pull/873)

##### Dependency updates:

- Bump braces from 3.0.2 to 3.0.3 and undici from 5.28.3 to 5.28.4 by
[@&#8203;dependabot](https://togithub.com/dependabot) in
[https://github.com/actions/setup-python/pull/893](https://togithub.com/actions/setup-python/pull/893)

##### New Contributors

- [@&#8203;gowridurgad](https://togithub.com/gowridurgad) made their
first contribution in
[https://github.com/actions/setup-python/pull/873](https://togithub.com/actions/setup-python/pull/873)

**Full Changelog**:
actions/setup-python@v5...v5.1.1

</details>

<details>
<summary>github/codeql-action (github/codeql-action)</summary>

###
[`v3.25.13`](https://togithub.com/github/codeql-action/compare/v3.25.12...v3.25.13)

[Compare
Source](https://togithub.com/github/codeql-action/compare/v3.25.12...v3.25.13)

###
[`v3.25.12`](https://togithub.com/github/codeql-action/compare/v3.25.11...v3.25.12)

[Compare
Source](https://togithub.com/github/codeql-action/compare/v3.25.11...v3.25.12)

</details>

<details>
<summary>ruby/setup-ruby (ruby/setup-ruby)</summary>

###
[`v1.187.0`](https://togithub.com/ruby/setup-ruby/releases/tag/v1.187.0)

[Compare
Source](https://togithub.com/ruby/setup-ruby/compare/v1.186.0...v1.187.0)

#### What's Changed

- Update CRuby releases on Windows by
[@&#8203;ruby-builder-bot](https://togithub.com/ruby-builder-bot) in
[https://github.com/ruby/setup-ruby/pull/622](https://togithub.com/ruby/setup-ruby/pull/622)

**Full Changelog**:
ruby/setup-ruby@v1.186.0...v1.187.0

###
[`v1.186.0`](https://togithub.com/ruby/setup-ruby/releases/tag/v1.186.0)

[Compare
Source](https://togithub.com/ruby/setup-ruby/compare/v1.185.0...v1.186.0)

#### What's Changed

- Add ruby-3.3.4 by
[@&#8203;ruby-builder-bot](https://togithub.com/ruby-builder-bot) in
[https://github.com/ruby/setup-ruby/pull/620](https://togithub.com/ruby/setup-ruby/pull/620)

**Full Changelog**:
ruby/setup-ruby@v1.185.0...v1.186.0

</details>

<details>
<summary>shivammathur/setup-php (shivammathur/setup-php)</summary>

###
[`v2.31.1`](https://togithub.com/shivammathur/setup-php/releases/tag/2.31.1)

[Compare
Source](https://togithub.com/shivammathur/setup-php/compare/2.31.0...2.31.1)

##### Changelog

- Fix installing PECL extensions on Windows with a build version
[#&#8203;855](https://togithub.com/shivammathur/setup-php/issues/855)

- Fix cache support for ioncube extension
[#&#8203;856](https://togithub.com/shivammathur/setup-php/issues/856)

-   Updated Node.js dependencies.

For the complete list of changes, please refer to the [Full
Changelog](https://togithub.com/shivammathur/setup-php/compare/2.31.0...2.31.1)

<p>
  <h4>Follow for updates</h4>
<a href="https://reddit.com/r/setup_php" title="setup-php reddit"><img
alt="setup-php reddit"
src="https://img.shields.io/badge/reddit-join-FF5700?logo=reddit&logoColor=FF5700&labelColor=555555"></a>
<a href="https://twitter.com/setup_php" title="setup-php twitter"><img
alt="setup-php twitter"
src="https://img.shields.io/badge/twitter-follow-1DA1F2?logo=twitter&logoColor=1DA1F2&labelColor=555555"></a>
<a href="https://status.setup-php.com" title="setup-php status"><img
alt="setup-php status"
src="https://img.shields.io/badge/status-subscribe-28A745?logo=statuspage&logoColor=28A745&labelColor=555555"></a>
</p>

</details>

---

### Configuration

📅 **Schedule**: Branch creation - "before 6am on monday" in timezone
Australia/Sydney, Automerge - At any time (no schedule defined).

🚦 **Automerge**: Disabled by config. Please merge this manually once you
are satisfied.

♻ **Rebasing**: Whenever PR becomes conflicted, or you tick the
rebase/retry checkbox.

👻 **Immortal**: This PR will be recreated if closed unmerged. Get
[config help](https://togithub.com/renovatebot/renovate/discussions) if
that's undesired.

---

- [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check
this box

---

This PR has been generated by [Mend
Renovate](https://www.mend.io/free-developer-tools/renovate/). View
repository job log
[here](https://developer.mend.io/github/google/osv-scanner).

<!--renovate-debug:eyJjcmVhdGVkSW5WZXIiOiIzNy40MzEuNCIsInVwZGF0ZWRJblZlciI6IjM3LjQzMS40IiwidGFyZ2V0QnJhbmNoIjoibWFpbiIsImxhYmVscyI6WyJkZXBlbmRlbmNpZXMiXX0=-->
Such issues will never not be stale right up until work on v2 starts
(and even then they'll likely be stale on and off)

(note I'm not entirely sure if this will work re the spaces - I've found
some issues on the action repo that suggest it should, but no actual
example docs; I think we just need to try it and see 🤷)
Replicate #1109 more like #1030 to avoid Renovate failures like
#1120 (comment)

The Docker files are already at 1.22.5, not sure if we want to update to
this globally?
[![Mend
Renovate](https://app.renovatebot.com/images/banner.svg)](https://renovatebot.com)

This PR contains the following updates:

| Package | Change | Age | Adoption | Passing | Confidence | Type |
Update |
|---|---|---|---|---|---|---|---|
|
[github.com/charmbracelet/lipgloss](https://togithub.com/charmbracelet/lipgloss)
| `v0.11.0` -> `v0.12.1` |
[![age](https://developer.mend.io/api/mc/badges/age/go/github.com%2fcharmbracelet%2flipgloss/v0.12.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![adoption](https://developer.mend.io/api/mc/badges/adoption/go/github.com%2fcharmbracelet%2flipgloss/v0.12.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![passing](https://developer.mend.io/api/mc/badges/compatibility/go/github.com%2fcharmbracelet%2flipgloss/v0.11.0/v0.12.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![confidence](https://developer.mend.io/api/mc/badges/confidence/go/github.com%2fcharmbracelet%2flipgloss/v0.11.0/v0.12.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
| require | minor |
|
[github.com/gkampitakis/go-snaps](https://togithub.com/gkampitakis/go-snaps)
| `v0.5.4` -> `v0.5.5` |
[![age](https://developer.mend.io/api/mc/badges/age/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.5?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![adoption](https://developer.mend.io/api/mc/badges/adoption/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.5?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![passing](https://developer.mend.io/api/mc/badges/compatibility/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.4/v0.5.5?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![confidence](https://developer.mend.io/api/mc/badges/confidence/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.4/v0.5.5?slim=true)](https://docs.renovatebot.com/merge-confidence/)
| require | patch |
|
[github.com/google/go-containerregistry](https://togithub.com/google/go-containerregistry)
| `v0.19.2` -> `v0.20.1` |
[![age](https://developer.mend.io/api/mc/badges/age/go/github.com%2fgoogle%2fgo-containerregistry/v0.20.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![adoption](https://developer.mend.io/api/mc/badges/adoption/go/github.com%2fgoogle%2fgo-containerregistry/v0.20.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![passing](https://developer.mend.io/api/mc/badges/compatibility/go/github.com%2fgoogle%2fgo-containerregistry/v0.19.2/v0.20.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![confidence](https://developer.mend.io/api/mc/badges/confidence/go/github.com%2fgoogle%2fgo-containerregistry/v0.19.2/v0.20.1?slim=true)](https://docs.renovatebot.com/merge-confidence/)
| require | minor |
|
[github.com/owenrumney/go-sarif/v2](https://togithub.com/owenrumney/go-sarif)
| `v2.3.2` -> `v2.3.3` |
[![age](https://developer.mend.io/api/mc/badges/age/go/github.com%2fowenrumney%2fgo-sarif%2fv2/v2.3.3?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![adoption](https://developer.mend.io/api/mc/badges/adoption/go/github.com%2fowenrumney%2fgo-sarif%2fv2/v2.3.3?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![passing](https://developer.mend.io/api/mc/badges/compatibility/go/github.com%2fowenrumney%2fgo-sarif%2fv2/v2.3.2/v2.3.3?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![confidence](https://developer.mend.io/api/mc/badges/confidence/go/github.com%2fowenrumney%2fgo-sarif%2fv2/v2.3.2/v2.3.3?slim=true)](https://docs.renovatebot.com/merge-confidence/)
| require | patch |
| golang.org/x/exp | `46b0784` -> `8a7402a` |
[![age](https://developer.mend.io/api/mc/badges/age/go/golang.org%2fx%2fexp/v0.0.0-20240719175910-8a7402abbf56?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![adoption](https://developer.mend.io/api/mc/badges/adoption/go/golang.org%2fx%2fexp/v0.0.0-20240719175910-8a7402abbf56?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![passing](https://developer.mend.io/api/mc/badges/compatibility/go/golang.org%2fx%2fexp/v0.0.0-20240707233637-46b078467d37/v0.0.0-20240719175910-8a7402abbf56?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![confidence](https://developer.mend.io/api/mc/badges/confidence/go/golang.org%2fx%2fexp/v0.0.0-20240707233637-46b078467d37/v0.0.0-20240719175910-8a7402abbf56?slim=true)](https://docs.renovatebot.com/merge-confidence/)
| require | digest |

---

### Release Notes

<details>
<summary>charmbracelet/lipgloss
(github.com/charmbracelet/lipgloss)</summary>

###
[`v0.12.1`](https://togithub.com/charmbracelet/lipgloss/releases/tag/v0.12.1)

[Compare
Source](https://togithub.com/charmbracelet/lipgloss/compare/v0.12.0...v0.12.1)

This release fixes a regression with regard to border calculations
introduced in Lip Gloss v0.11.1.

***

<a href="https://charm.sh/"><img alt="The Charm logo"
src="https://stuff.charm.sh/charm-badge.jpg" width="400"></a>

Thoughts? Questions? We love hearing from you. Feel free to reach out on
[Twitter](https://twitter.com/charmcli), [The
Fediverse](https://mastodon.technology/@&#8203;charm), or on
[Discord](https://charm.sh/chat).

###
[`v0.12.0`](https://togithub.com/charmbracelet/lipgloss/releases/tag/v0.12.0)

[Compare
Source](https://togithub.com/charmbracelet/lipgloss/compare/v0.11.1...v0.12.0)

### Lists, Check ✓

This release adds a new sub-package for rendering trees and lists.

```go
import "github.com/charmbracelet/lipgloss/list"
```

Define a new list.

```go
l := list.New("A", "B", "C")
```

Print the list.

```go
fmt.Println(l)

// • A
// • B
// • C
```

Lists have the ability to nest.

```go
l := list.New(
  "A", list.New("Artichoke"),
  "B", list.New("Baking Flour", "Bananas", "Barley", "Bean Sprouts"),
  "C", list.New("Cashew Apple", "Cashews", "Coconut Milk", "Curry Paste", "Currywurst"),
  "D", list.New("Dill", "Dragonfruit", "Dried Shrimp"),
  "E", list.New("Eggs"),
  "F", list.New("Fish Cake", "Furikake"),
  "J", list.New("Jicama"),
  "K", list.New("Kohlrabi"),
  "L", list.New("Leeks", "Lentils", "Licorice Root"),
)
```

Print the list.

```go
fmt.Println(l)
```

<p align="center">
<img width="600" alt="image"
src="https://github.com/charmbracelet/lipgloss/assets/42545625/0dc9f440-0748-4151-a3b0-7dcf29dfcdb0">
</p>

Lists can be customized via their enumeration function as well as using
`lipgloss.Style`s.

```go
enumeratorStyle := lipgloss.NewStyle().Foreground(lipgloss.Color("99")).MarginRight(1)
itemStyle := lipgloss.NewStyle().Foreground(lipgloss.Color("212")).MarginRight(1)

l := list.New(
  "Glossier",
  "Claire’s Boutique",
  "Nyx",
  "Mac",
  "Milk",
).
  Enumerator(list.Roman).
  EnumeratorStyle(enumeratorStyle).
  ItemStyle(itemStyle)
```

Print the list.

<p align="center">
<img width="600" alt="List example"
src="https://github.com/charmbracelet/lipgloss/assets/42545625/360494f1-57fb-4e13-bc19-0006efe01561">
</p>

In addition to the predefined enumerators (`Arabic`, `Alphabet`,
`Roman`, `Bullet`, `Tree`),
you may also define your own custom enumerator:

```go
l := list.New("Duck", "Duck", "Duck", "Duck", "Goose", "Duck", "Duck")

func DuckDuckGooseEnumerator(l list.Items, i int) string {
    if l.At(i).Value() == "Goose" {
        return "Honk →"
    }
    return ""
}

l = l.Enumerator(DuckDuckGooseEnumerator)
```

Print the list:

<p align="center">
<img width="600" alt="image"
src="https://github.com/charmbracelet/lipgloss/assets/42545625/157aaf30-140d-4948-9bb4-dfba46e5b87e">
</p>

If you need, you can also build lists incrementally:

```go
l := list.New()

for i := 0; i < repeat; i++ {
    l.Item("Lip Gloss")
}
```

***

<a href="https://charm.sh/"><img alt="The Charm logo"
src="https://stuff.charm.sh/charm-badge.jpg" width="400"></a>

Thoughts? Questions? We love hearing from you. Feel free to reach out on
[Twitter](https://twitter.com/charmcli), [The
Fediverse](https://mastodon.technology/@&#8203;charm), or on
[Discord](https://charm.sh/chat).

###
[`v0.11.1`](https://togithub.com/charmbracelet/lipgloss/releases/tag/v0.11.1)

[Compare
Source](https://togithub.com/charmbracelet/lipgloss/compare/v0.11.0...v0.11.1)

This release is a small patch release to fix text truncation in table
cells. For details see:
[https://github.com/charmbracelet/lipgloss/issues/324](https://togithub.com/charmbracelet/lipgloss/issues/324).

#### Other stuff

- chore: remove deprecated Copy() calls by
[@&#8203;meowgorithm](https://togithub.com/meowgorithm) in
[https://github.com/charmbracelet/lipgloss/pull/306](https://togithub.com/charmbracelet/lipgloss/pull/306)
- feat: deprecate Style.ColorWhitespace by
[@&#8203;meowgorithm](https://togithub.com/meowgorithm) in
[https://github.com/charmbracelet/lipgloss/pull/311](https://togithub.com/charmbracelet/lipgloss/pull/311)
- feat: deprecate Style.ColorWhitespace by
[@&#8203;meowgorithm](https://togithub.com/meowgorithm) in
[https://github.com/charmbracelet/lipgloss/pull/314](https://togithub.com/charmbracelet/lipgloss/pull/314)
- fix: Deprecate UnsetBorderTopBackgroundColor in favor of
UnsetBorderTopBackground by [@&#8203;nervo](https://togithub.com/nervo)
in
[https://github.com/charmbracelet/lipgloss/pull/315](https://togithub.com/charmbracelet/lipgloss/pull/315)

**Full Changelog**:
charmbracelet/lipgloss@v0.11.0...v0.11.1

***

<a href="https://charm.sh/"><img alt="The Charm logo"
src="https://stuff.charm.sh/charm-badge.jpg" width="400"></a>

Thoughts? Questions? We love hearing from you. Feel free to reach out on
[Twitter](https://twitter.com/charmcli), [The
Fediverse](https://mastodon.technology/@&#8203;charm), or
[Discord](https://charm.sh/discord).

</details>

<details>
<summary>gkampitakis/go-snaps
(github.com/gkampitakis/go-snaps)</summary>

###
[`v0.5.5`](https://togithub.com/gkampitakis/go-snaps/compare/v0.5.4...v0.5.5)

[Compare
Source](https://togithub.com/gkampitakis/go-snaps/compare/v0.5.4...v0.5.5)

</details>

<details>
<summary>google/go-containerregistry
(github.com/google/go-containerregistry)</summary>

###
[`v0.20.1`](https://togithub.com/google/go-containerregistry/releases/tag/v0.20.1)

[Compare
Source](https://togithub.com/google/go-containerregistry/compare/v0.20.0...v0.20.1)

#### What's Changed

- Create `remote.Push` by
[@&#8203;mattmoor](https://togithub.com/mattmoor) in
[https://github.com/google/go-containerregistry/pull/1978](https://togithub.com/google/go-containerregistry/pull/1978)

**Full Changelog**:
google/go-containerregistry@v0.20.0...v0.20.1

###
[`v0.20.0`](https://togithub.com/google/go-containerregistry/releases/tag/v0.20.0)

[Compare
Source](https://togithub.com/google/go-containerregistry/compare/v0.19.2...v0.20.0)

#### What's Changed

- Referrer API must return correct Content-Type by
[@&#8203;GregoireW](https://togithub.com/GregoireW) in
[https://github.com/google/go-containerregistry/pull/1968](https://togithub.com/google/go-containerregistry/pull/1968)
- 🚨 POTENTIALLY BREAKING: Restore blind-write to remote.Put by
[@&#8203;jonjohnsonjr](https://togithub.com/jonjohnsonjr) in
[https://github.com/google/go-containerregistry/pull/1970](https://togithub.com/google/go-containerregistry/pull/1970)

#### New Contributors

- [@&#8203;GregoireW](https://togithub.com/GregoireW) made their first
contribution in
[https://github.com/google/go-containerregistry/pull/1968](https://togithub.com/google/go-containerregistry/pull/1968)

**Full Changelog**:
google/go-containerregistry@v0.19.2...v0.20.0

</details>

<details>
<summary>owenrumney/go-sarif
(github.com/owenrumney/go-sarif/v2)</summary>

###
[`v2.3.3`](https://togithub.com/owenrumney/go-sarif/releases/tag/v2.3.3)

[Compare
Source](https://togithub.com/owenrumney/go-sarif/compare/v2.3.2...v2.3.3)

#### What's Changed

- fix: Update removed goreleaser flag by
[@&#8203;kaiwenleee](https://togithub.com/kaiwenleee) in
[https://github.com/owenrumney/go-sarif/pull/79](https://togithub.com/owenrumney/go-sarif/pull/79)

**Full Changelog**:
owenrumney/go-sarif@v2.3.2...v2.3.3

</details>

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Copying the `EcosystemSpecific` data from the `Manifest` to the
`ManifestPatch` is a bit cumbersome for the override strategy, and
`ManifestPatch` already has a field for the original manifest.

I don't think the current Maven `EcosystemSpecific` data is ever going
to differ from the what's in the original manifest?
Currently, Maven dependency management is not added to the override
client so they are not considered when computing Maven dependency graph.

This PR adds all direct dependency management to override client so that
transitive dependencies are resolved correctly.
…er group (#1132)

Bumps the bundler group in /docs with 1 update:
[rexml](https://github.com/ruby/rexml).

Updates `rexml` from 3.3.1 to 3.3.2
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/ruby/rexml/releases">rexml's
releases</a>.</em></p>
<blockquote>
<h2>REXML 3.3.2 - 2024-07-16</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/160">GH-160</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/169">GH-169</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/170">GH-170</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/171">GH-171</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/172">GH-172</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/173">GH-173</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/174">GH-174</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/175">GH-175</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/176">GH-176</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/177">GH-177</a></li>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Added support for raising a parse exception when an XML has extra
content after the root element.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/161">GH-161</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added support for raising a parse exception when an XML
declaration exists in wrong position.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/162">GH-162</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Removed needless a space after XML declaration in pretty print
mode.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/164">GH-164</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Stopped to emit <code>:text</code> event after the root element.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/167">GH-167</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>Fixed a bug that SAX2 parser doesn't expand predefined entities for
<code>characters</code> callback.
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/168">GH-168</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>Watson</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/ruby/rexml/blob/master/NEWS.md">rexml's
changelog</a>.</em></p>
<blockquote>
<h2>3.3.2 - 2024-07-16 {#version-3-3-2}</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/160">GH-160</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/169">GH-169</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/170">GH-170</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/171">GH-171</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/172">GH-172</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/173">GH-173</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/174">GH-174</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/175">GH-175</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/176">GH-176</a></li>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/177">GH-177</a></li>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Added support for raising a parse exception when an XML has extra
content after the root element.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/161">GH-161</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added support for raising a parse exception when an XML
declaration exists in wrong position.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/162">GH-162</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Removed needless a space after XML declaration in pretty print
mode.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/164">GH-164</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Stopped to emit <code>:text</code> event after the root element.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/167">GH-167</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>Fixed a bug that SAX2 parser doesn't expand predefined entities for
<code>characters</code> callback.
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/168">GH-168</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>Watson</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/ruby/rexml/commit/2b285ac0804f2918de642f7ed4646dc6d645a7fc"><code>2b285ac</code></a>
Add 3.3.2 entry</li>
<li><a
href="https://github.com/ruby/rexml/commit/0e33d3adfb5069b20622e5ed9393d10b8cc17b40"><code>0e33d3a</code></a>
test: improve linear performance test names</li>
<li><a
href="https://github.com/ruby/rexml/commit/910e5a2b487cb5a30989884a39f9cad2cc499cfc"><code>910e5a2</code></a>
Fix performance issue caused by using repeated <code>&gt;</code>
characters inside `&lt;xml&gt;&lt;!...</li>
<li><a
href="https://github.com/ruby/rexml/commit/1f1e6e9b40bf339894e843dfd679c2fb1a5ddbf2"><code>1f1e6e9</code></a>
Fix ReDoS by using repeated space characters inside `&lt;!DOCTYPE name
[&lt;!ATTLIS...</li>
<li><a
href="https://github.com/ruby/rexml/commit/1cc1d9a74ede52f3d9ce774cafb11c57b3905165"><code>1cc1d9a</code></a>
Suppress have_root not initialized warnings on Ruby &lt; 3</li>
<li><a
href="https://github.com/ruby/rexml/commit/67efb5951ed09dbb575c375b130a1e469f437d1f"><code>67efb59</code></a>
Fix performance issue caused by using repeated <code>&gt;</code>
characters inside `&lt;!DOCTY...</li>
<li><a
href="https://github.com/ruby/rexml/commit/a79ac8b4b42a9efabe33a0be31bd82d33fd50347"><code>a79ac8b</code></a>
Fix performance issue caused by using repeated <code>&gt;</code>
characters inside `&lt;!DOCTY...</li>
<li><a
href="https://github.com/ruby/rexml/commit/c33ea498102be65082940e8b7d6d31cb2c6e6ee2"><code>c33ea49</code></a>
Fix performance issue caused by using repeated <code>&gt;</code>
characters after ` &lt;!DOCTY...</li>
<li><a
href="https://github.com/ruby/rexml/commit/9f1415a2616c77cad44a176eee90e8457b4774b6"><code>9f1415a</code></a>
Fix performance issue caused by using repeated <code>&gt;</code>
characters inside `CDATA [...</li>
<li><a
href="https://github.com/ruby/rexml/commit/c1b64c174ec2e8ca2174c51332670e3be30c865f"><code>c1b64c1</code></a>
Fix performance issue caused by using repeated <code>&gt;</code>
characters inside comments...</li>
<li>Additional commits viewable in <a
href="https://github.com/ruby/rexml/compare/v3.3.1...v3.3.2">compare
view</a></li>
</ul>
</details>
<br />


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Dependabot will resolve any conflicts with this PR as long as you don't
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<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
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You can disable automated security fix PRs for this repo from the
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Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Xueqin Cui <[email protected]>
This adds a new "vertical" output format that is designed for humans and
based on the output of `osv-detector`, which effectively aims to group
the output relating to each entity being scanned in vertical slices:

<img width="898" alt="image"
src="https://github.com/google/osv-scanner/assets/3151613/61297153-5c22-43a4-a78e-e07ce648142a">

Unfortunately I think it suffers significantly due to the assumptions
made by the rest of the codebase for outputting that made sense when the
final output was a table i.e. we dump a lot of information as we go
about scanning, config files, vulnerability filtering, and so on that
really should be grouped but currently cannot because they're all
outputted at different stages - I think a way to address that could be
using some sort of event-emitter type pattern so that the reporters
could be responsible for deciding what they actually do (e.g.
`r.Emit("filtered-vulnerability", ...)` and then most reporters could
choose to just print immediately, and ones like "vertical" could choose
to add it to an internal struct), but I think that'll involve a lot more
work; for now I'm just going to ignore the pre-results output.

Resolves #85
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This PR contains the following updates:

| Package | Type | Update | Change |
|---|---|---|---|
| alpine | final | digest | `b89d9c9` -> `0a4eaa0` |

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This PR contains the following updates:

| Package | Change | Age | Adoption | Passing | Confidence |
|---|---|---|---|---|---|
|
[github.com/gkampitakis/go-snaps](https://togithub.com/gkampitakis/go-snaps)
| `v0.5.5` -> `v0.5.6` |
[![age](https://developer.mend.io/api/mc/badges/age/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.6?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![adoption](https://developer.mend.io/api/mc/badges/adoption/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.6?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![passing](https://developer.mend.io/api/mc/badges/compatibility/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.5/v0.5.6?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
[![confidence](https://developer.mend.io/api/mc/badges/confidence/go/github.com%2fgkampitakis%2fgo-snaps/v0.5.5/v0.5.6?slim=true)](https://docs.renovatebot.com/merge-confidence/)
|
| [github.com/urfave/cli/v2](https://togithub.com/urfave/cli) |
`v2.27.2` -> `v2.27.3` |
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|
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|

---

### Release Notes

<details>
<summary>gkampitakis/go-snaps
(github.com/gkampitakis/go-snaps)</summary>

###
[`v0.5.6`](https://togithub.com/gkampitakis/go-snaps/releases/tag/v0.5.6)

[Compare
Source](https://togithub.com/gkampitakis/go-snaps/compare/v0.5.5...v0.5.6)

#### What's Changed

- feat: support matchStandaloneSnapshot by
[@&#8203;gkampitakis](https://togithub.com/gkampitakis) in
[https://github.com/gkampitakis/go-snaps/pull/102](https://togithub.com/gkampitakis/go-snaps/pull/102)
- feat: support setting file extension by
[@&#8203;gkampitakis](https://togithub.com/gkampitakis) in
[https://github.com/gkampitakis/go-snaps/pull/102](https://togithub.com/gkampitakis/go-snaps/pull/102)

**Full Changelog**:
gkampitakis/go-snaps@v0.5.5...v0.5.6

</details>

<details>
<summary>urfave/cli (github.com/urfave/cli/v2)</summary>

### [`v2.27.3`](https://togithub.com/urfave/cli/releases/tag/v2.27.3)

[Compare
Source](https://togithub.com/urfave/cli/compare/v2.27.2...v2.27.3)

#### What's Changed

- v2 Docs: Mention value from env as default value by
[@&#8203;sj14](https://togithub.com/sj14) in
[https://github.com/urfave/cli/pull/1910](https://togithub.com/urfave/cli/pull/1910)
- Bump github.com/xrash/smetrics dependency by
[@&#8203;elezar](https://togithub.com/elezar) in
[https://github.com/urfave/cli/pull/1911](https://togithub.com/urfave/cli/pull/1911)
- fix: disable bash completion if double dash is included in arguments
(v2) by [@&#8203;suzuki-shunsuke](https://togithub.com/suzuki-shunsuke)
in
[https://github.com/urfave/cli/pull/1938](https://togithub.com/urfave/cli/pull/1938)
- Fix improper whitespace formatting in usageTemplate, AppHelpTemplate …
by [@&#8203;caeret](https://togithub.com/caeret) in
[https://github.com/urfave/cli/pull/1947](https://togithub.com/urfave/cli/pull/1947)

#### New Contributors

- [@&#8203;sj14](https://togithub.com/sj14) made their first
contribution in
[https://github.com/urfave/cli/pull/1910](https://togithub.com/urfave/cli/pull/1910)
- [@&#8203;elezar](https://togithub.com/elezar) made their first
contribution in
[https://github.com/urfave/cli/pull/1911](https://togithub.com/urfave/cli/pull/1911)
- [@&#8203;caeret](https://togithub.com/caeret) made their first
contribution in
[https://github.com/urfave/cli/pull/1947](https://togithub.com/urfave/cli/pull/1947)

**Full Changelog**:
urfave/cli@v2.27.2...v2.27.3

</details>

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### Configuration

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### Release Notes

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…return an non zero exit code in osv-reporter (#1152)

If all vulnerabilities are not called, don't return an non zero exit
code in osv-reporter.
hogo6002 and others added 10 commits August 1, 2024 10:55
When Maven looks for the parent POM, it first looks up the specified
relative path, then look for the default relative path which is
`../pom.xml`, and lastly in the remote repository. If only a directory
is specified in relative path, `pom.xml` will be looked automatically.

Reference:
https://maven.apache.org/ref/3.9.8/maven-model/maven.html#parent

Currently, OSV-Scanner only do some steps above, this PR corrects this.

Also, considering both `internal/manifest` and
`internal/resolution/manifest` require basically the same logic for
merging parent POM, I would like to refactor this in a following PR.
…ave defined `<classifier>` or `<type>` (#1151)

There is currently no way in the deps.dev API to determine the Maven
classifier/type that exist for a given version of a package. Not knowing
this, the override strategy can end up bumping to a version that does
not exist, which would cause a compilation failure that can't be
detected in-code.

I'm avoiding the bigger issue here by just explicitly preventing
remediation for those artifacts...

This will also prevent the infinite loop I mentioned in
#1025 (comment)
There are two places we read Maven pom.xml:
 - Transitive scanning in `internal/manifest`
 - Guided remediation in `internal/resolution/manifest`

Both share the same logic to merge parents, so this PR consolidates the
implementation in `internal/manifest`.

This PR also updates `deps.dev` dependencies to the latest version.
Fix updated snapshots to make merging possible.
This way they're easily identifiable for later review

Add a nudge to encourage contribution for stale issues.

Convert message text to multiline strings for ease of future maintenance

Aggregate related configuration for ease of comprehension and future
maintenance
…erride (#1136)

#1141 
Adds `--strategy=override` for `osv-scanner fix --non-interactive` for
`pom.xml` manifest files. For now interactive mode will print an error
telling you to use non-interactive mode if you try `pom.xml`.

Also, made non-interactive mode decide which strategy to use if not
explicitly specified based on the provided manifests / lockfiles.
…er group (#1158)

Bumps the bundler group in /docs with 1 update:
[rexml](https://github.com/ruby/rexml).

Updates `rexml` from 3.3.2 to 3.3.3
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/ruby/rexml/releases">rexml's
releases</a>.</em></p>
<blockquote>
<h2>REXML 3.3.3 - 2024-08-01</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Added support for detecting invalid XML that has unsupported
content before root element</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/184">GH-184</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added support for
<code>REXML::Security.entity_expansion_limit=</code> and
<code>REXML::Security.entity_expansion_text_limit=</code> in SAX2 and
pull
parsers</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/187">GH-187</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added more tests for invalid XMLs.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/183">GH-183</a></li>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Added more performance tests.</p>
<ul>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/186">GH-186</a></li>
<li>Patch by tomoya ishida.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>Watson</p>
</li>
<li>
<p>tomoya ishida</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/ruby/rexml/blob/master/NEWS.md">rexml's
changelog</a>.</em></p>
<blockquote>
<h2>3.3.3 - 2024-08-01 {#version-3-3-3}</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Added support for detecting invalid XML that has unsupported
content before root element</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/184">GH-184</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added support for
<code>REXML::Security.entity_expansion_limit=</code> and
<code>REXML::Security.entity_expansion_text_limit=</code> in SAX2 and
pull
parsers</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/187">GH-187</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added more tests for invalid XMLs.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/183">GH-183</a></li>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Added more performance tests.</p>
<ul>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a
href="https://redirect.github.com/ruby/rexml/issues/186">GH-186</a></li>
<li>Patch by tomoya ishida.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>Watson</p>
</li>
<li>
<p>tomoya ishida</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/ruby/rexml/commit/e4a067e11235a2ec7a00616d41350485e384ec05"><code>e4a067e</code></a>
Add 3.3.3 entry</li>
<li><a
href="https://github.com/ruby/rexml/commit/17ff3e78745b31db4e841357e8eed2f6669bea7b"><code>17ff3e7</code></a>
test: add a performance test for attribute list declaration</li>
<li><a
href="https://github.com/ruby/rexml/commit/be86b3de0aca8394534b715a83a63bf51c5195f5"><code>be86b3d</code></a>
test: fix wrong test name</li>
<li><a
href="https://github.com/ruby/rexml/commit/b93d790b36c065a3f7f3e0c3f5b2b71254a4d96d"><code>b93d790</code></a>
test: use double quote for string literal</li>
<li><a
href="https://github.com/ruby/rexml/commit/0fbe7d5a0eac8cfaffa6c3b27f3b9a90061a0fbc"><code>0fbe7d5</code></a>
test: don't use abbreviated name</li>
<li><a
href="https://github.com/ruby/rexml/commit/1599e8785f2d7734169aeb37a0b5d94f8212356d"><code>1599e87</code></a>
test: add a performance test for PI with many tabs</li>
<li><a
href="https://github.com/ruby/rexml/commit/e2546e6ecade16b04c9ee528e5be8509fe16c2d6"><code>e2546e6</code></a>
parse pi: improve invalid case detection</li>
<li><a
href="https://github.com/ruby/rexml/commit/73661ef281f5a829f7fec4ea673d42436c533ded"><code>73661ef</code></a>
test: fix a typo</li>
<li><a
href="https://github.com/ruby/rexml/commit/850488abf20f9327ebc00094cd3bb64eea400a59"><code>850488a</code></a>
test: use double quote for string literal</li>
<li><a
href="https://github.com/ruby/rexml/commit/46c6397d5c647a700fb1817d0093471621d92a27"><code>46c6397</code></a>
test: add performance tests for entity declaration</li>
<li>Additional commits viewable in <a
href="https://github.com/ruby/rexml/compare/v3.3.2...v3.3.3">compare
view</a></li>
</ul>
</details>
<br />


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Pre-release is failing due to a vulnerability on dependency
`github.com/docker/docker` and this PR updates it to the latest version.
Update changelog for v1.8.3
@hogo6002 hogo6002 requested review from cuixq and another-rex August 7, 2024 04:40
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@@ -0,0 +1,32 @@
name: "Close stale issues and PRs"

Check failure

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Token-Permissions High

score is 0: no topLevel permission defined
Remediation tip: Visit https://app.stepsecurity.io/secureworkflow.
Tick the 'Restrict permissions for GITHUB_TOKEN'
Untick other options
NOTE: If you want to resolve multiple issues at once, you can visit https://app.stepsecurity.io/securerepo instead.
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stale:
runs-on: ubuntu-latest
steps:
- uses: actions/stale@v9

Check warning

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@hogo6002 hogo6002 requested a review from andrewpollock August 7, 2024 04:50
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hogo6002 commented Aug 7, 2024

We will fix the token permission issue on main branch.

@hogo6002 hogo6002 merged commit 5593981 into docs Aug 7, 2024
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