setting-up-reproducible-analysis

npx skills add K-Dense-AI/science-superpowers --skill setting-up-reproducible-analysis --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Setting Up a Reproducible Analysis ## Overview Ensure the analysis happens in an isolated workspace that another person (or future you) can reproduce exactly: same code, same environment, same seed, same immutable input data. **Core principle:** A result you cannot reproduce is not a result. Set up reproducibility before you run anything. **Announce at start:** "I'm using the setting-up-reproducible-analysis skill to set up an isolated, reproducible workspace." ## Step 0: Detect Existing Isolation Before creating anything, check whether you're already in an isolated workspace. ```bash GIT_DIR=$(cd "$(git rev-parse --git-dir)" 2>/dev/null && pwd -P) GIT_COMMON=$(cd "$(git rev-parse --git-common-dir)" 2>/dev/null && pwd -P) BRANCH=$(git branch --show-current) ``` **Submodule guard:** `GIT_DIR != GIT_COMMON` is also true in submodules. Verify you're not in one: ```bash git rev-parse --show-superproject-working-tree 2>/dev/null ``` **If `GIT_DIR != GIT_COMMON` (and not a submodule):** already in a linked worktree. Skip to Step 2 (Environment). Don't create another. **If `GIT_DIR == GIT_COMMON`:** normal checkout. If your human partner hasn't already stated a preference, ask before cr

git rev-parse --show-superproject-working-tree 2>/dev/null
Prefer an existing .worktrees/ (must be git-ignored), else default to it
git check-ignore -q .worktrees 2>/dev/null || echo ".worktrees/" >> .gitignore
git worktree add ".worktrees/$BRANCH_NAME" -b "$BRANCH_NAME"
cd ".worktrees/$BRANCH_NAME"
Python
if [ -f environment.yml ]; then conda env create -f environment.yml || conda env update -f environment.yml; fi
if [ -f requirements.txt ]; then python -m venv .venv && . .venv/bin/activate && pip install -r requirements.txt; fi
if [ -f pyproject.toml ]; then python -m venv .venv && . .venv/bin/activate && pip install -e .; fi
R