sanger / limber

A config-driven LIMS built on Sequencescape, primarily for running library preparation pipelines in the laboratory
MIT License
4 stars 8 forks source link

🚨 [security] [ruby] Update rails 7.1.4 → 7.1.5 (patch) #2041

Closed depfu[bot] closed 2 weeks ago

depfu[bot] commented 3 weeks ago

🚨 Your current dependencies have known security vulnerabilities 🚨

This dependency update fixes known security vulnerabilities. Please see the details below and assess their impact carefully. We recommend to merge and deploy this as soon as possible!


Here is everything you need to know about this update. Please take a good look at what changed and the test results before merging this pull request.

What changed?

✳️ rails (7.1.4 → 7.1.5) · Repo

Release Notes

7.1.5

Active Support

  • No changes.

Active Model

  • Fix regression in alias_attribute to work with user defined methods.

    alias_attribute would wrongly assume the attribute accessor was generated by Active Model.

    class Person
      include ActiveModel::AttributeMethods
    
      define_attribute_methods :name
      attr_accessor :name
    
      alias_attribute :full_name, :name
    end
    
    person.full_name # => NoMethodError: undefined method `attribute' for an instance of Person

    Jean Boussier

Active Record

  • Fix marshalling of unsaved associated records in 7.1 format.

    The 7.1 format would only marshal associated records if the association was loaded.
    But associations that would only contain unsaved records would be skipped.

    Jean Boussier

  • Fix an issue where .left_outer_joins used with multiple associations that have
    the same child association but different parents does not join all parents.

    Previously, using .left_outer_joins with the same child association would only join one of the parents.

    Now it will correctly join both parents.

    Fixes #41498.

    Garrett Blehm

  • Ensure ActiveRecord::Encryption.config is always ready before access.

    Previously, ActiveRecord::Encryption configuration was deferred until ActiveRecord::Base
    was loaded. Therefore, accessing ActiveRecord::Encryption.config properties before
    ActiveRecord::Base was loaded would give incorrect results.

    ActiveRecord::Encryption now has its own loading hook so that its configuration is set as
    soon as needed.

    When ActiveRecord::Base is loaded, even lazily, it in turn triggers the loading of
    ActiveRecord::Encryption, thus preserving the original behavior of having its config ready
    before any use of ActiveRecord::Base.

    Maxime Réty

  • Add TimeZoneConverter#== method, so objects will be properly compared by
    their type, scale, limit & precision.

    Address #52699.

    Ruy Rocha

Action View

  • No changes.

Action Pack

  • No changes.

Active Job

  • No changes.

Action Mailer

  • No changes.

Action Cable

  • No changes.

Active Storage

  • No changes.

Action Mailbox

  • No changes.

Action Text

  • No changes.

Railties

  • No changes.

Guides

  • No changes.

7.1.4.2

Active Support

  • No changes.

Active Model

  • No changes.

Active Record

  • No changes.

Action View

  • No changes.

Action Pack

  • No changes.

Active Job

  • No changes.

Action Mailer

  • Fix NoMethodError in block_format helper

    Michael Leimstaedtner

Action Cable

  • No changes.

Active Storage

  • No changes.

Action Mailbox

  • No changes.

Action Text

  • No changes.

Railties

  • No changes.

Guides

  • No changes.

7.1.4.1

Active Support

  • No changes.

Active Model

  • No changes.

Active Record

  • No changes.

Action View

  • No changes.

Action Pack

  • Avoid regex backtracking in HTTP Token authentication

    [CVE-2024-47887]

  • Avoid regex backtracking in query parameter filtering

    [CVE-2024-41128]

Active Job

  • No changes.

Action Mailer

Action Cable

  • No changes.

Active Storage

  • No changes.

Action Mailbox

  • No changes.

Action Text

  • Avoid backtracing in plain_text_for_blockquote_node

    [CVE-2024-47888]

Railties

  • No changes.

Guides

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ actioncable (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ actionmailbox (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

↗️ actionmailer (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Security Advisories 🚨

🚨 Possible ReDoS vulnerability in block_format in Action Mailer

There is a possible ReDoS vulnerability in the block_format helper in Action Mailer. This vulnerability has been assigned the CVE identifier CVE-2024-47889.

Impact

Carefully crafted text can cause the block_format helper to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.

Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 requires Ruby 3.2 or greater so is unaffected.

Releases

The fixed releases are available at the normal locations.

Workarounds

Users can avoid calling the block_format helper or upgrade to Ruby 3.2

Credits

Thanks to ooooooo_q for the report!

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • Fix NoMethodError in block_format helper

    Michael Leimstaedtner

7.1.4.1 (from changelog)

  • Avoid regex backtracking in block_format helper

    [CVE-2024-47889]

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ actionpack (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Security Advisories 🚨

🚨 Possible ReDoS vulnerability in HTTP Token authentication in Action Controller

There is a possible ReDoS vulnerability in Action Controller's HTTP Token authentication. This vulnerability has been assigned the CVE identifier CVE-2024-47887.

Impact

For applications using HTTP Token authentication via authenticate_or_request_with_http_token or similar, a carefully crafted header may cause header parsing to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.

Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 depends on Ruby 3.2 or greater so is unaffected.

Releases

The fixed releases are available at the normal locations.

Workarounds

Users on Ruby 3.2 are unaffected by this issue.

Credits

Thanks to scyoon for reporting

🚨 Possible ReDoS vulnerability in query parameter filtering in Action Dispatch

There is a possible ReDoS vulnerability in the query parameter filtering routines of Action Dispatch. This vulnerability has been assigned the CVE identifier CVE-2024-41128.

Impact

Carefully crafted query parameters can cause query parameter filtering to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.

Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 depends on Ruby 3.2 or greater so is unaffected.

Releases

The fixed releases are available at the normal locations.

Workarounds

Users on Ruby 3.2 are unaffected by this issue.

Credits

Thanks to scyoon for the report and patches!

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • Avoid regex backtracking in HTTP Token authentication

    [CVE-2024-47887]

  • Avoid regex backtracking in query parameter filtering

    [CVE-2024-41128]

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ actiontext (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Security Advisories 🚨

🚨 Possible ReDoS vulnerability in plain_text_for_blockquote_node in Action Text

There is a possible ReDoS vulnerability in the plain_text_for_blockquote_node helper in Action Text. This vulnerability has been assigned the CVE identifier CVE-2024-47888.

Impact

Carefully crafted text can cause the plain_text_for_blockquote_node helper to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.

Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 depends on Ruby 3.2 or greater so is unaffected.

Releases

The fixed releases are available at the normal locations.

Workarounds

Users can avoid calling plain_text_for_blockquote_node or upgrade to Ruby 3.2

Credits

Thanks to ooooooo_q for the report!

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • Avoid backtracing in plain_text_for_blockquote_node

    [CVE-2024-47888]

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ actionview (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ activejob (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ activemodel (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • Fix regression in alias_attribute to work with user defined methods.

    alias_attribute would wrongly assume the attribute accessor was generated by Active Model.

    class Person
    include ActiveModel::AttributeMethods

    define_attribute_methods :name
    attr_accessor :name

    alias_attribute :full_name, :name
    end

    person.full_name # => NoMethodError: undefined method `attribute' for an instance of Person

    Jean Boussier

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ activerecord (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • Fix marshalling of unsaved associated records in 7.1 format.

    The 7.1 format would only marshal associated records if the association was loaded. But associations that would only contain unsaved records would be skipped.

    Jean Boussier

  • Fix an issue where .left_outer_joins used with multiple associations that have the same child association but different parents does not join all parents.

    Previously, using .left_outer_joins with the same child association would only join one of the parents.

    Now it will correctly join both parents.

    Fixes #41498.

    Garrett Blehm

  • Ensure ActiveRecord::Encryption.config is always ready before access.

    Previously, ActiveRecord::Encryption configuration was deferred until ActiveRecord::Base was loaded. Therefore, accessing ActiveRecord::Encryption.config properties before ActiveRecord::Base was loaded would give incorrect results.

    ActiveRecord::Encryption now has its own loading hook so that its configuration is set as soon as needed.

    When ActiveRecord::Base is loaded, even lazily, it in turn triggers the loading of ActiveRecord::Encryption, thus preserving the original behavior of having its config ready before any use of ActiveRecord::Base.

    Maxime Réty

  • Add TimeZoneConverter#== method, so objects will be properly compared by their type, scale, limit & precision.

    Address #52699.

    Ruy Rocha

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ activestorage (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ activesupport (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ date (indirect, 3.3.4 → 3.4.0) · Repo

Release Notes

3.4.0

What's Changed

  • Provide a 'Changelog' link on rubygems.org/gems/date by @mark-young-atg in #101
  • Remove the unintentional ability to parse Symbol by @nobu in #102
  • Prevent converted gregorian date from GC by @nobu in #103
  • [DOC] Specify the unit of return value for Date#- by @p0pemaru in #97
  • Update gperf by @nobu in #104

New Contributors

Full Changelog: v3.3.4...v3.4.0

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ loofah (indirect, 2.22.0 → 2.23.1) · Repo · Changelog

Release Notes

2.23.1

2.23.1 / 2024-10-25

Added

  • Allow CSS properties min-height and max-height. [#288] @lazyatom

Full Changelog: v2.23.0...v2.23.1

2.23.0

2.23.0 / 2024-10-24

Added

New Contributors

Full Changelog: v2.22.0...v2.23.0

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ net-imap (indirect, 0.4.14 → 0.5.0) · Repo

Release Notes

0.5.0

What's Changed

Breaking Changes

  • 💥 Drop ruby 2.7 and 3.0 support, and require ruby 3.1 by @nevans in #276
  • 💥⚡ Simplify header-fld-name parser (backward incompatible) by @nevans in #216
    For example, HEADER.FIELDS(Content-Type) or HEADER.FIELDS("Content-Type") are semantically identical, and a server may choose to return the quoted version.
    • Before this change, the FetchData attr header name would be quoted if the server sent the field name quoted.
    • After this change, the header field names will always be unquoted by the parser, so the result will always available via fetch_data.header_fields("Content-Type") or fetch_data.attr_upcase["HEADER.FIELDS(CONTENT-TYPE)"].
  • 💥 Replace MessageSet with SequenceSet by @nevans in #282
    Most of the changes are bugfixes or allow something new to work that didn't work before. See the PR for more details.
    This affects #search, #uid_search, #sort, #uid_sort, #fetch, #uid_fetch, #store, #uid_store, #copy, #uid_copy, #move, #uid_move, and #uid_expunge.
  • 💥 SequenceSet input validation for Set, Array, and enumerables by @nevans in #319
    • Array inputs can still be deeply nested.
    • Set inputs can only contain integers and "*" or :*, to be consistent with SequenceSet#to_set.
    • Other Enumerables will only be converted if they implement #to_sequence_set.
  • 🔥 Remove deprecated #client_thread attr_reader by @nevans in #321
    #client_thread was deprecated by v0.4.0.
  • 🔥 Drop deprecated BodyType structs by @nevans in #323
    These structs were deprecated by v0.4.0.

Added

  • ✨ Add #extract_responses method by @nevans in #330 Also backported to v0.4.17.
  • ✨ New config option to return frozen dup from #responses by @nevans in #334 Also backported to v0.4.17.
  • 🥅 Improve SequenceSet frozen errors by @nevans in #331 Also backported to v0.4.17.
  • 📚 SequenceSet API is considered stable now by @nevans in #318
  • 🔒 Enforce LOGINDISABLED requirement by @nevans in #307
    To workaround buggy servers, config.enforce_logindisabled can be set to :when_capabilities_cached or false.
  • 🔒 SASL DIGEST-MD5: realm, host, service_name, etc by @nevans in #284
    Please note that the DIGEST-MD5 SASL mechanism is insecure and deprecated.

Deprecations

  • 🔊 Warn about deprecated #responses usage by @nevans in #97
    To silence these warnings:
    • pass a block to #responses (supported since v0.4.0),
    • pass a response type to #responses for a frozen copied array (since v0.4.17),
    • set config.responses_without_block to :silence_deprecation_warning (since v0.4.13),
    • set config.responses_without_block to :frozen_dup for a frozen copy (since v0.4.17),
    • use #clear_responses instead (since v0.4.0),
    • use #extract_responses instead (since v0.4.17).
  • 🗑️ Deprecate MessageSet by @nevans in #282
    MessageSet was only intended for internal use, and all internal usage has been replaced.

Fixed

  • 🐛 Fix #send_data to send DateTime as time by @taku0 in #313
    Also backported to v0.4.15.
  • 🐛 Fix #header_fld_name to handle quoted strings correctly by @taku0 in #315
    Also backported to v0.4.16.
  • 🐛 Fix SequenceSet[input] when input is a SequenceSet by @nevans in #326
    Also backported to v0.4.17.
  • 🐛 Fix Set inputs for SequenceSet by @nevans in #332
    This bug was introduced by #319, which had not been previously released.

Other Changes

  • 🔧 Update default config for v0.5 by @nevans in #305
  • ♻️ Use Integer.try_convert (new in ruby 3.1+) by @nevans in #316
  • 🗑️ Add category: :deprecated to calls to warn by @nevans in #322
  • ♻️ Extract SASL::Authenticators#normalize_name by @nevans in #309
  • 🔒 📚 Improvements and docs for SASL::ClientAdapter by @nevans in #320
  • ♻️ Use SASL::ClientAdapter by @nevans in #194

Documentation

  • 📚 Update Config rdoc for v0.5 by @nevans in #306
  • 📚 Update SASL documentation by @nevans in #308
  • 📚 SequenceSet API is considered stable now by @nevans in #318
  • 🔒 📚 Improvements and docs for SASL::ClientAdapter by @nevans in #320

Miscellaneous

  • ✅ Add a Mutex to FakeServer (for tests only) by @nevans in #317
    Also backported to v0.4.17.
  • ⬆️ Bump step-security/harden-runner from 2.8.1 to 2.9.0 by @dependabot in #311
  • ⬆️ Bump step-security/harden-runner from 2.9.0 to 2.9.1 by @dependabot in #312
  • Bump step-security/harden-runner from 2.9.1 to 2.10.1 by @dependabot in #325
  • 🔨📚 Fix rdoc => ghpages workflow by @nevans in #335
  • ✅ Fix GH action for rubygems Trusted Publishing by @nevans in #340
    Also backported to v0.4.17.
  • ✅ Setup simplecov by @nevans in #328

New Contributors

Full Changelog: v0.4.14...v0.5.0
(Note that v0.4.x releases since v0.4.14 have used the v0.4-stable branch.)

0.4.17

What's Changed

Added features

  • ✨ Add #extract_responses method by @nevans in #337 (backports #330)
  • ✨ New config option to return frozen dup from #responses by @nevans in #339 (backports #334)
    This will become the default in v0.6.0.

Bug fixes

  • 🐛 Fix SequenceSet[input] when input is a SequenceSet by @nevans in #327 (backports #326)

Other Changes

  • 🥅 Improve SequenceSet frozen errors by @nevans in #338 (backports #331)

Miscellaneous

  • ✅ Add a Mutex to FakeServer (for tests only) by @nevans in #336 (backports #317)
  • ✅ Fix GH action for Rubygems Trusted Publishing by @nevans in #341 (backports #340)

Full Changelog: v0.4.16...v0.4.17

0.4.16

What's Changed

Fixed

  • 🐛 Fix #header_fld_name to handle quoted strings correctly by @taku0 in #315

Full Changelog: v0.4.15...v0.4.16

0.4.15

What's Changed

Fixed

  • 🐛 Fix #send_data to send DateTime as time by @taku0 in #313

New Contributors

Full Changelog: v0.4.14...v0.4.15

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ nio4r (indirect, 2.7.3 → 2.7.4) · Repo · Changelog

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ rackup (indirect, 2.1.0 → 2.2.0) · Repo

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ railties (indirect, 7.1.4 → 7.1.5) · Repo · Changelog

Release Notes

7.1.5 (from changelog)

  • No changes.

7.1.4.2 (from changelog)

  • No changes.

7.1.4.1 (from changelog)

  • No changes.

Does any of this look wrong? Please let us know.

Commits

See the full diff on Github. The new version differs by more commits than we can show here.

↗️ zeitwerk (indirect, 2.6.18 → 2.7.1) · Repo · Changelog

Release Notes

2.7.1 (from changelog)

  • Micro-optimization in a hot path.

  • Raises Zeitwerk::Error if an autoloaded constant expected to represent a namespace does not store a class or module object.

  • Adds truffleruby-head to CI, except for autoloading thread-safety (see why in oracle/truffleruby#2431).

2.7.0 (from changelog)

  • Explicit namespaces can now also be defined using constant assignments.

    While constant assignments like

    # coordinates.rb

    Coordinates = Data.define(:x, :y)

    worked for most objects, they did not for classes and modules that were also namespaces (i.e., those defined by a file and matching subdirectories). In such cases, their child constants could not be autoloaded.

    This limitation has been removed.

  • TracePoint is no longer used.

  • Requires Ruby 3.2 or later.

    Gems that work with previous versions of Zeitwerk also work with this one. If they support Ruby versions older than 3.2 they can specify a relaxed version constraint for Zeitwerk like "~> 2.6", for example.

    In client projects, Bundler takes the Ruby requirement into account when resolving dependencies, so Gemfile.lock will get one compatible with the Ruby version being used.

Does any of this look wrong? Please let us know.

Commits

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🆕 benchmark (added, 0.3.0)

🆕 securerandom (added, 0.3.1)

🗑️ webrick (removed)


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codecov[bot] commented 3 weeks ago

Codecov Report

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

Project coverage is 78.21%. Comparing base (7db5324) to head (5af4eb7). Report is 2 commits behind head on develop.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #2041 +/- ## ======================================== Coverage 78.21% 78.21% ======================================== Files 471 471 Lines 18226 18226 Branches 262 262 ======================================== Hits 14255 14255 Misses 3969 3969 Partials 2 2 ``` | [Flag](https://app.codecov.io/gh/sanger/limber/pull/2041/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sanger) | Coverage Δ | | |---|---|---| | [javascript](https://app.codecov.io/gh/sanger/limber/pull/2041/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sanger) | `70.43% <ø> (ø)` | | | [pull_request](https://app.codecov.io/gh/sanger/limber/pull/2041/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sanger) | `78.21% <ø> (ø)` | | | [push](https://app.codecov.io/gh/sanger/limber/pull/2041/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sanger) | `78.21% <ø> (ø)` | | | [ruby](https://app.codecov.io/gh/sanger/limber/pull/2041/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sanger) | `91.16% <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=sanger#carryforward-flags-in-the-pull-request-comment) to find out more.

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StephenHulme commented 2 weeks ago

@depfu rebase