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[Snyk] Fix for 16 vulnerabilities #200

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@Fab-T Fab-T commented Aug 30, 2024

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Snyk has created this PR to fix 16 vulnerabilities in the pip dependencies of this project.

Snyk changed the following file(s):

  • Explore an HCA Data Set in Scanpy (Nov 2018)/requirements.txt
⚠️ Warning
umap-learn 0.5.6 requires scipy, which is not installed.
statsmodels 0.13.5 requires scipy, which is not installed.
statsmodels 0.13.5 requires scipy, which is not installed.
scikit-learn 1.0.2 requires scipy, which is not installed.
scanpy 1.9.3 requires scipy, which is not installed.
python-igraph 0.11.6 has requirement igraph==0.11.6, but you have igraph 0.10.8.
pynndescent 0.5.13 requires scipy, which is not installed.
notebook 6.5.7 requires pyzmq, which is not installed.
loompy 3.0.7 requires scipy, which is not installed.
jupyter-server 1.24.0 requires pyzmq, which is not installed.
jupyter-console 6.6.3 requires pyzmq, which is not installed.
jupyter-client 7.4.9 requires pyzmq, which is not installed.
ipykernel 6.16.2 requires pyzmq, which is not installed.
anndata 0.8.0 requires scipy, which is not installed.

Important

  • Check the changes in this PR to ensure they won't cause issues with your project.
  • Max score is 1000. Note that the real score may have changed since the PR was raised.
  • This PR was automatically created by Snyk using the credentials of a real user.
  • Some vulnerabilities couldn't be fully fixed and so Snyk will still find them when the project is tested again. This may be because the vulnerability existed within more than one direct dependency, but not all of the affected dependencies could be upgraded.

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs.

For more information:
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📚 Read about Snyk's upgrade logic


Learn how to fix vulnerabilities with free interactive lessons:

🦉 Remote Code Execution (RCE)
🦉 Access Control Bypass
🦉 Open Redirect
🦉 More lessons are available in Snyk Learn

[//]: # 'snyk:metadata:{"customTemplate":{"variablesUsed":[],"fieldsUsed":[]},"dependencies":[{"name":"anyio","from":"3.7.1","to":"4.4.0"},{"name":"ipython","from":"7.34.0","to":"8.10.0"},{"name":"jupyter-server","from":"1.24.0","to":"2.14.1"},{"name":"requests","from":"2.31.0","to":"2.32.2"},{"name":"setuptools","from":"40.5.0","to":"70.0.0"},{"name":"tornado","from":"6.2","to":"6.4.1"},{"name":"urllib3","from":"2.0.7","to":"2.2.2"},{"name":"zipp","from":"3.15.0","to":"3.19.1"}],"env":"prod","issuesToFix":[{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-ANYIO-7361842","priority_score":629,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"8.3","score":415},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Race Condition"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-ANYIO-7361842","priority_score":629,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"8.3","score":415},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Race Condition"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-ANYIO-7361842","priority_score":629,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"8.3","score":415},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Race Condition"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-ANYIO-7361842","priority_score":629,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"8.3","score":415},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Race Condition"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-ANYIO-7361842","priority_score":629,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"8.3","score":415},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Race Condition"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-IPYTHON-3318382","priority_score":531,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"4.2","score":210},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Remote Code Execution (RCE)"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-IPYTHON-3318382","priority_score":531,"priority_score_factors":[{"type":"exploit","label":"Proof of 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Information"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-JUPYTERSERVER-7217832","priority_score":653,"priority_score_factors":[{"type":"socialTrends","label":true,"score":111},{"type":"fixability","label":true,"score":167},{"type":"cvssScore","label":"7.5","score":375},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Information Exposure"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-JUPYTERSERVER-5862881","priority_score":444,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"4.6","score":230},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Access Control Bypass"},{"exploit_maturity":"No Known 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