init #3

NxPKG · 2024-08-03T10:33:26Z

User description

Description

This PR fixes #

Notes for Reviewers

Signed commits

[*] Yes, I signed my commits.

PR Type

Enhancement, Documentation

Description

Updated README to reflect MLHub integration and provided deployment instructions.
Modified hub and proxy deployment configurations for MLHub compatibility.
Updated RBAC rules to allow the hub to manage services.
Added SSH port configuration to hub service and deployment.
Changed default values and images in values.yaml to MLHub-specific versions.
Updated network policies and SSL configurations.

Changes walkthrough 📝

Relevant files

Documentation

1 files

README.md `Update README for MLHub integration and deployment instructions` README.md Updated the title and description to reflect the MLHub integration. Added a section detailing the modifications made for MLHub compatibility. Provided instructions for deploying the chart with MLHub.	+22/-11

Dependencies

1 files

requirements.txt `Update Kubespawner dependency to specific GitHub version` images/hub/requirements.txt Commented out the existing `jupyterhub-kubespawner` dependency. Added a GitHub link to install `kubespawner` with specific fixes.	+3/-1

Enhancement

9 files

deployment.yaml `Update hub deployment configuration for MLHub compatibility` jupyterhub/templates/hub/deployment.yaml Modified command and environment variables for hub container. Changed volume mount path for SQLite PVC. Added SSH port configuration.	+35/-30
rbac.yaml `Update RBAC rules to allow hub to manage services` jupyterhub/templates/hub/rbac.yaml Added permissions for the hub to create and delete services.	+3/-0
service.yaml `Add SSH port configuration to hub service` jupyterhub/templates/hub/service.yaml Added SSH port configuration to the hub service.	+6/-1
deployment.yaml `Update proxy deployment configuration for MLHub compatibility` jupyterhub/templates/proxy/deployment.yaml Modified command and environment variables for proxy container. Updated SSL mount path.	+31/-26
netpol.yaml `Update network policy for proxy port changes` jupyterhub/templates/proxy/netpol.yaml Updated network policy to reflect port changes.	+1/-0
secret.yaml `Update proxy secret configuration for additional SSL entries` jupyterhub/templates/proxy/secret.yaml Added additional SSL certificate and key entries.	+2/-0
service.yaml `Update proxy service target ports` jupyterhub/templates/proxy/service.yaml Changed target ports for HTTP and HTTPS services.	+3/-3
netpol.yaml `Update singleuser network policy port` jupyterhub/templates/singleuser/netpol.yaml Updated singleuser network policy port.	+1/-1
values.yaml `Update default values and images for MLHub` jupyterhub/values.yaml Updated default values for hub, proxy, and singleuser configurations. Changed image names and tags to MLHub-specific versions. Enabled network policy for singleuser.	+23/-19

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Summary by Sourcery

Refactor deployment configurations to support MLHub and ml-tooling images, introduce environment variables for better configurability, add SSH tunneling support, and update documentation to reflect these changes.

New Features:

Introduce environment variables for additional arguments and execution modes in hub and proxy deployments.
Add support for SSH tunneling by modifying ports and adding SSH-related environment variables.

Enhancements:

Refactor command fields in hub and proxy deployment YAMLs to use environment variables for better configurability.
Update default image names and tags to use ml-tooling images instead of JupyterHub images.
Modify default paths for SSL secrets and other configurations to align with ml-tooling standards.
Enable network policies for singleuser servers.

Documentation:

Update README to reflect changes from JupyterHub to MLHub, including new deployment instructions and modifications.

…tallable (the placeholder would have usually been replaced when chart is published via chartpress).

…false" instead of false - Add env variable to set execution mode to k8s for proxy

…se to route some urls to the workspaces directly)

…e not pushed yet

…ator

…Policy.enabled

…n our ml-workspace

…nfigured

…NAL_ARGS - Add missing slash to readiness probe path

…NAL_ARGS - allow setting extraEnv values for proxy - fix port issues

…s for new release

sourcery-ai · 2024-08-03T10:33:36Z

Reviewer's Guide by Sourcery

This pull request refactors the JupyterHub Helm chart to support MLHub and MLWorkspace images, modifies default values, and updates various configurations to enable SSH tunneling and other features.

File-Level Changes

Files	Changes
`jupyterhub/templates/hub/deployment.yaml` `jupyterhub/templates/proxy/deployment.yaml`	Refactored command fields to use ADDITIONAL_ARGS environment variable and added new environment variables for execution mode and SSH tunneling.
`jupyterhub/values.yaml` `README.md`	Updated default values and documentation to reflect changes for MLHub and MLWorkspace images.
`jupyterhub/templates/hub/service.yaml` `jupyterhub/templates/proxy/service.yaml`	Added new service ports for SSH and updated target ports for proxy service.

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codiumai-pr-agent-free · 2024-08-03T10:34:07Z

PR Reviewer Guide 🔍

⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪
🧪 No relevant tests
🔒 Security concerns Yes, Running as Root: The deployment configurations set the user ID (`uid`) and filesystem group ID (`fsGid`) to 0, which means the containers will run as the root user. This setup can lead to security vulnerabilities, especially if the containers are compromised. It is recommended to run services with least privilege to mitigate potential risks.
⚡ Key issues to review Security Concern Running containers with root privileges (`uid: 0` and `fsGid: 0`) can pose a significant security risk, especially in a multi-user environment like JupyterHub. Consider using a non-root user for running the containers. Possible Bug The environment variable `ADDITIONAL_ARGS` is being set in a complex way using Go templating, which might lead to errors or misconfigurations. Simplifying this configuration could reduce potential bugs. Configuration Complexity The proxy configuration has been significantly altered, including changes to command arguments and environment variables. This increases complexity and potential for misconfiguration. Review to ensure that all changes are necessary and correctly implemented. Inconsistent Ports There are inconsistencies in port configurations across different files, which could lead to connectivity issues or misconfigurations. For example, changes from port 8000 to 8080 and 8443 to 8080 need to be verified across all configurations to ensure consistency.

codiumai-pr-agent-free · 2024-08-03T10:34:39Z

PR Code Suggestions ✨

Category	Suggestion	Score
Possible issue	Ensure that the database path change does not affect other dependent services The `mountPath` for the volume mount `hub-db-dir` has been changed from `/srv/jupyterhub` to `/data`. This change might affect other parts of the application that expect the database to be at the original location. It's recommended to verify that all references to the database path have been updated accordingly or to maintain the original path if other services depend on it. jupyterhub/templates/hub/deployment.yaml [81] -- mountPath: /data +- mountPath: /srv/jupyterhub name: hub-db-dir Apply this suggestion Suggestion importance[1-10]: 8 Why: The suggestion correctly identifies a potential issue with changing the database path, which could affect other parts of the application. Ensuring consistency in the database path is crucial for the application's stability.	8
	Verify that the new TLS mount path is compatible with all parts of the application The `mountPath` for the TLS secrets has been changed from `/etc/chp/tls` to `/resources/ssl`. This change might lead to issues if other parts of the application are not updated to reflect this new path. It is advisable to either revert to the original path or ensure all dependent configurations are updated. jupyterhub/templates/proxy/deployment.yaml [56] -# mountPath: /etc/chp/tls -mountPath: /resources/ssl +mountPath: /etc/chp/tls Apply this suggestion Suggestion importance[1-10]: 8 Why: The suggestion highlights a critical change in the TLS secrets path, which could cause issues if not consistently updated across the application. Ensuring all configurations reflect this change is essential for maintaining security and functionality.	8
	Ensure that the HTTPS target port change aligns with standard practices and configurations The target port for HTTPS traffic has been changed from 8443 to 8080. This change might not align with the standard ports used for HTTPS and could lead to misconfigurations or accessibility issues. Consider using standard ports for HTTPS or ensure that all network configurations are adjusted accordingly. jupyterhub/templates/proxy/service.yaml [62] -targetPort: 8080 +targetPort: 8443 Apply this suggestion Suggestion importance[1-10]: 7 Why: The suggestion correctly points out that changing the HTTPS target port to a non-standard port could lead to misconfigurations. While not necessarily a bug, adhering to standard port practices is important for compatibility and security.	7
	Check that the new port setting in singleuser network policies does not disrupt network traffic The port for network policies in the singleuser profile has been changed from 8888 to 8080. This change might disrupt the expected network traffic flow for singleuser instances. It's recommended to verify that this new port configuration is correctly set up in the network policies or revert to the original port if it was set for specific reasons. jupyterhub/templates/singleuser/netpol.yaml [23] -port: 8080 +port: 8888 Apply this suggestion Suggestion importance[1-10]: 7 Why: The suggestion identifies a potential disruption in network traffic flow due to the port change. Verifying the new port configuration is crucial to ensure it does not interfere with the expected behavior of singleuser instances.	7

sourcery-ai

Hey @NxPKG - I've reviewed your changes and found some issues that need to be addressed.

Blocking issues:

Address security concerns with running containers as root (link)

Overall Comments:

Consider the security implications of setting UID and fsGid to 0 in the hub and singleuser configurations. Running containers as root is generally not recommended.
The changes are extensive and significantly alter the original JupyterHub setup. Please provide more documentation on the rationale behind major changes, especially regarding networking and authentication modifications.

Here's what I looked at during the review

🟢 General issues: all looks good
🔴 Security: 1 blocking issue, 2 other issues
🟢 Testing: all looks good
🟢 Complexity: all looks good
🟡 Documentation: 3 issues found

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sourcery-ai · 2024-08-03T10:35:15Z

jupyterhub/values.yaml

@@ -11,8 +11,8 @@ hub:
  cookieSecret:
  publicURL:
  initContainers: []
-  uid: 1000


🚨 issue (security): Address security concerns with running containers as root

Changing UID and fsGid to 0 means containers are running as root, which is a significant security risk. Please justify this change and consider reverting to non-root user if possible.

sourcery-ai · 2024-08-03T10:35:15Z

jupyterhub/values.yaml



 auth:
-  type: dummy


🚨 question (security): Explain the switch to custom authentication and its implications

The change from 'dummy' to 'custom' authentication with NativeAuthenticator could have security implications. Please provide details on how this affects user authentication and any additional setup required.

sourcery-ai · 2024-08-03T10:35:15Z

jupyterhub/templates/hub/rbac.yaml

@@ -19,6 +19,9 @@ rules:
  - apiGroups: [""]       # "" indicates the core API group
    resources: ["events"]
    verbs: ["get", "watch", "list"]
+  - apiGroups: [""]


🚨 question (security): Justify the addition of new RBAC permissions for the hub

The hub now has permissions to list, create, and delete services. Please explain why these new permissions are necessary and any potential security implications.

sourcery-ai · 2024-08-03T10:35:16Z

README.md

+For most parts you should be able to follow the comprehensive guide linked below.
+
+Most prominent changes: 
+- change of the command fields in hub and proxy yamls


suggestion (documentation): Consider rephrasing for specificity.

Consider rephrasing to: 'modification of the command fields in the hub and proxy YAML files.'

Suggested change

- change of the command fields in hub and proxy yamls

modification of the command fields in the hub and proxy YAML files

sourcery-ai · 2024-08-03T10:35:16Z

README.md

+We do not push the helm chart to a repository for now, so feel free to download it from the [mlhub releases page](https://github.com/ml-tooling/ml-hub/releases) or to create the package yourself via `helm package jupyterhub/`.
+
+You can then deploy the chart via `helm upgrade --install mlhub packaged-chart.tgz --namespace $namespace --values config.yaml`.
+The config.yaml can be used to overrride default values.


issue (documentation): Fix typo: 'overrride' should be 'override'.

sourcery-ai · 2024-08-03T10:35:16Z

README.md

+The config.yaml can be used to overrride default values.
+
+---
+<br/>


suggestion (documentation): Consider removing the HTML line break.

Markdown handles line breaks without needing HTML tags. Consider removing '
' for cleaner markdown.

Suggested change

<br/>

---

# Original Readme:

raethlein added 30 commits August 29, 2019 11:06

Modify chart so that it works with mlhub

a525f44

Replace placeholder with actual version to make the chart locally ins…

30156a9

…tallable (the placeholder would have usually been replaced when chart is published via chartpress).

- Fix issue with environment values that caused a yaml parse error: "…

b3209f5

…false" instead of false - Add env variable to set execution mode to k8s for proxy

Give the hub the permission to create and delete services (which we u…

b30bd42

…se to route some urls to the workspaces directly)

Add packaged chart archive to gitignore

fd12a48

Do not use the proxy's ssl but our nginx's one

452e903

Make the chart compatible with our ssl path

be1b3a2

Change https port to point also to nginx

382b127

Change port in networkpolicy to our default image port

5efd989

Install Kubespawner from github, as it contains some bugfixes that ar…

f028973

…e not pushed yet

Modify path of jupyterhub config in chart yaml based on our mlhub image

cd1bb59

Fix default values of proxy secret key and crt

8a0a96f

Set nativeauthenticator (installed in MLHub) as the default authentic…

649e24e

…ator

Set default values based on our mlhub

ac625e0

Set default values in chart based on MLHub

95e5604

Set singleuser.networkPolicy.enabled to true instead of proxy.network…

a49544a

…Policy.enabled

Modify default values for mlhub chart

49dae96

Update default value for mount path for singleuser workspaces based o…

634a654

…n our ml-workspace

Update readme including linking to our ml-hub repository

434acdd

Set default value for workspaceImages to indicate that this can be co…

3592733

…nfigured

Change port to 8091 also when https manual is set

fc032c2

Switch port to 8080 as the Hub's port is changed to 8080

c8e7549

Merge branch 'develop'

0095d13

Use the jupyterhub-config's default singleuser image

72c02d4

- Send additional arguments to the container via env variable ADDITIO…

f3921ab

…NAL_ARGS - Add missing slash to readiness probe path

- Send additional arguments to the container via env variable ADDITIO…

3d89e09

…NAL_ARGS - allow setting extraEnv values for proxy - fix port issues

Add missing slash

60205ea

Update default values for new release

f18a183

Rollback changes made to image-puller as we updated the default value…

6508d3a

…s for new release

Update ml-hub version

151cdac

raethlein added 3 commits November 13, 2019 15:11

Extend readme

63b1a50

Update default hub image

fffa370

Modify persisted paths in hub and singleuser servers

cc5cf31

codiumai-pr-agent-free bot added documentation Improvements or additions to documentation enhancement New feature or request Possible security concern Review effort [1-5]: 4 labels Aug 3, 2024

sourcery-ai bot reviewed Aug 3, 2024

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init #3

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	- change of the command fields in hub and proxy yamls
	modification of the command fields in the hub and proxy YAML files

-<br/>
+---
+# Original Readme:

init #3

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NxPKG commented Aug 3, 2024 • edited by sourcery-ai bot Loading

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PR Type

Description

Changes walkthrough 📝

Summary by Sourcery

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Reviewer's Guide by Sourcery

File-Level Changes

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PR Reviewer Guide 🔍

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PR Code Suggestions ✨

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