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@briehl briehl released this 26 Jun 15:01
· 88 commits to main since this release
v5.3.0
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Version 5.3.0

  • PTV-1845 - kbaseTabs now shows another tab after a closable tab is closed;
    previously it showed an empty space.
  • PTV-1909 - Narrative sign out does sign out
  • UIP-41 - Update Jupyter Notebook to version 6.5.6
  • UIP-41 - Fix Dropzone dependency issues, address problems with unit tests
  • UIP-41 - Removed unused Python dependencies

Notebook widget updates

  • The clustergrammer widget was updated to clustergrammer2; see the python dependency changes below for version information.

Dependency Changes

  • Updated to include all Python dependencies in the image built in this repo, and removed those that are not directly referenced in KBase code.

  • Retained scientific computing dependencies that may be useful to the community (SciPy, numpy, pandas, etc.)

  • Removed directly required dependencies that are really just used by the Jupyter Notebook.

  • Separated requirements into image dependencies (i.e. packages that are generally useful to have on the Narrative Docker image, ported from the narrative-base-image repo), application requirements and dev requirements.

  • Generally useful python packages are combined in the src/requirements-general.txt file.

  • the requirements in src/requirements.txt are needed for the Narrative to run.

  • the requirements in src/requirements-dev.txt are needed for Narrative development and testing.

  • flake8, isort, and black have been replaced by the multifunctional formatter and linter Ruff.

  • Python dependency updates

    • beautifulsoup4: 4.12.2 -> 4.12.3
    • black: 24.4.2 -> replaced by Ruff
    • certifi: 2022.12.7 -> 2024.6.2
    • coverage: 7.3.1 -> 7.5.3
    • clustergrammer_widget: removed
    • clustergrammer2: 0.18.0 (new)
    • cryptography: 41.0.4 -> 42.0.8
    • flake8: 7.0.0 -> replaced by Ruff
    • idna: 3.4 -> 3.7
    • isort: 5.13.2 -> replaced by Ruff
    • ipython: 8.10.0 -> 8.25.0
    • jinja2: 3.1.2 -> 3.1.4
    • markupsafe: 2.1.3 -> 2.1.4
    • pillow: 9.4.0 -> 10.3.0
    • pygments: 2.16.1 -> 2.17.2
    • pymongo: 4.5.0 -> 4.7.3
    • pyopenssl: 23.2.0 -> 24.0.0
    • pytest: 7.4.0 -> 8.2.2
    • pytest-cov: 4.1.0 -> 5.0.0
    • pytest-recording: 0.13.1 (new)
    • requests-mock: 1.11.0 -> 1.12.1
    • requests: 2.31.0 -> 2.32.3
    • ruff: 0.4.7 (new)
    • scikit-learn: 1.2.1 -> 1.5.0
    • statsmodels: 0.14.2 (new)
    • terminado: 0.17.1 -> 0.18.0
    • tornado: 6.2 -> 6.4.1
    • vcrpy: 5.1.0 -> 6.0.1

  • Javascript dependency updates

    • @babel/traverse: 7.22.8 -> 7.23.3
    • @wdio/browserstack-service: 8.12.2 -> 8.29.3
    • @wdio/cli: 8.12.2 -> 8.29.3
    • axios: 1.4.0 -> 1.6.1
    • chromedriver: 114.0.2 -> 123.0.0
    • commander: 10.0.0 -> 11.1.0
    • dropzone: 5.7.0 -> 5.9.3
    • eslint-config-prettier: 8.8.0 -> 9.1.0
    • follow-redirects: 1.15.2 -> 1.15.4
    • handlebars: 4.7.7 -> 4.7.8
    • karma: 6.4.1 -> 6.4.2
    • nunjucks: 2.4.3 -> 3.2.4 in /src/nodejs/NarrativeServer
    • plotly.js-dist-min: 2.18.2 -> 2.28.0
    • postcss: 8.4.27 -> 8.4.33
    • prettier: 3.0.0 -> 3.2.4
    • puppeteer: 20.8.2 -> 21.10.0
    • pure-uuid: 1.6.4 -> 1.8.1
    • selenium-webdriver: 4.10.0 -> 4.17.0
    • word-wrap: 1.2.3 -> 1.2.4
    • ws: 7.2.0 -> 7.4.6 in /src/nodejs/NarrativeServer
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