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[release] Merge Develop into Master for 2.13.4#629
github-actions[bot] wants to merge 88 commits intomasterfrom
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Proposed Changes

Instructions for Reviewers

  • Check stories are ready for release.
  • Check for any database migrations.
  • Check for debug code.
  • Check version is appropriate.

Everything above the horizontal rule will be overwritten on the next push
This PR was auto-generated on 2026-01-06T10:29:22+00:00

Additional Context

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dependabot bot and others added 30 commits May 20, 2025 08:42
@dependabot
Bump flask-cors from 5.0.1 to 6.0.0
42fc2d0 
Bumps [flask-cors](https://github.com/corydolphin/flask-cors) from 5.0.1 to 6.0.0.
- [Release notes](https://github.com/corydolphin/flask-cors/releases)
- [Changelog](https://github.com/corydolphin/flask-cors/blob/main/CHANGELOG.md)
- [Commits](corydolphin/flask-cors@5.0.1...6.0.0)

---
updated-dependencies:
- dependency-name: flask-cors
  dependency-version: 6.0.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump coverage from 7.8.1 to 7.8.2
30d1a76 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.8.1 to 7.8.2.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.8.1...7.8.2)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.8.2
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump mypy from 1.15.0 to 1.16.0
13f4f0a 
Bumps [mypy](https://github.com/python/mypy) from 1.15.0 to 1.16.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.15.0...v1.16.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.16.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
Merge pull request #586 from sanger/dependabot/pip/mypy-1.16.0
7650d5f 
build(deps-dev): bump mypy from 1.15.0 to 1.16.0
@dependabot
build(deps-dev): bump pytest from 8.3.5 to 8.4.0
5390e2a 
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.3.5 to 8.4.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.5...8.4.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-version: 8.4.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
Merge pull request #588 from sanger/dependabot/pip/pytest-8.4.0
533d4f1 
build(deps-dev): bump pytest from 8.3.5 to 8.4.0
@harrietc52
Merge pull request #579 from sanger/dependabot/pip/flask-cors-6.0.0
851e0bf 
Bump flask-cors from 5.0.1 to 6.0.0
@harrietc52
Merge pull request #585 from sanger/dependabot/pip/coverage-7.8.2
853d458 
Bump coverage from 7.8.1 to 7.8.2
@dependabot
Bump alembic from 1.15.2 to 1.16.1
5f09bcb 
Bumps [alembic](https://github.com/sqlalchemy/alembic) from 1.15.2 to 1.16.1.
- [Release notes](https://github.com/sqlalchemy/alembic/releases)
- [Changelog](https://github.com/sqlalchemy/alembic/blob/main/CHANGES)
- [Commits](https://github.com/sqlalchemy/alembic/commits)

---
updated-dependencies:
- dependency-name: alembic
  dependency-version: 1.16.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@harrietc52
Merge pull request #582 from sanger/dependabot/pip/alembic-1.16.1
5e0e8a4 
Bump alembic from 1.15.2 to 1.16.1
@dependabot
build(deps): bump flask-cors from 6.0.0 to 6.0.1
6cbcfe0 
Bumps [flask-cors](https://github.com/corydolphin/flask-cors) from 6.0.0 to 6.0.1.
- [Release notes](https://github.com/corydolphin/flask-cors/releases)
- [Changelog](https://github.com/corydolphin/flask-cors/blob/main/CHANGELOG.md)
- [Commits](corydolphin/flask-cors@6.0.0...6.0.1)

---
updated-dependencies:
- dependency-name: flask-cors
  dependency-version: 6.0.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump coverage from 7.8.2 to 7.9.1
65a1800 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.8.2 to 7.9.1.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.8.2...7.9.1)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.9.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
Merge pull request #593 from sanger/dependabot/pip/coverage-7.9.1
4fe5936 
build(deps-dev): bump coverage from 7.8.2 to 7.9.1
@dependabot
build(deps-dev): bump pytest-cov from 6.1.1 to 6.2.1
6b2089c 
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 6.1.1 to 6.2.1.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.1.1...v6.2.1)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-version: 6.2.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump mypy from 1.16.0 to 1.16.1
4a87e71 
Bumps [mypy](https://github.com/python/mypy) from 1.16.0 to 1.16.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.16.0...v1.16.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.16.1
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps): bump alembic from 1.16.1 to 1.16.2
8944149 
Bumps [alembic](https://github.com/sqlalchemy/alembic) from 1.16.1 to 1.16.2.
- [Release notes](https://github.com/sqlalchemy/alembic/releases)
- [Changelog](https://github.com/sqlalchemy/alembic/blob/main/CHANGES)
- [Commits](https://github.com/sqlalchemy/alembic/commits)

---
updated-dependencies:
- dependency-name: alembic
  dependency-version: 1.16.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump pytest from 8.4.0 to 8.4.1
9615138 
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.4.0 to 8.4.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.4.0...8.4.1)

---
updated-dependencies:
- dependency-name: pytest
  dependency-version: 8.4.1
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump flake8 from 7.2.0 to 7.3.0
db1452e 
Bumps [flake8](https://github.com/pycqa/flake8) from 7.2.0 to 7.3.0.
- [Commits](PyCQA/flake8@7.2.0...7.3.0)

---
updated-dependencies:
- dependency-name: flake8
  dependency-version: 7.3.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps): bump python-dotenv from 1.1.0 to 1.1.1
63be5c8 
Bumps [python-dotenv](https://github.com/theskumar/python-dotenv) from 1.1.0 to 1.1.1.
- [Release notes](https://github.com/theskumar/python-dotenv/releases)
- [Changelog](https://github.com/theskumar/python-dotenv/blob/main/CHANGELOG.md)
- [Commits](theskumar/python-dotenv@v1.1.0...v1.1.1)

---
updated-dependencies:
- dependency-name: python-dotenv
  dependency-version: 1.1.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@harrietc52
Merge pull request #591 from sanger/dependabot/pip/pytest-cov-6.2.1
1f12e50 
build(deps-dev): bump pytest-cov from 6.1.1 to 6.2.1
@harrietc52
Merge pull request #592 from sanger/dependabot/pip/flask-cors-6.0.1
d33948f 
build(deps): bump flask-cors from 6.0.0 to 6.0.1
@harrietc52
Merge pull request #594 from sanger/dependabot/pip/mypy-1.16.1
4eeef22 
build(deps-dev): bump mypy from 1.16.0 to 1.16.1
@harrietc52
Merge pull request #596 from sanger/dependabot/pip/pytest-8.4.1
a1c357c 
build(deps-dev): bump pytest from 8.4.0 to 8.4.1
@harrietc52
Merge pull request #595 from sanger/dependabot/pip/alembic-1.16.2
bdaf9ef 
build(deps): bump alembic from 1.16.1 to 1.16.2
@harrietc52
Merge pull request #597 from sanger/dependabot/pip/flake8-7.3.0
9a5021f 
build(deps-dev): bump flake8 from 7.2.0 to 7.3.0
@harrietc52
Merge pull request #598 from sanger/dependabot/pip/python-dotenv-1.1.1
193e425 
build(deps): bump python-dotenv from 1.1.0 to 1.1.1
@dependabot
build(deps-dev): bump coverage from 7.9.1 to 7.10.1
8bd8283 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.9.1 to 7.10.1.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.9.1...7.10.1)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.10.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
Merge pull request #605 from sanger/dependabot/pip/coverage-7.10.1
6d80f95 
build(deps-dev): bump coverage from 7.9.1 to 7.10.1
@dependabot
build(deps-dev): bump mypy from 1.16.1 to 1.17.1
17f8a24 
Bumps [mypy](https://github.com/python/mypy) from 1.16.1 to 1.17.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.16.1...v1.17.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.17.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump coverage from 7.10.1 to 7.10.3
3199785 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.10.1 to 7.10.3.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.10.1...7.10.3)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.10.3
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
dependabot bot and others added 4 commits October 17, 2025 09:37
@dependabot
build(deps): bump sqlalchemy from 2.0.43 to 2.0.44
edcc441 
Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 2.0.43 to 2.0.44.
- [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases)
- [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst)
- [Commits](https://github.com/sqlalchemy/sqlalchemy/commits)

---
updated-dependencies:
- dependency-name: sqlalchemy
  dependency-version: 2.0.44
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps): bump alembic from 1.16.5 to 1.17.0
85e026b 
Bumps [alembic](https://github.com/sqlalchemy/alembic) from 1.16.5 to 1.17.0.
- [Release notes](https://github.com/sqlalchemy/alembic/releases)
- [Changelog](https://github.com/sqlalchemy/alembic/blob/main/CHANGES)
- [Commits](https://github.com/sqlalchemy/alembic/commits)

---
updated-dependencies:
- dependency-name: alembic
  dependency-version: 1.17.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
ci: add release PR workflow
48f11e8
@StephenHulme
Merge pull request #628 from sanger/sh51/create-release-pr
e6aa5e5 
Add release PR workflow
@github-actions github-actions bot added the production release Pull requests for production release label Oct 21, 2025
dependabot bot and others added 25 commits October 23, 2025 06:02
@dependabot
build(deps-dev): bump coverage from 7.10.7 to 7.11.0
bdb91a6 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.10.7 to 7.11.0.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.10.7...7.11.0)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.11.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
Merge pull request #630 from sanger/dependabot/pip/coverage-7.11.0
76b0854 
build(deps-dev): bump coverage from 7.10.7 to 7.11.0
@harrietc52
Merge pull request #625 from sanger/dependabot/pip/sqlalchemy-2.0.44
29a9397 
build(deps): bump sqlalchemy from 2.0.43 to 2.0.44
@harrietc52
Merge pull request #626 from sanger/dependabot/pip/psycopg2-2.9.11
0235b79 
build(deps): bump psycopg2 from 2.9.10 to 2.9.11
@harrietc52
Merge pull request #627 from sanger/dependabot/pip/alembic-1.17.0
d9bba6e 
build(deps): bump alembic from 1.16.5 to 1.17.0
@dependabot
build(deps): bump colorlog from 6.9.0 to 6.10.1
aa96ade 
Bumps [colorlog](https://github.com/borntyping/python-colorlog) from 6.9.0 to 6.10.1.
- [Release notes](https://github.com/borntyping/python-colorlog/releases)
- [Commits](borntyping/python-colorlog@v6.9.0...v6.10.1)

---
updated-dependencies:
- dependency-name: colorlog
  dependency-version: 6.10.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@harrietc52
Merge pull request #631 from sanger/dependabot/pip/colorlog-6.10.1
f96b947 
build(deps): bump colorlog from 6.9.0 to 6.10.1
@dependabot
build(deps): bump python-dotenv from 1.1.1 to 1.2.1
8f935c2 
Bumps [python-dotenv](https://github.com/theskumar/python-dotenv) from 1.1.1 to 1.2.1.
- [Release notes](https://github.com/theskumar/python-dotenv/releases)
- [Changelog](https://github.com/theskumar/python-dotenv/blob/main/CHANGELOG.md)
- [Commits](theskumar/python-dotenv@v1.1.1...v1.2.1)

---
updated-dependencies:
- dependency-name: python-dotenv
  dependency-version: 1.2.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps): bump alembic from 1.17.0 to 1.17.1
51f0955 
Bumps [alembic](https://github.com/sqlalchemy/alembic) from 1.17.0 to 1.17.1.
- [Release notes](https://github.com/sqlalchemy/alembic/releases)
- [Changelog](https://github.com/sqlalchemy/alembic/blob/main/CHANGES)
- [Commits](https://github.com/sqlalchemy/alembic/commits)

---
updated-dependencies:
- dependency-name: alembic
  dependency-version: 1.17.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@harrietc52
Merge pull request #633 from sanger/dependabot/pip/alembic-1.17.1
5aeaa6c 
build(deps): bump alembic from 1.17.0 to 1.17.1
@dependabot
build(deps-dev): bump black from 25.9.0 to 25.11.0
925f372 
Bumps [black](https://github.com/psf/black) from 25.9.0 to 25.11.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@25.9.0...25.11.0)

---
updated-dependencies:
- dependency-name: black
  dependency-version: 25.11.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps): bump alembic from 1.17.1 to 1.17.2
777a223 
Bumps [alembic](https://github.com/sqlalchemy/alembic) from 1.17.1 to 1.17.2.
- [Release notes](https://github.com/sqlalchemy/alembic/releases)
- [Changelog](https://github.com/sqlalchemy/alembic/blob/main/CHANGES)
- [Commits](https://github.com/sqlalchemy/alembic/commits)

---
updated-dependencies:
- dependency-name: alembic
  dependency-version: 1.17.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump coverage from 7.11.0 to 7.12.0
449a1e2 
Bumps [coverage](https://github.com/coveragepy/coveragepy) from 7.11.0 to 7.12.0.
- [Release notes](https://github.com/coveragepy/coveragepy/releases)
- [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.11.0...7.12.0)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.12.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps): bump werkzeug from 3.1.3 to 3.1.4
ccd4504 
Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.1.3 to 3.1.4.
- [Release notes](https://github.com/pallets/werkzeug/releases)
- [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst)
- [Commits](pallets/werkzeug@3.1.3...3.1.4)

---
updated-dependencies:
- dependency-name: werkzeug
  dependency-version: 3.1.4
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump mypy from 1.18.2 to 1.19.0
5d6133e 
Bumps [mypy](https://github.com/python/mypy) from 1.18.2 to 1.19.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.18.2...v1.19.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.19.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
build(deps-dev): bump pytest from 8.4.2 to 9.0.0
1ebf81c 
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.4.2 to 9.0.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.4.2...9.0.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-version: 9.0.0
  dependency-type: direct:development
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@harrietc52
Merge pull request #632 from sanger/dependabot/pip/python-dotenv-1.2.1
bba553d 
build(deps): bump python-dotenv from 1.1.1 to 1.2.1
@harrietc52
Merge pull request #637 from sanger/dependabot/pip/black-25.11.0
f1f7049 
build(deps-dev): bump black from 25.9.0 to 25.11.0
@harrietc52
Merge pull request #638 from sanger/dependabot/pip/alembic-1.17.2
6099816 
build(deps): bump alembic from 1.17.1 to 1.17.2
@harrietc52
Merge pull request #639 from sanger/dependabot/pip/coverage-7.12.0
93b8588 
build(deps-dev): bump coverage from 7.11.0 to 7.12.0
@harrietc52
Merge pull request #640 from sanger/dependabot/pip/werkzeug-3.1.4
655d701 
build(deps): bump werkzeug from 3.1.3 to 3.1.4
@harrietc52
Merge pull request #641 from sanger/dependabot/pip/mypy-1.19.0
99d59ba 
build(deps-dev): bump mypy from 1.18.2 to 1.19.0
@harrietc52
Merge pull request #642 from sanger/dependabot/pip/pytest-9.0.0
b2d84c7 
build(deps-dev): bump pytest from 8.4.2 to 9.0.0
@dependabot
build(deps): bump aiohttp from 3.11.11 to 3.13.3
3109b95 
---
updated-dependencies:
- dependency-name: aiohttp
  dependency-version: 3.13.3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
@StephenHulme
Merge pull request #650 from sanger/dependabot/pip/aiohttp-3.13.3
05129b3 
build(deps): bump aiohttp from 3.11.11 to 3.13.3
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@StephenHulme @harrietc52