feat: adding a profile for cluster execution

[cmeesters]

This PR merely adds a profile for cluster execution. The first one to be added is for the Mogon NHR cluster in Mainz, Germany.

Summary by CodeRabbit

• New Features

  • Added a Mogon-NHR execution profile with default and task-specific resource allocations (partition, memory, runtime, tasks) to better match that environment.

• Chores

  • Removed obsolete cluster-related settings from the global configuration to simplify environment defaults while keeping paths, I/O directories, subsets, and other options intact.

[coderabbitai]

Walkthrough

Removed cluster-related resource blocks from global config/config.yaml and added a new profile profiles/Mogon-NHR/config.yaml that defines default and task-specific SLURM resource settings for docking, energy minimization, and results.

Changes

Cohort / File(s)	Summary of Changes
Global config cleanup config/config.yaml	Deleted cluster-related sections DOCKING, ENERGY_MIN, DOCKING_RESULTS and their keys (e.g., mem_mb_per_cpu, jobname, partition, ntasks, constraint, walltime_minutes, threads). Other config keys remain unchanged.
Mogon-NHR profile resources profiles/Mogon-NHR/config.yaml	Added new profile providing defaults (slurm_partition: smallcpu, mem_mb_per_cpu: 1800, runtime: "30m", clusters: "mogonnhr") and task-specific overrides: docking (mem_per_cpu 3000, partition: parallel, ntasks: 512), energyMin (mem 350, runtime: 90), results (mem 65000, runtime: 300).

Sequence Diagram(s)

sequenceDiagram
    participant U as User
    participant WF as Workflow Runner
    participant CL as Config Loader
    participant GC as Global Config\n(`config/config.yaml`)
    participant PR as Profile\n(`profiles/Mogon-NHR/config.yaml`)
    participant SC as Scheduler (SLURM)

    U->>WF: Start workflow with profile=Mogon-NHR
    WF->>CL: Load configuration
    CL->>GC: Read global settings (cluster blocks removed)
    CL->>PR: Read profile defaults & task overrides
    CL-->>WF: Return merged config (profile supplies cluster resources)
    rect rgba(200,230,255,0.5)
      note right of WF: Submit jobs using profile resources
      WF->>SC: Submit docking (partition: parallel, ntasks:512, mem_per_cpu:3000)
      WF->>SC: Submit energyMin (mem:350, runtime:90)
      WF->>SC: Submit results (mem:65000, runtime:300)
    end

Loading

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

I thump my paws — the fields refined,
Global clutter cleared, new paths designed.
Mogon queues hum, each job aligned,
Dock, mend, collect — tidy and kind.
A rabbit hops where YAMLs shine. 🐇✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The title clearly and succinctly identifies the primary change—adding a cluster execution profile—which matches the PR’s objective and content. It avoids unnecessary detail and uses direct phrasing that immediately informs reviewers of the feature being introduced.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feat/profile

---

📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between e30a5de and f6a7cfd.

📒 Files selected for processing (1)

• profiles/Mogon-NHR/config.yaml (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• profiles/Mogon-NHR/config.yaml

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[coderabbitai]

Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 5de1a87 and e30a5de.

📒 Files selected for processing (2)

• config/config.yaml (0 hunks)
• profiles/Mogon-NHR/config.yaml (1 hunks)

💤 Files with no reviewable changes (1)

• config/config.yaml