From 42a6fb552c7513e4d2ecef8e58b79217c1bcde40 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Sat, 25 Apr 2026 01:26:24 +0000
Subject: [PATCH] Add list_rules: populate quickfix window with all rules

M.list_rules() calls ensure_index(), collects every rule and checkpoint
from rule_cache into a quickfix list sorted by file then line number,
and opens the quickfix window. Each entry jumps directly to the rule
definition when selected with <CR>.

Returns a WARN notification if no rules are found (empty project or
cache not yet populated).

Suggested keymap: <Leader>r

https://claude.ai/code/session_019k8BeVivnvcEohfcZMttjZ
---
 README.md              | 14 +++++++++++++-
 lua/snakemake/init.lua | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d4dfc84..a07f628 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,11 @@ Place your cursor anywhere inside a Snakemake rule definition, press the keymap,
 
 **Subsequent uses:** if a `--forcerun` line is already present, the new rule name is appended to it (space-separated) — so you can build up a list of rules to force-rerun without editing `run.sh` by hand.
 
-### 2. Go to producer rule (`goto_producer`)
+### 2. Rule picker (`list_rules`)
+
+Press the keymap from anywhere and the plugin opens Neovim's built-in quickfix window listing every rule and checkpoint across all `Snakemake*`/`Snakefile*` files in the current working directory. Entries are sorted by file then line number. Navigate with standard quickfix commands (`<CR>` to jump, `:cn`/`:cp` to step through).
+
+### 3. Go to producer rule (`goto_producer`)
 
 Place your cursor on a quoted input filename inside any rule's `input:` block and press the keymap. The plugin will:
 
@@ -48,6 +52,10 @@ Both exact matches (pattern equals pattern) and concrete-to-wildcard matches are
     vim.keymap.set("n", "<Leader>o", function()
       require("snakemake").open_and_insert()
     end)
+    -- list all rules in the quickfix window
+    vim.keymap.set("n", "<Leader>r", function()
+      require("snakemake").list_rules()
+    end)
     -- jump to the rule that produces the file under cursor
     vim.keymap.set("n", "<Leader>g", function()
       require("snakemake").goto_producer()
@@ -58,6 +66,10 @@ Both exact matches (pattern equals pattern) and concrete-to-wildcard matches are
 
 ## Usage
 
+### Browsing all rules
+
+Press `<Leader>r` from anywhere. The quickfix window opens with every rule and checkpoint found across all Snakemake files, sorted by file and line number. Press `<CR>` on any entry to jump to that rule.
+
 ### Adding a rule to forcerun
 
 1. Open a Snakefile in Neovim
diff --git a/lua/snakemake/init.lua b/lua/snakemake/init.lua
index 8df32e4..b79d835 100644
--- a/lua/snakemake/init.lua
+++ b/lua/snakemake/init.lua
@@ -221,4 +221,36 @@ M.goto_producer = function()
   vim.notify("no rule found producing: " .. target, vim.log.levels.WARN)
 end
 
+-- Populate the quickfix list with every rule across all indexed Snakemake
+-- files and open the quickfix window.  Each entry jumps directly to the
+-- rule definition line when selected.
+M.list_rules = function()
+  ensure_index()
+
+  local items = {}
+  for _, rules in pairs(rule_cache) do
+    for _, rule in ipairs(rules) do
+      table.insert(items, {
+        filename = rule.file,
+        lnum     = rule.lnum,
+        col      = 1,
+        text     = rule.name,
+      })
+    end
+  end
+
+  if #items == 0 then
+    vim.notify("no rules found", vim.log.levels.WARN)
+    return
+  end
+
+  table.sort(items, function(a, b)
+    if a.filename ~= b.filename then return a.filename < b.filename end
+    return a.lnum < b.lnum
+  end)
+
+  vim.fn.setqflist({}, "r", { title = "Snakemake rules", items = items })
+  vim.cmd("copen")
+end
+
 return M