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Author SHA1 Message Date
copilot-swe-agent[bot]
31bc081831
fix: enable full Quarto support when R is activated
Agent-Logs-Url: https://github.com/dwinkler1/np/sessions/8f21e9a2-22be-44c9-aa37-bc4fd64b20a3

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>
2026-04-29 06:25:26 +00:00
13 changed files with 149 additions and 394 deletions

View file

@ -1,6 +1,20 @@
name: "Test RDE template"
on:
workflow_dispatch: # allows manual triggering
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

View file

@ -1,16 +1,9 @@
name: "Test ed template"
name: "Test ed template MacOS"
on:
workflow_dispatch:
workflow_dispatch: # allows manual triggering
push:
paths:
- 'templates/ed/**'
- 'tests/ed/**'
- '.github/workflows/check_ed.yml'
pull_request:
paths:
- 'templates/ed/**'
- 'tests/ed/**'
- '.github/workflows/check_ed.yml'
branches:
- 'update_rde'
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
@ -19,105 +12,15 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
os: [macos-latest, ubuntu-latest]
steps:
- uses: actions/checkout@v6
- uses: cachix/install-nix-action@v31
with:
github_access_token: ${{ github.token }}
github_access_token: ${{ secrets.GITHUB_TOKEN }}
- uses: cachix/cachix-action@v17
with:
name: rde
authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
extraPullNames: rstats-on-nix, nix-community
- name: Build template
run: nix build ./templates/ed
- name: Test R script
env:
NO_NUSHELL: '1'
run: |
cd templates/ed
nix develop --command bash -c "Rscript ${{ github.workspace }}/tests/ed/test.R"
- name: Test Python script (disabled by default)
env:
NO_NUSHELL: '1'
run: |
cd templates/ed
nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py" || echo "SKIP: Python packages not enabled"
test-with-python:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- uses: cachix/install-nix-action@v31
with:
github_access_token: ${{ github.token }}
- uses: cachix/cachix-action@v17
with:
name: rde
authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
extraPullNames: rstats-on-nix, nix-community
- name: Setup test directory with Python enabled
run: |
TEST_DIR=$(mktemp -d)
cp -r templates/ed/. "$TEST_DIR/"
cd "$TEST_DIR"
sed -i 's/python[[:space:]]*=[[:space:]]*false;/python = true;/' flake.nix
grep -q "python[[:space:]]*=[[:space:]]*true;" flake.nix || {
echo "Error: Failed to enable Python in flake.nix"
exit 1
}
echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
- name: Build with Python enabled
run: |
cd "$TEST_DIR"
nix build
- name: Test Python packages
env:
NO_NUSHELL: '1'
run: |
cd "$TEST_DIR"
nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py"
test-with-julia:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- uses: cachix/install-nix-action@v31
with:
github_access_token: ${{ github.token }}
- uses: cachix/cachix-action@v17
with:
name: rde
authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
extraPullNames: rstats-on-nix, nix-community
- name: Setup test directory with Julia enabled
run: |
TEST_DIR=$(mktemp -d)
cp -r templates/ed/. "$TEST_DIR/"
cd "$TEST_DIR"
sed -i 's/julia[[:space:]]*=[[:space:]]*false;/julia = true;/' flake.nix
grep -q "julia[[:space:]]*=[[:space:]]*true;" flake.nix || {
echo "Error: Failed to enable Julia in flake.nix"
exit 1
}
echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
- name: Build with Julia enabled
run: |
cd "$TEST_DIR"
nix build
- name: Test Julia packages
env:
NO_NUSHELL: '1'
run: |
cd "$TEST_DIR"
# nix develop --command bash -c "julia ${{ github.workspace }}/tests/ed/test.jl"
- run: nix build ./templates/ed

View file

@ -3,7 +3,7 @@ on:
workflow_dispatch: # allows manual triggering
push:
branches:
- 'update_ed'
- 'update_rde'
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
@ -23,4 +23,5 @@ jobs:
name: rde
authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
extraPullNames: rstats-on-nix, nix-community
- run: nix build ./templates/rde
- run: nix build ./templates/ed

View file

@ -22,11 +22,12 @@ jobs:
name: rde
authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
extraPullNames: rstats-on-nix, nix-community
- run: cd templates/rde/ && nix develop -c p-updateDeps
- name: Update ed flake.lock
uses: DeterminateSystems/update-flake-lock@v28
with:
token: ${{ secrets.GH_TOKEN_FOR_UPDATES }}
branch: update_ed
branch: update_rde
path-to-flake-dir: "templates/ed"
pr-title: "Update RDE flake.lock" # Title of PR to be created
pr-labels: | # Labels to be set on the PR

View file

@ -1,2 +1 @@
.nvimcom
.commandcode/

View file

@ -1,73 +0,0 @@
# Project Editor
A per-project Neovim wrapper built with [nix-wrapper-modules](https://birdeehub.github.io/nix-wrapper-modules/) and [nvimConfig](https://github.com/dwinkler1/nvimConfig).
## Setup
The flake provides two entry points:
| Command | What you get |
|---|---|
| `direnv allow` / `nix develop` | **(Recommended)** A shell with `nv` and all enabled language toolchains (R, Python, Julia, Quarto) on `PATH`. |
| `nix run` | Launches only the `nv` editor. Language toolchains (R, Python, etc.) are **not** on `PATH`. |
### With direnv (recommended)
```bash
direnv allow # enter the devShell automatically
nv # launch the pre-configured Neovim
R # R REPL is available (if enabled in flake.nix)
```
### Without direnv
```bash
nix develop # enter the devShell manually
nv # launch Neovim
R # R REPL is available (if enabled in flake.nix)
```
> **Why `nix run` only gives the editor:** The flake's `packages.default` is the wrapped Neovim binary. Language toolchains (R, radian, quarto, etc.) live in `devShells.default`. Use `nix develop` (or `direnv allow`) to get the full environment.
## Configuration
The `flake.nix` is the single source of truth. Key knobs:
| Option | What it controls |
|---|---|
| `cats` | Toggle language support (nix, r, python, julia, etc.) |
| `settings.lang_packages.<lang>` | Language-specific packages installed in the wrapper |
| `settings.colorscheme` | Neovim colorscheme |
| `settings.background` | `"dark"` or `"light"` |
| `settings.wrapRc` | When `true`, init.lua is embedded (rebuild to change); when `false`, init.lua is external (reload without rebuild) |
| `binName` | The wrapper binary name (`nv` by default) |
| `env` | Environment variables set in the wrapper |
| `extraPackages` | Extra system packages available in the wrapper's PATH |
| `specs.extraLua` | Inject lazy.nvim plugin specs |
### Adding packages without editing flake.nix
Create any of these optional files in the project root to add dependencies without modifying `flake.nix`:
- **`python-packages.nix`** — receives `python3Packages`, return a list of packages:
```nix
p: with p; [ numpy scipy ]
```
- **`r-packages.nix`** — receives `rpkgs` (includes `rPackages`), return a list:
```nix
p: with p.rPackages; [ ggplot2 data.table ]
```
- **`julia-packages.nix`** — no arguments, return a list of package name strings:
```nix
[ "DataFrames" "Plots" ]
```
## Formatting
```bash
nix fmt
```
Uses `nixfmt-rfc-style` pinned via the flake's `formatter` output.

View file

@ -22,15 +22,15 @@
},
"nixpkgs": {
"locked": {
"lastModified": 1779560665,
"narHash": "sha256-tpyBcxPpcQb8ukyNF7DoCwfSY3VPsxHoYwj00Cayv5o=",
"owner": "nixos",
"lastModified": 1776877367,
"narHash": "sha256-EHq1/OX139R1RvBzOJ0aMRT3xnWyqtHBRUBuO1gFzjI=",
"owner": "NixOS",
"repo": "nixpkgs",
"rev": "64c08a7ca051951c8eae34e3e3cb1e202fe36786",
"rev": "0726a0ecb6d4e08f6adced58726b95db924cef57",
"type": "github"
},
"original": {
"owner": "nixos",
"owner": "NixOS",
"ref": "nixos-unstable",
"repo": "nixpkgs",
"type": "github"
@ -45,18 +45,20 @@
"nixpkgs"
],
"plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
"r-nvim-nix": "r-nvim-nix",
"plugins-r": [
"plugins-r"
],
"rixpkgs": [
"rixpkgs"
],
"wrappers": "wrappers"
},
"locked": {
"lastModified": 1779544872,
"narHash": "sha256-AnuNQ9nbXrDYmL97TOejAds/FQOgD6FEOHABp/8dmsU=",
"lastModified": 1776413627,
"narHash": "sha256-pU3u7T4MqpjUWxflNvd4i47FURp756L7nMRL8MV+QEw=",
"owner": "dwinkler1",
"repo": "nvimConfig",
"rev": "aec9110e709e1aa50d78f06293c4bde14974b23f",
"rev": "2617face3b1be40534d2cae7f0a374a062b3710d",
"type": "github"
},
"original": {
@ -81,26 +83,20 @@
"type": "github"
}
},
"r-nvim-nix": {
"inputs": {
"nixpkgs": [
"nvimConfig",
"rixpkgs"
],
"rnvimsrc": "rnvimsrc"
},
"plugins-r": {
"flake": false,
"locked": {
"lastModified": 1779438909,
"narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
"owner": "dwinkler1",
"repo": "r_nvim_nix",
"rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
"lastModified": 1769881528,
"narHash": "sha256-oQSHHu6filJkAyH94yEvyTVuxA+5MU2dMOEAnsIjJKQ=",
"owner": "R-nvim",
"repo": "R.nvim",
"rev": "958b472d763cb258927c7ef69af4fd9945cc5469",
"type": "github"
},
"original": {
"owner": "dwinkler1",
"ref": "v0.99.4",
"repo": "r_nvim_nix",
"owner": "R-nvim",
"ref": "v0.99.3",
"repo": "R.nvim",
"type": "github"
}
},
@ -115,25 +111,8 @@
},
"original": {
"owner": "dwinkler1",
"ref": "nixpkgs",
"repo": "rixpkgs",
"rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
"type": "github"
}
},
"rnvimsrc": {
"flake": false,
"locked": {
"lastModified": 1776905071,
"narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
"owner": "R-nvim",
"repo": "R.nvim",
"rev": "582f2af11290ac067e49018db38e12a511325556",
"type": "github"
},
"original": {
"owner": "R-nvim",
"ref": "v0.99.4",
"repo": "R.nvim",
"type": "github"
}
},
@ -142,6 +121,7 @@
"fran": "fran",
"nixpkgs": "nixpkgs",
"nvimConfig": "nvimConfig",
"plugins-r": "plugins-r",
"rixpkgs": "rixpkgs"
}
},
@ -153,11 +133,11 @@
]
},
"locked": {
"lastModified": 1779297405,
"narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
"lastModified": 1776375800,
"narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
"owner": "BirdeeHub",
"repo": "nix-wrapper-modules",
"rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
"rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
"type": "github"
},
"original": {

View file

@ -6,36 +6,8 @@
nixpkgs,
nvimConfig,
...
}: let
systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
forAllSystems = nixpkgs.lib.genAttrs systems;
mkPkgs = system:
import nixpkgs {
inherit system;
config.allowUnfree = true;
overlays = [nvimConfig.overlays.dependencies];
};
projectModule = pkgs: let
baseConfig = nvimConfig.wrapperConfigs.default {inherit pkgs;};
extraRPackages =
if builtins.pathExists ./r-packages.nix
then import ./r-packages.nix pkgs.rpkgs
else [];
extraPythonPackages =
if builtins.pathExists ./python-packages.nix
then import ./python-packages.nix pkgs.python3Packages
else [];
extraJuliaPackages =
if builtins.pathExists ./julia-packages.nix
then import ./julia-packages.nix
else [];
projectName = builtins.baseNameOf (toString self.outPath);
in {
} @ inputs: let
projectSettings = {pkgs}: {
cats = {
clickhouse = false;
gitPlugins = false;
@ -45,117 +17,123 @@
nix = true;
optional = false;
python = false;
r = true;
r = false;
};
settings = {
settings = let
# With `replace` packages are replaced otherwise they are merged with base packages
replace = pkgs.lib.mkForce;
in {
lang_packages = {
python = with pkgs.python3Packages;
[
requests
]
++ extraPythonPackages;
r =
(with pkgs.rpkgs.rPackages; [
arrow
data_table
fixest
pkgs.nvimcom
python = replace (
(with pkgs.python3Packages; [
duckdb
polars
])
++ extraRPackages;
++ (
if builtins.pathExists ./python-packages.nix
# p: with p; [ ... ]
then import ./python-packages.nix pkgs.python3Packages
else []
)
);
julia =
["StatsBase"]
++ extraJuliaPackages;
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 = "tokyonight"; #"kanagawa";
colorscheme = "kanagawa";
background = "dark";
wrapRc = true;
};
binName = "vv";
binName = "nv";
env.IS_PROJECT_EDITOR = "1";
catPkgs = {
always = [
pkgs.git
pkgs.pre-commit
pkgs.cowsay
];
nix = [
pkgs.nil
pkgs.nixfmt
];
env = {
IS_PROJECT_EDITOR = "1";
R_LIBS_USER = "./.nvimcom";
};
specs.extraLua = {
extraPackages = with pkgs; [
cowsay
];
specs.extraLua = let
name = builtins.baseNameOf (builtins.toString ./.);
in {
data = pkgs.vimPlugins.mini-notify;
before = ["INIT_MAIN"];
data = pkgs.writeText "project-startup.lua" ''
config = ''
require("mini.notify").setup()
vim.notify = MiniNotify.make_notify()
vim.notify("Welcome to ${projectName}!")
vim.notify("Welcome to ${name}!")
'';
};
};
in {
formatter = forAllSystems (system: (mkPkgs system).nixfmt-tree);
packages = forAllSystems (system: let
pkgs = mkPkgs system;
systems = nixpkgs.lib.systems.flakeExposed;
forAllSystems = nixpkgs.lib.genAttrs systems;
overlays = [inputs.nvimConfig.overlays.dependencies];
in {
default = nvimConfig.lib.mkWrapper {
inherit pkgs;
modules = [(projectModule pkgs)];
};
packages = forAllSystems (system: let
pkgs = import nixpkgs {inherit system overlays;};
baseNvim = nvimConfig.packages.${system}.default;
nvim = (baseNvim.eval (projectSettings {inherit pkgs;})).config.wrapper;
default = nvim;
in {
default = nvim;
});
devShells = forAllSystems (system: let
pkgs = mkPkgs system;
evalResult = nvimConfig.lib.eval {
inherit pkgs;
modules = [(projectModule pkgs)];
};
nv = evalResult.config.wrap {inherit pkgs;};
pkgs = import nixpkgs {inherit system overlays;};
nv = self.packages.${system}.default;
in {
default = pkgs.mkShell {
packages =
[
nv
pkgs.nushell
]
++ nvimConfig.lib.devShellPackages evalResult.config;
shellHook =
nvimConfig.lib.shellHook evalResult.config
+ ''
if [ -z "''${NO_NUSHELL:-}" ]; then
exec nu
fi
'';
packages = [nv pkgs.updateR];
};
});
};
inputs = {
nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
fran = {
url = "github:dwinkler1/fran";
inputs.nixpkgs.follows = "rixpkgs";
inputs = {
nixpkgs.follows = "rixpkgs";
};
};
nvimConfig = {
url = "github:dwinkler1/nvimConfig";
inputs = {
nixpkgs.follows = "nixpkgs";
rixpkgs.follows = "rixpkgs";
nixpkgs.follows = "nixpkgs";
fran.follows = "fran";
"plugins-r".follows = "plugins-r";
};
};
"plugins-r" = {
url = "github:R-nvim/R.nvim/v0.99.3";
flake = false;
};
};
}

View file

@ -185,6 +185,10 @@
julia = config.enabledLanguages.julia;
python = config.enabledLanguages.python;
r = config.enabledLanguages.r;
# Enable markdown/quarto plugins whenever R is active so that
# .qmd buffers get proper syntax highlighting and chunk
# recognition via quarto-nvim and otter-nvim.
markdown = config.enabledLanguages.r;
project = true;
gitPlugins = config.enabledPackages.gitPlugins;
background = config.theme.background;
@ -202,11 +206,22 @@
# Development shell configuration
devShells = forSystems (system: let
pkgs = import nixpkgs {inherit system;};
# When R is enabled, build an overlaid pkgs that includes the R-enhanced
# quarto (with knitr and other R packages baked in via extraRPackages).
# This ensures `quarto render` from the terminal also works correctly.
rPkgs =
if config.enabledLanguages.r
then
import nixpkgs {
inherit system;
overlays = [rixOverlay rOverlay];
}
else pkgs;
# Language-specific packages that should be available in shell
languagePackages = with pkgs;
languagePackages =
[]
++ (if config.enabledLanguages.r then [quarto] else [])
++ (if config.enabledLanguages.python then [uv] else [])
++ (if config.enabledLanguages.r then [rPkgs.quarto] else [])
++ (if config.enabledLanguages.python then [pkgs.uv] else [])
++ (if config.enabledLanguages.julia then [] else []);
in {
default = pkgs.mkShell {

View file

@ -18,8 +18,10 @@ final: prev: let
broom # Tidy model outputs
data_table # Fast data manipulation
janitor # Data cleaning helpers
knitr # Required by Quarto to execute R code chunks
languageserver # LSP for IDE support
reprex # Reproducible examples
rmarkdown # Required by Quarto for R-based rendering
styler # Code formatting
tidyverse # Data science ecosystem
]

View file

@ -1,29 +0,0 @@
#!/usr/bin/env Rscript
packages <- c("arrow", "data.table", "fixest", "nvimcom")
failed <- character(0)
for (pkg in packages) {
ok <- tryCatch(
{
# nvimcom requires Neovim; skip loading but check it's installed
if (pkg == "nvimcom") {
requireNamespace(pkg, quietly = TRUE)
} else {
library(pkg, character.only = TRUE, quietly = TRUE)
}
TRUE
},
error = function(e) FALSE
)
if (!ok) {
failed <- c(failed, pkg)
}
}
if (length(failed) > 0) {
cat(sprintf("FAIL: %s\n", paste(failed, collapse = ", ")))
quit(status = 1)
}
cat("PASS: all packages loaded\n")

View file

@ -1,19 +0,0 @@
#!/usr/bin/env julia
packages = ["StatsBase"]
failed = String[]
for pkg in packages
try
@eval using $pkg
catch
push!(failed, pkg)
end
end
if !isempty(failed)
@error "FAIL: $(join(failed, ", "))"
exit(1)
end
println("PASS: all packages loaded")

View file

@ -1,17 +0,0 @@
#!/usr/bin/env python3
import sys
packages = ["requests"]
failed = []
for pkg in packages:
try:
__import__(pkg)
except ImportError:
failed.append(pkg)
if failed:
sys.stderr.write(f"FAIL: {', '.join(failed)}\n")
sys.exit(1)
print("PASS: all packages loaded")