mirror of
https://github.com/dwinkler1/np.git
synced 2026-02-19 22:40:57 -05:00
Refactor template: extract scripts, overlays, and hosts into separate modules
Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>
This commit is contained in:
copilot-swe-agent[bot]
parent
5e8f07c560
commit
3398a72241
17 changed files with 1185 additions and 422 deletions
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@ -50,241 +50,24 @@
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};
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};
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};
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# R packages
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rOverlay = final: prev: let
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reqPkgs = with final.rpkgs.rPackages;
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[
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broom
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data_table
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janitor
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languageserver
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reprex
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styler
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tidyverse
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]
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++ (with final.extraRPackages; [
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httpgd
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])
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++ (prev.lib.optional (builtins.pathExists ./r-packages.nix) (import ./r-packages.nix final.rpkgs));
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in {
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quarto = final.rpkgs.quarto.override {extraRPackages = reqPkgs;};
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rWrapper = final.rpkgs.rWrapper.override {packages = reqPkgs;};
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};
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# Python packages
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pythonOverlay = final: prev: {
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python = prev.python3.withPackages (pyPackages:
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with pyPackages; [
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requests
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]);
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};
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###################################
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## ⬆️ BASIC CONFIG ABOVE HERE ⬆️ ##
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###################################
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rixOverlay = final: prev: {rpkgs = inputs.rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};};
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extraPkgOverlay = final: prev: let
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extraTheme = {
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plugin = prev.vimPlugins."${config.theme.extraColorschemePackage.plugin}";
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name = config.theme.extraColorschemePackage.name;
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config = {
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lua = config.theme.extraColorschemePackage.extraLua;
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};
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};
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in {
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inherit extraTheme;
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};
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projectScriptsOverlay = final: prev: let
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initPython = ''
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#!/usr/bin/env bash
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set -euo pipefail
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if [[ ! -f "pyproject.toml" ]]; then
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echo "🐍 Initializing UV project..."
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uv init
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echo "📦 Adding IPython and Marimo..."
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uv add ipython
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uv add marimo
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echo "--------------------------------------------------------------------------"
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echo "✅ Python project initialized!"
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echo "run 'uv add PACKAGE' to add more python packages."
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echo "--------------------------------------------------------------------------"
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else
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echo "--------------------------------------------------------------------------"
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echo "🔄 Existing Python project detected."
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echo "📦 Ensuring IPython and Marimo are installed..."
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uv add ipython
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uv add marimo
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echo "Run '${config.defaultPackageName}-updateDeps' to update dependencies."
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echo "--------------------------------------------------------------------------"
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fi
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'';
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initProjectScript = ''
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#!/usr/bin/env bash
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set -euo pipefail
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PROJECT_NAME="''${1:-${config.defaultPackageName}}"
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echo "🚀 Setting up project: $PROJECT_NAME"
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# Create directory structure
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directories=(
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"data/raw"
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"data/processed"
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"data/interim"
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"docs"
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"figures"
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"tables"
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"src/analysis"
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"src/data_prep"
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"src/explore"
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"src/utils"
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)
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for dir in "''${directories[@]}"; do
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if [[ ! -d "$dir" ]]; then
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mkdir -p "$dir"
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echo "✓ Created $dir/"
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fi
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done
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# Create essential files
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if [[ ! -f "README.md" ]]; then
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cat > README.md << 'EOF'
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# RDE
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## Project Structure
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- `data/`: Data files (gitignored)
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- `docs/`: Documentation
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- `figures/`: Output figures
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- `tables/`: Output tables
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- `src/`: Source code
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EOF
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fi
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# Initialize git
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if [[ ! -d ".git" ]]; then
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git init
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echo "✓ Initialized Git repository and added: flake.nix, flake.lock"
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fi
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# Check if files are already staged/tracked before adding
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if ! git diff --cached --name-only | grep -q "flake.nix\|flake.lock" &&
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! git ls-files --error-unmatch flake.nix flake.lock >/dev/null 2>&1; then
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echo "✓ Adding flake.nix, flake.lock to Git repository"
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git add flake.nix flake.lock
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else
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echo "✓ flake.nix, flake.lock already tracked/staged in Git"
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fi
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# Create .gitignore
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if [[ ! -f ".gitignore" ]]; then
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cat > .gitignore << 'EOF'
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# Data files
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data/
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*.csv
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*.docx
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*.xlsx
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*.parquet
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# R specific
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.Rproj.user/
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.Rhistory
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.RData
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.Ruserdata
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*.Rproj
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.Rlibs/
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# Python specific
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__pycache__/
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*.pyc
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.pytest_cache/
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.venv/
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# Jupyter
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.ipynb_checkpoints/
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# IDE
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.vscode/
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.idea/
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# OS
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.DS_Store
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Thumbs.db
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# Devenv
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.devenv*
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devenv.local.nix
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# direnv
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.direnv
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# pre-commit
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.pre-commit-config.yaml
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EOF
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fi
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echo "✅ Project setup completed successfully!"
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'';
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updateDepsScript = ''
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#!/usr/bin/env bash
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set -euo pipefail
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echo "🔄 Updating project dependencies..."
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RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' ) &&\
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sed -i "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix
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echo "✅ R date is $RVER"
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nix flake update
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echo "✅ Flake inputs updated"
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if [[ -f "pyproject.toml" ]]; then
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uv sync --upgrade
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echo "✅ Python dependencies updated"
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fi
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if [[ -f "Project.toml" ]]; then
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${config.defaultPackageName}-jl -e "using Pkg; Pkg.update()"
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echo "✅ Julia dependencies updated"
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fi
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if [[ -f "devenv.nix" ]]; then
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devenv update
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echo "✅ Devenv dependencies updated"
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fi
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echo "🎉 All dependencies updated!"
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'';
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activateDevenv = ''
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#!/usr/bin/env bash
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set -euo pipefail
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if [[ -f "devenv.nix" ]]; then
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echo "🚀 Activating devenv environment..."
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exec ${config.defaultPackageName}-devenv shell
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else
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echo "❌ No devenv.nix file found in the current directory."
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echo "To create one, run '${config.defaultPackageName}-initDevenv'"
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exit 1
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fi
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'';
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in {
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initPython = prev.writeShellScriptBin "initPython" initPython;
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initProject = prev.writeShellScriptBin "initProject" initProjectScript;
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updateDeps = prev.writeShellScriptBin "updateDeps" updateDepsScript;
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activateDevenv = prev.writeShellScriptBin "activateDevenv" activateDevenv;
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};
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# Import overlays from separate files
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rOverlay = import ./overlays/r.nix;
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pythonOverlay = import ./overlays/python.nix;
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rixOverlay = import ./overlays/rix.nix inputs;
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extraPkgOverlay = import ./overlays/theme.nix config;
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projectScriptsOverlay = import ./overlays/project-scripts.nix config;
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supportedSystems = [
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"x86_64-linux"
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"aarch64-linux"
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"aarch64-darwin"
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];
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forSystems = nixpkgs.lib.genAttrs supportedSystems;
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projectConfig = forSystems (
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system: let
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inherit (nixCats) utils;
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@ -303,6 +86,7 @@
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pythonOverlay
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projectScriptsOverlay
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];
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categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
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{
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pkgs,
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@ -314,28 +98,14 @@
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...
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} @ packageDef: {
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lspsAndRuntimeDeps = {
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project = with pkgs; [
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];
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julia = with pkgs; [
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julia-bin
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];
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python = with pkgs; [
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python
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nodejs
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basedpyright
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uv
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];
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r = with pkgs; [
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rWrapper
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quarto
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air-formatter
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];
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project = with pkgs; [];
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julia = with pkgs; [julia-bin];
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python = with pkgs; [python nodejs basedpyright uv];
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r = with pkgs; [rWrapper quarto air-formatter];
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};
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startupPlugins = {
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project = with pkgs.vimPlugins; [
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pkgs.extraTheme
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];
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project = with pkgs.vimPlugins; [pkgs.extraTheme];
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gitPlugins = with pkgs.neovimPlugins; [
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{
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plugin = r;
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@ -345,13 +115,13 @@
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};
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optionalPlugins = {
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project = with pkgs.vimPlugins; [
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];
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project = with pkgs.vimPlugins; [];
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gitPlugins = with pkgs.neovimPlugins; [
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cmp-r
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cmp-pandoc-references
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];
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};
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optionalLuaPreInit = {
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project = [
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''
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@ -370,37 +140,27 @@
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''
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];
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};
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optionalLuaAdditions = {
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project = [
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"vim.notify('Project loaded: ${name}')"
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];
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project = ["vim.notify('Project loaded: ${name}')"];
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};
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sharedLibraries = {
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project = {
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};
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project = {};
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};
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environmentVariables = {
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project = {
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};
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julia = {
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JULIA_NUM_THREADS = "auto";
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};
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project = {};
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julia = {JULIA_NUM_THREADS = "auto";};
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python = {
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# Prevent uv from managing Python downloads
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UV_PYTHON_DOWNLOADS = "never";
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# Force uv to use nixpkgs Python interpreter
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UV_PYTHON = pkgs.python.interpreter;
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};
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r = {
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R_LIBS_USER = "./.Rlibs";
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};
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r = {R_LIBS_USER = "./.Rlibs";};
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};
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extraWrapperArgs = {
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python = [
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"--unset PYTHONPATH"
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];
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python = ["--unset PYTHONPATH"];
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};
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}
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);
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@ -417,166 +177,8 @@
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settings = {
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suffix-path = false;
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suffix-LD = false;
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# your alias may not conflict with your other packages.
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aliases = ["pvim"];
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hosts = {
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g = {
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enable = true;
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path = {
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value = "${pkgs.neovide}/bin/neovide";
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args = [
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"--add-flags"
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"--neovim-bin ${name}"
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];
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};
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};
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marimo = let
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marimoInit = ''
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set -euo pipefail
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if [[ ! -f "pyproject.toml" ]]; then
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echo "🐍 Initializing UV project..."
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uv init
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echo "📦 Adding Marimo..."
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uv add marimo
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echo "--------------------------------------------------------------------------"
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echo "✅ Python project initialized!"
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echo "run 'uv add PACKAGE' to add more python packages."
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echo "--------------------------------------------------------------------------"
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else
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echo "--------------------------------------------------------------------------"
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echo "🔄 Syncing existing project..."
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uv sync
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echo "🐍 Launching Marimo..."
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echo "--------------------------------------------------------------------------"
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fi
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'';
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in {
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enable = config.enabledLanguages.python;
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path = {
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value = "${pkgs.uv}/bin/uv";
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args = [
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"--run"
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"${marimoInit}"
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"--add-flags"
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"run marimo edit \"$@\""
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];
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};
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};
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py = {
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enable = config.enabledLanguages.python;
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path = {
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value = "${pkgs.python.interpreter}";
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};
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};
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ipy = let
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ipythonInit = ''
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set -euo pipefail
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if [[ ! -f "pyproject.toml" ]]; then
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echo "🐍 Initializing UV project..."
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uv init
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echo "📦 Adding IPython..."
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uv add ipython
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echo "--------------------------------------------------------------------------"
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echo "✅ Python project initialized!"
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echo "run 'uv add PACKAGE' to add more python packages."
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echo "--------------------------------------------------------------------------"
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else
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echo "--------------------------------------------------------------------------"
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echo "🔄 Syncing existing project..."
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echo "📦 Ensuring IPython is installed..."
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uv add ipython
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uv sync
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echo "🐍 Launching IPython..."
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echo "--------------------------------------------------------------------------"
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fi
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'';
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in {
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enable = config.enabledLanguages.python;
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path = {
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value = "${pkgs.uv}/bin/uv";
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args = [
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"--run"
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"${ipythonInit}"
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"--add-flags"
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"run ipython \"$@\""
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];
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};
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};
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jl = {
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enable = config.enabledLanguages.julia;
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path = {
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value = "${pkgs.julia-bin}/bin/julia";
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args = ["--add-flags" "--project=."];
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};
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};
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initJl = {
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enable = config.enabledLanguages.julia;
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path = {
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value = "${pkgs.julia-bin}/bin/julia";
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args = ["--add-flags" "--project=. -e 'using Pkg; Pkg.instantiate(); Pkg.add(\"Pluto\")'"];
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};
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};
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pluto = let
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runPluto = ''
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import Pkg; import TOML; Pkg.instantiate();
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if !isfile("Project.toml") || !haskey(TOML.parsefile(Base.active_project())["deps"], "Pluto")
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Pkg.add("Pluto");
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end
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import Pluto; Pluto.run();
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'';
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in {
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enable = config.enabledLanguages.julia;
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path = {
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value = "${pkgs.julia-bin}/bin/julia";
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args = ["--add-flags" "--project=. -e '${runPluto}'"];
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};
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};
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r = {
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enable = config.enabledLanguages.r;
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path = {
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value = "${pkgs.rWrapper}/bin/R";
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args = ["--add-flags" "--no-save --no-restore"];
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};
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};
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initPython = {
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enable = config.enabledLanguages.python;
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path.value = "${pkgs.initPython}/bin/initPython";
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};
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initProject = {
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enable = true;
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path = {
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value = "${pkgs.initProject}/bin/initProject";
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};
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};
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initDevenv = {
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enable = config.enabledPackages.devenv;
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path = {
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value = "${pkgs.devenv}/bin/devenv";
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args = ["--add-flags" "init"];
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};
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};
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activateDevenv = {
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enable = config.enabledPackages.devenv;
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path = {
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value = "${pkgs.activateDevenv}/bin/activateDevenv";
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};
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};
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devenv = {
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enable = config.enabledPackages.devenv;
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path = {
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value = "${pkgs.devenv}/bin/devenv";
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};
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};
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updateDeps = {
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enable = true;
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path = {
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value = "${pkgs.updateDeps}/bin/updateDeps";
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};
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};
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node.enable = true;
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perl.enable = true;
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ruby.enable = true;
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};
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hosts = import ./hosts config pkgs;
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};
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categories = {
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julia = config.enabledLanguages.julia;
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