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Snyk has created this PR to fix 38 vulnerabilities in the pip dependencies of this project.

Snyk changed the following file(s):

  • Python Workshop/requirements.txt
⚠️ Warning
vfb-connect 2.1.8 requires pysolr, which is not installed.
skeletor 1.3.0 requires scipy, which is not installed.
scikit-learn 1.0.2 requires scipy, which is not installed.
python-catmaid 2.4.0 requires scipy, which is not installed.
nptyping 2.5.0 has requirement numpy==1.21.5; python_version < "3.8", but you have numpy 1.21.3.
notebook 6.5.7 requires pyzmq, which is not installed.
neuprint-python 0.4.26 requires scipy, which is not installed.
navis 1.4.0 requires scipy, which is not installed.
morphops 0.1.13 requires scipy, which is not installed.
molesq 0.4.0 requires scipy, which is not installed.
jupyter-server 1.24.0 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.

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.

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Learn how to fix vulnerabilities with free interactive lessons:

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[//]: # 'snyk:metadata:{"customTemplate":{"variablesUsed":[],"fieldsUsed":[]},"dependencies":[{"name":"certifi","from":"2021.10.8","to":"2024.7.4"},{"name":"idna","from":"2.10","to":"3.7"},{"name":"ipython","from":"5.10.0","to":"8.10.0"},{"name":"jinja2","from":"2.11.3","to":"3.1.4"},{"name":"jupyter-core","from":"4.6.3","to":"4.11.2"},{"name":"mistune","from":"0.8.4","to":"2.0.3"},{"name":"nbconvert","from":"5.6.1","to":"6.3.0b0"},{"name":"networkx","from":"2.2","to":"2.6"},{"name":"notebook","from":"5.7.16","to":"6.4.12"},{"name":"numpy","from":"1.16.6","to":"1.22.2"},{"name":"prompt-toolkit","from":"1.0.18","to":"3.0.13"},{"name":"pygments","from":"2.5.2","to":"2.15.0"},{"name":"requests","from":"2.27.1","to":"2.31.0"},{"name":"scipy","from":"1.2.3","to":"1.10.0rc1"},{"name":"setuptools","from":"40.5.0","to":"70.0.0"},{"name":"tornado","from":"5.1.1","to":"6.4.1"},{"name":"tqdm","from":"4.64.1","to":"4.66.3"},{"name":"ujson","from":"2.0.3","to":"5.4.0"},{"name":"zipp","from":"1.2.0","to":"3.19.1"}],"env":"prod","issuesToFix":[{"exploit_maturity":"No 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Concept","id":"SNYK-PYTHON-TORNADO-7217828","priority_score":646,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Improper Neutralization of CRLF Sequences ('CRLF Injection')"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217829","priority_score":586,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.3","score":265},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-5537286","priority_score":384,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"3.4","score":170},{"type":"scoreVersion","label":"v1","score":1}],"severity":"low","title":"Open Redirect"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-5840803","priority_score":494,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.6","score":280},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-6041512","priority_score":539,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217828","priority_score":646,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Improper Neutralization of CRLF Sequences ('CRLF Injection')"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217829","priority_score":586,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.3","score":265},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-5537286","priority_score":384,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"3.4","score":170},{"type":"scoreVersion","label":"v1","score":1}],"severity":"low","title":"Open Redirect"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-5840803","priority_score":494,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.6","score":280},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-6041512","priority_score":539,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217828","priority_score":646,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Improper Neutralization of CRLF Sequences ('CRLF Injection')"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217829","priority_score":586,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.3","score":265},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-5537286","priority_score":384,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"3.4","score":170},{"type":"scoreVersion","label":"v1","score":1}],"severity":"low","title":"Open Redirect"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-5840803","priority_score":494,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.6","score":280},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-TORNADO-6041512","priority_score":539,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217828","priority_score":646,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Improper Neutralization of CRLF Sequences ('CRLF Injection')"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TORNADO-7217829","priority_score":586,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.3","score":265},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"HTTP Request Smuggling"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-TQDM-6807582","priority_score":561,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"4.8","score":240},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Injection"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-UJSON-2359034","priority_score":589,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"7.5","score":375},{"type":"scoreVersion","label":"v1","score":1}],"severity":"high","title":"Out-of-Bounds Write"},{"exploit_maturity":"No Known Exploit","id":"SNYK-PYTHON-UJSON-2940619","priority_score":509,"priority_score_factors":[{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"5.9","score":295},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Double Free"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-UJSON-2942122","priority_score":646,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.5","score":325},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Improper Handling of Syntactically Invalid Structure"},{"exploit_maturity":"Proof of Concept","id":"SNYK-PYTHON-ZIPP-7430899","priority_score":666,"priority_score_factors":[{"type":"exploit","label":"Proof of Concept","score":107},{"type":"fixability","label":true,"score":214},{"type":"cvssScore","label":"6.9","score":345},{"type":"scoreVersion","label":"v1","score":1}],"severity":"medium","title":"Infinite loop"}],"prId":"a5197c0a-f13b-45f3-9a2c-bdf7c2e2f121","prPublicId":"a5197c0a-f13b-45f3-9a2c-bdf7c2e2f121","packageManager":"pip","priorityScoreList":[554,704,519,524,624,531,484,484,604,589,726,654,434,589,449,506,506,399,506,399,696,589,479,519,489,686,509,736,384,494,539,646,586,561,589,509,646,666],"projectPublicId":"8704a93c-458e-4e98-9691-5aa4087bf342","projectUrl":"https://app.snyk.io/org/virtualflybrain/project/8704a93c-458e-4e98-9691-5aa4087bf342?utm_source=github&utm_medium=referral&page=fix-pr","prType":"fix","templateFieldSources":{"branchName":"default","commitMessage":"default","description":"default","title":"default"},"templateVariants":["pr-warning-shown","priorityScore"],"type":"auto","upgrade":[],"vulns":["SNYK-PYTHON-CERTIFI-3164749","SNYK-PYTHON-CERTIFI-5805047","SNYK-PYTHON-CERTIFI-7430173","SNYK-PYTHON-IDNA-6597975","SNYK-PYTHON-IPYTHON-2348630","SNYK-PYTHON-IPYTHON-3318382","SNYK-PYTHON-JINJA2-6150717","SNYK-PYTHON-JINJA2-6809379","SNYK-PYTHON-JUPYTERCORE-3063766","SNYK-PYTHON-MISTUNE-2940625","SNYK-PYTHON-NBCONVERT-2979829","SNYK-PYTHON-NETWORKX-1062709","SNYK-PYTHON-NOTEBOOK-1041707","SNYK-PYTHON-NOTEBOOK-2441824","SNYK-PYTHON-NOTEBOOK-2928995","SNYK-PYTHON-NUMPY-2321969","SNYK-PYTHON-NUMPY-2321964","SNYK-PYTHON-NUMPY-2321966","SNYK-PYTHON-NUMPY-2321970","SNYK-PYTHON-PROMPTTOOLKIT-6141120","SNYK-PYTHON-PYGMENTS-1086606","SNYK-PYTHON-PYGMENTS-1088505","SNYK-PYTHON-PYGMENTS-5750273","SNYK-PYTHON-REQUESTS-5595532","SNYK-PYTHON-SCIPY-5756497","SNYK-PYTHON-SCIPY-5759266","SNYK-PYTHON-SETUPTOOLS-3180412","SNYK-PYTHON-SETUPTOOLS-7448482","SNYK-PYTHON-TORNADO-5537286","SNYK-PYTHON-TORNADO-5840803","SNYK-PYTHON-TORNADO-6041512","SNYK-PYTHON-TORNADO-7217828","SNYK-PYTHON-TORNADO-7217829","SNYK-PYTHON-TQDM-6807582","SNYK-PYTHON-UJSON-2359034","SNYK-PYTHON-UJSON-2940619","SNYK-PYTHON-UJSON-2942122","SNYK-PYTHON-ZIPP-7430899"],"patch":[],"isBreakingChange":false,"remediationStrategy":"vuln"}'

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-3164749
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-5805047
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-7430173
- https://snyk.io/vuln/SNYK-PYTHON-IDNA-6597975
- https://snyk.io/vuln/SNYK-PYTHON-IPYTHON-2348630
- https://snyk.io/vuln/SNYK-PYTHON-IPYTHON-3318382
- https://snyk.io/vuln/SNYK-PYTHON-JINJA2-6150717
- https://snyk.io/vuln/SNYK-PYTHON-JINJA2-6809379
- https://snyk.io/vuln/SNYK-PYTHON-JUPYTERCORE-3063766
- https://snyk.io/vuln/SNYK-PYTHON-MISTUNE-2940625
- https://snyk.io/vuln/SNYK-PYTHON-NBCONVERT-2979829
- https://snyk.io/vuln/SNYK-PYTHON-NETWORKX-1062709
- https://snyk.io/vuln/SNYK-PYTHON-NOTEBOOK-1041707
- https://snyk.io/vuln/SNYK-PYTHON-NOTEBOOK-2441824
- https://snyk.io/vuln/SNYK-PYTHON-NOTEBOOK-2928995
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321964
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321966
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321969
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321970
- https://snyk.io/vuln/SNYK-PYTHON-PROMPTTOOLKIT-6141120
- https://snyk.io/vuln/SNYK-PYTHON-PYGMENTS-1086606
- https://snyk.io/vuln/SNYK-PYTHON-PYGMENTS-1088505
- https://snyk.io/vuln/SNYK-PYTHON-PYGMENTS-5750273
- https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-5595532
- https://snyk.io/vuln/SNYK-PYTHON-SCIPY-5756497
- https://snyk.io/vuln/SNYK-PYTHON-SCIPY-5759266
- https://snyk.io/vuln/SNYK-PYTHON-SETUPTOOLS-3180412
- https://snyk.io/vuln/SNYK-PYTHON-SETUPTOOLS-7448482
- https://snyk.io/vuln/SNYK-PYTHON-TORNADO-5537286
- https://snyk.io/vuln/SNYK-PYTHON-TORNADO-5840803
- https://snyk.io/vuln/SNYK-PYTHON-TORNADO-6041512
- https://snyk.io/vuln/SNYK-PYTHON-TORNADO-7217828
- https://snyk.io/vuln/SNYK-PYTHON-TORNADO-7217829
- https://snyk.io/vuln/SNYK-PYTHON-TQDM-6807582
- https://snyk.io/vuln/SNYK-PYTHON-UJSON-2359034
- https://snyk.io/vuln/SNYK-PYTHON-UJSON-2940619
- https://snyk.io/vuln/SNYK-PYTHON-UJSON-2942122
- https://snyk.io/vuln/SNYK-PYTHON-ZIPP-7430899
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