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Develop -> Main for 5.5.0 release#3706

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briehl merged 22 commits intomainfrom
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Aug 14, 2025
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Develop -> Main for 5.5.0 release#3706
briehl merged 22 commits intomainfrom
develop

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@briehl briehl commented Aug 14, 2025

Description of PR purpose/changes

Everything's already vetted on develop, should be good to go.

briehl and others added 21 commits December 18, 2024 16:51
@briehl
add DTS importer path and selector
9ba16cd
@briehl
add gff_genome to bulk importers
012e5ac
@briehl
add staging upload config
320dc0e
@briehl
Merge branch 'develop' into URO-352-dts-import
01e4a1b
@briehl
do dts file path tweaking on the front end
b958129
@briehl
Merge branch 'develop' into URO-352-dts-import
beecb8e
@exnehilo7
Add focus on open. Tweak display icon.
a386eed
@briehl
Merge pull request #3697 from kbase/URO-366-users-should-be-able-to-p…
5935fba 
…aste-usernames-into-the-s

URO-366 Add focus on open. Tweak display icon.
@briehl
fix a couple tests
d593c24
@briehl
add tests for dts_manifest importer
c1e7d28
@briehl
Merge branch 'develop' into URO-352-dts-import
5833adc
@briehl
fdescribe -> describe
36551e5
@dependabot
Bump the pip group across 1 directory with 25 updates
e91b7b8 
Bumps the pip group with 25 updates in the /src directory:

| Package | From | To |
| --- | --- | --- |
| [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) | `4.13.3` | `4.13.4` |
| [certifi](https://github.com/certifi/python-certifi) | `2025.1.31` | `2025.7.14` |
| [cryptography](https://github.com/pyca/cryptography) | `44.0.1` | `45.0.5` |
| [jsonschema](https://github.com/python-jsonschema/jsonschema) | `4.23.0` | `4.25.0` |
| [markdown](https://github.com/Python-Markdown/markdown) | `3.7` | `3.8.2` |
| [pillow](https://github.com/python-pillow/Pillow) | `11.1.0` | `11.3.0` |
| [plotly](https://github.com/plotly/plotly.py) | `5.24.1` | `6.2.0` |
| [pycurl](https://github.com/pycurl/pycurl) | `7.45.4` | `7.45.6` |
| [pygments](https://github.com/pygments/pygments) | `2.19.1` | `2.19.2` |
| [pyopenssl](https://github.com/pyca/pyopenssl) | `25.0.0` | `25.1.0` |
| [rsa](https://github.com/sybrenstuvel/python-rsa) | `4.9` | `4.9.1` |
| [setuptools](https://github.com/pypa/setuptools) | `75.8.2` | `80.9.0` |
| [sympy](https://github.com/sympy/sympy) | `1.13.3` | `1.14.0` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.5` | `8.1.7` |
| [jinja2](https://github.com/pallets/jinja) | `3.1.5` | `3.1.6` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.2.3` | `2.3.1` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.11.1` | `4.13.2` |
| [requests](https://github.com/psf/requests) | `2.32.3` | `2.32.4` |
| [statsmodels](https://github.com/statsmodels/statsmodels) | `0.14.4` | `0.14.5` |
| [tornado](https://github.com/tornadoweb/tornado) | `6.4.2` | `6.5.1` |
| [coverage](https://github.com/nedbat/coveragepy) | `7.6.12` | `7.10.1` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.4` | `8.4.1` |
| [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `6.0.0` | `6.2.1` |
| [pytest-recording](https://github.com/kiwicom/pytest-recording) | `0.13.2` | `0.13.4` |
| [ruff](https://github.com/astral-sh/ruff) | `0.9.9` | `0.12.7` |



Updates `beautifulsoup4` from 4.13.3 to 4.13.4

Updates `certifi` from 2025.1.31 to 2025.7.14
- [Commits](certifi/python-certifi@2025.01.31...2025.07.14)

Updates `cryptography` from 44.0.1 to 45.0.5
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@44.0.1...45.0.5)

Updates `jsonschema` from 4.23.0 to 4.25.0
- [Release notes](https://github.com/python-jsonschema/jsonschema/releases)
- [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst)
- [Commits](python-jsonschema/jsonschema@v4.23.0...v4.25.0)

Updates `markdown` from 3.7 to 3.8.2
- [Release notes](https://github.com/Python-Markdown/markdown/releases)
- [Changelog](https://github.com/Python-Markdown/markdown/blob/master/docs/changelog.md)
- [Commits](Python-Markdown/markdown@3.7...3.8.2)

Updates `pillow` from 11.1.0 to 11.3.0
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@11.1.0...11.3.0)

Updates `plotly` from 5.24.1 to 6.2.0
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md)
- [Commits](plotly/plotly.py@v5.24.1...v6.2.0)

Updates `pycurl` from 7.45.4 to 7.45.6
- [Changelog](https://github.com/pycurl/pycurl/blob/master/ChangeLog)
- [Commits](https://github.com/pycurl/pycurl/commits)

Updates `pygments` from 2.19.1 to 2.19.2
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](pygments/pygments@2.19.1...2.19.2)

Updates `pyopenssl` from 25.0.0 to 25.1.0
- [Changelog](https://github.com/pyca/pyopenssl/blob/main/CHANGELOG.rst)
- [Commits](pyca/pyopenssl@25.0.0...25.1.0)

Updates `rsa` from 4.9 to 4.9.1
- [Changelog](https://github.com/sybrenstuvel/python-rsa/blob/main/CHANGELOG.md)
- [Commits](https://github.com/sybrenstuvel/python-rsa/commits)

Updates `setuptools` from 75.8.2 to 80.9.0
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v75.8.2...v80.9.0)

Updates `sympy` from 1.13.3 to 1.14.0
- [Release notes](https://github.com/sympy/sympy/releases)
- [Commits](sympy/sympy@sympy-1.13.3...sympy-1.14.0)

Updates `ipywidgets` from 8.1.5 to 8.1.7
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](jupyter-widgets/ipywidgets@8.1.5...8.1.7)

Updates `jinja2` from 3.1.5 to 3.1.6
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.5...3.1.6)

Updates `pandas` from 2.2.3 to 2.3.1
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.2.3...v2.3.1)

Updates `pymongo` from 4.11.1 to 4.13.2
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](mongodb/mongo-python-driver@4.11.1...4.13.2)

Updates `requests` from 2.32.3 to 2.32.4
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.32.3...v2.32.4)

Updates `statsmodels` from 0.14.4 to 0.14.5
- [Release notes](https://github.com/statsmodels/statsmodels/releases)
- [Changelog](https://github.com/statsmodels/statsmodels/blob/main/CHANGES.md)
- [Commits](statsmodels/statsmodels@v0.14.4...v0.14.5)

Updates `tornado` from 6.4.2 to 6.5.1
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.4.2...v6.5.1)

Updates `coverage` from 7.6.12 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@7.6.12...7.10.1)

Updates `pytest` from 8.3.4 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@8.3.4...8.4.1)

Updates `pytest-cov` from 6.0.0 to 6.2.1
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.0.0...v6.2.1)

Updates `pytest-recording` from 0.13.2 to 0.13.4
- [Release notes](https://github.com/kiwicom/pytest-recording/releases)
- [Changelog](https://github.com/kiwicom/pytest-recording/blob/master/docs/changelog.rst)
- [Commits](kiwicom/pytest-recording@v0.13.2...v0.13.4)

Updates `ruff` from 0.9.9 to 0.12.7
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.9.9...0.12.7)

---
updated-dependencies:
- dependency-name: beautifulsoup4
  dependency-version: 4.13.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: certifi
  dependency-version: 2025.7.14
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: cryptography
  dependency-version: 45.0.5
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: jsonschema
  dependency-version: 4.25.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: markdown
  dependency-version: 3.8.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pillow
  dependency-version: 11.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: plotly
  dependency-version: 6.2.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: pycurl
  dependency-version: 7.45.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pygments
  dependency-version: 2.19.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pyopenssl
  dependency-version: 25.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: rsa
  dependency-version: 4.9.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: setuptools
  dependency-version: 80.9.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: sympy
  dependency-version: 1.14.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: ipywidgets
  dependency-version: 8.1.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: jinja2
  dependency-version: 3.1.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pandas
  dependency-version: 2.3.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pymongo
  dependency-version: 4.13.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: requests
  dependency-version: 2.32.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: statsmodels
  dependency-version: 0.14.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: tornado
  dependency-version: 6.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: coverage
  dependency-version: 7.10.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest
  dependency-version: 8.4.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest-cov
  dependency-version: 6.2.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest-recording
  dependency-version: 0.13.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: ruff
  dependency-version: 0.12.7
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
@briehl
Merge pull request #3677 from kbase/URO-352-dts-import
844c5b8 
URO-352 DTS importer setup for narrative
@briehl
version bump to 5.5.0
8d3721c
@briehl
Merge pull request #3701 from kbase/version-bump
2ae69c4 
Version bump to 5.5.0
@briehl
Merge branch 'develop' into update-python-deps-aug-2025
854e190
@briehl
update release notes
ab977ba
@briehl
Merge pull request #3703 from kbase/update-python-deps-aug-2025
4b83cbf 
Update python deps aug 2025
@briehl
update js deps
73d279f
@ialarmedalien
Merge pull request #3704 from kbase/update-js-deps-aug-2025
3962b1a 
Update JavaScript dependencies Aug 2025
@briehl briehl requested a review from ialarmedalien August 14, 2025 14:52
@sonarqubecloud
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sonarqubecloud bot commented Aug 14, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

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codecov bot commented Aug 14, 2025 •
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Codecov Report

❌ Patch coverage is 95.91837% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 25.96%. Comparing base (9b350a5) to head (fe5f7bc).
⚠️ Report is 25 commits behind head on main.

Files with missing lines Patch % Lines
kbase-extension/static/kbase/js/kbaseNarrative.js 0.00% 2 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #3706      +/-   ##
==========================================
+ Coverage   25.91%   25.96%   +0.04%     
==========================================
  Files         461      461              
  Lines       46660    46691      +31     
==========================================
+ Hits        12094    12122      +28     
- Misses      34566    34569       +3
Files with missing lines Coverage Δ
...ension/static/kbase/js/api/StagingServiceClient.js 100.00% <ø> (ø)
.../widgets/narrative_core/kbaseNarrativeWorkspace.js 67.66% <100.00%> (ø)
...se/js/widgets/narrative_core/upload/importSetup.js 98.11% <100.00%> (+0.42%) ⬆️
kbase-extension/static/kbase/js/kbaseNarrative.js 48.30% <0.00%> (-0.26%) ⬇️

... and 5 files with indirect coverage changes

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@briehl briehl merged commit 97bc661 into main Aug 14, 2025
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3 participants

@briehl @ialarmedalien @exnehilo7