heading towards targeted chunk sizes, made sure updated files have old copies cleaned up

ReadMe.md

@@ -19,19 +19,22 @@ Opens `similarities.json`, reverses the sort order, and saves it as
 
 ### `refresh_sources.lua`
 Creates/Maintains a store of chunked data with embeddings based on configurable
-sources. Example:
+`sources.json`. Example:
 
 ```json
 {
   "source name":{
+    "embedding_model":"qwen3-embedding:0.6b",
     "filters":{
       "blacklist":[".git"],
       "extension_whitelist":["md"]
     },
     "initialize_command":"git clone REMOTE .",
+    "max_chunk_size":32768,
     "path":"will be created before initialize_command is run",
     "strip_frontmatter":true,
-    "refresh_command":"git reset --hard origin/main"
+    "target_chunk_size":3072,
+    "refresh_command":"git fetch origin && git reset --hard origin/main"
   }
 }
 ```
@@ -41,6 +44,9 @@ The filters are based on `utility.tree`'s filter options (optional).
 while `refresh_command` is run each time (optional).
 Commands will be run in the specified `path`.
 `strip_frontmatter` will remove YAML frontmatter (common in Markdown files).
+`embedding_model` and `max_chunk_size` are self-explanatory (optional).
+`target_chunk_size` (optional) allows for finer-grained chunks to be generated
+alongside the maximum overviews for more precise retrieval.
 
 The embeddings are stored like so:
 
@@ -55,7 +61,11 @@ The embeddings are stored like so:
 }
 ```
 
-TODO
+SHA2 512-bit sums are used to link a text chunk with its embedding. All file
+names reference a list of text chunks so they can handle being too large. Every
+file that is too large for a single chunk has a whole-file embedding calculated
+first (it is the first element of the array), so that if a whole file becomes
+relevant, it can still show up instead of only chunks.
 
 ### `synopsis_generator.lua`
 Chooses a random file within `notebook`, and generates a novel synopsis from it.
@@ -64,6 +74,25 @@ Arguments:
 - `refresh_file_list`: Refreshes the cached file list to choose from.
 - `export_ordered_list_of_prompts`: Makes an epub to review generated synopses.
 
+## JSON config
+This repo uses my utility library's config system, using a `config.json` file in
+the repo root that is excluded from commits.
+
+```json
+{
+  "models":{
+    "embedding":{
+      "model":"qwen3-embedding:0.6b",
+      "max_chunk_size":32768
+    },
+    "initialized_sources":{}
+  }
+}
+```
+
+`refresh_sources.lua` uses `models` to store default embedding model information
+and `initialized_sources` to store which sources have been initialized.
+
 ## Tasks
 - [ ] The whitelisting/blacklisting of tree should be in list too.
 - [ ] synopsis_generator should be able to blacklist files it already tried?

refresh_sources.lua

@@ -61,7 +61,7 @@ end
 
 
 local refresh_file_list = function(source_name, data_source)
-  timing.mark("Assembling file list for " .. source_name .. ".")
+  timing.mark("Assembling file list for \"" .. source_name .. "\"")
 
   local full_path = "PRIVATE_DATA" .. utility.path_separator .. data_source.path
   if data_source.initialize_command and (not config.models.initialized_sources[data_source.path]) then
@@ -87,7 +87,7 @@ local refresh_file_list = function(source_name, data_source)
     file_list[#file_list + 1] = file_name
   end)
 
-  timing.mark("Finished assembling file list for " .. source_name .. ".")
+  timing.mark("Finished assembling file list for \"" .. source_name .. "\"")
   return file_list
 end
 
@@ -104,20 +104,9 @@ local generate_embeddings = function(data_source, text)
   return json.decode(result)
 end
 
--- returns nothing for empty files and errors
+local make_chunks = function(text, chunk_size)
-local process_file = function(data_source, file_name)
+  assert(chunk_size, "make_chunks() requires chunk_size")
-  local text = utility.read_file(file_name)
 
-  if data_source.strip_frontmatter then
-    text = text_processing.strip_frontmatter(text)
-  end
-
-  if #text == 0 then
-    log("empty", file_name .. "\n is empty and being skipped.")
-    return
-  end
-
-  local chunk_size = data_source.max_chunk_size or config.models.embedding.max_chunk_size
   local half_chunk_size = math.floor(chunk_size / 2)
   local chunks = { text }
 
@@ -135,6 +124,25 @@ local process_file = function(data_source, file_name)
     end
   end
 
+  return chunks
+end
+
+-- returns nothing for empty files and errors
+local process_file = function(data_source, file_name)
+  local text = utility.read_file(file_name)
+
+  if data_source.strip_frontmatter then
+    text = text_processing.strip_frontmatter(text)
+  end
+
+  if #text == 0 then
+    log("empty", file_name .. "\n is empty and being skipped.")
+    return
+  end
+
+  local chunk_size = data_source.max_chunk_size or config.models.embedding.max_chunk_size
+  local chunks = make_chunks(text, chunk_size)
+
   local new_embeddings = {}
   for i = 1, #chunks do
     log("debug", "Embedding length:", #chunks[i])
@@ -202,6 +210,15 @@ local memorize_file = function(data_source, file_name)
   return file_sums
 end
 
+local delete_memories = function(sha512sum_list)
+  -- if true then return end -- TEMP disabling removal to compare and verify function
+  for i = 1, #sha512sum_list do
+    local sha512sum = sha512sum_list[i]
+    embeddings.vectors[sha512sum] = nil
+    os.execute("rm " .. (memory_path .. utility.path_separator .. sha512sum):enquote())
+  end
+end
+
 local refresh_sources = function()
   os.execute("mkdir -p " .. memory_path:enquote())
 
@@ -230,6 +247,7 @@ local refresh_sources = function()
       local function loop()
         local sha512sum = utility.sha512sum(file_name)
         log("sha", file_name, sha512sum, "\n Sum present? " .. tostring(embeddings.vectors[sha512sum]))
+
         if embeddings.vectors[sha512sum] then
           log("debug", file_name .. "\n has already been embedded, skipping.")
           -- add file reference if it was missing
@@ -239,7 +257,13 @@ local refresh_sources = function()
           return
         end
 
-        log("debug", "Generating embeddings for " .. file_name .. ".")
+        if embeddings.files[file_name] then
+          log("debug", file_name .. "\n Removing old embeddings for modified file.")
+          delete_memories(embeddings.files[file_name])
+          embeddings.files[file_name] = nil
+        end
+
+        log("debug", file_name .. "\n Generating embeddings..")
         local file_sums = memorize_file(data_source, file_name)
         embeddings.files[file_name] = file_sums
       end