Conda Env Manager

Conda Environment Manager (Tool Layer)

Overview

Conda is the backbone for reproducible, cross-platform environments in NeuroClaw — especially for CUDA-dependent deep learning stacks (PyTorch, TensorFlow, MONAI, nnU-Net), neuroimaging tools (ANTs, FSL wrappers, nipype), and scientific computing packages.

This skill acts as the interface-layer orchestrator for all common conda operations, preventing accidental modification of the base environment, reducing version conflicts, and enforcing best practices (isolated environments per project, environment.yml for reproducibility, explicit version pinning, dry-run previews).

Strict workflow (never skipped):

1. Parse user intent from the request or context (create / export / update / remove / clone / list / activate guidance).
2. Detect current conda setup (conda info, active environment, disk space, conda version).
3. Propose a safe, best-practice plan:
   • Prefer --name over --prefix for readability
   • Always suggest creating a new environment instead of modifying base or existing ones
   • Recommend environment.yml for reproducibility and sharing
   • Use --yes only after explicit user confirmation
   • Warn about large downloads (CUDA stacks, large models)
   • Suggest channel priority: conda-forge > pytorch/nvidia > defaults
4. Show numbered plan + exact commands + estimated time/size + risks.
5. Wait for explicit user confirmation (“YES”, “execute”, “proceed”).
6. On approval: execute safely (with logging), capture output, report success/failure, and suggest next steps.

Core safety & best-practice rules

• Never modify the base environment unless explicitly requested (and double-warned)
• Prefer conda env export --from-history > environment.yml for clean, reproducible specs
• Use --dry-run / plan preview by default
• Integrate with dependency-planner for post-creation package installation
• Log all actions to ./logs/conda_YYYYMMDD_HHMMSS.log

Quick Reference (Common NeuroClaw Tasks)

Installation

This skill is pure Python orchestration — no external binaries needed beyond a working conda installation.

Required prerequisites (must exist before activation):

• Working conda / mamba / micromamba installation
• dependency-planner (recommended companion for package installation after env creation)
• Basic subprocess / shell access

To register in NeuroClaw:

# Place files in: skills/conda-env-manager/
# Update SOUL.md and/or USER.md with trigger phrases

NeuroClaw recommended wrapper script

# conda_env_manager.py
import subprocess
import argparse
import sys
from pathlib import Path
from datetime import datetime

def run_conda_cmd(cmd, dry_run=False):
    full_cmd = ["conda"] + cmd
    if dry_run:
        full_cmd.insert(1, "--dry-run")
    print("Would run:", " ".join(full_cmd))
    # In real implementation: subprocess.run(full_cmd, check=True) after confirmation

def get_conda_info():
    try:
        out = subprocess.check_output(["conda", "info", "--json"]).decode()
        return out
    except:
        return "Conda not found or error."

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="NeuroClaw Conda Environment Manager")
    parser.add_argument("--request", required=True, help="User request (create/export/update/remove...)")
    parser.add_argument("--dry-run", action="store_true", help="Only show plan")
    args = parser.parse_args()

    print("Conda snapshot:")
    print(get_conda_info()[:500], "...")  # truncated

    print("\nRequest:", args.request)
    print("Generating safe conda plan following NeuroClaw best practices...")
    print("Plan preview would appear here.")
    print("Waiting for explicit user confirmation before any real execution.")

Reproducible Environment Specification Standard

All conda environments created/managed by this skill must include comprehensive reproducibility metadata following the NeuroClaw standard.

Environment Archival Format

After each environment creation or significant update, conda-env-manager generates the following audit trail:

1. Canonical environment file (environment-{env_name}-lock.yml):

name: neuroclaw-dl
channels:
  - pytorch
  - conda-forge  
  - defaults
dependencies:
  - python=3.11.0=h6de4bd8_0_cpython
  - pytorch::pytorch::=2.1.2=py3.11_cuda12.1_cudnn8.9.5_0
  - pytorch::cudatoolkit=12.1=h6de4bd8_0
  - conda-forge::numpy=1.24.3=py311h8315ce3_0
  - conda-forge::scipy=1.11.4=py311hf2f185e_3
  - pip
  - pip::nibabel==5.1.0
  - pip::torch-geometric==2.3.1
variables:
  CUDA_HOME: /opt/conda/envs/neuroclaw-dl
platforms:
  - linux-64
metadata:
  created_at: "2026-04-05T14:22:00Z"
  created_by: "conda-env-manager/NeuroClaw"
  python_version: "3.11.0"
  pytorch_cuda: "12.1"
  system_hash: "sha256:abc123..."

2. Machine-portable environment file (environment-{env_name}-portable.yml):

name: neuroclaw-dl
channels:
  - pytorch
  - conda-forge
  - defaults
dependencies:
  - python=3.11.*
  - pytorch::pytorch=2.1.*
  - pytorch::torchvision
  - conda-forge::numpy>=1.24
  - conda-forge::scipy>=1.11
  - pip
  - pip::nibabel>=5.1.0
# Use this for cross-platform recreations

3. Environment metadata manifest (environment-{env_name}-manifest.json):

{
  "environment_name": "neuroclaw-dl",
  "created_at": "2026-04-05T14:22:00Z",
  "created_by": "conda-env-manager",
  "conda_version": "23.3.1",
  "python_version": "3.11.0",
  "system_info": {
    "os": "Linux",
    "kernel": "5.15.0-106-generic",
    "arch": "x86_64"
  },
  "cuda_config": {
    "cuda_version": "12.1",
    "cudnn_version": "8.9.5",
    "gpu_compute_capability": "8.6"
  },
  "package_count": 42,
  "total_size_mb": 8320,
  "dependencies": {
    "python": {
      "version": "3.11.0",
      "build_string": "h6de4bd8_0_cpython",
      "hash_sha256": "abc123...",
      "channel": "defaults"
    },
    "pytorch": {
      "version": "2.1.2",
      "build_string": "py3.11_cuda12.1_cudnn8.9.5_0",
      "hash_sha256": "def456...",
      "channel": "pytorch"
    }
  },
  "integrity": {
    "manifest_hash": "sha256:xyz789...",
    "lockfile_hash": "sha256:uvw456...",
    "verification_timestamp": "2026-04-05T14:23:00Z"
  },
  "installation_method": "conda_env_create",
  "notes": []
}

Reproducibility Verification Protocol

When recreating an environment from lock file, conda-env-manager automatically:

1. Pre-creation validation:

   • Parse lock file SHA256 hash and verify integrity
   • Check CUDA version compatibility with host system
   • Estimate required disk space and verify availability

2. Post-creation verification (automated after conda env create):

   • Run conda list --json and compare package versions against lock file
   • Verify all pip packages match with pip list --format=json
   • Execute Python import test: python -c "import torch; print(torch.__version__)"
   • Compare against stored manifest hash

3. Generate verification report (environment-{env_name}-verify-report.json):

{
  "environment_name": "neuroclaw-dl",
  "verified_at": "2026-04-05T14:25:00Z",
  "verification_status": "SUCCESS",
  "package_count": 42,
  "conda_packages_verified": 42,
  "pip_packages_verified": 3,
  "failed_imports": [],
  "warnings": [],
  "reproducibility_score": 1.0,
  "lock_file_match": true
}

Environment Snapshot at Experiment Checkpoints

Every experiment executed with this conda environment automatically captures:

experiment_20260405_143000_checkpoint/
├── environment_locked.yml (exact snapshot at checkpoint time)
├── environment_manifest.json
├── python_packages_frozenlist.txt
├── pip_freeze_output.txt
├── cuda_info.json
│   {
│     "nvcc_version": "12.1",
│     "driver_version": "555.42",
│     "gcc_version": "11.4.0"
│   }
└── environment_restoration_guide.md
    # Instructions for reproducing this exact environment on another machine

Environment Branching & Experiment Variants

For ablation studies or variant experiments, conda-env-manager supports safe environment cloning:

# Clone environment for variant testing
conda create --name neuroclaw-dl-v2 --clone neuroclaw-dl

# Auto-generates:
# - environment-neuroclaw-dl-v2-lock.yml (exact clone specification)
# - environment-neuroclaw-dl-v2-manifest.json
# - clone-metadata.json (tracks parent environment + clone timestamp)

Cloned environments remain independent but traceable for result comparison and rollback.

Important Notes & Limitations

• User confirmation is mandatory — no silent destructive actions
• Prefer --from-history exports for minimal, reproducible yml files
• Large environments / CUDA stacks → warn about disk space and time
• Windows users are encouraged to use WSL2 for best compatibility
• If mamba is detected, the skill can suggest the faster mamba replacement
• Rollback support: keep yml backups before major updates
• Do not auto-activate environments — only print instructions (shell session safety)

When to Call This Skill

• Any request containing “conda”, “environment”, “env create”, “yml”, “export env”
• Before running deep-learning or model skills that require specific package versions
• When dependency-planner detects conflicts best solved by a new environment
• Reproducibility, sharing, or team collaboration tasks

Complementary / Related Skills

• dependency-planner → package installation after environment creation
• multi-search-engine → lookup latest conda channel / solver advice
• claw-shell → execution of conda commands

Reference

Custom interface-layer skill for NeuroClaw, addressing environment setup gaps identified in the MedicalClaw / OpenClaw evaluation and aligned with 2025–2026 conda best practices (isolated environments, yml reproducibility, dry-run safety).

Created At: 2026-03-19 01:45 HKT
Last Updated At: 2026-04-05 02:01 HKT Author: chengwang96