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snakemake / snakemake-executor-plugin-kubernetes

A snakemake executor plugin for submission of jobs to Kubernetes
MIT License
2 stars 6 forks source link

feat: PVC support for kubernetes (continuation of #9) #22

Closed johanneskoester closed 1 month ago

johanneskoester commented 1 month ago

@saulobejo in PR #9:

With this pull request I add the capability to mount a PVC in the K8S executor. It expects the PVC to be created in advance. The goal is to be able to mount arbitrary storages as disks.

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago

Walkthrough

The recent updates to the snakemake_executor_plugin_kubernetes module enhance Kubernetes job execution through significant improvements to the ExecutorSettings class. By introducing new attributes such as privileged and persistent_volumes, the changes provide users with greater flexibility in container configurations and streamline the management of Persistent Volume Claims (PVCs). This empowers users to tailor job execution with elevated permissions and effective volume handling.

Changes

Files Change Summary
snakemake_executor_plugin_kubernetes/__init__.py Enhanced ExecutorSettings with privileged and persistent_volumes attributes for better container and volume configuration. Updated run_job method to properly handle volume mounts.
tests/tests.py Removed specific Docker image assignment in get_remote_execution_settings, indicating a move towards a more stable deployment strategy for remote execution settings.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant ExecutorSettings
    participant Kubernetes

    User->>ExecutorSettings: Set privileged and persistent volumes
    ExecutorSettings->>Kubernetes: Validate and configure settings
    Kubernetes->>Kubernetes: Create privileged container (if enabled)
    Kubernetes->>Kubernetes: Mount persistent volumes (if defined)
    Kubernetes-->>User: Execute job with configured settings

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