This PR was automatically created by Snyk using the credentials of a real user.
Snyk has created this PR to fix one or more vulnerable packages in the `pip` dependencies of this project.
#### Changes included in this PR
- Changes to the following files to upgrade the vulnerable dependencies to a fixed version:
- requirements.txt
⚠️ Warning
```
Werkzeug 2.2.2 requires MarkupSafe, which is not installed.
requests 2.20.0 has requirement urllib3<1.25,>=1.21.1, but you have urllib3 1.26.12.
PyGithub 1.57 requires pynacl, which is not installed.
Jinja2 2.11.3 requires MarkupSafe, which is not installed.
hca 6.5.1 requires cryptography, which is not installed.
hca 6.5.1 has requirement dcplib<3,>=2.0.2, but you have dcplib 3.12.0.
hca 6.5.1 has requirement PyJWT<2,>=1.6.4, but you have PyJWT 2.6.0.
hca 6.5.1 has requirement jsonschema<3,>=2.6, but you have jsonschema 4.17.0.
google-auth-oauthlib 0.7.1 has requirement google-auth>=2.14.0, but you have google-auth 1.35.0.
Flask 2.2.2 has requirement Jinja2>=3.0, but you have Jinja2 2.11.3.
dcplib 3.12.0 requires cryptography, which is not installed.
dcplib 3.12.0 has requirement termcolor<2,>=1.1.0, but you have termcolor 2.1.0.
botocore 1.12.208 has requirement jmespath<1.0.0,>=0.7.1, but you have jmespath 1.0.1.
botocore 1.12.208 has requirement urllib3<1.26,>=1.20; python_version >= "3.4", but you have urllib3 1.26.12.
boto3 1.26.8 has requirement botocore<1.30.0,>=1.29.8, but you have botocore 1.12.208.
argcomplete 1.12.3 has requirement importlib-metadata<5,>=0.23; python_version == "3.7", but you have importlib-metadata 5.0.0.
```
#### Vulnerabilities that will be fixed
##### By pinning:
Severity | Priority Score (*) | Issue | Upgrade | Breaking Change | Exploit Maturity
:-------------------------:|-------------------------|:-------------------------|:-------------------------|:-------------------------|:-------------------------
 | **589/1000** **Why?** Has a fix available, CVSS 7.5 | Timing Attack [SNYK-PYTHON-CRYPTOGRAPHY-1022152](https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-1022152) | `cryptography:` `2.9.2 -> 3.2` | No | No Known Exploit
 | **691/1000** **Why?** Proof of Concept exploit, Has a fix available, CVSS 7.4 | Use of a Broken or Risky Cryptographic Algorithm [SNYK-PYTHON-PYJWT-2840625](https://snyk.io/vuln/SNYK-PYTHON-PYJWT-2840625) | `pyjwt:` `1.7.1 -> 2.4.0` | No | Proof of Concept
 | **479/1000** **Why?** Has a fix available, CVSS 5.3 | Regular Expression Denial of Service (ReDoS) [SNYK-PYTHON-URLLIB3-1533435](https://snyk.io/vuln/SNYK-PYTHON-URLLIB3-1533435) | `urllib3:` `1.25.11 -> 1.26.5` | No | No Known Exploit
(*) Note that the real score may have changed since the PR was raised.
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.
Check the changes in this PR to ensure they won't cause issues with your project.
------------
**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:
🧐 [View latest project report](https://app.snyk.io/org/humancellatlas/project/bae6750a-1c90-43f6-a860-4652f2409304?utm_source=github&utm_medium=referral&page=fix-pr)
🛠 [Adjust project settings](https://app.snyk.io/org/humancellatlas/project/bae6750a-1c90-43f6-a860-4652f2409304?utm_source=github&utm_medium=referral&page=fix-pr/settings)
📚 [Read more about Snyk's upgrade and patch logic](https://support.snyk.io/hc/en-us/articles/360003891078-Snyk-patches-to-fix-vulnerabilities)
[//]: # (snyk:metadata:{"prId":"1cbab55b-fdd9-4851-83cc-473e0aeea612","prPublicId":"1cbab55b-fdd9-4851-83cc-473e0aeea612","dependencies":[{"name":"cryptography","from":"2.9.2","to":"3.2"},{"name":"pyjwt","from":"1.7.1","to":"2.4.0"},{"name":"urllib3","from":"1.25.11","to":"1.26.5"}],"packageManager":"pip","projectPublicId":"bae6750a-1c90-43f6-a860-4652f2409304","projectUrl":"https://app.snyk.io/org/humancellatlas/project/bae6750a-1c90-43f6-a860-4652f2409304?utm_source=github&utm_medium=referral&page=fix-pr","type":"auto","patch":[],"vulns":["SNYK-PYTHON-CRYPTOGRAPHY-1022152","SNYK-PYTHON-PYJWT-2840625","SNYK-PYTHON-URLLIB3-1533435"],"upgrade":[],"isBreakingChange":false,"env":"prod","prType":"fix","templateVariants":["pr-warning-shown","priorityScore"],"priorityScoreList":[589,691,479]})
---
**Learn how to fix vulnerabilities with free interactive lessons:**
🦉 [Use of a Broken or Risky Cryptographic Algorithm](https://learn.snyk.io/lessons/insecure-hash/python/?loc=fix-pr)
🦉 [Regular Expression Denial of Service (ReDoS)](https://learn.snyk.io/lessons/redos/javascript/?loc=fix-pr)
This PR was automatically created by Snyk using the credentials of a real user.
Snyk has created this PR to fix one or more vulnerable packages in the `pip` dependencies of this project.
#### Changes included in this PR - Changes to the following files to upgrade the vulnerable dependencies to a fixed version: - requirements.txt⚠️ Warning
``` Werkzeug 2.2.2 requires MarkupSafe, which is not installed. requests 2.20.0 has requirement urllib3<1.25,>=1.21.1, but you have urllib3 1.26.12. PyGithub 1.57 requires pynacl, which is not installed. Jinja2 2.11.3 requires MarkupSafe, which is not installed. hca 6.5.1 requires cryptography, which is not installed. hca 6.5.1 has requirement dcplib<3,>=2.0.2, but you have dcplib 3.12.0. hca 6.5.1 has requirement PyJWT<2,>=1.6.4, but you have PyJWT 2.6.0. hca 6.5.1 has requirement jsonschema<3,>=2.6, but you have jsonschema 4.17.0. google-auth-oauthlib 0.7.1 has requirement google-auth>=2.14.0, but you have google-auth 1.35.0. Flask 2.2.2 has requirement Jinja2>=3.0, but you have Jinja2 2.11.3. dcplib 3.12.0 requires cryptography, which is not installed. dcplib 3.12.0 has requirement termcolor<2,>=1.1.0, but you have termcolor 2.1.0. botocore 1.12.208 has requirement jmespath<1.0.0,>=0.7.1, but you have jmespath 1.0.1. botocore 1.12.208 has requirement urllib3<1.26,>=1.20; python_version >= "3.4", but you have urllib3 1.26.12. boto3 1.26.8 has requirement botocore<1.30.0,>=1.29.8, but you have botocore 1.12.208. argcomplete 1.12.3 has requirement importlib-metadata<5,>=0.23; python_version == "3.7", but you have importlib-metadata 5.0.0. ```**Why?** Has a fix available, CVSS 7.5 | Timing Attack
[SNYK-PYTHON-CRYPTOGRAPHY-1022152](https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-1022152) | `cryptography:`
`2.9.2 -> 3.2`
| No | No Known Exploit  | **691/1000**
**Why?** Proof of Concept exploit, Has a fix available, CVSS 7.4 | Use of a Broken or Risky Cryptographic Algorithm
[SNYK-PYTHON-PYJWT-2840625](https://snyk.io/vuln/SNYK-PYTHON-PYJWT-2840625) | `pyjwt:`
`1.7.1 -> 2.4.0`
| No | Proof of Concept  | **479/1000**
**Why?** Has a fix available, CVSS 5.3 | Regular Expression Denial of Service (ReDoS)
[SNYK-PYTHON-URLLIB3-1533435](https://snyk.io/vuln/SNYK-PYTHON-URLLIB3-1533435) | `urllib3:`
`1.25.11 -> 1.26.5`
| No | No Known Exploit (*) Note that the real score may have changed since the PR was raised. 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. Check the changes in this PR to ensure they won't cause issues with your project. ------------ **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: