diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..7617f61 --- /dev/null +++ b/.Rprofile @@ -0,0 +1,5 @@ +if (Sys.getenv("RNVIM_TMPDIR") == "") { + options(defaultPackages = c("utils", "grDevices", "graphics", "stats", "methods")) +} else { + options(defaultPackages = c("utils", "grDevices", "graphics", "stats", "methods", "nvimcom")) +} diff --git a/.commandcode/taste/taste.md b/.commandcode/taste/taste.md new file mode 100644 index 0000000..54e4488 --- /dev/null +++ b/.commandcode/taste/taste.md @@ -0,0 +1,9 @@ +# nix +- For R.nvim in the Nix wrapper, both RNVIM_COMPLDIR (C server compilation) and a writable R_LIBS_USER directory (nvimcom R package installation) must be configured — fixing only one leaves permission errors in the other. Confidence: 0.65 +- For R.nvim writable directories (RNVIM_COMPLDIR, R_LIBS_USER, TMPDIR), prefer project-local paths (e.g., $PWD/.Rlibs) over global cache paths — the cache approach may let the build succeed but still fail at runtime. Confidence: 0.70 +- Do not use lib.mkDefault on values consumed by lib.optionals or other boolean-checking functions — mkDefault wraps values in a priority set that fails "expected a Boolean" at evaluation time. Use plain booleans for inline conditionals, reserving mkDefault for module options resolved by the merge system. Confidence: 0.70 + +# Taste (Continuously Learned by [CommandCode][cmd]) + +[cmd]: https://commandcode.ai/ + diff --git a/flake.lock b/flake.lock index 78a5bd8..698ccf9 100644 --- a/flake.lock +++ b/flake.lock @@ -22,11 +22,11 @@ }, "nixpkgs": { "locked": { - "lastModified": 1776169885, - "narHash": "sha256-l/iNYDZ4bGOAFQY2q8y5OAfBBtrDAaPuRQqWaFHVRXM=", + "lastModified": 1778869304, + "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=", "owner": "nixos", "repo": "nixpkgs", - "rev": "4bd9165a9165d7b5e33ae57f3eecbcb28fb231c9", + "rev": "d233902339c02a9c334e7e593de68855ad26c4cb", "type": "github" }, "original": { @@ -55,19 +55,43 @@ "plugins-r": { "flake": false, "locked": { - "lastModified": 1776340770, - "narHash": "sha256-o/8UZIc/Bq9dWTjA+MpSR5uMUpE7KHTErk+TwWID8Ww=", + "lastModified": 1776905071, + "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=", "owner": "R-nvim", "repo": "R.nvim", - "rev": "b9cfffeb9b4e484aa9e13f01c0eb80230aada455", + "rev": "582f2af11290ac067e49018db38e12a511325556", "type": "github" }, "original": { "owner": "R-nvim", + "ref": "v0.99.4", "repo": "R.nvim", "type": "github" } }, + "r-nvim-nix": { + "inputs": { + "nixpkgs": [ + "rixpkgs" + ], + "rnvimsrc": [ + "plugins-r" + ] + }, + "locked": { + "lastModified": 1778684156, + "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=", + "owner": "dwinkler1", + "repo": "r_nvim_nix", + "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82", + "type": "github" + }, + "original": { + "owner": "dwinkler1", + "repo": "r_nvim_nix", + "type": "github" + } + }, "rixpkgs": { "locked": { "lastModified": 1771303851, @@ -79,8 +103,8 @@ }, "original": { "owner": "dwinkler1", - "ref": "nixpkgs", "repo": "rixpkgs", + "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e", "type": "github" } }, @@ -90,6 +114,7 @@ "nixpkgs": "nixpkgs", "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references", "plugins-r": "plugins-r", + "r-nvim-nix": "r-nvim-nix", "rixpkgs": "rixpkgs", "wrappers": "wrappers" } @@ -101,11 +126,11 @@ ] }, "locked": { - "lastModified": 1776375800, - "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=", + "lastModified": 1779297405, + "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=", "owner": "BirdeeHub", "repo": "nix-wrapper-modules", - "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57", + "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1", "type": "github" }, "original": { diff --git a/flake.nix b/flake.nix index cce0107..2780328 100644 --- a/flake.nix +++ b/flake.nix @@ -1,16 +1,19 @@ -# Copyright (c) 2026 BirdeeHub +# Copyright (c) 2026 Daniel # Licensed under the MIT license { description = "Daniel's NixCats"; inputs = { nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable"; - #nixpkgs.url = "github:nixos/nixpkgs/nixos-25.11"; wrappers = { url = "github:BirdeeHub/nix-wrapper-modules"; inputs.nixpkgs.follows = "nixpkgs"; }; - rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs"; + rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e"; + + r-nvim-nix.url = "github:dwinkler1/r_nvim_nix"; + r-nvim-nix.inputs.rnvimsrc.follows = "plugins-r"; + r-nvim-nix.inputs.nixpkgs.follows = "rixpkgs"; fran = { url = "github:dwinkler1/fran"; @@ -20,7 +23,7 @@ }; "plugins-r" = { - url = "github:R-nvim/R.nvim"; + url = "github:R-nvim/R.nvim/v0.99.4"; flake = false; }; @@ -36,45 +39,34 @@ wrappers, ... } @ inputs: let + mkWrapperConfig = pkgs: { + cats = { + clickhouse = false; + gitPlugins = true; + julia = false; + lua = true; + markdown = true; + nix = true; + optional = false; + python = false; + r = true; + }; + settings = { + lang_packages = { + python = []; + r = []; + julia = []; + }; + }; + binName = "vv"; + }; + wrapperSettings = pkgs: let - def = pkgs.lib.mkDefault; + cfg = mkWrapperConfig pkgs; in wrapper.config.wrap { inherit pkgs; - cats = { - clickhouse = def false; - gitPlugins = def true; - julia = def false; - lua = def true; - markdown = def false; - nix = def true; - optional = def false; - python = def false; - r = def false; - }; - - settings = { - lang_packages = { - python = with pkgs.python3Packages; [ - duckdb - polars - ]; - - r = with pkgs.rpkgs.rPackages; [ - arrow - broom - data_table - janitor - styler - ]; - - julia = ["DataFramesMeta" "QuackIO"]; - }; - colorscheme = def "cyberdream"; - background = def "dark"; - wrapRc = def true; - }; - binName = def "vv"; + inherit (cfg) settings binName; }; systems = [ @@ -85,54 +77,39 @@ forAllSystems = nixpkgs.lib.genAttrs systems; - extra_pkg_config = { - # allowUnfree = true; - }; - overlayDefs = import ./overlays inputs; - dependencyOverlays = overlayDefs.dependencyOverlays; - - dependencyOverlay = overlayDefs.dependencyOverlay; - mkPkgs = system: import nixpkgs { inherit system; - config = extra_pkg_config; - overlays = [dependencyOverlay]; + config = { allowUnfree = true; }; + overlays = [ overlayDefs.dependencyOverlay ]; }; - module = nixpkgs.lib.modules.importApply ./modules/neovim.nix inputs; + module = (import ./modules/neovim.nix) inputs; wrapper = wrappers.lib.evalModule module; in { overlays = { + # overlay `vv` wraps the module with default settings only. + # For the fully-configured binary (including mkWrapperConfig overrides), + # use `packages..default` instead. default = nixpkgs.lib.composeManyExtensions [ - dependencyOverlay + overlayDefs.dependencyOverlay (final: prev: { vv = wrapper.config.wrap {pkgs = final;}; }) ]; - dependencies = dependencyOverlay; - vv = self.overlays.default; + dependencies = overlayDefs.dependencyOverlay; }; - wrapperModules = { - default = module; - neovim = self.wrapperModules.default; - }; - - wrappers = { - default = wrapper.config; - neovim = self.wrappers.default; - }; + wrapperModules.default = module; + wrapperConfigs.default = wrapper.config; packages = forAllSystems ( system: let pkgs = mkPkgs system; - nvimPkg = wrapperSettings pkgs; in { - default = nvimPkg; - vv = nvimPkg; + default = wrapperSettings pkgs; } ); @@ -147,13 +124,79 @@ system: let pkgs = mkPkgs system; nvimPkg = wrapperSettings pkgs; + + pythonPkgs = with pkgs.python3Packages; [ + duckdb + polars + ]; + + rPkgs = (with pkgs.rpkgs.rPackages; [ + arrow + broom + data_table + janitor + languageserver + styler + ]) ++ [ pkgs.nvimcom ]; + + juliaPkgs = ["DataFramesMeta" "QuackIO"]; + + pythonPackages = let + python_packages_fn = + if pkgs ? basePythonPackages + then ps: pkgs.basePythonPackages ps ++ pythonPkgs + else _: pythonPkgs; + in + with pkgs; [ + (python3.withPackages python_packages_fn) + nodejs + ruff + basedpyright + uv + ]; + + rPackages = let + r_packages = (pkgs.baseRPackages or []) ++ rPkgs; + in + with pkgs; [ + (rWrapper.override {packages = r_packages;}) + radianWrapper + (quarto.override {extraRPackages = r_packages;}) + air-formatter + yaml-language-server + updateR + nvimcom + rnvimserver + ]; + + juliaPackages = let + julia_with_packages = pkgs.julia-bin.withPackages juliaPkgs; + in [julia_with_packages]; + + markdownPackages = with pkgs; [ + python313Packages.pylatexenc + quarto + zk + ]; + + shellPackages = + [nvimPkg] + ++ pkgs.lib.optionals wrapper.config.cats.python pythonPackages + ++ pkgs.lib.optionals wrapper.config.cats.r rPackages + ++ pkgs.lib.optionals wrapper.config.cats.julia juliaPackages + ++ pkgs.lib.optionals wrapper.config.cats.markdown markdownPackages; in { default = pkgs.mkShell { name = "vShell"; - packages = [nvimPkg]; - nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals self.wrappers.default.cats.optional [devenv]); - inputsFrom = []; - shellHook = ""; + packages = shellPackages; + nativeBuildInputs = pkgs.lib.optionals wrapper.config.cats.optional [ pkgs.devenv ]; + shellHook = '' + echo 'I am a NixShell' + export R_HOME=$(R RHOME) + export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' | sort -u | paste -sd: -) + export R_LIBS_USER="$PWD/.r-libs" + mkdir -p "$R_LIBS_USER" + ''; }; } ); @@ -163,18 +206,11 @@ pkgs = mkPkgs system; nvimPkg = wrapperSettings pkgs; in { - default = nvimPkg; - module-eval = let - _ = wrapper.config; - in - pkgs.runCommand "check-module-eval" {} '' - echo "Module evaluation successful" > $out - ''; - package-build = pkgs.runCommand "check-vv" {} '' + default = pkgs.runCommand "check-vv" {} '' BINARY_PATH="${nvimPkg}/bin/vv" if [ ! -x "$BINARY_PATH" ]; then - echo "Error: Binary n not found or not executable" + echo "Error: Binary not found or not executable" exit 1 fi @@ -187,6 +223,11 @@ cat version_output.txt >> $out fi ''; + module-eval = + let _ = wrapper.config; + in pkgs.runCommand "check-module-eval" {} '' + echo "Module evaluation successful" > $out + ''; } ); diff --git a/ftplugin/markdown.lua b/ftplugin/markdown.lua index b673b60..db316fc 100644 --- a/ftplugin/markdown.lua +++ b/ftplugin/markdown.lua @@ -1,32 +1,35 @@ -- Add the key mappings only for Markdown files in a zk notebook. -if require("zk.util").notebook_root(vim.fn.expand('%:p')) ~= nil then - local map = vim.keymap.set - -- Open the link under the caret. - map("n", "", "lua vim.lsp.buf.definition()", { noremap = true, silent = false, buffer = true }) +local nix = require("config.nix") +if nix.get_cat("markdown", false) then + if require("zk.util").notebook_root(vim.fn.expand('%:p')) ~= nil then + local map = vim.keymap.set + -- Open the link under the caret. + map("n", "", "lua vim.lsp.buf.definition()", { noremap = true, silent = false, buffer = true }) - -- Create a new note after asking for its title. - -- This overrides the global `zn` mapping to create the note in the same directory as the current buffer. - map("n", "zhn", "ZkNew { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }", - { noremap = true, silent = false, buffer = true, desc = "Note (here)" }) - -- Create a new note in the same directory as the current buffer, using the current selection for title. - map("v", "zhnt", ":'<,'>ZkNewFromTitleSelection { dir = vim.fn.expand('%:p:h') }", - { noremap = true, silent = false, buffer = true, desc = "Note from selection (title)" }) - -- Create a new note in the same directory as the current buffer, using the current selection for note content and asking for its title. - map("v", "zhnc", - ":'<,'>ZkNewFromContentSelection { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }", - { noremap = true, silent = false, buffer = true, desc = "Note from selection (content)" }) + -- Create a new note after asking for its title. + -- This overrides the global `zn` mapping to create the note in the same directory as the current buffer. + map("n", "zhn", "ZkNew { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }", + { noremap = true, silent = false, buffer = true, desc = "Note (here)" }) + -- Create a new note in the same directory as the current buffer, using the current selection for title. + map("v", "zhnt", ":'<,'>ZkNewFromTitleSelection { dir = vim.fn.expand('%:p:h') }", + { noremap = true, silent = false, buffer = true, desc = "Note from selection (title)" }) + -- Create a new note in the same directory as the current buffer, using the current selection for note content and asking for its title. + map("v", "zhnc", + ":'<,'>ZkNewFromContentSelection { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }", + { noremap = true, silent = false, buffer = true, desc = "Note from selection (content)" }) - -- Open notes linking to the current buffer. - map("n", "zb", "ZkBacklinks", { noremap = true, silent = false, buffer = true, desc = "Backlinks" }) - -- Alternative for backlinks using pure LSP and showing the source context. - --map('n', 'zb', 'lua vim.lsp.buf.references()', opts) - -- Open notes linked by the current buffer. - map("n", "zL", "ZkLinks", { noremap = true, silent = false, buffer = true, desc = "Links" }) - map("n", "zi", "ZkInsertLink", { noremap = true, silent = false, buffer = true, desc = "Insert link" }) + -- Open notes linking to the current buffer. + map("n", "zb", "ZkBacklinks", { noremap = true, silent = false, buffer = true, desc = "Backlinks" }) + -- Alternative for backlinks using pure LSP and showing the source context. + --map('n', 'zb', 'lua vim.lsp.buf.references()', opts) + -- Open notes linked by the current buffer. + map("n", "zL", "ZkLinks", { noremap = true, silent = false, buffer = true, desc = "Links" }) + map("n", "zi", "ZkInsertLink", { noremap = true, silent = false, buffer = true, desc = "Insert link" }) - -- Preview a linked note. - -- Open the code actions for a visual selection. - map("v", "za", ":'<,'>lua vim.lsp.buf.range_code_action()", - { noremap = true, silent = false, buffer = true, desc = "Code actions" }) + -- Preview a linked note. + -- Open the code actions for a visual selection. + map("v", "za", ":'<,'>lua vim.lsp.buf.range_code_action()", + { noremap = true, silent = false, buffer = true, desc = "Code actions" }) + end end diff --git a/modules/module/settings/cats.nix b/modules/module/settings/cats.nix index 22b3638..13758d4 100644 --- a/modules/module/settings/cats.nix +++ b/modules/module/settings/cats.nix @@ -14,7 +14,6 @@ Available categories: - clickhouse: Clickhouse client and tools - - customPlugins: local plugin specs - external: external tools and integrations - general: core Neovim plugins/features - gitPlugins: git-related plugins @@ -25,7 +24,6 @@ - optional: optional tools and utilities - python: Python tooling and plugins - r: R tooling and plugins - - test: test-only tooling (disabled by default) - treesitterParsers: Treesitter parsers - utils: general utilities ''; @@ -33,18 +31,16 @@ config.cats = { clickhouse = lib.mkDefault false; - customPlugins = lib.mkDefault true; external = lib.mkDefault true; general = lib.mkDefault true; gitPlugins = lib.mkDefault true; julia = lib.mkDefault false; lua = lib.mkDefault true; - markdown = lib.mkDefault false; + markdown = lib.mkDefault true; nix = lib.mkDefault true; optional = lib.mkDefault false; python = lib.mkDefault false; - r = lib.mkDefault false; - test = lib.mkDefault false; + r = lib.mkDefault true; treesitterParsers = lib.mkDefault true; utils = lib.mkDefault true; }; diff --git a/modules/module/settings/core.nix b/modules/module/settings/core.nix index 42e9e11..ec9bb5c 100644 --- a/modules/module/settings/core.nix +++ b/modules/module/settings/core.nix @@ -16,7 +16,7 @@ # Lua packages available to neovim (for :lua require()) config.settings.nvim_lua_env = lp: - lib.optionals (config.cats.general or false) [ lp.tiktoken_core ]; + lib.optionals (config.cats.general or true) [ lp.tiktoken_core ]; # Binary name for the wrapper config.binName = lib.mkDefault "vv"; @@ -25,10 +25,10 @@ config.settings.block_normal_config = true; # Don't symlink the config (we wrap it instead) - config.settings.dont_link = false; + config.settings.dont_link = lib.mkDefault false; # Create additional aliases for the binary - config.settings.aliases = [ "vvim" ]; + config.settings.aliases = lib.mkDefault [ "vvim" ]; # Enable wrapper handling of spec runtimeDeps (template pattern). config.settings.autowrapRuntimeDeps = true; diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix index 2ae4b9c..2fcab8a 100644 --- a/modules/module/settings/env.nix +++ b/modules/module/settings/env.nix @@ -7,16 +7,21 @@ # Environment variables set for the wrapper. # These are available when running neovim. config.env = lib.mkMerge [ - (lib.mkIf (config.cats.python or false) { + (lib.mkIf (config.cats.python or true) { UV_PYTHON_DOWNLOADS = "never"; UV_PYTHON = pkgs.python.interpreter; }) + (lib.mkIf (config.cats.r or true) { + RNVIM_COMPLDIR = "$PWD/.r-compl"; + R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs"; + TMPDIR = "$PWD/.r-tmp"; + }) ]; # Environment variables with defaults (can be overridden by user) config.envDefault = lib.mkMerge [ - (lib.mkIf (config.cats.r or false) { - R_LIBS_USER = "./.Rlibs"; + (lib.mkIf (config.cats.r or true) { + R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs"; }) ]; } diff --git a/modules/module/settings/hosts.nix b/modules/module/settings/hosts.nix index 0743979..f248a00 100644 --- a/modules/module/settings/hosts.nix +++ b/modules/module/settings/hosts.nix @@ -15,7 +15,7 @@ nvim-host.enable = true; nvim-host.package = "${pkgs.neovide}/bin/neovide"; nvim-host.argv0 = "neovide"; - nvim-host.flags."--neovim-bin" = "${placeholder "out"}/bin/${config.binName}"; + nvim-host.flags."--neovim-bin" = "${builtins.placeholder "out"}/bin/${config.binName}"; }; m = { diff --git a/modules/module/settings/lang-packages.nix b/modules/module/settings/lang-packages.nix index 3315363..531b811 100644 --- a/modules/module/settings/lang-packages.nix +++ b/modules/module/settings/lang-packages.nix @@ -26,7 +26,7 @@ }; default = { }; description = '' - Language-specific package overrides appended to each language spec's extraPackages. + Language-specific package overrides appended to each language spec's runtimePackages. Intended for flake.nix overrides via wrapper.config.wrap. ''; }; diff --git a/modules/module/settings/runtime-path.nix b/modules/module/settings/runtime-path.nix index 96c5d0f..b321019 100644 --- a/modules/module/settings/runtime-path.nix +++ b/modules/module/settings/runtime-path.nix @@ -10,14 +10,13 @@ let let is_enabled = if spec ? enable then spec.enable else true; has_runtime_deps = (spec.runtimeDeps or false) == runtime_deps_type; - packages = spec.extraPackages or [ ]; + packages = spec.runtimePackages or [ ]; in acc ++ lib.optionals (is_enabled && has_runtime_deps) packages ) [ ]; prefix_packages = collect_runtime_packages "prefix"; - suffix_packages = collect_runtime_packages "suffix"; to_path_specs = packages: [ { @@ -31,5 +30,4 @@ let in { config.prefixVar = lib.optionals (prefix_packages != [ ]) (to_path_specs prefix_packages); - config.suffixVar = lib.optionals (suffix_packages != [ ]) (to_path_specs suffix_packages); } diff --git a/modules/module/specs/cats-enable.nix b/modules/module/specs/cats-enable.nix deleted file mode 100644 index f5a9826..0000000 --- a/modules/module/specs/cats-enable.nix +++ /dev/null @@ -1,51 +0,0 @@ -{ config, lib, ... }: -{ - # This module implements category-based enabling of specs. - # It runs early (order 200) so other specMaps can see the enable flags. - # - # How it works: - # 1. For each spec, extract its name (removing -lazy suffix if present) - # 2. Check if there's a corresponding cats. toggle - # 3. Set spec.value.enable based on the cats toggle (default: true) - # 4. This allows specs to be conditionally included based on config.cats settings - # - # Example: If config.cats.python = false, then specs.python.enable = false - - config.specMaps = lib.mkOrder 200 [ - { - name = "CATS_ENABLE"; - data = - list: - map ( - v: - if v.type == "spec" || v.type == "parent" then - let - # Extract spec name, handling lazy specs (remove -lazy suffix) - specName = - if v.name == null then - null - else if lib.hasSuffix "-lazy" v.name then - lib.removeSuffix "-lazy" v.name - else - v.name; - - # Check if this spec has a corresponding cat toggle - catEnabled = - if specName != null && builtins.hasAttr specName config.cats then - config.cats.${specName} - else - true; # Default to enabled if no cat toggle exists - in - v - // { - value = v.value // { - # Use explicit enable if set, otherwise use cat toggle - enable = if v.value ? enable then v.value.enable else catEnabled; - }; - } - else - v - ) list; - } - ]; -} diff --git a/modules/module/specs/deps.nix b/modules/module/specs/deps.nix index a8bfaf6..c3a40ea 100644 --- a/modules/module/specs/deps.nix +++ b/modules/module/specs/deps.nix @@ -5,24 +5,14 @@ wlib, ... }: { - # ============================================================================ - # SPEC MODULE DEFAULTS - # ============================================================================ - # Define default options available to all specs - config.specMods = {parentSpec ? null, ...}: { - options.extraPackages = lib.mkOption { + options.runtimePkgs = lib.mkOption { type = lib.types.listOf wlib.types.stringable; default = []; - description = "a extraPackages spec field to put packages to suffix to the PATH"; + description = "a runtimePkgs spec field to put packages to suffix to the PATH"; }; }; - # ============================================================================ - # EXTERNAL TOOLS SPEC - # ============================================================================ - # Core system tools and utilities - config.specs.external = { data = lib.mkDefault null; before = ["INIT_MAIN"]; @@ -30,7 +20,7 @@ vim.o.shell = "${pkgs.zsh}/bin/zsh" ''; runtimeDeps = "prefix"; - extraPackages = with pkgs; [ + runtimePkgs = with pkgs; [ perl ruby shfmt @@ -39,15 +29,11 @@ ]; }; - # ============================================================================ - # OPTIONAL TOOLS SPEC - # ============================================================================ - config.specs.optional = lib.mkIf (config.cats.optional or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; before = ["INIT_MAIN"]; - extraPackages = with pkgs; [ + runtimePkgs = with pkgs; [ bat broot devenv @@ -76,54 +62,38 @@ ]; }; - # ============================================================================ - # MARKDOWN SPEC - # ============================================================================ - config.specs.markdown = lib.mkIf (config.cats.markdown or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = with pkgs; [ + runtimePkgs = with pkgs; [ python313Packages.pylatexenc quarto zk ]; }; - # ============================================================================ - # NIX SPEC - # ============================================================================ - config.specs.nix = lib.mkIf (config.cats.nix or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = with pkgs; [ + runtimePkgs = with pkgs; [ alejandra nix-doc nixd ]; }; - # ============================================================================ - # LUA SPEC - # ============================================================================ - config.specs.lua = lib.mkIf (config.cats.lua or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = with pkgs; [ + runtimePkgs = with pkgs; [ lua-language-server ]; }; - # ============================================================================ - # PYTHON SPEC - # ============================================================================ - config.specs.python = lib.mkIf (config.cats.python or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = let + runtimePkgs = let python_packages_fn = if pkgs ? basePythonPackages then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python @@ -139,14 +109,10 @@ ]; }; - # ============================================================================ - # R SPEC - # ============================================================================ - config.specs.r = lib.mkIf (config.cats.r or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = let + runtimePkgs = let r_packages = (pkgs.baseRPackages or []) ++ config.settings.lang_packages.r; in with pkgs; [ @@ -159,30 +125,22 @@ ]; }; - # ============================================================================ - # JULIA SPEC - # ============================================================================ - config.specs.julia = lib.mkIf (config.cats.julia or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = let + runtimePkgs = let julia_with_packages = pkgs.julia-bin.withPackages config.settings.lang_packages.julia; in [julia_with_packages]; }; - # ============================================================================ - # CLICKHOUSE SPEC - # ============================================================================ - config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) { data = lib.mkDefault null; runtimeDeps = "prefix"; - extraPackages = with pkgs; [ + runtimePkgs = with pkgs; [ clickhouse-lts ]; }; - config.extraPackages = config.specCollect (acc: v: acc ++ (v.extraPackages or [])) []; + config.runtimePkgs = config.specCollect (acc: v: acc ++ (v.runtimePkgs or [])) []; } diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix index ded8195..ff00a72 100644 --- a/modules/module/specs/plugins.nix +++ b/modules/module/specs/plugins.nix @@ -3,15 +3,14 @@ pkgs, lib, ... -}: -{ - config.specs.gitPlugins = { - data = [ ]; +}: { + config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or true) { + data = []; }; - config.specs.r = { + config.specs.r = lib.mkIf (config.cats.r or true) { data = with pkgs.vimPlugins; [ - config.nvim-lib.neovimPlugins.r + pkgs.r-nvim quarto-nvim { data = otter-nvim; @@ -20,14 +19,14 @@ ]; }; - config.specs.markdown-lazy = { + config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or true) { lazy = true; data = [ config.nvim-lib.neovimPlugins.cmp-pandoc-references ]; }; - config.specs.general = { + config.specs.general = lib.mkIf (config.cats.general or true) { data = with pkgs.vimPlugins; [ lze lzextras @@ -80,7 +79,7 @@ ]; }; - config.specs.lua = { + config.specs.lua = lib.mkIf (config.cats.lua or true) { data = with pkgs.vimPlugins; [ luvit-meta { @@ -90,7 +89,7 @@ ]; }; - config.specs.markdown = { + config.specs.markdown = lib.mkIf (config.cats.markdown or true) { data = with pkgs.vimPlugins; [ quarto-nvim render-markdown-nvim @@ -105,20 +104,22 @@ ]; }; - config.specs.utils = { + config.specs.utils = lib.mkIf (config.cats.utils or true) { data = with pkgs.vimPlugins; [ blink-cmp nvim-lspconfig nvim-treesitter-context nvim-treesitter-textobjects { - data = pkgs.codecompanion-nvim; + data = pkgs.codecompanion-nvim.overrideAttrs (old: { + doCheck = false; + }); pname = "codecompanion"; } ]; }; - config.specs.treesitterParsers = { + config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or true) { data = with pkgs.vimPlugins.nvim-treesitter-parsers; [ bash c @@ -157,7 +158,7 @@ ]; }; - config.specs.utils-lazy = { + config.specs.utils-lazy = lib.mkIf (config.cats.utils or true) { lazy = true; data = with pkgs.vimPlugins; [ blink-compat @@ -174,8 +175,8 @@ ]; }; - config.specs.gitPlugins-lazy = { + config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or true) { lazy = true; - data = [ ]; + data = []; }; } diff --git a/modules/neovim.nix b/modules/neovim.nix index ba0361c..64d2cda 100644 --- a/modules/neovim.nix +++ b/modules/neovim.nix @@ -7,16 +7,10 @@ inputs: ... }: { - # ============================================================================ - # IMPORTS - # ============================================================================ - # Import the base neovim wrapper module and all configuration modules - imports = [ wlib.wrapperModules.neovim ./module/specs/deps.nix ./module/specs/plugins.nix - ./module/specs/cats-enable.nix ./module/settings/core.nix ./module/settings/cats.nix ./module/settings/env.nix @@ -25,11 +19,6 @@ inputs: ./module/settings/runtime-path.nix ]; - # ============================================================================ - # HELPER FUNCTIONS - # ============================================================================ - # Utilities for working with plugin inputs - options.nvim-lib.neovimPlugins = lib.mkOption { readOnly = true; type = lib.types.attrsOf wlib.types.stringable; @@ -58,11 +47,6 @@ inputs: ]; }; - # ============================================================================ - # CONFIGURATION - # ============================================================================ - # Pass cats configuration to neovim and expose metadata - config.settings.cats = config.cats; config.info.cats = config.cats; config.info.nixCats_config_location = config.settings.config_directory; diff --git a/overlays/default.nix b/overlays/default.nix index 821ff88..5a4cc6c 100644 --- a/overlays/default.nix +++ b/overlays/default.nix @@ -3,39 +3,33 @@ let lib = nixpkgs.lib; rOverlay = import ./r.nix {inherit inputs;}; - franOverlay = inputs.fran.overlays.default; - pythonOverlay = import ./python.nix inputs; - pluginsOverlay = import ./plugins.nix inputs; + rNvimNixOverlay = inputs.r-nvim-nix.overlays.default; + pythonOverlay = import ./python.nix {inherit inputs;}; + pluginsOverlay = import ./plugins.nix {inherit inputs;}; dependencyOverlays = [ rOverlay + rNvimNixOverlay pythonOverlay pluginsOverlay ]; dependencyOverlay = lib.composeManyExtensions dependencyOverlays; + + # franOverlay provides R-specific tooling (radianWrapper, air-formatter). + # It is scoped to rixpkgs (via overlays/r.nix) rather than the global + # package set, since it only applies to R package derivations. + franOverlay = inputs.fran.overlays.default; in { inherit rOverlay + rNvimNixOverlay franOverlay pythonOverlay pluginsOverlay dependencyOverlays dependencyOverlay; - # Named exports for downstream composition. default = dependencyOverlay; dependencies = dependencyOverlays; - - overlays = { - inherit - rOverlay - franOverlay - pythonOverlay - pluginsOverlay - dependencyOverlays - dependencyOverlay; - default = dependencyOverlay; - dependencies = dependencyOverlays; - }; } diff --git a/overlays/r.nix b/overlays/r.nix index 2fb71c8..14c02eb 100644 --- a/overlays/r.nix +++ b/overlays/r.nix @@ -1,52 +1,15 @@ -# R packages overlay (rix) -# -# This overlay provides access to R packages from rstats-on-nix. -# -# rstats-on-nix maintains snapshots of CRAN packages built with Nix: -# - Provides reproducible R package versions -# - Ensures binary cache availability for faster builds -# - Maintained by the rstats-on-nix community -# -# Available attributes after applying this overlay: -# - pkgs.rpkgs: R packages from rstats-on-nix -# - pkgs.rpkgs.rPackages: All CRAN packages -# - pkgs.rpkgs.quarto: Quarto publishing system -# - pkgs.rpkgs.rWrapper: R with package management -# - pkgs.rWrapper: R wrapper with standard packages pre-configured -# - pkgs.quarto: Quarto with R integration and standard packages -# -# Custom R packages and tools (radianWrapper, air-formatter) come from -# the fran overlay which should be applied separately. -# -# To use specific R packages, reference them via: -# with pkgs.rpkgs.rPackages; [ package1 package2 ] -# -# Update the R snapshot date in flake.nix inputs section: -# rixpkgs.url = "github:rstats-on-nix/nixpkgs/YYYY-MM-DD" { inputs, ... }: final: prev: let - # R packages from rstats-on-nix for the current system rpkgs = import inputs.rixpkgs { system = prev.stdenv.hostPlatform.system; overlays = [inputs.fran.overlays.default]; - }; # rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system}; - - # Standard R packages used by default in rWrapper and quarto - reqPkgs = with rpkgs.rPackages; [ - # languageserver - ]; + }; in { inherit rpkgs; - baseRPackages = reqPkgs; - - # R wrapper with standard packages - rWrapper = rpkgs.rWrapper.override {packages = reqPkgs;}; - - # Quarto with R integration - quarto = rpkgs.quarto.override {extraRPackages = reqPkgs;}; - - # Update helper for rix + baseRPackages = [ ]; + rWrapper = rpkgs.rWrapper.override {packages = [ ];}; + quarto = rpkgs.quarto.override {extraRPackages = [ ];}; updateR = import ../scripts/updater.nix {pkgs = final;}; } diff --git a/plugin/20_startup.lua b/plugin/20_startup.lua index ca18bd8..0404b2c 100644 --- a/plugin/20_startup.lua +++ b/plugin/20_startup.lua @@ -390,23 +390,25 @@ end) -- zk now_if_args(function() - require("zk").setup({ - picker = "minipick", - lsp = { - -- `config` is passed to `vim.lsp.start_client(config)` - config = { - cmd = { "zk", "lsp" }, - name = "zk", - -- on_attach = ... - -- etc, see `:h vim.lsp.start_client()` - }, + if nix.get_cat("markdown", false) then + require("zk").setup({ + picker = "minipick", + lsp = { + -- `config` is passed to `vim.lsp.start_client(config)` + config = { + cmd = { "zk", "lsp" }, + name = "zk", + -- on_attach = ... + -- etc, see `:h vim.lsp.start_client()` + }, - -- automatically attach buffers in a zk notebook that match the given filetypes - auto_attach = { - enabled = true, - filetypes = { "markdown" }, - }, + -- automatically attach buffers in a zk notebook that match the given filetypes + auto_attach = { + enabled = true, + filetypes = { "markdown" }, + }, - }, - }) + }, + }) + end end) diff --git a/plugin/21_datascience.lua b/plugin/21_datascience.lua index 118ee20..2e9f86c 100644 --- a/plugin/21_datascience.lua +++ b/plugin/21_datascience.lua @@ -44,6 +44,12 @@ end) -- r now(function() if nix.get_cat("r", false) then + local cwd = vim.fn.getcwd(-1) + vim.env.RNVIM_COMPLDIR = cwd .. "/.r-compl" + vim.env.R_LIBS_USER = (vim.env.R_LIBS_USER or ""):gsub("%$PWD", cwd) + vim.env.TMPDIR = cwd .. "/.r-tmp" + vim.fn.mkdir(vim.env.RNVIM_COMPLDIR, "p") + vim.fn.mkdir(vim.env.TMPDIR, "p") vim.g.rout_follow_colorscheme = true require("r").setup({ -- Create a table with the options to be passed to setup() @@ -65,41 +71,45 @@ end) now(function() vim.treesitter.language.register("markdown", { "quarto", "rmd" }) - vim.api.nvim_create_autocmd("FileType", { - pattern = { "quarto" }, - callback = function() - require("otter").activate() - end, - }) + if nix.get_cat({ "r", "markdown" }, false) then + vim.api.nvim_create_autocmd("FileType", { + pattern = { "quarto" }, + callback = function() + require("otter").activate() + end, + }) - require("otter").setup({ - lsp = { - diagnostic_update_events = { "BufWritePost", "InsertLeave" }, - }, - buffers = { - set_filetype = true, - write_to_disk = true, - }, - }) + require("otter").setup({ + lsp = { + diagnostic_update_events = { "BufWritePost", "InsertLeave" }, + }, + buffers = { + set_filetype = true, + write_to_disk = true, + }, + }) + end end) later(function() - require("quarto").setup({ - lspFeatures = { - enabled = true, - chunks = "curly", - languages = { "r", "python", "julia" }, - diagnostics = { + if nix.get_cat({ "r", "markdown" }, false) then + require("quarto").setup({ + lspFeatures = { enabled = true, - triggers = { "BufWritePost" }, + chunks = "curly", + languages = { "r", "python", "julia" }, + diagnostics = { + enabled = true, + triggers = { "BufWritePost" }, + }, + completion = { + enabled = true, + }, }, - completion = { + codeRunner = { enabled = true, + default_method = "slime", }, - }, - codeRunner = { - enabled = true, - default_method = "slime", - }, - }) + }) + end end) diff --git a/plugin/22_languages.lua b/plugin/22_languages.lua index 1983b25..ed4682a 100644 --- a/plugin/22_languages.lua +++ b/plugin/22_languages.lua @@ -1,6 +1,7 @@ local add = Config.add local now_if_args = Config.now_if_args local later = MiniDeps.later +local nix = require('config.nix') if not Config.isNixCats then local m_add = MiniDeps.add @@ -12,19 +13,21 @@ end -- lua later(function() - add("luvit-meta") - add("lazydev") - require("lazydev").setup({ - library = { - -- See the configuration section for more details - -- Load luvit types when the `vim.uv` word is found - "lua", - "mini.nvim", - "MiniDeps", - { path = "luvit-meta/library", words = { "vim%.uv" } }, - { path = "${3rd}/luv/library", words = { "vim%.uv" } }, - }, - }) + if nix.get_cat("lua", false) then + add("luvit-meta") + add("lazydev") + require("lazydev").setup({ + library = { + -- See the configuration section for more details + -- Load luvit types when the `vim.uv` word is found + "lua", + "mini.nvim", + "MiniDeps", + { path = "luvit-meta/library", words = { "vim%.uv" } }, + { path = "${3rd}/luv/library", words = { "vim%.uv" } }, + }, + }) + end end) -- Markdown diff --git a/plugin/25_lsp.lua b/plugin/25_lsp.lua index 8c67295..f3c4c50 100644 --- a/plugin/25_lsp.lua +++ b/plugin/25_lsp.lua @@ -15,17 +15,17 @@ now_if_args(function() marksman = { filetypes = { "markdown", "markdown_inline", "codecompanion" }, }, - -- r_language_server = { - -- filetypes = { 'r', 'rmd', 'rmarkdown' }, - -- settings = { - -- ['r_language_server'] = { - -- lsp = { - -- rich_documentation = true, - -- enable = true, - -- }, - -- }, - -- } - -- }, + r_ls = { + filetypes = { 'r', 'rmd', 'rmarkdown' }, + settings = { + ['r_ls'] = { + lsp = { + rich_documentation = true, + enable = true, + }, + }, + } + }, julials = { settings = { julia = {