Maintain dependencies and workspace lint coverage

.config/nextest.toml

@@ -7,15 +7,7 @@
 # whole job was SIGTERM-killed at the runner level) — nextest reports it as a
 # clean per-test timeout failure instead of stalling the job.
 #
-# The large headroom (300s, not a tight ~10s) is deliberate. The subprocess
-# example tests in tests/suites/examples.rs shell out to `cargo run --example
-# … --features ilp-highs`:
-#   - In the Test job, CI pre-builds those examples (see ci.yml) so the
-#     subprocess reuses artifacts and each test runs in well under a second.
-#   - In the Code Coverage job, the subprocess inherits llvm-cov's
-#     `-C instrument-coverage` RUSTFLAGS, so it recompiles the examples
-#     *instrumented* (a non-instrumented pre-build would not match its
-#     fingerprint, so pre-building there is pointless). That instrumented
-#     recompile legitimately takes >120s, hence the 300s bound.
+# The large headroom (300s, not a tight ~10s) is deliberate: this is a final
+# safety bound for genuinely hung tests, not the expected runtime budget.
 [profile.default]
 slow-timeout = { period = "60s", terminate-after = 5 }

.github/workflows/ci.yml

@@ -38,7 +38,7 @@ jobs:
       - name: Check formatting
         run: cargo fmt --all --check
 
-  # Lints.
+  # Lints every workspace crate with every feature (CLI `mcp`, `benchmarks`).
   clippy:
     name: Clippy
     runs-on: ubuntu-latest
@@ -49,7 +49,7 @@ jobs:
           components: clippy
       - uses: Swatinem/rust-cache@v2
       - name: Run clippy
-        run: cargo clippy --all-targets --features example-db -- -D warnings
+        run: cargo clippy --workspace --all-targets --all-features -- -D warnings
 
   # Build and exercise the HiGHS-backed CLI natively on Apple Silicon.
   macos-arm64:

Cargo.toml

@@ -21,25 +21,24 @@ example-db = []
 benchmarks = ["dep:criterion"]
 
 [dependencies]
-petgraph = { version = "0.8", features = ["serde-1"] }
-bitvec = "1.0"
-serde = { version = "1.0", features = ["derive"] }
+petgraph = { version = "0.8.3", features = ["serde-1"] }
+bitvec = "1.1.1"
+serde = { version = "1.0.229", features = ["derive"] }
 # Persisted problem and reduction data must preserve every finite f64 on replay.
-serde_json = { version = "1.0", features = ["float_roundtrip"] }
-thiserror = "2.0"
-num-bigint = "0.4"
-num-rational = "0.4"
-num-traits = "0.2"
+serde_json = { version = "1.0.151", features = ["float_roundtrip"] }
+thiserror = "2.0.20"
+num-bigint = "0.4.8"
+num-rational = "0.4.2"
+num-traits = "0.2.19"
 good_lp = { version = "=1.14.2", default-features = false, features = ["highs"] }
-inventory = "0.3"
-ordered-float = "5.0"
-rand = "0.10"
-criterion = { version = "0.8", optional = true }
+inventory = "0.3.24"
+rand = "0.10.2"
+criterion = { version = "0.8.2", optional = true }
 problemreductions-macros = { version = "0.6.0", path = "problemreductions-macros" }
 problemreductions-expr = { version = "0.6.0", path = "problemreductions-expr" }
 
 [dev-dependencies]
-proptest = "1.0"
+proptest = "1.11.0"
 
 [[bench]]
 name = "solver_benchmarks"

Makefile

@@ -89,7 +89,7 @@ fmt-check:
 
 # Run clippy
 clippy:
-	cargo clippy --all-targets --features "$(TEST_FEATURES)" -- -D warnings
+	cargo clippy --workspace --all-targets --all-features -- -D warnings
 
 node_modules/elkjs/package.json: package.json package-lock.json
 	npm ci

codecov.yml

@@ -10,11 +10,11 @@ coverage:
     project:
       default:
         target: 95%
-        threshold: 2%
+        threshold: 0%
     patch:
       default:
         target: 95%
-        threshold: 2%
+        threshold: 0%
 
 # Exclude proc-macro crate from coverage since it runs at compile time
 # and traditional runtime coverage tools cannot measure it.

problemreductions-cli/Cargo.toml

@@ -17,19 +17,18 @@ path = "src/bin/pred_sym.rs"
 
 [features]
 all = ["mcp"]
-mcp = ["dep:rmcp", "dep:tokio", "dep:schemars", "dep:tracing", "dep:tracing-subscriber"]
+mcp = ["dep:rmcp", "dep:tokio", "dep:schemars", "dep:tracing-subscriber"]
 
 [dependencies]
 problemreductions = { version = "0.6.0", path = "..", features = ["example-db"] }
-clap = { version = "4", features = ["derive", "string"] }
-anyhow = "1"
-serde = { version = "1", features = ["derive"] }
-serde_json = "1"
-num-bigint = "0.4"
-clap_complete = "4"
-owo-colors = { version = "4", features = ["supports-colors"] }
-rmcp = { version = "1.2", features = ["server", "macros", "transport-io"], optional = true }
-tokio = { version = "1", features = ["full"], optional = true }
-schemars = { version = "1.0", optional = true }
-tracing = { version = "0.1", optional = true }
-tracing-subscriber = { version = "0.3", optional = true }
+clap = { version = "4.6.7", features = ["derive", "string"] }
+anyhow = "1.0.104"
+serde = { version = "1.0.229", features = ["derive"] }
+serde_json = "1.0.151"
+num-bigint = "0.4.8"
+clap_complete = "4.6.11"
+owo-colors = { version = "4.4.0", features = ["supports-colors"] }
+rmcp = { version = "3.4.0", features = ["server", "macros", "transport-io"], optional = true }
+tokio = { version = "1.53.1", features = ["rt-multi-thread"], optional = true }
+schemars = { version = "1.2.2", optional = true }
+tracing-subscriber = { version = "0.3.23", optional = true }

problemreductions-cli/src/mcp/prompts.rs

@@ -1,4 +1,4 @@
-use rmcp::model::{GetPromptResult, Prompt, PromptArgument, PromptMessage, PromptMessageRole};
+use rmcp::model::{GetPromptResult, Prompt, PromptArgument, PromptMessage, Role};
 
 /// Return the list of available MCP prompt templates.
 pub fn list_prompts() -> Vec<Prompt> {
@@ -88,11 +88,8 @@ pub fn list_prompts() -> Vec<Prompt> {
 }
 
 fn prompt_result(description: &str, user_message: &str) -> GetPromptResult {
-    GetPromptResult::new(vec![PromptMessage::new_text(
-        PromptMessageRole::User,
-        user_message,
-    )])
-    .with_description(description)
+    GetPromptResult::new(vec![PromptMessage::new_text(Role::User, user_message)])
+        .with_description(description)
 }
 
 /// Return the content for the named prompt, or `None` if the name is unknown.

problemreductions-cli/src/mcp/tools.rs

@@ -615,14 +615,14 @@ impl McpServer {
 
 #[rmcp::tool_handler]
 impl rmcp::ServerHandler for McpServer {
-    fn get_info(&self) -> rmcp::model::ServerInfo {
+    fn get_info(&self) -> rmcp::model::ServerConfig {
         let capabilities = rmcp::model::ServerCapabilities::builder()
             .enable_tools()
             .enable_prompts()
             .build();
         let server_info =
             rmcp::model::Implementation::new("problemreductions", env!("CARGO_PKG_VERSION"));
-        rmcp::model::ServerInfo::new(capabilities)
+        rmcp::model::ServerConfig::new(capabilities)
             .with_server_info(server_info)
             .with_instructions(
                 "MCP server for NP-hard problem reductions. \
@@ -647,11 +647,13 @@ impl rmcp::ServerHandler for McpServer {
         &self,
         request: rmcp::model::GetPromptRequestParams,
         _context: rmcp::service::RequestContext<rmcp::RoleServer>,
-    ) -> Result<rmcp::model::GetPromptResult, rmcp::ErrorData> {
+    ) -> Result<rmcp::model::GetPromptResponse, rmcp::ErrorData> {
         let args = request.arguments.unwrap_or_default();
-        super::prompts::get_prompt(&request.name, &args).ok_or_else(|| {
-            rmcp::ErrorData::invalid_params(format!("Unknown prompt: {}", request.name), None)
-        })
+        super::prompts::get_prompt(&request.name, &args)
+            .map(Into::into)
+            .ok_or_else(|| {
+                rmcp::ErrorData::invalid_params(format!("Unknown prompt: {}", request.name), None)
+            })
     }
 }
 

problemreductions-cli/tests/mcp_integration.rs

@@ -115,7 +115,7 @@ mod mcp_tests {
     }
 
     #[test]
-    fn test_mcp_server_initialize_and_list_tools() {
+    fn test_mcp_server_initialize_list_and_call_tools() {
         let (mut stdin, mut reader, child) = spawn_mcp();
         initialize(&mut stdin, &mut reader);
 
@@ -192,11 +192,30 @@ mod mcp_tests {
             );
         }
 
+        send(
+            &mut stdin,
+            &serde_json::json!({
+                "jsonrpc": "2.0",
+                "id": 3,
+                "method": "tools/call",
+                "params": {"name": "list_problems", "arguments": {}}
+            }),
+        );
+        let call_resp = read_response(&mut reader);
+        assert_eq!(call_resp["id"], 3);
+        assert!(call_resp.get("error").is_none(), "{call_resp}");
+        assert_ne!(call_resp["result"]["isError"], true);
+        assert!(call_resp["result"]["content"][0]["text"]
+            .as_str()
+            .unwrap()
+            .contains("MaximumIndependentSet"));
+        assert!(call_resp["result"].get("resultType").is_none());
+
         shutdown(stdin, child);
     }
 
     #[test]
-    fn test_mcp_server_prompts_list() {
+    fn test_mcp_server_prompts_list_and_get() {
         let (mut stdin, mut reader, child) = spawn_mcp();
         initialize(&mut stdin, &mut reader);
 
@@ -244,6 +263,39 @@ mod mcp_tests {
         assert!(prompt_names.contains(&"find_reduction"));
         assert!(prompt_names.contains(&"overview"));
 
+        send(
+            &mut stdin,
+            &serde_json::json!({
+                "jsonrpc": "2.0",
+                "id": 3,
+                "method": "prompts/get",
+                "params": {"name": "what_is", "arguments": {"problem": "QUBO"}}
+            }),
+        );
+        let prompt_resp = read_response(&mut reader);
+        assert_eq!(prompt_resp["id"], 3);
+        let message = &prompt_resp["result"]["messages"][0];
+        assert_eq!(message["role"], "user");
+        assert_eq!(message["content"]["type"], "text");
+        assert!(message["content"]["text"]
+            .as_str()
+            .unwrap()
+            .contains("QUBO"));
+
+        send(
+            &mut stdin,
+            &serde_json::json!({
+                "jsonrpc": "2.0",
+                "id": 4,
+                "method": "prompts/get",
+                "params": {"name": "unknown"}
+            }),
+        );
+        let error_resp = read_response(&mut reader);
+        assert_eq!(error_resp["id"], 4);
+        assert_eq!(error_resp["error"]["code"], -32602);
+        assert_eq!(error_resp["error"]["message"], "Unknown prompt: unknown");
+
         shutdown(stdin, child);
     }
 }

problemreductions-expr/Cargo.toml

@@ -7,11 +7,11 @@ license = "MIT"
 repository = "https://github.com/CodingThrust/problem-reductions"
 
 [dependencies]
-num-bigint = { version = "0.4", features = ["serde"] }
-num-rational = { version = "0.4", features = ["serde"] }
-num-traits = "0.2"
-serde = { version = "1.0", features = ["derive"] }
-thiserror = "2.0"
+num-bigint = { version = "0.4.8", features = ["serde"] }
+num-rational = { version = "0.4.2", features = ["serde"] }
+num-traits = "0.2.19"
+serde = { version = "1.0.229", features = ["derive"] }
+thiserror = "2.0.20"
 
 [dev-dependencies]
-serde_json = "1.0"
+serde_json = "1.0.151"

problemreductions-macros/Cargo.toml

@@ -10,8 +10,8 @@ repository = "https://github.com/CodingThrust/problem-reductions"
 proc-macro = true
 
 [dependencies]
-syn = { version = "2.0", features = ["full", "parsing"] }
-quote = "1.0"
-proc-macro2 = "1.0"
+syn = { version = "3.0.6", features = ["full", "parsing"] }
+quote = "1.0.47"
+proc-macro2 = "1.0.107"
 problemreductions-expr = { version = "0.6.0", path = "../problemreductions-expr" }
-num-traits = "0.2"
+num-traits = "0.2.19"

problemreductions-macros/src/lib.rs

@@ -503,7 +503,7 @@ fn generate_reduction_entry(
     let trait_path = impl_block
         .trait_
         .as_ref()
-        .map(|(_, path, _)| path)
+        .map(|(path, _)| path)
         .ok_or_else(|| syn::Error::new_spanned(impl_block, "Expected impl ReduceTo<T> for S"))?;
 
     // Extract target type from ReduceTo<Target>