diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md deleted file mode 100644 index 9a9a73c..0000000 --- a/.github/copilot-instructions.md +++ /dev/null @@ -1,194 +0,0 @@ -# GitHub Copilot Instructions for np Repository - -## Repository Overview - -This repository provides Nix flake templates for setting up Research Development Environments (RDE). The primary template is located in `templates/rde/` and is designed for data science and research projects supporting R, Python, and Julia. - -## Project Structure - -- `flake.nix` - Root flake defining available templates -- `templates/rde/` - Main RDE template with Neovim-based development environment - - `flake.nix` - Template flake configuration with language support and tooling - - `flake.lock` - Locked dependencies for reproducibility - - `.envrc` - direnv configuration for automatic environment loading -- `.github/workflows/` - CI/CD workflows for testing and updates - - `check.yml` - Tests RDE template on Ubuntu - - `check_macos.yml` - Tests RDE template on macOS - - `update.yml` - Automated daily dependency updates - -## Key Technologies - -- **Nix Flakes**: Reproducible development environments -- **nixCats**: Custom Neovim configuration framework -- **direnv**: Automatic environment loading -- **Cachix**: Binary cache for faster builds (using `rde`, `rstats-on-nix`, and `nix-community` caches) - -## Language Support - -The RDE template supports multiple languages, controlled via `config.enabledLanguages` in `templates/rde/flake.nix`: - -- **R**: R wrapper, Quarto, air-formatter, language server, and custom R packages via overlays -- **Python**: Python 3, basedpyright LSP, UV package manager -- **Julia**: Julia REPL with Pluto.jl support - -## Development Commands - -The template provides project-specific commands (prefix with package name, default is `p`): - -- `p` - Launch Neovim -- `p-g` - Launch Neovide GUI -- `p-initProject` - Initialize project structure (data/, src/, docs/) -- `p-updateDeps` - Update all dependencies (flake inputs, R packages, Python packages) -- `p-r` - Launch R console -- `p-py` / `p-ipy` - Launch Python/IPython REPL -- `p-marimo` - Launch Marimo notebook -- `p-jl` - Launch Julia REPL -- `p-pluto` - Launch Pluto.jl notebook -- `p-devenv` - Devenv integration (when enabled) - -## Nix Flake Conventions - -### Configuration Structure - -The RDE template uses a centralized `config` object at the top of `flake.nix`: - -```nix -config = rec { - defaultPackageName = "p"; - enabledLanguages = { julia = false; python = false; r = true; }; - enabledPackages = { gitPlugins = enabledLanguages.r; devenv = false; }; - theme = { colorscheme = "kanagawa"; background = "dark"; }; -}; -``` - -### Overlays Pattern - -The template uses multiple overlays to extend nixpkgs: - -- `rOverlay` - Adds R packages via rix/rstats-on-nix -- `pythonOverlay` - Configures Python packages -- `rixOverlay` - Integrates R package snapshots from rstats-on-nix -- `projectScriptsOverlay` - Custom shell scripts for project management -- `extraPkgOverlay` - Additional theme and plugin configuration - -### Package Categories - -nixCats uses categories to organize functionality: - -- `lspsAndRuntimeDeps` - Language servers and runtime dependencies -- `startupPlugins` - Neovim plugins loaded at startup -- `optionalPlugins` - Plugins loaded on demand -- `environmentVariables` - Language-specific environment setup -- `extraWrapperArgs` - Additional wrapper arguments (e.g., unset PYTHONPATH for Python) - -## Testing & CI/CD - -### Local Testing - -```bash -# Build the RDE template -nix build ./templates/rde - -# Check the RDE template -nix flake check ./templates/rde - -# Enter development shell -nix develop ./templates/rde -``` - -### CI Workflows - -- **check.yml**: Runs on pushes to `templates/rde/flake.lock`, builds and checks the template on Ubuntu -- **check_macos.yml**: Tests on macOS when `update_rde` branch is pushed -- **update.yml**: Daily cron job that updates dependencies via `p-updateDeps` and creates PRs - -## Dependency Management - -### R Packages - -R packages are managed through rstats-on-nix pinned snapshots. The date is specified in the `rixpkgs.url` input: - -```nix -rixpkgs.url = "github:rstats-on-nix/nixpkgs/2025-12-15"; -``` - -Custom R packages can be added in `rOverlay` or via `r-packages.nix` file. - -### Python Packages - -Python packages use UV for management with nixpkgs Python as the interpreter: - -- Environment variables force UV to use nix Python: `UV_PYTHON_DOWNLOADS = "never"` and `UV_PYTHON = pkgs.python.interpreter` -- PYTHONPATH is explicitly unset via `extraWrapperArgs` - -### Flake Inputs - -Dependencies are tracked in `flake.lock`. Key inputs include: - -- `nixpkgs` - NixOS 25.11 -- `rixpkgs` - R package snapshots from rstats-on-nix -- `nixCats` - Custom Neovim configuration framework -- `fran` - Extra R packages overlay -- Plugin inputs for R.nvim ecosystem - -## Coding Style & Conventions - -1. **Nix Code**: - - Use `rec` for recursive attribute sets when needed - - Prefer `let...in` for local bindings - - Use `lib.optional` and `lib.optionalString` for conditional inclusion - - Keep configuration at the top of the file for easy customization - -2. **Shell Scripts** (in overlays): - - Always use `set -euo pipefail` for safety - - Provide user-friendly output with emojis and clear messages - - Check for existing files/directories before creating - -3. **Workflows**: - - Use `workflow_dispatch` for manual triggering - - Configure concurrency to cancel in-progress runs - - Use Cachix for binary caching with multiple caches - -## Common Patterns - -### Adding a New Language - -1. Add to `config.enabledLanguages` -2. Create overlay for language-specific packages -3. Add to `categoryDefinitions.lspsAndRuntimeDeps` -4. Add command aliases in `packageDefinitions.hosts` -5. Update `shellHook` with available commands - -### Adding Custom Scripts - -Add to `projectScriptsOverlay`: - -```nix -myScript = prev.writeShellScriptBin "myScript" '' - #!/usr/bin/env bash - set -euo pipefail - # script content -''; -``` - -### Plugin Integration - -For git-based plugins: -1. Add flake input with `flake = false` -2. Reference in nixCats inputs -3. Add to `startupPlugins` or `optionalPlugins` categories - -## Important Notes - -- The template creates a `.gitignore` that excludes data files by default -- R packages are installed to project-local `.Rlibs/` directory -- Python UV is configured to never download Python, always using nixpkgs version -- The template supports multiple platforms: x86_64-linux, aarch64-linux, aarch64-darwin -- Neovim is wrapped with language-specific environment variables and PATH additions - -## File Generation - -When asked to initialize projects or generate common files, follow the patterns in: -- `initProjectScript` for project structure -- `.gitignore` template for what to exclude -- `README.md` template for documentation structure diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index a231159..e228877 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -4,17 +4,6 @@ on: push: paths: - 'templates/rde/flake.lock' - - 'templates/rde/**/*.nix' - - 'templates/rde/**/*.sh' - - 'templates/rde/**/*.lua' - - '.github/workflows/check.yml' - pull_request: - paths: - - 'templates/rde/flake.lock' - - 'templates/rde/**/*.nix' - - 'templates/rde/**/*.sh' - - 'templates/rde/**/*.lua' - - '.github/workflows/check.yml' concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true @@ -25,199 +14,13 @@ jobs: matrix: os: [ubuntu-latest] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v5 - uses: wimpysworld/nothing-but-nix@main with: hatchet-protocol: 'carve' - uses: cachix/install-nix-action@v31 with: github_access_token: ${{ secrets.GITHUB_TOKEN }} - - uses: cachix/cachix-action@v16 - with: - name: rde - authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}' - extraPullNames: rstats-on-nix, nix-community -# - uses: DeterminateSystems/magic-nix-cache-action@main - - # Build and basic checks - - name: Build template - run: nix build ./templates/rde - - name: Run flake check - run: nix flake check ./templates/rde - - # Test development shell functionality - - name: Test dev shell enters successfully - run: | - cd templates/rde - nix develop --command bash -c "echo 'Dev shell works'" - - # Test R functionality (default enabled) - - name: Test R command is available - run: | - cd templates/rde - nix develop --command bash -c "which p-r" - - - name: Test R launches and runs basic command - run: | - cd templates/rde - nix develop --command bash -c "p-r --version" - - - name: Test R can execute simple code - run: | - cd templates/rde - nix develop --command bash -c "p-r -e 'print(1+1)'" - - - name: Test Quarto is available in R environment - run: | - cd templates/rde - nix develop --command bash -c "quarto --version" - - # Test Neovim functionality - - name: Test Neovim command is available - run: | - cd templates/rde - nix develop --command bash -c "which p" - - - name: Test Neovim launches in headless mode - run: | - cd templates/rde - nix develop --command bash -c "p --headless --version" - - # Test utility commands - - name: Test p-initProject command is available - run: | - cd templates/rde - nix develop --command bash -c "which p-initProject" - - - name: Test p-initProject creates project structure - run: | - TEST_DIR=$(mktemp -d) - cd "$TEST_DIR" - nix develop $GITHUB_WORKSPACE/templates/rde --command bash -c "p-initProject" - # Verify directories were created - test -d data/raw || exit 1 - test -d data/processed || exit 1 - test -d src || exit 1 - test -f README.md || exit 1 - test -f .gitignore || exit 1 - echo "Project structure created successfully" - # Cleanup - rm -rf "$TEST_DIR" - - - name: Test p-updateDeps command is available - run: | - cd templates/rde - nix develop --command bash -c "which p-updateDeps" - - # Test that package is built correctly - - name: Test default package can be run - run: | - cd templates/rde - nix run . -- --headless --version - - test-with-python: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v6 - - uses: wimpysworld/nothing-but-nix@main - with: - hatchet-protocol: 'carve' - - uses: cachix/install-nix-action@v31 - with: - github_access_token: ${{ secrets.GITHUB_TOKEN }} - - uses: cachix/cachix-action@v16 - with: - name: rde - authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}' - extraPullNames: rstats-on-nix, nix-community - - # Create a temporary directory with Python enabled - - name: Setup test directory with Python enabled - run: | - TEST_DIR=$(mktemp -d) - cp -r templates/rde/. "$TEST_DIR/" - cd "$TEST_DIR" - # Enable Python in the config (handle variations in whitespace) - sed -i 's/python[[:space:]]*=[[:space:]]*false;/python = true;/' flake.nix - # Verify the change was successful - grep -q "python[[:space:]]*=[[:space:]]*true;" flake.nix || { - echo "Error: Failed to enable Python in flake.nix" - exit 1 - } - echo "TEST_PYTHON_DIR=$TEST_DIR" >> $GITHUB_ENV - - - name: Build with Python enabled - run: | - cd "$TEST_PYTHON_DIR" - nix build - - - name: Test Python commands are available - run: | - cd "$TEST_PYTHON_DIR" - nix develop --command bash -c "which p-py && which p-ipy && which p-initPython" - - - name: Test Python launches - run: | - cd "$TEST_PYTHON_DIR" - nix develop --command bash -c "p-py --version" - - - name: Test Python can execute code - run: | - cd "$TEST_PYTHON_DIR" - nix develop --command bash -c "p-py -c 'print(1+1)'" - - - name: Test UV package manager is available - run: | - cd "$TEST_PYTHON_DIR" - nix develop --command bash -c "uv --version" - - test-with-julia: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v6 - - uses: wimpysworld/nothing-but-nix@main - with: - hatchet-protocol: 'carve' - - uses: cachix/install-nix-action@v31 - with: - github_access_token: ${{ secrets.GITHUB_TOKEN }} - - uses: cachix/cachix-action@v16 - with: - name: rde - authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}' - extraPullNames: rstats-on-nix, nix-community - - # Create a temporary directory with Julia enabled - - name: Setup test directory with Julia enabled - run: | - TEST_DIR=$(mktemp -d) - cp -r templates/rde/. "$TEST_DIR/" - cd "$TEST_DIR" - # Enable Julia in the config (handle variations in whitespace) - sed -i 's/julia[[:space:]]*=[[:space:]]*false;/julia = true;/' flake.nix - # Verify the change was successful - grep -q "julia[[:space:]]*=[[:space:]]*true;" flake.nix || { - echo "Error: Failed to enable Julia in flake.nix" - exit 1 - } - echo "TEST_JULIA_DIR=$TEST_DIR" >> $GITHUB_ENV - - - name: Build with Julia enabled - run: | - cd "$TEST_JULIA_DIR" - nix build - - - name: Test Julia commands are available - run: | - cd "$TEST_JULIA_DIR" - nix develop --command bash -c "which p-jl && which p-initJl" - - - name: Test Julia launches - run: | - cd "$TEST_JULIA_DIR" - nix develop --command bash -c "p-jl --version" - - - name: Test Julia can execute code - run: | - cd "$TEST_JULIA_DIR" - nix develop --command bash -c "p-jl -e 'println(1+1)'" + - uses: DeterminateSystems/magic-nix-cache-action@main + - run: nix build ./templates/rde + - run: nix flake check ./templates/rde diff --git a/.github/workflows/check_macos.yml b/.github/workflows/check_macos.yml index 06578c7..958426d 100644 --- a/.github/workflows/check_macos.yml +++ b/.github/workflows/check_macos.yml @@ -14,14 +14,9 @@ jobs: matrix: os: [macos-latest] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v5 - uses: cachix/install-nix-action@v31 with: github_access_token: ${{ secrets.GITHUB_TOKEN }} - - uses: cachix/cachix-action@v16 - with: - name: rde - authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}' - extraPullNames: rstats-on-nix, nix-community + - uses: DeterminateSystems/magic-nix-cache-action@main - run: nix build ./templates/rde - - run: nix build ./templates/ed diff --git a/.github/workflows/flakehub-publish-rolling.yml b/.github/workflows/flakehub-publish-rolling.yml index 80ff807..8403bbe 100644 --- a/.github/workflows/flakehub-publish-rolling.yml +++ b/.github/workflows/flakehub-publish-rolling.yml @@ -10,7 +10,7 @@ jobs: id-token: "write" contents: "read" steps: - - uses: "actions/checkout@v6" + - uses: "actions/checkout@v5" with: persist-credentials: false - uses: "DeterminateSystems/determinate-nix-action@v3" diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml index 891e992..a72d5f3 100644 --- a/.github/workflows/update.yml +++ b/.github/workflows/update.yml @@ -3,33 +3,23 @@ name: update-flake-lock on: workflow_dispatch: # allows manual triggering schedule: - - cron: '0 6 * * *' + - cron: '0 3 * * *' jobs: lockfile: runs-on: ubuntu-latest steps: - name: Checkout repository - uses: actions/checkout@v6 - - uses: wimpysworld/nothing-but-nix@main - with: - hatchet-protocol: 'carve' - - uses: cachix/install-nix-action@v31 - with: - github_access_token: ${{ secrets.GITHUB_TOKEN }} - - uses: cachix/cachix-action@v16 - with: - name: rde - authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}' - extraPullNames: rstats-on-nix, nix-community - - run: cd templates/rde/ && nix develop -c p-updateDeps - - run: cd templates/ed/ && nix develop -c updateR + uses: actions/checkout@v5 + - name: Install Determinate Nix + uses: DeterminateSystems/determinate-nix-action@v3 + - uses: DeterminateSystems/magic-nix-cache-action@main - name: Update n flake.lock - uses: DeterminateSystems/update-flake-lock@v28 + uses: DeterminateSystems/update-flake-lock@v27 with: token: ${{ secrets.GH_TOKEN_FOR_UPDATES }} branch: update_rde - path-to-flake-dir: "templates/ed" + path-to-flake-dir: "templates/rde" pr-title: "Update RDE flake.lock" # Title of PR to be created pr-labels: | # Labels to be set on the PR dependencies diff --git a/README.md b/README.md deleted file mode 100644 index bfa3c32..0000000 --- a/README.md +++ /dev/null @@ -1,70 +0,0 @@ -# Nix Project Templates (np) - -A collection of Nix flake templates for reproducible development environments. - -## Templates - -### RDE (Research Development Environment) - -The default template for data science and research projects with support for R, Python, and Julia. - -**Quick start:** -```bash -nix flake init -t github:dwinkler1/np#rde -nix develop -``` - -**Features:** -- đŸ”Ŧ Multi-language support (R, Python, Julia) -- đŸ“Ļ Reproducible with Nix -- 🎨 Neovim-based IDE with LSP support -- 📊 Research-focused workflows -- 🔧 Modular and customizable - -See [templates/rde/README.md](templates/rde/README.md) for full documentation. - -## CI/CD - -All templates are automatically tested to ensure functionality: - -- **Build Tests**: Templates build successfully on Linux and macOS -- **Functionality Tests**: All commands and language support are verified -- **Configuration Tests**: Multiple configurations (R, Python, Julia) are tested -- **Automated Updates**: Dependencies are updated daily via automated PRs - -### CI Workflows - -- `.github/workflows/check.yml` - Comprehensive functionality tests (Ubuntu) -- `.github/workflows/check_macos.yml` - macOS compatibility tests -- `.github/workflows/update.yml` - Automated dependency updates - -## Usage - -1. **Initialize a new project:** - ```bash - nix flake init -t github:dwinkler1/np#rde - ``` - -2. **Enter development environment:** - ```bash - nix develop - # or with direnv - echo "use flake" > .envrc && direnv allow - ``` - -3. **Start working:** - ```bash - p-initProject # Create project structure - p # Launch Neovim - ``` - -## Contributing - -Contributions are welcome! Please ensure: -- All templates pass CI tests -- Documentation is updated for new features -- Code follows existing patterns - -## License - -See [LICENSE](LICENSE) file for details. diff --git a/flake.nix b/flake.nix index 7b723a7..e2cb7cc 100644 --- a/flake.nix +++ b/flake.nix @@ -6,11 +6,7 @@ path = ./templates/rde; description = "Research Development Environment"; }; - ed = { - path = ./templates/ed; - description = "Simple nvim Environment"; - }; }; - defaultTemplate = self.templates.ed; + defaultTemplate = self.templates.rde; }; } diff --git a/templates/ed/.envrc b/templates/ed/.envrc deleted file mode 100644 index 3550a30..0000000 --- a/templates/ed/.envrc +++ /dev/null @@ -1 +0,0 @@ -use flake diff --git a/templates/ed/.gitignore b/templates/ed/.gitignore deleted file mode 100644 index 52e8a70..0000000 --- a/templates/ed/.gitignore +++ /dev/null @@ -1 +0,0 @@ -.nvimcom diff --git a/templates/ed/flake.lock b/templates/ed/flake.lock deleted file mode 100644 index 5839626..0000000 --- a/templates/ed/flake.lock +++ /dev/null @@ -1,148 +0,0 @@ -{ - "nodes": { - "fran": { - "inputs": { - "nixpkgs": [ - "rixpkgs" - ] - }, - "locked": { - "lastModified": 1771133455, - "narHash": "sha256-DvHfkW3DctWV+YnigY4+5Stn9NgI38JqR2IScXDX8z8=", - "owner": "dwinkler1", - "repo": "fran", - "rev": "68b189ab981adae06590ee1929a70c8b86afd2b8", - "type": "github" - }, - "original": { - "owner": "dwinkler1", - "repo": "fran", - "type": "github" - } - }, - "nixpkgs": { - "locked": { - "lastModified": 1771043024, - "narHash": "sha256-O1XDr7EWbRp+kHrNNgLWgIrB0/US5wvw9K6RERWAj6I=", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "3aadb7ca9eac2891d52a9dec199d9580a6e2bf44", - "type": "github" - }, - "original": { - "owner": "NixOS", - "ref": "nixos-25.11", - "repo": "nixpkgs", - "type": "github" - } - }, - "nvimConfig": { - "inputs": { - "fran": [ - "fran" - ], - "nixpkgs": [ - "nixpkgs" - ], - "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references", - "plugins-r": "plugins-r", - "rixpkgs": [ - "rixpkgs" - ], - "wrappers": "wrappers" - }, - "locked": { - "lastModified": 1770172480, - "narHash": "sha256-gem34C89cocBGuWLj7cdrAS5WkrOBp6V+ycQM/RhcCw=", - "owner": "dwinkler1", - "repo": "nvimConfig", - "rev": "8f5c05252e914cb3738039a7ec13eb7d5955227a", - "type": "github" - }, - "original": { - "owner": "dwinkler1", - "repo": "nvimConfig", - "type": "github" - } - }, - "plugins-cmp-pandoc-references": { - "flake": false, - "locked": { - "lastModified": 1743491695, - "narHash": "sha256-XsdneGNJzmRBggk8lz9JNDQYk7wbYfUAF2oZLXzFb9c=", - "owner": "jmbuhr", - "repo": "cmp-pandoc-references", - "rev": "130eae4f75029d6495808e0ea4b769fa1ce4c9ac", - "type": "github" - }, - "original": { - "owner": "jmbuhr", - "repo": "cmp-pandoc-references", - "type": "github" - } - }, - "plugins-r": { - "flake": false, - "locked": { - "lastModified": 1769736135, - "narHash": "sha256-T4QgcBL+LCXvrEiRE2JW4jtUKl8DKzFHk8czGUO1jgY=", - "owner": "R-nvim", - "repo": "R.nvim", - "rev": "2701ec64f5485e17c0e057081a9ae2058d776464", - "type": "github" - }, - "original": { - "owner": "R-nvim", - "repo": "R.nvim", - "type": "github" - } - }, - "rixpkgs": { - "locked": { - "lastModified": 1770035835, - "narHash": "sha256-Pi8f3LPTFmG7SZeAJEAamOWly1SZhEofT92uBqS4atY=", - "owner": "rstats-on-nix", - "repo": "nixpkgs", - "rev": "0d3fe7afce51d2126fdccf0b717d8048b90e4781", - "type": "github" - }, - "original": { - "owner": "rstats-on-nix", - "ref": "2026-02-02", - "repo": "nixpkgs", - "type": "github" - } - }, - "root": { - "inputs": { - "fran": "fran", - "nixpkgs": "nixpkgs", - "nvimConfig": "nvimConfig", - "rixpkgs": "rixpkgs" - } - }, - "wrappers": { - "inputs": { - "nixpkgs": [ - "nvimConfig", - "nixpkgs" - ] - }, - "locked": { - "lastModified": 1769745458, - "narHash": "sha256-Fq6THKEiAKx+wWQ4wTg9HvOAyD6i8JkWfHVQDZH7Byo=", - "owner": "BirdeeHub", - "repo": "nix-wrapper-modules", - "rev": "cc5e052dd1e93ae75dc06e3fabf46f0820c272f2", - "type": "github" - }, - "original": { - "owner": "BirdeeHub", - "repo": "nix-wrapper-modules", - "type": "github" - } - } - }, - "root": "root", - "version": 7 -} diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix deleted file mode 100644 index 46b9141..0000000 --- a/templates/ed/flake.nix +++ /dev/null @@ -1,134 +0,0 @@ -{ - description = "Project Editor"; - - outputs = { - self, - nixpkgs, - nvimConfig, - ... - } @ inputs: let - projectSettings = {pkgs}: { - cats = { - clickhouse = false; - gitPlugins = false; - julia = false; - lua = false; - markdown = false; - nix = true; - optional = false; - python = false; - r = false; - }; - - settings = let - # With `replace` packages are replaced otherwise they are merged with base packages - replace = pkgs.lib.mkForce; - in { - lang_packages = { - python = replace ( - (with pkgs.python3Packages; [ - duckdb - polars - ]) - ++ ( - if builtins.pathExists ./python-packages.nix - # p: with p; [ ... ] - then import ./python-packages.nix pkgs.python3Packages - else [] - ) - ); - - r = replace ( - (with pkgs.rpkgs.rPackages; [ - fixest - # pkgs.extraRPackages.musicMetadata - ]) - ++ ( - if builtins.pathExists ./r-packages.nix - # p: with p.rPackages; [ ... ] - then import ./r-packages.nix pkgs.rpkgs - else [] - ) - ); - - julia = replace ([ - "StatsBase" - ] - ++ ( - if builtins.pathExists ./julia-packages.nix - # [ ... ] - then import ./julia-packages.nix - else [] - )); - }; - colorscheme = "kanagawa"; - background = "dark"; - wrapRc = true; - }; - binName = "vv"; - - env = { - IS_PROJECT_EDITOR = "1"; - R_LIBS_USER = "./.nvimcom"; - }; - - extraPackages = with pkgs; [ - cowsay - ]; - - specs.extraLua = let - name = builtins.baseNameOf (builtins.toString ./.); - in { - data = pkgs.vimPlugins.mini-notify; - before = ["INIT_MAIN"]; - config = '' - require("mini.notify").setup() - vim.notify = MiniNotify.make_notify() - vim.notify("Welcome to ${name}!") - ''; - }; - }; - - systems = nixpkgs.lib.systems.flakeExposed; - forAllSystems = nixpkgs.lib.genAttrs systems; - overlays = [inputs.nvimConfig.overlays.dependencies]; - in { - packages = forAllSystems (system: let - pkgs = import nixpkgs {inherit system overlays;}; - baseNvim = nvimConfig.packages.${system}.default; - - nvim = (baseNvim.eval (projectSettings {inherit pkgs;})).config.wrapper; - default = nvim; - in { - default = nvim; - }); - - devShells = forAllSystems (system: let - pkgs = import nixpkgs {inherit system overlays;}; - nv = self.packages.${system}.default; - in { - default = pkgs.mkShell { - packages = [nv pkgs.updateR]; - }; - }); - }; - - inputs = { - nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.11"; - rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs"; - fran = { - url = "github:dwinkler1/fran"; - inputs = { - nixpkgs.follows = "rixpkgs"; - }; - }; - nvimConfig = { - url = "github:dwinkler1/nvimConfig"; - inputs = { - rixpkgs.follows = "rixpkgs"; - nixpkgs.follows = "nixpkgs"; - fran.follows = "fran"; - }; - }; - }; -} diff --git a/templates/rde/.envrc b/templates/rde/.envrc index e66fd99..3550a30 100644 --- a/templates/rde/.envrc +++ b/templates/rde/.envrc @@ -1,3 +1 @@ -export DIRENV_WARN_TIMEOUT=20s - use flake diff --git a/templates/rde/README.md b/templates/rde/README.md deleted file mode 100644 index d3a4cbf..0000000 --- a/templates/rde/README.md +++ /dev/null @@ -1,378 +0,0 @@ -# Research Development Environment (RDE) Template - -A modular Nix flake template for reproducible research environments with support for R, Python, and Julia. Designed for data science, statistical analysis, and computational research. - -## Features - -- đŸ”Ŧ **Multi-language support**: R, Python, Julia with integrated tooling -- đŸ“Ļ **Reproducible**: Nix ensures consistent environments across machines -- 🎨 **Neovim-based**: Powerful editor with LSP, completion, and more -- 📊 **Research-focused**: Pre-configured for data analysis workflows -- 🔧 **Modular**: Enable only the languages you need -- 📝 **Documented**: Comprehensive inline documentation - -## Quick Start - -### Installation - -```bash -# Initialize a new project with this template -nix flake init -t github:dwinkler1/np#rde - -# Enter the development environment -nix develop - -# Or use direnv for automatic activation -echo "use flake" > .envrc -direnv allow -``` - -### First Steps - -```bash -# Initialize project structure (creates directories, git repo) -p-initProject - -# Enable Python (if needed) -# Edit flake.nix: set enabledLanguages.python = true - -# Initialize Python project -p-initPython - -# Update all dependencies -p-updateDeps -``` - -## Structure - -The template is organized into several directories for better maintainability: - -``` -templates/rde/ -├── flake.nix # Main flake configuration (261 lines) -├── README.md # This file -├── overlays/ # Nix overlays for packages -│ ├── r.nix # R packages configuration -│ ├── python.nix # Python packages configuration -│ ├── rix.nix # rstats-on-nix integration -│ ├── theme.nix # Neovim theme configuration -│ └── project-scripts.nix # Project initialization scripts -├── hosts/ # Host/command configurations -│ ├── default.nix # Merges all host configs -│ ├── python.nix # Python commands (marimo, ipy, etc.) -│ ├── julia.nix # Julia commands (jl, pluto, etc.) -│ ├── r.nix # R commands -│ └── utils.nix # Utility commands (initProject, etc.) -├── lib/ # Helper functions -│ ├── shell-hook.nix # Dev shell welcome message -│ └── mini-notify-config.lua # Neovim notification filtering -└── scripts/ # Shell scripts - ├── initPython.sh # Initialize Python project - ├── initProject.sh # Initialize project structure - ├── updateDeps.sh # Update all dependencies - └── activateDevenv.sh # Activate devenv shell -``` - -## Configuration - -Edit the `config` section in `flake.nix` to customize your environment: - -### Basic Settings - -```nix -config = rec { - # Name for your project commands (e.g., myproject-r, myproject-py) - defaultPackageName = "p"; - - # Enable/disable language support - enabledLanguages = { - julia = false; # Julia with Pluto notebooks - python = false; # Python with uv package manager - r = true; # R with tidyverse and friends - }; - - # Additional features - enabledPackages = { - gitPlugins = enabledLanguages.r; # R.nvim plugin - devenv = false; # Additional dev environment - }; - - # Neovim color scheme - theme = rec { - colorscheme = "kanagawa"; # cyberdream, onedark, tokyonight, kanagawa - background = "dark"; # dark or light - }; -}; -``` - -### Language-Specific Configuration - -#### R Configuration - -Edit `overlays/r.nix` to add/remove R packages: - -```nix -reqPkgs = with final.rpkgs.rPackages; [ - tidyverse # Add your packages here - data_table - # ... more packages -]; -``` - -Or create `r-packages.nix` in your project: - -```nix -rpkgs: with rpkgs.rPackages; [ - ggplot2 - dplyr -] -``` - -#### Python Configuration - -Python packages are managed via `uv`: - -```bash -# Add packages to your project -uv add numpy pandas matplotlib - -# Or edit pyproject.toml directly -``` - -#### Julia Configuration - -Julia packages use the built-in package manager: - -```bash -# In Julia REPL (p-jl) -using Pkg -Pkg.add("DataFrames") -``` - -## Available Commands - -Commands are prefixed with your `defaultPackageName` (default: `p`). - -### Editor - -- `p` or `p-pvim`: Launch Neovim -- `p-g`: Launch Neovide (GUI) - -### R (when enabled) - -- `p-r`: R console with pre-loaded packages -- Includes: tidyverse, data.table, languageserver, quarto - -### Python (when enabled) - -- `p-py`: Python interpreter -- `p-ipy`: IPython REPL (enhanced interactive shell) -- `p-marimo`: Marimo notebooks (reactive notebooks) -- `p-initPython`: Initialize Python project with uv - -### Julia (when enabled) - -- `p-jl`: Julia REPL with project environment -- `p-pluto`: Pluto.jl notebooks (reactive notebooks) -- `p-initJl`: Initialize Julia project - -### Utilities - -- `p-initProject`: Create project directory structure -- `p-updateDeps`: Update all dependencies (R, Python, Julia, flake) - -## Project Workflow - -### 1. Initialize Project - -```bash -# Create standardized directory structure -p-initProject - -# Creates: -# - data/{raw,processed,interim}/ -# - docs/ -# - figures/ -# - tables/ -# - src/{analysis,data_prep,explore,utils}/ -# - .gitignore -# - README.md -``` - -### 2. Set Up Language Environment - -**For R:** -```bash -# R is enabled by default -# Just start using it -p-r -``` - -**For Python:** -```bash -# 1. Enable in flake.nix -# 2. Initialize project -p-initPython -# 3. Add packages -uv add numpy pandas scikit-learn -``` - -**For Julia:** -```bash -# 1. Enable in flake.nix -# 2. Initialize project -p-initJl -# 3. Packages are managed in Julia REPL -``` - -### 3. Development - -```bash -# Start Neovim -p - -# Or use notebooks -p-marimo # Python notebooks -p-pluto # Julia notebooks - -# R scripts work with p (Neovim has R support) -``` - -### 4. Keep Dependencies Updated - -```bash -# Update everything at once -p-updateDeps - -# This updates: -# - R packages (rixpkgs snapshot) -# - Python packages (via uv) -# - Julia packages (via Pkg) -# - Flake inputs -``` - -## Benefits of This Structure - -1. **Modularity**: Each component is in its own file, making it easier to understand and modify -2. **Maintainability**: Changes to one language or feature don't affect others -3. **Readability**: Main flake.nix is ~261 lines instead of 688 (62% reduction) -4. **Reusability**: Individual modules can be easily reused or replaced -5. **Testability**: Smaller files are easier to test and debug -6. **Documentation**: Comprehensive inline comments explain how everything works - -## Extending the Template - -### Add New R Packages - -**System-wide** (edit `overlays/r.nix`): -```nix -reqPkgs = with final.rpkgs.rPackages; [ - tidyverse - yourNewPackage # Add here -]; -``` - -**Project-specific** (create `r-packages.nix`): -```nix -rpkgs: with rpkgs.rPackages; [ - projectSpecificPackage -] -``` - -### Add New Python Packages - -```bash -uv add package-name -``` - -### Add New Commands - -Edit the appropriate file in `hosts/`: -- `hosts/python.nix` - Python commands -- `hosts/julia.nix` - Julia commands -- `hosts/r.nix` - R commands -- `hosts/utils.nix` - General utilities - -### Add New Scripts - -1. Create script in `scripts/` -2. Add to `overlays/project-scripts.nix` -3. Add to appropriate host file - -### Customize Neovim - -The template uses a pre-configured Neovim (nixCats). To customize: -- Edit theme in `config.theme` section -- Add plugins in `flake.nix` categoryDefinitions -- Modify LSP settings in `categoryDefinitions.lspsAndRuntimeDeps` - -## Troubleshooting - -### Nix Build Fails - -```bash -# Update flake inputs -nix flake update - -# Clear cache -nix-collect-garbage -``` - -### Python Packages Not Found - -```bash -# Sync environment -uv sync - -# Or re-initialize -p-initPython -``` - -### R Packages Not Available - -```bash -# Update R snapshot -p-updateDeps - -# Or check overlays/r.nix for package name -``` - -## CI and Testing - -This template is automatically tested on every change to ensure all functionality works correctly. The CI workflow (`.github/workflows/check.yml`) runs comprehensive tests including: - -### Default Configuration Tests (R enabled) -- ✅ Template builds successfully -- ✅ Flake check passes -- ✅ Development shell enters without errors -- ✅ Neovim launches in headless mode -- ✅ R console is available and runs code -- ✅ Utility commands (initProject, updateDeps) are available -- ✅ Project structure creation works correctly - -### Python Configuration Tests -- ✅ Template builds with Python enabled -- ✅ Python commands (p-py, p-ipy, p-initPython) are available -- ✅ Python interpreter launches and executes code - -### Julia Configuration Tests -- ✅ Template builds with Julia enabled -- ✅ Julia commands (p-jl, p-initJl) are available -- ✅ Julia REPL launches and executes code - -The CI runs on: -- Every push to template files (`.nix`, `.sh`, `.lua`, `flake.lock`) -- Every pull request affecting the template -- Manual dispatch for testing - -This ensures that users can confidently use the template knowing that all advertised functionality has been verified. - -## Usage - -Use this template with: - -```bash -nix flake init -t github:dwinkler1/np#rde -``` - -Then run `direnv allow` or enter the dev shell with `nix develop`. diff --git a/templates/rde/flake.lock b/templates/rde/flake.lock index 7617db3..90be7b2 100644 --- a/templates/rde/flake.lock +++ b/templates/rde/flake.lock @@ -1,53 +1,24 @@ { "nodes": { - "fran": { - "inputs": { - "nixpkgs": [ - "rixpkgs" - ] - }, - "locked": { - "lastModified": 1771133455, - "narHash": "sha256-DvHfkW3DctWV+YnigY4+5Stn9NgI38JqR2IScXDX8z8=", - "owner": "dwinkler1", - "repo": "fran", - "rev": "68b189ab981adae06590ee1929a70c8b86afd2b8", - "type": "github" - }, - "original": { - "owner": "dwinkler1", - "repo": "fran", - "type": "github" - } - }, "nixCats": { "inputs": { - "fran": [ - "fran" - ], "nixCats": "nixCats_2", "nixpkgs": [ "nixpkgs" ], - "plugins-cmp-pandoc-references": [ - "plugins-cmp-pandoc-references" - ], - "plugins-cmp-r": [ - "plugins-cmp-r" - ], - "plugins-r": [ - "plugins-r" - ], + "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references", + "plugins-cmp-r": "plugins-cmp-r", + "plugins-r": "plugins-r", "rixpkgs": [ "rixpkgs" ] }, "locked": { - "lastModified": 1770172580, - "narHash": "sha256-l/fKPLdKxq7PLRbExDxsS4Esel4yos/NFJOFcDpsm2E=", + "lastModified": 1756388494, + "narHash": "sha256-Y06QA/XZ8+4nmjwZfFUWMf80slfIxOnylLn8GCmXjew=", "owner": "dwinkler1", "repo": "nixCatsConfig", - "rev": "98079a0844e53afd0c593c8f4d1ee5381baf36f0", + "rev": "c1aa16d681ac53298477e78097fefabdaacc16a7", "type": "github" }, "original": { @@ -58,11 +29,11 @@ }, "nixCats_2": { "locked": { - "lastModified": 1769085828, - "narHash": "sha256-TjhFIAtS628+/r3IuYWPcNa++mUMMDDG8PbSfFHXBiA=", + "lastModified": 1756094250, + "narHash": "sha256-Bkghd2NdQqQfKwSftABMDjnfRMFTJXA/XvvfKVonV/Q=", "owner": "BirdeeHub", "repo": "nixCats-nvim", - "rev": "43fbf4d12b0a613f1a792503da4bb2bf270173c7", + "rev": "7496b06144a15e44301aacea31c3e1ccdb81546e", "type": "github" }, "original": { @@ -73,16 +44,16 @@ }, "nixpkgs": { "locked": { - "lastModified": 1771043024, - "narHash": "sha256-O1XDr7EWbRp+kHrNNgLWgIrB0/US5wvw9K6RERWAj6I=", + "lastModified": 1756288264, + "narHash": "sha256-Om8adB1lfkU7D33VpR+/haZ2gI5r3Q+ZbIPzE5sYnwE=", "owner": "nixos", "repo": "nixpkgs", - "rev": "3aadb7ca9eac2891d52a9dec199d9580a6e2bf44", + "rev": "ddd1826f294a0ee5fdc198ab72c8306a0ea73aa9", "type": "github" }, "original": { "owner": "nixos", - "ref": "nixos-25.11", + "ref": "nixpkgs-unstable", "repo": "nixpkgs", "type": "github" } @@ -103,14 +74,46 @@ "type": "github" } }, + "plugins-cmp-pandoc-references_2": { + "flake": false, + "locked": { + "lastModified": 1743491695, + "narHash": "sha256-XsdneGNJzmRBggk8lz9JNDQYk7wbYfUAF2oZLXzFb9c=", + "owner": "jmbuhr", + "repo": "cmp-pandoc-references", + "rev": "130eae4f75029d6495808e0ea4b769fa1ce4c9ac", + "type": "github" + }, + "original": { + "owner": "jmbuhr", + "repo": "cmp-pandoc-references", + "type": "github" + } + }, "plugins-cmp-r": { "flake": false, "locked": { - "lastModified": 1764700377, - "narHash": "sha256-xb7VFWM/BKAkN7fg62y8n618t2qkQjdYbPwhBhLJwtk=", + "lastModified": 1746709841, + "narHash": "sha256-TwmLSILu1H3RyRivCQlbsgUN4dsEqO1E8Hx71N/lFws=", "owner": "R-nvim", "repo": "cmp-r", - "rev": "70bfe8f4c062acc10266e24825439c009a0b1b89", + "rev": "602f399c4efde01147cadfebcc884b7aa154f8b7", + "type": "github" + }, + "original": { + "owner": "R-nvim", + "repo": "cmp-r", + "type": "github" + } + }, + "plugins-cmp-r_2": { + "flake": false, + "locked": { + "lastModified": 1746709841, + "narHash": "sha256-TwmLSILu1H3RyRivCQlbsgUN4dsEqO1E8Hx71N/lFws=", + "owner": "R-nvim", + "repo": "cmp-r", + "rev": "602f399c4efde01147cadfebcc884b7aa154f8b7", "type": "github" }, "original": { @@ -122,44 +125,54 @@ "plugins-r": { "flake": false, "locked": { - "lastModified": 1763419698, - "narHash": "sha256-GUnRsFF6MlUcFfEsNmm0zXauG3+Pf22OOJNXszOvs+M=", + "lastModified": 1755532199, + "narHash": "sha256-mb8HCaMasPUP9JZUkH1sPrtdbhM2HMUkJEKDsRt6wTs=", "owner": "R-nvim", "repo": "R.nvim", - "rev": "b40fca202f26be4c83875dae489c655f2b834df6", + "rev": "fd992e1c13ad3df794a30af2e937b994bf7bf4db", + "type": "github" + }, + "original": { + "owner": "R-nvim", + "repo": "R.nvim", + "type": "github" + } + }, + "plugins-r_2": { + "flake": false, + "locked": { + "lastModified": 1755532199, + "narHash": "sha256-mb8HCaMasPUP9JZUkH1sPrtdbhM2HMUkJEKDsRt6wTs=", + "owner": "R-nvim", + "repo": "R.nvim", + "rev": "fd992e1c13ad3df794a30af2e937b994bf7bf4db", "type": "github" }, "original": { "owner": "R-nvim", - "ref": "v0.99.1", "repo": "R.nvim", "type": "github" } }, "rixpkgs": { "locked": { - "lastModified": 1770035835, - "narHash": "sha256-Pi8f3LPTFmG7SZeAJEAamOWly1SZhEofT92uBqS4atY=", - "owner": "rstats-on-nix", - "repo": "nixpkgs", - "rev": "0d3fe7afce51d2126fdccf0b717d8048b90e4781", - "type": "github" + "lastModified": 1754915244, + "narHash": "sha256-WtdFq/HbvAgq03AMhSAJW35go6R5bqhGNf2KBzXqH2U=", + "type": "tarball", + "url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-08-11.tar.gz" }, "original": { - "owner": "rstats-on-nix", - "ref": "2026-02-02", - "repo": "nixpkgs", - "type": "github" + "type": "tarball", + "url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-08-11.tar.gz" } }, "root": { "inputs": { - "fran": "fran", "nixCats": "nixCats", "nixpkgs": "nixpkgs", - "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references", - "plugins-cmp-r": "plugins-cmp-r", - "plugins-r": "plugins-r", + "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references_2", + "plugins-cmp-r": "plugins-cmp-r_2", + "plugins-r": "plugins-r_2", "rixpkgs": "rixpkgs" } } diff --git a/templates/rde/flake.nix b/templates/rde/flake.nix index a6aa9a3..97f893e 100644 --- a/templates/rde/flake.nix +++ b/templates/rde/flake.nix @@ -1,6 +1,27 @@ { description = "New Project"; - + inputs = { + rixpkgs.url = "https://github.com/rstats-on-nix/nixpkgs/archive/2025-08-11.tar.gz"; + nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-unstable"; + nixCats = { + url = "github:dwinkler1/nixCatsConfig"; + inputs.nixpkgs.follows = "nixpkgs"; + inputs.rixpkgs.follows = "rixpkgs"; + }; + ## Git Plugins + "plugins-r" = { + url = "github:R-nvim/R.nvim"; + flake = false; + }; + "plugins-cmp-r" = { + url = "github:R-nvim/cmp-r"; + flake = false; + }; + "plugins-cmp-pandoc-references" = { + url = "github:jmbuhr/cmp-pandoc-references"; + flake = false; + }; + }; outputs = { self, nixpkgs, @@ -18,7 +39,7 @@ enabledLanguages = { julia = false; python = false; - r = true; + r = false; }; ## Enable packages enabledPackages = { @@ -26,52 +47,199 @@ ### Always enable when R is enabled ### You can use your own R installation and just enable the plugin gitPlugins = enabledLanguages.r; - ## Create additional dev shells in the project - devenv = false; - }; - theme = rec { - ## set colortheme and background here - ### "cyberdream", "onedark", and "tokyonight" are pre-installed - colorscheme = "kanagawa"; - background = "dark"; - ## Add other colortheme packages and config here - ## The default is a best guess - extraColorschemePackage = rec { - name = colorscheme; - extraLua = '' - vim.notify("Loading ${colorscheme} with extra config...") - require('${name}').setup({ - commentStyle = {italic = false}, - keywordStyle = {italic = false}, - theme = 'dragon' - }) - ''; - plugin = name + "-nvim"; - }; }; }; + # R packages + rixOverlay = final: prev: {rpkgs = inputs.rixpkgs.legacyPackages.${prev.system};}; + rOverlay = final: prev: let + reqPkgs = with final.rpkgs.rPackages; [ + broom + data_table + janitor + languageserver + reprex + styler + tidyverse + (buildRPackage { + name = "nvimcom"; + src = inputs.plugins-r; + sourceRoot = "source/nvimcom"; + buildInputs = with prev.rpkgs; [ + R + stdenv.cc.cc + gnumake + ]; + propagatedBuildInputs = []; + }) + ]; + in { + quarto = final.rpkgs.quarto.override {extraRPackages = reqPkgs;}; + rWrapper = final.rpkgs.rWrapper.override {packages = reqPkgs;}; + }; + + # Python packages + pythonOverlay = final: prev: { + python = prev.python3.withPackages (pyPackages: + with pyPackages; [ + requests + ]); + }; ################################### ## âŦ†ī¸ BASIC CONFIG ABOVE HERE âŦ†ī¸ ## ################################### - # Import overlays from separate files - # Each overlay adds specific packages or configurations - rOverlay = import ./overlays/r.nix; - pythonOverlay = import ./overlays/python.nix; - rixOverlay = import ./overlays/rix.nix inputs; - extraPkgOverlay = import ./overlays/theme.nix config; - projectScriptsOverlay = import ./overlays/project-scripts.nix config; + projectScriptsOverlay = final: prev: let + initPython = '' + #!/usr/bin/env bash + set -euo pipefail + if [[ ! -f "pyproject.toml" ]]; then + echo "🐍 Initializing UV project..." + uv init + echo "đŸ“Ļ Adding IPython and Marimo..." + uv add ipython + uv add marimo + echo "--------------------------------------------------------------------------" + echo "✅ Python project initialized!" + echo "run 'uv add PACKAGE' to add more python packages." + echo "--------------------------------------------------------------------------" + else + echo "--------------------------------------------------------------------------" + echo "🔄 Existing Python project detected." + echo "đŸ“Ļ Ensuring IPython and Marimo are installed..." + uv add ipython + uv add marimo + echo "Run '${config.defaultPackageName}-updateDeps' to update dependencies." + echo "--------------------------------------------------------------------------" + fi + ''; - supportedSystems = [ - "x86_64-linux" - "aarch64-linux" - "aarch64-darwin" - ]; - forSystems = nixpkgs.lib.genAttrs supportedSystems; + initProjectScript = '' + #!/usr/bin/env bash + set -euo pipefail - # Main package configuration - # This configures the Neovim environment with language support + PROJECT_NAME="''${1:-${config.defaultPackageName}}" + + echo "🚀 Setting up project: $PROJECT_NAME" + + # Create directory structure + directories=( + "data/raw" + "data/processed" + "data/interim" + "docs" + "figures" + "tables" + "src/analysis" + "src/data_prep" + "src/explore" + "src/utils" + ) + + for dir in "''${directories[@]}"; do + if [[ ! -d "$dir" ]]; then + mkdir -p "$dir" + echo "✓ Created $dir/" + fi + done + + # Create essential files + if [[ ! -f "README.md" ]]; then + cat > README.md << 'EOF' + # RDE + + ## Project Structure + - `data/`: Data files (gitignored) + - `docs/`: Documentation + - `figures/`: Output figures + - `tables/`: Output tables + - `src/`: Source code + + EOF + fi + + # Initialize git + if [[ ! -d ".git" ]]; then + git init + echo "✓ Initialized Git repository and added: flake.nix, flake.lock" + fi + # Check if files are already staged/tracked before adding + if ! git diff --cached --name-only | grep -q "flake.nix\|flake.lock" && + ! git ls-files --error-unmatch flake.nix flake.lock >/dev/null 2>&1; then + echo "✓ Adding flake.nix, flake.lock to Git repository" + git add flake.nix flake.lock + else + echo "✓ flake.nix, flake.lock already tracked/staged in Git" + fi + # Create .gitignore + if [[ ! -f ".gitignore" ]]; then + cat > .gitignore << 'EOF' + # Data files + data/ + *.csv + *.docx + *.xlsx + *.parquet + + # R specific + .Rproj.user/ + .Rhistory + .RData + .Ruserdata + *.Rproj + .Rlibs/ + + # Python specific + __pycache__/ + *.pyc + .pytest_cache/ + .venv/ + + # Jupyter + .ipynb_checkpoints/ + + # IDE + .vscode/ + .idea/ + + # OS + .DS_Store + Thumbs.db + EOF + fi + + echo "✅ Project setup completed successfully!" + ''; + + updateDepsScript = '' + #!/usr/bin/env bash + set -euo pipefail + + echo "🔄 Updating project dependencies..." + + if [[ -f "flake.lock" ]]; then + nix flake update + echo "✅ Flake inputs updated" + fi + + if [[ -f "pyproject.toml" ]]; then + uv sync --upgrade + echo "✅ Python dependencies updated" + fi + + if [[ -f "Project.toml" ]]; then + ${config.defaultPackageName}-jl -e "using Pkg; Pkg.update()" + echo "✅ Julia dependencies updated" + fi + + echo "🎉 All dependencies updated!" + ''; + in { + initPython = prev.writeShellScriptBin "initPython" initPython; + initProject = prev.writeShellScriptBin "initProject" initProjectScript; + updateDeps = prev.writeShellScriptBin "updateDeps" updateDepsScript; + }; + forSystems = nixpkgs.lib.genAttrs nixpkgs.lib.platforms.all; projectConfig = forSystems ( system: let inherit (nixCats) utils; @@ -83,14 +251,11 @@ prev.dependencyOverlays ++ [ (utils.standardPluginOverlay inputs) - extraPkgOverlay rixOverlay - inputs.fran.overlays.default rOverlay pythonOverlay projectScriptsOverlay ]; - categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions ( { pkgs, @@ -101,17 +266,28 @@ mkPlugin, ... } @ packageDef: { - # Language servers and runtime dependencies lspsAndRuntimeDeps = { - project = with pkgs; []; - julia = with pkgs; [julia-bin]; - python = with pkgs; [python nodejs basedpyright uv]; - r = with pkgs; [rWrapper quarto air-formatter]; + project = with pkgs; [ + ]; + julia = with pkgs; [ + julia-bin + ]; + python = with pkgs; [ + python + nodejs + pyright + uv + ]; + r = with pkgs; [ + rWrapper + quarto + air-formatter + ]; }; - # Plugins that load automatically startupPlugins = { - project = with pkgs.vimPlugins; [pkgs.extraTheme]; + project = with pkgs.vimPlugins; [ + ]; gitPlugins = with pkgs.neovimPlugins; [ { plugin = r; @@ -120,44 +296,63 @@ ]; }; - # Plugins that load on-demand optionalPlugins = { - project = with pkgs.vimPlugins; []; + project = with pkgs.vimPlugins; [ + ]; gitPlugins = with pkgs.neovimPlugins; [ cmp-r cmp-pandoc-references ]; }; - - # Lua code to run before main config optionalLuaPreInit = { project = [ - (builtins.readFile ./lib/mini-notify-config.lua) + '' + local predicate = function(notif) + if not (notif.data.source == "lsp_progress" and notif.data.client_name == "lua_ls") then + return true + end + -- Filter out some LSP progress notifications from 'lua_ls' + return notif.msg:find("Diagnosing") == nil and notif.msg:find("semantic tokens") == nil + end + local custom_sort = function(notif_arr) + return MiniNotify.default_sort(vim.tbl_filter(predicate, notif_arr)) + end + require("mini.notify").setup({ content = { sort = custom_sort } }) + vim.notify = MiniNotify.make_notify() + '' ]; }; - - # Lua code to run after main config optionalLuaAdditions = { - project = ["vim.notify('Project loaded: ${name}')"]; + project = [ + "vim.notify('Project loaded: ${name}')" + ]; }; - sharedLibraries = { - project = {}; + project = { + }; }; - # Environment variables for each language environmentVariables = { - project = {}; - julia = {JULIA_NUM_THREADS = "auto";}; + project = { + }; + julia = { + JULIA_NUM_THREADS = "auto"; + }; python = { + # Prevent uv from managing Python downloads UV_PYTHON_DOWNLOADS = "never"; + # Force uv to use nixpkgs Python interpreter UV_PYTHON = pkgs.python.interpreter; }; - r = {R_LIBS_USER = "./.Rlibs";}; + r = { + R_LIBS_USER = "./.Rlibs"; + }; }; extraWrapperArgs = { - python = ["--unset PYTHONPATH"]; + python = [ + "--unset PYTHONPATH" + ]; }; } ); @@ -165,8 +360,6 @@ packageDefinitions = prev.packageDefinitions // { - # Main package definition - # This creates the command with configured languages and tools "${config.defaultPackageName}" = utils.mergeCatDefs prev.packageDefinitions.n ( { pkgs, @@ -176,19 +369,133 @@ settings = { suffix-path = false; suffix-LD = false; + # your alias may not conflict with your other packages. aliases = ["pvim"]; - # Import all host commands from hosts/ directory - hosts = import ./hosts config pkgs; + hosts = { + g = { + enable = true; + path = { + value = "${pkgs.neovide}/bin/neovide"; + args = [ + "--add-flags" + "--neovim-bin ${name}" + ]; + }; + }; + m = let + marimoInit = '' + set -euo pipefail + if [[ ! -f "pyproject.toml" ]]; then + echo "🐍 Initializing UV project..." + uv init + echo "đŸ“Ļ Adding Marimo..." + uv add marimo + echo "--------------------------------------------------------------------------" + echo "✅ Python project initialized!" + echo "run 'uv add PACKAGE' to add more python packages." + echo "--------------------------------------------------------------------------" + else + echo "--------------------------------------------------------------------------" + echo "🔄 Syncing existing project..." + uv sync + echo "🐍 Launching Marimo..." + echo "--------------------------------------------------------------------------" + fi + ''; + in { + enable = config.enabledLanguages.python; + path = { + value = "${pkgs.uv}/bin/uv"; + args = [ + "--run" + "${marimoInit}" + "--add-flags" + "run marimo edit \"$@\"" + ]; + }; + }; + py = let + ipythonInit = '' + set -euo pipefail + if [[ ! -f "pyproject.toml" ]]; then + echo "🐍 Initializing UV project..." + uv init + echo "đŸ“Ļ Adding IPython..." + uv add ipython + echo "--------------------------------------------------------------------------" + echo "✅ Python project initialized!" + echo "run 'uv add PACKAGE' to add more python packages." + echo "--------------------------------------------------------------------------" + else + echo "--------------------------------------------------------------------------" + echo "🔄 Syncing existing project..." + echo "đŸ“Ļ Ensuring IPython is installed..." + uv add ipython + uv sync + echo "🐍 Launching IPython..." + echo "--------------------------------------------------------------------------" + fi + ''; + in { + enable = config.enabledLanguages.python; + path = { + value = "${pkgs.uv}/bin/uv"; + args = [ + "--run" + "${ipythonInit}" + "--add-flags" + "run ipython \"$@\"" + ]; + }; + }; + jl = { + enable = config.enabledLanguages.julia; + path = { + value = "${pkgs.julia-bin}/bin/julia"; + args = ["--add-flags" "--project=."]; + }; + }; + initJl = { + enable = config.enabledLanguages.julia; + path = { + value = "${pkgs.julia-bin}/bin/julia"; + args = ["--add-flags" "--project=. -e 'using Pkg; Pkg.instantiate()'"]; + }; + }; + r = { + enable = config.enabledLanguages.r; + path = { + value = "${pkgs.rWrapper}/bin/R"; + args = ["--add-flags" "--no-save --no-restore"]; + }; + }; + initPython = { + enable = config.enabledLanguages.python; + path.value = "${pkgs.initPython}/bin/initPython"; + }; + initProject = { + enable = true; + path = { + value = "${pkgs.initProject}/bin/initProject"; + }; + }; + updateDeps = { + enable = true; + path = { + value = "${pkgs.updateDeps}/bin/updateDeps"; + }; + }; + node.enable = true; + perl.enable = true; + ruby.enable = true; + }; }; - # Enable/disable features based on config categories = { julia = config.enabledLanguages.julia; python = config.enabledLanguages.python; r = config.enabledLanguages.r; project = true; gitPlugins = config.enabledPackages.gitPlugins; - background = config.theme.background; - colorscheme = config.theme.colorscheme; }; } ); @@ -199,68 +506,41 @@ ); in { packages = projectConfig; - # Development shell configuration devShells = forSystems (system: let pkgs = import nixpkgs {inherit system;}; - # Language-specific packages that should be available in shell - languagePackages = with pkgs; - [] - ++ (if config.enabledLanguages.r then [quarto] else []) - ++ (if config.enabledLanguages.python then [uv] else []) - ++ (if config.enabledLanguages.julia then [] else []); in { - default = pkgs.mkShell { - name = config.defaultPackageName; - packages = [projectConfig.${system}.default] ++ languagePackages; - inputsFrom = []; - # Welcome message when entering the shell - shellHook = import ./lib/shell-hook.nix config pkgs; - }; + default = let + shellCmds = pkgs.lib.concatLines (pkgs.lib.filter (cmd: cmd != "") [ + (pkgs.lib.optionalString config.enabledLanguages.r " - ${config.defaultPackageName}-r: Launch R console") + (pkgs.lib.optionalString config.enabledLanguages.julia " - ${config.defaultPackageName}-jl: Launch Julia REPL") + (pkgs.lib.optionalString config.enabledLanguages.julia " - ${config.defaultPackageName}-initJl: Init existing Julia project") + (pkgs.lib.optionalString config.enabledLanguages.python " - ${config.defaultPackageName}-m: Launch Marimo notebook") + (pkgs.lib.optionalString config.enabledLanguages.python " - ${config.defaultPackageName}-py: Launch IPython REPL") + (pkgs.lib.optionalString config.enabledLanguages.python " - ${config.defaultPackageName}-initPython: Init python project") + " " + "To adjust options run: ${config.defaultPackageName} flake.nix" + ]); + in + pkgs.mkShell { + name = config.defaultPackageName; + packages = [projectConfig.${system}.default]; + inputsFrom = []; + shellHook = '' + echo "" + echo "==========================================================================" + echo "đŸŽ¯ ${config.defaultPackageName} Development Environment" + echo "---" + echo "📝 Run '${config.defaultPackageName}-initProject' to set up project structure" + echo "🔄 Run '${config.defaultPackageName}-updateDeps' to update all dependencies" + echo "---" + echo "🚀 Available commands:" + echo " - ${config.defaultPackageName}: Launch Neovim" + echo " - ${config.defaultPackageName}-g: Launch Neovide" + echo "${shellCmds}" + echo "==========================================================================" + echo "" + ''; + }; }); }; - inputs = { - rixpkgs.url = "github:rstats-on-nix/nixpkgs/2026-02-02"; - nixpkgs.url = "github:nixos/nixpkgs/nixos-25.11"; - nixCats = { - url = "github:dwinkler1/nixCatsConfig"; - inputs = { - nixpkgs.follows = "nixpkgs"; - rixpkgs.follows = "rixpkgs"; - fran.follows = "fran"; - plugins-cmp-pandoc-references.follows = "plugins-cmp-pandoc-references"; - plugins-cmp-r.follows = "plugins-cmp-r"; - plugins-r.follows = "plugins-r"; - }; - }; - ## Extra R packages - fran = { - url = "github:dwinkler1/fran"; - inputs = { - nixpkgs.follows = "rixpkgs"; - }; - }; - ## Git Plugins - "plugins-r" = { - url = "github:R-nvim/R.nvim/v0.99.1"; - flake = false; - }; - "plugins-cmp-r" = { - url = "github:R-nvim/cmp-r"; - flake = false; - }; - "plugins-cmp-pandoc-references" = { - url = "github:jmbuhr/cmp-pandoc-references"; - flake = false; - }; - }; - nixConfig = { - extra-substituters = [ - "https://rstats-on-nix.cachix.org" - "https://rde.cachix.org" - ]; - extra-trusted-public-keys = [ - "rstats-on-nix.cachix.org-1:vdiiVgocg6WeJrODIqdprZRUrhi1JzhBnXv7aWI6+F0=" - "rde.cachix.org-1:yRxQYM+69N/dVER6HNWRjsjytZnJVXLS/+t/LI9d1D4=" - ]; - }; } diff --git a/templates/rde/hosts/default.nix b/templates/rde/hosts/default.nix deleted file mode 100644 index 9639c8b..0000000 --- a/templates/rde/hosts/default.nix +++ /dev/null @@ -1,27 +0,0 @@ -# Merges all host configurations from separate modules -# -# This file combines host definitions from language-specific modules. -# It serves as the single entry point for all command definitions. -# -# Structure: -# - python.nix: Python commands (marimo, ipy, py, initPython) -# - julia.nix: Julia commands (jl, pluto, initJl) -# - r.nix: R commands (r console) -# - utils.nix: Utility commands (initProject, updateDeps, etc.) -# -# Usage: -# This file is imported in flake.nix: -# hosts = import ./hosts config pkgs; -# -# The merged result provides all commands in a single attribute set. -# Commands are enabled/disabled based on config.enabledLanguages settings. -config: pkgs: let - # Import individual host modules - pythonHosts = import ./python.nix config pkgs; - juliaHosts = import ./julia.nix config pkgs; - rHosts = import ./r.nix config pkgs; - utilsHosts = import ./utils.nix config pkgs; -in - # Merge all hosts into single attribute set - # Later definitions override earlier ones in case of conflicts - pythonHosts // juliaHosts // rHosts // utilsHosts diff --git a/templates/rde/hosts/julia.nix b/templates/rde/hosts/julia.nix deleted file mode 100644 index 1ac861e..0000000 --- a/templates/rde/hosts/julia.nix +++ /dev/null @@ -1,66 +0,0 @@ -# Julia-related host configurations -# -# This module defines all Julia-related commands available in the dev shell. -# Julia is configured with project-local package management. -# -# Available commands (when Julia is enabled): -# - -jl: Launch Julia REPL with project environment -# - -pluto: Launch Pluto.jl notebook server -# - -initJl: Initialize Julia project and install Pluto -# -# How it works: -# - All commands use --project=. to activate local Project.toml -# - JULIA_NUM_THREADS=auto enables multi-threading -# - Packages are managed via Julia's built-in Pkg manager -# -# Project setup: -# 1. Run -initJl to create Project.toml -# 2. Add packages: julia --project=. -e 'using Pkg; Pkg.add("PackageName")' -# 3. Packages are stored in Project.toml and Manifest.toml -# -# Dependencies: julia-bin (configured in flake.nix) -config: pkgs: { - # jl: Julia REPL with project environment - # Activates local Project.toml for package management - # Use Pkg.add("PackageName") to install packages - jl = { - enable = config.enabledLanguages.julia; - path = { - value = "${pkgs.julia-bin}/bin/julia"; - args = ["--add-flags" "--project=."]; - }; - }; - - # initJl: Initialize Julia project - # Creates Project.toml and installs Pluto.jl notebook - # Run this once to set up Julia package management - initJl = { - enable = config.enabledLanguages.julia; - path = { - value = "${pkgs.julia-bin}/bin/julia"; - args = ["--add-flags" "--project=. -e 'using Pkg; Pkg.instantiate(); Pkg.add(\"Pluto\")'"]; - }; - }; - - # pluto: Launch Pluto.jl interactive notebook - # Auto-installs Pluto if not present in Project.toml - # Opens browser with notebook interface - # Notebooks are reactive - cells update automatically - pluto = let - runPluto = '' - import Pkg; import TOML; Pkg.instantiate(); - proj = isfile("Project.toml") ? TOML.parsefile(Base.active_project()) : Dict(); - deps = get(proj, "deps", Dict()); - if !haskey(deps, "Pluto") - Pkg.add("Pluto"); - end - import Pluto; Pluto.run(); - ''; - in { - enable = config.enabledLanguages.julia; - path = { - value = "${pkgs.julia-bin}/bin/julia"; - args = ["--add-flags" "--project=. -e '${runPluto}'"]; - }; - }; -} diff --git a/templates/rde/hosts/python.nix b/templates/rde/hosts/python.nix deleted file mode 100644 index d1c7b16..0000000 --- a/templates/rde/hosts/python.nix +++ /dev/null @@ -1,96 +0,0 @@ -# Python-related host configurations -# -# This module defines all Python-related commands available in the dev shell. -# Each command is configured with enable conditions and execution paths. -# -# Available commands (when Python is enabled): -# - -marimo: Launch Marimo notebook (interactive Python notebooks) -# - -py: Run Python interpreter -# - -ipy: Launch IPython REPL (enhanced interactive shell) -# - -initPython: Initialize Python project with uv -# -# How it works: -# - Commands are enabled based on config.enabledLanguages.python -# - UV (Python package manager) handles project dependencies -# - Each command auto-initializes project if pyproject.toml doesn't exist -# -# Dependencies: uv, python, nodejs, basedpyright (configured in flake.nix) -config: pkgs: { - # Marimo: Interactive notebook environment for Python - # Auto-initializes UV project and installs marimo on first run - marimo = let - marimoInit = '' - set -euo pipefail - if [[ ! -f "pyproject.toml" ]]; then - echo "🐍 Initializing UV project..." - uv init - echo "đŸ“Ļ Adding Marimo..." - uv add marimo - echo "--------------------------------------------------------------------------" - echo "✅ Python project initialized!" - echo "run 'uv add PACKAGE' to add more python packages." - echo "--------------------------------------------------------------------------" - else - echo "--------------------------------------------------------------------------" - echo "🔄 Syncing existing project..." - uv sync - echo "🐍 Launching Marimo..." - echo "--------------------------------------------------------------------------" - fi - uv run marimo edit "$@" - ''; - in { - enable = config.enabledLanguages.python; - path = { - value = "${pkgs.writeShellScriptBin "marimo-wrapper" marimoInit}/bin/marimo-wrapper"; - }; - }; - - # py: Standard Python interpreter - # Direct access to Python REPL for quick experiments - py = { - enable = config.enabledLanguages.python; - path = { - value = "${pkgs.python.interpreter}"; - }; - }; - - # ipy: IPython - Enhanced interactive Python shell - # Features: syntax highlighting, tab completion, magic commands - # Auto-initializes UV project and installs IPython on first run - ipy = let - ipythonInit = '' - set -euo pipefail - if [[ ! -f "pyproject.toml" ]]; then - echo "🐍 Initializing UV project..." - uv init - echo "đŸ“Ļ Adding IPython..." - uv add ipython - echo "--------------------------------------------------------------------------" - echo "✅ Python project initialized!" - echo "run 'uv add PACKAGE' to add more python packages." - echo "--------------------------------------------------------------------------" - else - echo "--------------------------------------------------------------------------" - echo "🔄 Syncing existing project..." - uv sync - echo "🐍 Launching IPython..." - echo "--------------------------------------------------------------------------" - fi - uv run ipython "$@" - ''; - in { - enable = config.enabledLanguages.python; - path = { - value = "${pkgs.writeShellScriptBin "ipy-wrapper" ipythonInit}/bin/ipy-wrapper"; - }; - }; - - # initPython: Initialize Python project - # Creates pyproject.toml and adds IPython and Marimo - # Use this to set up Python tooling in an existing project - initPython = { - enable = config.enabledLanguages.python; - path.value = "${pkgs.initPython}/bin/initPython"; - }; -} diff --git a/templates/rde/hosts/r.nix b/templates/rde/hosts/r.nix deleted file mode 100644 index 21f2030..0000000 --- a/templates/rde/hosts/r.nix +++ /dev/null @@ -1,31 +0,0 @@ -# R-related host configurations -# -# This module defines R-related commands available in the dev shell. -# R is configured with project-local package library and Quarto support. -# -# Available commands (when R is enabled): -# - -r: Launch R console with packages -# -# How it works: -# - Uses rWrapper which includes all packages from overlays/r.nix -# - R_LIBS_USER=./.Rlibs enables project-local package installation -# - --no-save --no-restore ensures clean session startup -# -# Package management: -# - System packages: Edit overlays/r.nix -# - Project packages: Install with install.packages() in R -# - Custom packages: Create r-packages.nix in project root -# -# Dependencies: rWrapper, quarto, air-formatter (configured in flake.nix) -config: pkgs: { - # r: R console with pre-configured packages - # Includes tidyverse, data.table, and other common packages - # Session starts without saving/restoring workspace - r = { - enable = config.enabledLanguages.r; - path = { - value = "${pkgs.rWrapper}/bin/R"; - args = ["--add-flags" "--no-save --no-restore"]; - }; - }; -} diff --git a/templates/rde/hosts/utils.nix b/templates/rde/hosts/utils.nix deleted file mode 100644 index 2071ee0..0000000 --- a/templates/rde/hosts/utils.nix +++ /dev/null @@ -1,90 +0,0 @@ -# Utility and common host configurations -# -# This module defines general-purpose commands and utilities. -# These commands are available regardless of enabled languages. -# -# Available commands: -# - : Launch Neovim editor (default command) -# - -g: Launch Neovide (GUI for Neovim) -# - -initProject: Initialize project directory structure -# - -updateDeps: Update all dependencies (R, Python, Julia, flake) -# - -initDevenv: Initialize devenv project (if enabled) -# - -devenv: Run devenv commands (if enabled) -# - -activateDevenv: Activate devenv shell (if enabled) -# -# Note: node, perl, ruby are also available but have minimal configuration -# -# Dependencies: neovide, devenv (if enabled), project scripts -config: pkgs: { - # g: Neovide - GUI frontend for Neovim - # Provides smooth scrolling, animations, and GUI features - # Automatically connects to the configured Neovim instance - g = { - enable = true; - path = { - value = "${pkgs.neovide}/bin/neovide"; - args = [ - "--add-flags" - "--neovim-bin ${config.defaultPackageName}" - ]; - }; - }; - - # initProject: Initialize research project structure - # Creates standardized directory layout for data analysis - # Sets up: data/, docs/, figures/, tables/, src/ - # Also initializes git repository and .gitignore - initProject = { - enable = true; - path = { - value = "${pkgs.initProject}/bin/initProject"; - }; - }; - - # initDevenv: Initialize devenv project - # Devenv provides additional development environment features - # Only available if config.enabledPackages.devenv = true - initDevenv = { - enable = config.enabledPackages.devenv; - path = { - value = "${pkgs.devenv}/bin/devenv"; - args = ["--add-flags" "init"]; - }; - }; - - # activateDevenv: Activate devenv shell - # Automatically runs when entering dev shell if devenv.nix exists - # Only available if config.enabledPackages.devenv = true - activateDevenv = { - enable = config.enabledPackages.devenv; - path = { - value = "${pkgs.activateDevenv}/bin/activateDevenv"; - }; - }; - - # devenv: Run devenv commands - # Access to full devenv CLI for managing development environments - # Only available if config.enabledPackages.devenv = true - devenv = { - enable = config.enabledPackages.devenv; - path = { - value = "${pkgs.devenv}/bin/devenv"; - }; - }; - - # updateDeps: Update all project dependencies - # Updates: R packages (rixpkgs), Python (uv), Julia (Pkg), flake inputs - # Automatically detects which languages are in use - updateDeps = { - enable = true; - path = { - value = "${pkgs.updateDeps}/bin/updateDeps"; - }; - }; - - # Additional language runtimes with minimal configuration - # These are available but not heavily used by this template - node.enable = true; # Node.js runtime (used by some LSPs) - perl.enable = true; # Perl runtime - ruby.enable = true; # Ruby runtime -} diff --git a/templates/rde/lib/mini-notify-config.lua b/templates/rde/lib/mini-notify-config.lua deleted file mode 100644 index fd258ff..0000000 --- a/templates/rde/lib/mini-notify-config.lua +++ /dev/null @@ -1,42 +0,0 @@ --- Neovim notification configuration using mini.notify --- --- This file configures the mini.notify plugin to filter out verbose LSP messages. --- It reduces noise from the Lua language server during development. --- --- What it does: --- - Sets up mini.notify as the notification handler --- - Filters out "Diagnosing" and "semantic tokens" messages from lua_ls --- - Keeps all other notifications visible --- --- Usage: --- Loaded automatically via flake.nix: --- optionalLuaPreInit.project = [(builtins.readFile ./lib/mini-notify-config.lua)] --- --- Customization: --- - Add more patterns to filter in the predicate function --- - Filter notifications from other LSP servers by client_name --- - Adjust notification display settings in setup() call - --- Predicate function to filter notifications --- Returns true if notification should be shown, false to hide it -local predicate = function(notif) - -- Keep all non-LSP notifications - if not (notif.data.source == "lsp_progress" and notif.data.client_name == "lua_ls") then - return true - end - -- Filter out specific verbose LSP progress notifications from lua_ls - -- These messages are too frequent and not useful during development - return notif.msg:find("Diagnosing") == nil and notif.msg:find("semantic tokens") == nil -end - --- Custom sort function that applies filtering --- Filters notification array before sorting -local custom_sort = function(notif_arr) - return MiniNotify.default_sort(vim.tbl_filter(predicate, notif_arr)) -end - --- Initialize mini.notify with custom configuration -require("mini.notify").setup({ content = { sort = custom_sort } }) - --- Set mini.notify as the default notification handler -vim.notify = MiniNotify.make_notify() diff --git a/templates/rde/lib/shell-hook.nix b/templates/rde/lib/shell-hook.nix deleted file mode 100644 index a4dcdfa..0000000 --- a/templates/rde/lib/shell-hook.nix +++ /dev/null @@ -1,56 +0,0 @@ -# Shell hook configuration -# -# This module generates the welcome message displayed when entering the dev shell. -# It provides information about available commands and how to get started. -# -# The message includes: -# - Project name and welcome banner -# - Quick start instructions (initProject, updateDeps) -# - List of all available commands based on enabled languages -# - Instructions for editing configuration -# -# Commands are conditionally shown based on config.enabledLanguages settings. -# This ensures users only see commands relevant to their configuration. -# -# Usage: -# Imported in flake.nix as: -# shellHook = import ./lib/shell-hook.nix config pkgs; -# -# Generates the help message displayed when entering the dev shell -config: pkgs: let - inherit (config) defaultPackageName enabledLanguages enabledPackages; - - # Build dynamic list of available commands based on enabled languages - # Filters out empty strings for disabled languages - shellCmds = pkgs.lib.concatLines (pkgs.lib.filter (cmd: cmd != "") [ - (pkgs.lib.optionalString enabledLanguages.r " - ${defaultPackageName}-r: Launch R console") - (pkgs.lib.optionalString enabledLanguages.julia " - ${defaultPackageName}-jl: Launch Julia REPL") - (pkgs.lib.optionalString enabledLanguages.julia " - ${defaultPackageName}-pluto: Launch Pluto.jl notebook") - (pkgs.lib.optionalString enabledLanguages.julia " - ${defaultPackageName}-initJl: Init existing Julia project") - (pkgs.lib.optionalString enabledLanguages.python " - ${defaultPackageName}-marimo: Launch Marimo notebook") - (pkgs.lib.optionalString enabledLanguages.python " - ${defaultPackageName}-py: Run python") - (pkgs.lib.optionalString enabledLanguages.python " - ${defaultPackageName}-ipy: Launch IPython REPL") - (pkgs.lib.optionalString enabledLanguages.python " - ${defaultPackageName}-initPython: Init python project") - (pkgs.lib.optionalString enabledPackages.devenv " - ${defaultPackageName}-initDevenv: Init devenv project") - (pkgs.lib.optionalString enabledPackages.devenv " - ${defaultPackageName}-devenv: Run devenv") - " " - "To adjust options run: ${defaultPackageName} flake.nix" - ]); -in '' - echo "" - echo "==========================================================================" - echo "đŸŽ¯ ${defaultPackageName} Development Environment" - echo "---" - echo "📝 Run '${defaultPackageName}-initProject' to set up project structure" - echo "🔄 Run '${defaultPackageName}-updateDeps' to update all dependencies" - echo "---" - echo "🚀 Available commands:" - echo " - ${defaultPackageName}: Launch Neovim" - echo " - ${defaultPackageName}-g: Launch Neovide" - echo "${shellCmds}" - echo "==========================================================================" - echo "" - # Auto-activate devenv shell if devenv.nix exists (can be disabled in config) - ${pkgs.lib.optionalString enabledPackages.devenv "${defaultPackageName}-activateDevenv"} - echo "" -'' diff --git a/templates/rde/overlays/project-scripts.nix b/templates/rde/overlays/project-scripts.nix deleted file mode 100644 index c13ca90..0000000 --- a/templates/rde/overlays/project-scripts.nix +++ /dev/null @@ -1,39 +0,0 @@ -# Project scripts overlay -# -# This overlay wraps shell scripts from the scripts/ directory as Nix packages. -# Scripts are made available as executable commands with the project name prefix. -# -# How it works: -# 1. Reads shell scripts from scripts/ directory -# 2. Substitutes @defaultPackageName@ with actual package name -# 3. Creates executable packages via writeShellScriptBin -# 4. Scripts become available as: - -# -# Available scripts: -# - initPython: Initialize Python project with uv -# - initProject: Set up project directory structure -# - updateDeps: Update all dependencies (R, Python, Julia, flake) -# - activateDevenv: Activate devenv shell if available -# -# Usage: Scripts are automatically available in the dev shell -config: final: prev: let - # Helper function to substitute config placeholders in scripts - # Replaces @defaultPackageName@ with the actual package name from config - substituteScript = scriptPath: - prev.lib.replaceStrings - ["@defaultPackageName@"] - [config.defaultPackageName] - (builtins.readFile scriptPath); -in { - # Python project initialization (creates pyproject.toml, adds packages) - initPython = prev.writeShellScriptBin "initPython" (substituteScript ../scripts/initPython.sh); - - # Project structure setup (creates directories, git repo, .gitignore) - initProject = prev.writeShellScriptBin "initProject" (substituteScript ../scripts/initProject.sh); - - # Update all dependencies (R packages, Python packages, flake inputs) - updateDeps = prev.writeShellScriptBin "updateDeps" (substituteScript ../scripts/updateDeps.sh); - - # Activate devenv environment if devenv.nix exists - activateDevenv = prev.writeShellScriptBin "activateDevenv" (substituteScript ../scripts/activateDevenv.sh); -} diff --git a/templates/rde/overlays/python.nix b/templates/rde/overlays/python.nix deleted file mode 100644 index 7f9c64e..0000000 --- a/templates/rde/overlays/python.nix +++ /dev/null @@ -1,22 +0,0 @@ -# Python packages overlay -# -# This overlay configures the Python environment with essential packages. -# Note: Most Python packages should be managed via uv (pyproject.toml) -# This overlay is for packages needed at the system level. -# -# Usage: -# - Add system-level Python packages to the list below -# - For project-specific packages, use uv (e.g., 'uv add package-name') -# - The Python interpreter is available via pkgs.python -# -# Example additions: -# - numpy, pandas, scipy for scientific computing -# - pytest, black, mypy for development tools -final: prev: { - # Python 3 with system-level packages - python = prev.python3.withPackages (pyPackages: - with pyPackages; [ - requests # HTTP library for making API calls - # Add more system-level packages here - ]); -} diff --git a/templates/rde/overlays/r.nix b/templates/rde/overlays/r.nix deleted file mode 100644 index 255079b..0000000 --- a/templates/rde/overlays/r.nix +++ /dev/null @@ -1,39 +0,0 @@ -# R packages overlay -# -# This overlay configures the R environment with essential packages for data analysis. -# It combines packages from rstats-on-nix (rpkgs) with custom packages. -# -# Usage: -# - Edit the package list below to add/remove R packages -# - Create r-packages.nix in your project root to add custom packages -# - Custom file format: rpkgs: with rpkgs.rPackages; [ package1 package2 ] -# -# The overlay exports: -# - quarto: Quarto with R packages -# - rWrapper: R executable with all packages available -final: prev: let - # Core R packages for data analysis and development - reqPkgs = with final.rpkgs.rPackages; - [ - broom # Tidy model outputs - data_table # Fast data manipulation - janitor # Data cleaning helpers - languageserver # LSP for IDE support - reprex # Reproducible examples - styler # Code formatting - tidyverse # Data science ecosystem - ] - # Additional packages from fran overlay - ++ (with final.extraRPackages; [ - httpgd # HTTP graphics device for interactive plots - ]) - # Import custom R packages from project root if file exists - # Users can create r-packages.nix in their project to add more packages - # Example r-packages.nix: rpkgs: with rpkgs.rPackages; [ ggplot2 dplyr ] - ++ (prev.lib.optional (builtins.pathExists ./r-packages.nix) (import ./r-packages.nix final.rpkgs)); -in { - # Quarto with R support and all required packages - quarto = final.rpkgs.quarto.override {extraRPackages = reqPkgs;}; - # R wrapper with all packages pre-loaded - rWrapper = final.rpkgs.rWrapper.override {packages = reqPkgs;}; -} diff --git a/templates/rde/overlays/rix.nix b/templates/rde/overlays/rix.nix deleted file mode 100644 index 068ec86..0000000 --- a/templates/rde/overlays/rix.nix +++ /dev/null @@ -1,21 +0,0 @@ -# Rix overlay for R packages from rstats-on-nix -# -# This overlay provides access to R packages from the rstats-on-nix project. -# rstats-on-nix maintains snapshots of CRAN packages built with Nix. -# -# Purpose: -# - Provides reproducible R package versions -# - Ensures binary cache availability for faster builds -# - Maintained by the rstats-on-nix community -# -# The rpkgs attribute gives access to: -# - rpkgs.rPackages: All CRAN packages -# - rpkgs.quarto: Quarto publishing system -# - rpkgs.rWrapper: R with package management -# -# Update the R snapshot date in flake.nix inputs section: -# rixpkgs.url = "github:rstats-on-nix/nixpkgs/YYYY-MM-DD" -inputs: final: prev: { - # R packages from rstats-on-nix for the current system - rpkgs = inputs.rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system}; -} diff --git a/templates/rde/overlays/theme.nix b/templates/rde/overlays/theme.nix deleted file mode 100644 index 7410bf0..0000000 --- a/templates/rde/overlays/theme.nix +++ /dev/null @@ -1,30 +0,0 @@ -# Extra theme packages overlay -# -# This overlay configures the Neovim color scheme based on user configuration. -# It transforms the theme config from flake.nix into a Neovim plugin structure. -# -# Usage: -# - Configure theme in flake.nix config.theme section -# - Specify colorscheme name, background (dark/light) -# - Add custom Lua configuration in extraColorschemePackage -# -# The overlay exports: -# - extraTheme: Plugin structure with theme configuration -# -# Built-in themes: cyberdream, onedark, tokyonight, kanagawa -config: final: prev: let - # Transform user theme config into Neovim plugin format - extraTheme = { - # Get the plugin package from nixpkgs - plugin = prev.vimPlugins."${config.theme.extraColorschemePackage.plugin}"; - # Theme name for identification - name = config.theme.extraColorschemePackage.name; - # Lua configuration to run when theme loads - config = { - lua = config.theme.extraColorschemePackage.extraLua; - }; - }; -in { - # Export theme for use in Neovim configuration - inherit extraTheme; -} diff --git a/templates/rde/scripts/activateDevenv.sh b/templates/rde/scripts/activateDevenv.sh deleted file mode 100644 index 8b8113a..0000000 --- a/templates/rde/scripts/activateDevenv.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env bash -set -euo pipefail -if [[ -f "devenv.nix" ]]; then - echo "🚀 Activating devenv environment..." - if ! command -v @defaultPackageName@-devenv &> /dev/null; then - echo "❌ Command '@defaultPackageName@-devenv' not found." - echo "Ensure devenv is properly configured in your environment." - exit 1 - fi - exec @defaultPackageName@-devenv shell -else - echo "❌ No devenv.nix file found in the current directory." - echo "To create one, run '@defaultPackageName@-initDevenv'" - exit 1 -fi diff --git a/templates/rde/scripts/initProject.sh b/templates/rde/scripts/initProject.sh deleted file mode 100644 index ebaf8e8..0000000 --- a/templates/rde/scripts/initProject.sh +++ /dev/null @@ -1,120 +0,0 @@ -#!/usr/bin/env bash -set -euo pipefail - -PROJECT_NAME="${1:-@defaultPackageName@}" - -echo "🚀 Setting up project: $PROJECT_NAME" - -# Create directory structure -directories=( - "data/raw" - "data/processed" - "data/interim" - "docs" - "figures" - "tables" - "src/analysis" - "src/data_prep" - "src/explore" - "src/utils" -) - -for dir in "${directories[@]}"; do - if [[ ! -d "$dir" ]]; then - mkdir -p "$dir" - echo "✓ Created $dir/" - fi -done - -# Create essential files -if [[ ! -f "README.md" ]]; then - cat > README.md << 'EOF' -# RDE - -## Project Structure -- `data/`: Data files (gitignored) -- `docs/`: Documentation -- `figures/`: Output figures -- `tables/`: Output tables -- `src/`: Source code - -EOF -fi - -# Initialize git -if [[ ! -d ".git" ]]; then - if ! command -v git &> /dev/null; then - echo "⚠ī¸ Warning: 'git' command not found. Skipping git initialization." - echo "Install git to enable version control." - else - git init - echo "✓ Initialized Git repository" - fi -fi - -# Check if files exist and are not already staged/tracked before adding -if command -v git &> /dev/null && [[ -d ".git" ]]; then - if [[ -f "flake.nix" ]] && ! git diff --cached --name-only 2>/dev/null | grep -q "flake.nix" && - ! git ls-files --error-unmatch flake.nix >/dev/null 2>&1; then - echo "✓ Adding flake.nix to Git repository" - git add flake.nix - elif [[ -f "flake.nix" ]]; then - echo "✓ flake.nix already tracked/staged in Git" - fi - - if [[ -f "flake.lock" ]] && ! git diff --cached --name-only 2>/dev/null | grep -q "flake.lock" && - ! git ls-files --error-unmatch flake.lock >/dev/null 2>&1; then - echo "✓ Adding flake.lock to Git repository" - git add flake.lock - elif [[ -f "flake.lock" ]]; then - echo "✓ flake.lock already tracked/staged in Git" - fi -fi -# Create .gitignore -if [[ ! -f ".gitignore" ]]; then - cat > .gitignore << 'EOF' -# Data files -data/ -*.csv -*.docx -*.xlsx -*.parquet - -# R specific -.Rproj.user/ -.Rhistory -.RData -.Ruserdata -*.Rproj -.Rlibs/ - -# Python specific -__pycache__/ -*.pyc -.pytest_cache/ -.venv/ - -# Jupyter -.ipynb_checkpoints/ - -# IDE -.vscode/ -.idea/ - -# OS -.DS_Store -Thumbs.db - -# Devenv -.devenv* -devenv.local.nix - -# direnv -.direnv - -# pre-commit -.pre-commit-config.yaml -EOF -fi - -echo "✅ Project setup completed successfully!" diff --git a/templates/rde/scripts/initPython.sh b/templates/rde/scripts/initPython.sh deleted file mode 100644 index 6c560a5..0000000 --- a/templates/rde/scripts/initPython.sh +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env bash -set -euo pipefail - -# Check if uv command is available -if ! command -v uv &> /dev/null; then - echo "❌ Command 'uv' not found." - echo "UV is required for Python project management." - echo "Ensure UV is properly installed in your environment." - exit 1 -fi - -if [[ ! -f "pyproject.toml" ]]; then - echo "🐍 Initializing UV project..." - uv init - echo "đŸ“Ļ Adding IPython and Marimo..." - uv add ipython - uv add marimo - echo "--------------------------------------------------------------------------" - echo "✅ Python project initialized!" - echo "run 'uv add PACKAGE' to add more python packages." - echo "--------------------------------------------------------------------------" -else - echo "--------------------------------------------------------------------------" - echo "🔄 Existing Python project detected." - echo "đŸ“Ļ Ensuring IPython and Marimo are installed..." - uv add ipython - uv add marimo - echo "Run '@defaultPackageName@-updateDeps' to update dependencies." - echo "--------------------------------------------------------------------------" -fi diff --git a/templates/rde/scripts/updateDeps.sh b/templates/rde/scripts/updateDeps.sh deleted file mode 100644 index c4d6c60..0000000 --- a/templates/rde/scripts/updateDeps.sh +++ /dev/null @@ -1,98 +0,0 @@ -#!/usr/bin/env bash -set -euo pipefail - -echo "🔄 Updating project dependencies..." - -# Check for required commands -if ! command -v wget &> /dev/null; then - echo "❌ Error: 'wget' command not found." - echo "Please install wget to fetch R version information." - exit 1 -fi - -if ! command -v sed &> /dev/null; then - echo "❌ Error: 'sed' command not found." - echo "Please install sed to update flake.nix." - exit 1 -fi - -if ! command -v nix &> /dev/null; then - echo "❌ Error: 'nix' command not found." - echo "Please install Nix to update flake inputs." - exit 1 -fi - -# Ensure we're in the repository root -if [[ ! -f "flake.nix" ]]; then - # Try to find git root - if command -v git &> /dev/null && git rev-parse --show-toplevel >/dev/null 2>&1; then - cd "$(git rev-parse --show-toplevel)" - if [[ ! -f "flake.nix" ]]; then - echo "❌ Error: flake.nix not found in repository root" - exit 1 - fi - else - echo "❌ Error: Not in a git repository and flake.nix not found" - exit 1 - fi -fi - -# Fetch latest R version from rstats-on-nix -# This command chain: downloads CSV, extracts last line, gets 4th field (date), removes quotes -echo "📡 Fetching latest R version from rstats-on-nix..." -RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' ) - -# Validate RVER matches YYYY-MM-DD format -if [[ ! "$RVER" =~ ^[0-9]{4}-[0-9]{2}-[0-9]{2}$ ]]; then - echo "❌ Error: Failed to fetch valid R version date. Got: '$RVER'" - exit 1 -fi - -echo "✅ R date is $RVER" - -# Create backup of flake.nix before modifying -cp flake.nix flake.nix.backup - -# Update rixpkgs date in flake.nix -if sed -i "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix; then - echo "✅ Updated rixpkgs date in flake.nix" - rm flake.nix.backup -else - echo "⚠ī¸ Warning: Failed to update flake.nix, restoring backup" - mv flake.nix.backup flake.nix -fi - -nix flake update -echo "✅ Flake inputs updated" - -# Update Python dependencies if pyproject.toml exists and uv is available -if [[ -f "pyproject.toml" ]]; then - if command -v uv >/dev/null 2>&1; then - uv sync --upgrade - echo "✅ Python dependencies updated" - else - echo "ℹī¸ pyproject.toml found but uv command not available, skipping Python update" - fi -fi - -# Update Julia dependencies if Project.toml exists and julia is available -if [[ -f "Project.toml" ]]; then - if command -v @defaultPackageName@-jl >/dev/null 2>&1; then - @defaultPackageName@-jl -e "using Pkg; Pkg.update()" - echo "✅ Julia dependencies updated" - else - echo "ℹī¸ Project.toml found but @defaultPackageName@-jl command not available, skipping Julia update" - fi -fi - -# Update devenv dependencies if devenv.nix exists and devenv is available -if [[ -f "devenv.nix" ]]; then - if command -v devenv >/dev/null 2>&1; then - devenv update - echo "✅ Devenv dependencies updated" - else - echo "ℹī¸ devenv.nix found but devenv command not available, skipping devenv update" - fi -fi - -echo "🎉 All dependencies updated!"