codingest 0.2.2__tar.gz → 0.2.3__tar.gz

{codingest-0.2.2 → codingest-0.2.3}/Cargo.lock

@@ -308,7 +308,7 @@ dependencies = [
 
 [[package]]
 name = "codingest"
-version = "0.2.2"
+version = "0.2.3"
 dependencies = [
  "aho-corasick",
  "base64 0.22.1",
@@ -330,8 +330,10 @@ dependencies = [
  "tree-sitter-html",
  "tree-sitter-java",
  "tree-sitter-javascript",
+ "tree-sitter-julia",
  "tree-sitter-php",
  "tree-sitter-python",
+ "tree-sitter-r",
  "tree-sitter-rust",
  "tree-sitter-swift",
  "tree-sitter-typescript",
@@ -340,7 +342,7 @@ dependencies = [
 
 [[package]]
 name = "codingest-cli"
-version = "0.2.2"
+version = "0.2.3"
 dependencies = [
  "anyhow",
  "clap",
@@ -352,7 +354,7 @@ dependencies = [
 
 [[package]]
 name = "codingest-mcp"
-version = "0.2.2"
+version = "0.2.3"
 dependencies = [
  "anyhow",
  "codingest",
@@ -361,7 +363,7 @@ dependencies = [
 
 [[package]]
 name = "codingest-py"
-version = "0.2.2"
+version = "0.2.3"
 dependencies = [
  "codingest",
  "codingest-cli",
@@ -1388,9 +1390,9 @@ dependencies = [
 
 [[package]]
 name = "kglite"
-version = "0.15.13"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "30cb58ba44e467d5f0892ad1d2ccb70747b0b72c9e6264d3516fd179eb4e7d7c"
+checksum = "929b7d190017068c56ffd40e74f3f8eebd5ddf57c5da6f17d33ab4f5aa30bc10"
 dependencies = [
  "bzip2",
  "chrono",
@@ -1423,9 +1425,9 @@ dependencies = [
 
 [[package]]
 name = "kglite-mcp-server"
-version = "0.15.13"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a5d069a5d728179b2b5e7045caa3e0e4ad1d81e6220d33d7b7de8d32b988334"
+checksum = "f2dc4bfa9bc451a1d9c18768216a7fe1d8a68f9bab6ed6375365ce75c90c163e"
 dependencies = [
  "anyhow",
  "bytes",
@@ -2739,6 +2741,16 @@ dependencies = [
  "tree-sitter-language",
 ]
 
+[[package]]
+name = "tree-sitter-julia"
+version = "0.23.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4144731a178812ee867619b1e98b3b91e54c1652304b26e5ebe3175b701de323"
+dependencies = [
+ "cc",
+ "tree-sitter-language",
+]
+
 [[package]]
 name = "tree-sitter-language"
 version = "0.1.7"
@@ -2765,6 +2777,16 @@ dependencies = [
  "tree-sitter-language",
 ]
 
+[[package]]
+name = "tree-sitter-r"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ffc9954ec870dcad6cffdd302b405306c68cf031ed79a78cd9746f6740d9fe20"
+dependencies = [
+ "cc",
+ "tree-sitter-language",
+]
+
 [[package]]
 name = "tree-sitter-rust"
 version = "0.24.2"

{codingest-0.2.2 → codingest-0.2.3}/Cargo.toml

@@ -3,7 +3,7 @@ members = ["crates/codingest", "crates/codingest-cli", "crates/codingest-mcp", "
 resolver = "2"
 
 [workspace.package]
-version = "0.2.2"
+version = "0.2.3"
 edition = "2021"
 rust-version = "1.88"
 license = "MIT"
@@ -12,11 +12,27 @@ repository = "https://github.com/kkollsga/codingest"
 [workspace.dependencies]
 base64 = "0.22"
 sha2 = "0.11"
-# kglite engine + MCP server — imported as crates.io libraries. The 0.15.13
-# floor adds 0.15.13's planner fix for joins filtered on a type's title/id field
-# (anchored traversals 5.7-327x faster here; see BENCHMARKS.md 0.2.1) on top of
-# the 0.15.11 floor, which brought three things, only one of which changed what
-# we run:
+# kglite engine + MCP server — imported as crates.io libraries. The 0.16.1
+# floor picks up the wire-JSON break (kglite_value_to_json emits real JSON for
+# nine variants — our CLI renders through it, so expectations pin the NEW
+# shapes and an older engine would fail them) on top of the 0.16.0
+# base, which is a HARD floor, not a preference: 0.16.0 writes `.kgl` container v6,
+# which kglite 0.15.14 and earlier refuse by version number. Because
+# `codingest.build()` writes the bytes with the Rust engine compiled in here and
+# reads them back through the separately-installed Python `kglite` wheel, the
+# two sides must be on the same side of that break — hence `>=0.16.1,<0.17` in
+# pyproject.toml, and hence a reader on 0.15.x is not "old but workable", it is
+# a hard failure with `FileFormatError`.
+# 0.16.0 also removed `DirGraph::enable_columnar` from the public API (every
+# graph is columnar from its first node now); the two sites that open-coded
+# `prepare_save` + `enable_columnar` before a `.kgl` write moved to the
+# purpose-built `kglite::api::io::prepare_kgl_write`, which also keeps the
+# graph's copy-on-write lineage across that mutation — our `Arc::make_mut`
+# spelling did not.
+# It sits on top of the 0.15.13 floor, which added a planner fix for joins
+# filtered on a type's title/id field (anchored traversals 5.7-327x faster here;
+# see BENCHMARKS.md 0.2.1), and the 0.15.11 floor before it, which brought three
+# things, only one of which changed what we run:
 #   * 0.15.10's `add_connections` resolves its edge-property columns once per
 #     call instead of once per cell — upstream measured 66.7ms -> 30.4ms
 #     (-54%) on 60k edges x 10 property columns. That is exactly the shape of
@@ -69,8 +85,8 @@ sha2 = "0.11"
 # and no disk storage. Neither 0.15.7 nor 0.15.8 changes the `kglite::api` we
 # call, graph output, property encoding, or `.kgl` serialization.
 # Keep both libraries aligned so the graph and server share one engine release.
-kglite = { version = "0.15.13", default-features = false }
-kglite-mcp-server = { version = "0.15.13", default-features = false }
+kglite = { version = "0.16.1", default-features = false }
+kglite-mcp-server = { version = "0.16.1", default-features = false }
 
 # Mirror KGLite's release codegen so the standalone builder has
 # performance parity with the in-tree component (see KGLite

{codingest-0.2.2 → codingest-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codingest
-Version: 0.2.2
+Version: 0.2.3
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Rust
 Classifier: Topic :: Software Development
 Classifier: Topic :: Software Development :: Libraries
-Requires-Dist: kglite>=0.15.13,<0.16
+Requires-Dist: kglite>=0.16.1,<0.17
 License-File: LICENSE
 Summary: Build fast, queryable code graphs for AI agents, MCP code review, and local or GitHub repository analysis.
 Keywords: ai-agents,mcp,code-review,knowledge-graph,code-analysis,github,tree-sitter,cypher
@@ -53,7 +53,7 @@ graph.cypher("MATCH (f:Function) RETURN f.name LIMIT 10")
 ```
 
 No language servers, databases, or repository-specific build steps are
-required. The native Rust builder bundles parsers for 15 languages and returns
+required. The native Rust builder bundles parsers for 17 languages and returns
 a real `kglite.KnowledgeGraph`, ready for Cypher queries.
 
 ## Built for agents and code analysis
@@ -69,8 +69,9 @@ a real `kglite.KnowledgeGraph`, ready for Cypher queries.
 - **Open-source intelligence:** clone and analyse a GitHub repository with one
   Python call, or let an agent manage cached public repositories through MCP.
 - **Polyglot by default:** one graph across Python, Rust, TypeScript,
-  JavaScript, Java, Go, C/C++, C#, Swift, PHP, HTML, CSS, Dart, and AGC
-  assembly.
+  JavaScript, Java, Go, C/C++, C#, Swift, PHP, HTML, CSS, Dart, Julia, R,
+  and AGC assembly — capabilities per language in
+  [docs/languages.md](docs/languages.md).
 - **Revision-aware:** analyse a tag, branch, commit, or multiple revisions in
   one graph and query what changed.
 
@@ -191,7 +192,7 @@ codingest skill install        # code-review Agent Skill
 ```
 
 The wheel bundles every grammar plus the `codingest` and `codingest-mcp`
-commands. KGLite ≥0.15.13 is installed automatically as the query/storage
+commands. KGLite ≥0.16.1 is installed automatically as the query/storage
 engine; its MCP server and the transitive `mcp-methods` framework power the
 builder-aware Codingest server. Nothing else needs to be installed.
 
@@ -203,8 +204,8 @@ Python prerequisites.
 
 ```toml
 [dependencies]
-codingest = "0.1"
-kglite = "0.15.13"
+codingest = "0.2"
+kglite = "0.16.1"
 ```
 
 ```rust
@@ -276,7 +277,7 @@ diagnostic.
 ## Dependency policy
 
 `kglite` and `kglite-mcp-server` use matching crates.io requirements with a
-0.15.13 minimum and a shared lockfile. This keeps the builder, persistence
+0.16.1 minimum and a shared lockfile. This keeps the builder, persistence
 handoff, and embedded MCP server on one compatible engine patch line.
 
 ## Parity with the (now-removed) in-tree component

{codingest-0.2.2 → codingest-0.2.3}/README.md

@@ -26,7 +26,7 @@ graph.cypher("MATCH (f:Function) RETURN f.name LIMIT 10")
 ```
 
 No language servers, databases, or repository-specific build steps are
-required. The native Rust builder bundles parsers for 15 languages and returns
+required. The native Rust builder bundles parsers for 17 languages and returns
 a real `kglite.KnowledgeGraph`, ready for Cypher queries.
 
 ## Built for agents and code analysis
@@ -42,8 +42,9 @@ a real `kglite.KnowledgeGraph`, ready for Cypher queries.
 - **Open-source intelligence:** clone and analyse a GitHub repository with one
   Python call, or let an agent manage cached public repositories through MCP.
 - **Polyglot by default:** one graph across Python, Rust, TypeScript,
-  JavaScript, Java, Go, C/C++, C#, Swift, PHP, HTML, CSS, Dart, and AGC
-  assembly.
+  JavaScript, Java, Go, C/C++, C#, Swift, PHP, HTML, CSS, Dart, Julia, R,
+  and AGC assembly — capabilities per language in
+  [docs/languages.md](docs/languages.md).
 - **Revision-aware:** analyse a tag, branch, commit, or multiple revisions in
   one graph and query what changed.
 
@@ -164,7 +165,7 @@ codingest skill install        # code-review Agent Skill
 ```
 
 The wheel bundles every grammar plus the `codingest` and `codingest-mcp`
-commands. KGLite ≥0.15.13 is installed automatically as the query/storage
+commands. KGLite ≥0.16.1 is installed automatically as the query/storage
 engine; its MCP server and the transitive `mcp-methods` framework power the
 builder-aware Codingest server. Nothing else needs to be installed.
 
@@ -176,8 +177,8 @@ Python prerequisites.
 
 ```toml
 [dependencies]
-codingest = "0.1"
-kglite = "0.15.13"
+codingest = "0.2"
+kglite = "0.16.1"
 ```
 
 ```rust
@@ -249,7 +250,7 @@ diagnostic.
 ## Dependency policy
 
 `kglite` and `kglite-mcp-server` use matching crates.io requirements with a
-0.15.13 minimum and a shared lockfile. This keeps the builder, persistence
+0.16.1 minimum and a shared lockfile. This keeps the builder, persistence
 handoff, and embedded MCP server on one compatible engine patch line.
 
 ## Parity with the (now-removed) in-tree component

{codingest-0.2.2 → codingest-0.2.3}/crates/codingest/Cargo.toml

@@ -10,7 +10,7 @@ keywords = ["knowledge-graph", "code-analysis", "tree-sitter", "cypher", "kglite
 categories = ["development-tools", "parser-implementations"]
 
 # Requires the kglite 0.15 engine API (`kglite::api::code_entities`); the
-# workspace pins the current 0.15 patch floor (0.15.13).
+# workspace pins the current engine floor (0.16.1).
 
 [lib]
 name = "codingest"
@@ -63,6 +63,11 @@ tree-sitter-php = "0.24.2"
 tree-sitter-html = "0.23.2"
 tree-sitter-css = "0.25.0"
 tree-sitter-dart = "0.2.0"
+tree-sitter-r = "1.3.0"
+# 0.23.1 is the newest release (2024-09); it binds via tree-sitter-language
+# 0.1 (runtime-agnostic LanguageFn), so it carries no tree-sitter runtime
+# ceiling and links cleanly against tree-sitter 0.26.
+tree-sitter-julia = "0.23.1"
 toml = "1.1.3"
 walkdir = "2.5.0"
 tempfile = "3.27.0"

{codingest-0.2.2 → codingest-0.2.3}/crates/codingest/src/bin/codingest_stats.rs

@@ -132,7 +132,7 @@ fn edge_breakdown(graph: &DirGraph) -> BTreeMap<String, usize> {
         let Some((s, t)) = graph.graph.edge_endpoints(e) else {
             continue;
         };
-        let (Some(sn), Some(tn)) = (graph.graph.node_weight(s), graph.graph.node_weight(t)) else {
+        let (Some(sn), Some(tn)) = (graph.node_view(s), graph.node_view(t)) else {
             continue;
         };
         let key = edge_breakdown_key(
@@ -577,7 +577,7 @@ mod tests {
                     return None;
                 }
                 let (_, t) = graph.graph.edge_endpoints(e)?;
-                Some(short_name(&id_string(graph.graph.node_weight(t)?.id())).to_string())
+                Some(short_name(&id_string(graph.node_view(t)?.id())).to_string())
             })
             .collect();
         assert!(all.len() > 1, "need several distinct callees to prove sort");

{codingest-0.2.2 → codingest-0.2.3}/crates/codingest/src/builder/load.rs

@@ -603,7 +603,7 @@ impl<'a> LoadPipeline<'a> {
         // detectors live under `builder/routes/`. Adding a new framework is
         // one new file in that directory plus a line in routes/mod.rs.
         let (route_nodes, route_edges) =
-            super::routes::build_routes(&result.functions, &result.constants);
+            super::routes::build_routes(&result.files, &result.functions, &result.constants);
         if !route_nodes.is_empty() {
             maintain::add_nodes(
                 graph,
@@ -1481,6 +1481,22 @@ mod tests {
         assert!(qnames.contains(&"Foo.Bar.V2"));
     }
 
+    /// AGC's registry `module_sep` is `/` and that is LOAD-BEARING, not a
+    /// typo: the AGC parser emits slash-shaped module paths
+    /// (`"Comanche055/MAIN"`, see `parsers::agc::module_path`), and this is
+    /// the string `build_modules` splits. Its *qualified names* are dotted
+    /// (`"Comanche055.FIRST"`), but qnames never pass through the separator
+    /// fields — they only informed the `LangGroup::PythonJava` placement.
+    /// Switching the field to `.` would collapse the hierarchy below into a
+    /// single unparented `Comanche055/MAIN` module.
+    #[test]
+    fn build_modules_splits_agc_paths_on_slash() {
+        let files = vec![file_with_module("agc", "Comanche055/MAIN")];
+        let modules = build_modules(&files);
+        let qnames: Vec<&str> = modules.iter().map(|m| m.qualified_name.as_str()).collect();
+        assert_eq!(qnames, vec!["Comanche055", "Comanche055/MAIN"]);
+    }
+
     #[test]
     fn is_numeric_segment_detection() {
         assert!(is_numeric_segment("0"));