Feat/codelist systems

.github/workflows/run_preflight.yml

@@ -37,3 +37,6 @@ jobs:
       - name: Clippy check
         working-directory: rust
         run: cargo clippy --all-targets --all-features -- -D warnings
+
+      - name: Unused dependency check
+        uses: bnjbvr/cargo-machete@main

.github/workflows/run_python_unit_tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
       - uses: actions/checkout@v3

Cargo.toml

@@ -1,6 +1,8 @@
 [workspace]
+resolver = "3"
 members = [
     "rust/codelist-rs",
+    "rust/codelist-systems-rs",
     "rust/codelist-validator-rs",
     "rust/codelist-builder-rs",
     "bindings/python",

Justfile

@@ -1,15 +1,27 @@
+# Default recipe: list all available recipes when you run `just` with no args
+default:
+    @just --list
+
+# List all available recipes
+list:
+    @just --list
+
 # Ensure Rust code is formatted
 fmt:
     cargo fmt
 
 # Check if Rust code is formatted (used in CI)
 fmt-check:
-    cargo fmt -- --check
+    cargo fmt --all -- --check
 
 # Run Clippy with warnings treated as errors
 clippy:
     cargo clippy -- -D warnings
 
+# Scan Cargo.toml files for unused dependencies
+machete:
+    cargo machete
+
 # Run Prettier on Markdown files
 prettier:
     npx prettier --write "**/*.md"
@@ -18,17 +30,18 @@ prettier:
 prettier-check:
     npx prettier --check "**/*.md"
 
-# CI task: check formatting and linting and all tests
-ci: fmt-check clippy prettier-check test-python test-rust
+# CI task: check formatting, linting, unused deps, and all tests
+ci: fmt-check clippy machete prettier-check test-python test-rust
 
-# Run python tests.
 # Requires an active Python venv (run `source bindings/python/.venv/bin/activate`
 # first). `maturin develop` builds the extension and installs it into the
 # active venv so the tests exercise the current Rust code, not a stale wheel.
+#
+# Run python tests
 test-python:
     maturin develop --manifest-path bindings/python/Cargo.toml
     sh bindings/python/tests/run.sh
 
 # Run rust tests
 test-rust:
-    cargo test --all-features
+    cargo test --all-features

bindings/python/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "codelists_rs"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 
 [lib]
 name = "codelists_rs"

bindings/python/src/codelist.rs

@@ -15,10 +15,10 @@ use codelist_rs::{
 use codelist_validator_rs::validator::Validator;
 use indexmap::IndexSet;
 use pyo3::{
+    PyErr, PyResult,
     exceptions::PyValueError,
     prelude::*,
     types::{PyDict, PySet},
-    PyErr, PyResult,
 };
 use regex::Regex;
 
@@ -53,7 +53,7 @@ impl PyCodeList {
             _ => {
                 return Err(PyErr::new::<pyo3::exceptions::PyValueError, _>(format!(
                     "Invalid codelist type: {codelist_type}"
-                )))
+                )));
             }
         };
 

bindings/python/src/factory.rs

@@ -29,7 +29,7 @@ impl PyCodeListFactory {
             _ => {
                 return Err(PyValueError::new_err(format!(
                     "Invalid codelist type: {codelist_type}"
-                )))
+                )));
             }
         };
 

bindings/r/src/rust/Cargo.toml

@@ -2,8 +2,8 @@
 name = 'codelist'
 publish = false
 version = '0.1.0'
-edition = '2021'
-rust-version = '1.65'
+edition = '2024'
+rust-version = '1.85'
 
 [lib]
 crate-type = [ 'staticlib' ]

rust/codelist-builder-rs/Cargo.toml

@@ -1,19 +1,17 @@
 [package]
 name = "codelist-builder-rs"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 authors = ["Caroline Morton <caroline@parakeetconsulting.com>"]
 description = "Builder library for medical codelists"
 
 [dependencies]
-codelist-rs = { path = "../codelist-rs" }
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 thiserror = { version = "2.0.9" }
 thiserror-ext = { version = "0.2.1" }
 reqwest = { version = "0.12.2" }
 csv = { version = "1.3.1" }
-async-trait = "0.1"
 
 [dev-dependencies]
 tokio = { version = "1.0", features = ["full"] }

rust/codelist-rs/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "codelist-rs"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 authors = ["Caroline Morton <caroline@parakeetconsulting.com>", "Emma Bagshaw"]
 description = "Base library for medical code list handling"
 

rust/codelist-rs/src/codelist.rs

@@ -100,11 +100,7 @@ impl CodeList {
     ///   found
     pub fn remove_entry(&mut self, code: &str) -> Result<(), CodeListError> {
         let removed = self.entries.remove(code);
-        if removed.is_some() {
-            Ok(())
-        } else {
-            Err(CodeListError::entry_not_found(code))
-        }
+        if removed.is_some() { Ok(()) } else { Err(CodeListError::entry_not_found(code)) }
     }
 
     /// Get the full entries of the codelist, including code, optional term and

rust/codelist-rs/src/codelist_factory.rs

@@ -290,17 +290,16 @@ impl CodeListFactory {
             let path = entry.path();
 
             // Skips if not csv/json
-            if let Some(ext) = path.extension().and_then(|e| e.to_str()) {
-                if ext == "csv" || ext == "json" {
-                    if let Some(path_str) = path.to_str() {
-                        // TODO: We are using the file name as the codelist name, but this may not
-                        // be the best approach
-                        if let Ok(codelist) =
-                            self.load_codelist_from_file(folder_path.to_string(), path_str)
-                        {
-                            codelists.push(codelist);
-                        }
-                    }
+            if let Some(ext) = path.extension().and_then(|e| e.to_str())
+                && (ext == "csv" || ext == "json")
+                && let Some(path_str) = path.to_str()
+            {
+                // TODO: We are using the file name as the codelist name, but this may not
+                // be the best approach
+                if let Ok(codelist) =
+                    self.load_codelist_from_file(folder_path.to_string(), path_str)
+                {
+                    codelists.push(codelist);
                 }
             }
         }
@@ -482,18 +481,24 @@ C03,Test Disease 3,Description 3";
         assert_eq!(codelist.entries.len(), 3);
 
         // Test individual entries exist
-        assert!(codelist
-            .entries
-            .iter()
-            .any(|e| e.0 == "A01" && e.1 .0 == Some("Test Disease 1".to_string())));
-        assert!(codelist
-            .entries
-            .iter()
-            .any(|e| e.0 == "B02" && e.1 .0 == Some("Test Disease 2".to_string())));
-        assert!(codelist
-            .entries
-            .iter()
-            .any(|e| e.0 == "C03" && e.1 .0 == Some("Test Disease 3".to_string())));
+        assert!(
+            codelist
+                .entries
+                .iter()
+                .any(|e| e.0 == "A01" && e.1.0 == Some("Test Disease 1".to_string()))
+        );
+        assert!(
+            codelist
+                .entries
+                .iter()
+                .any(|e| e.0 == "B02" && e.1.0 == Some("Test Disease 2".to_string()))
+        );
+        assert!(
+            codelist
+                .entries
+                .iter()
+                .any(|e| e.0 == "C03" && e.1.0 == Some("Test Disease 3".to_string()))
+        );
 
         assert!(!codelist.codelist_options.allow_duplicates);
         assert_eq!(codelist.codelist_options.code_column_name, "code".to_string());
@@ -690,18 +695,24 @@ A01"; // Missing columns
         assert_eq!(codelist.entries.len(), 3);
 
         // Test individual entries exist
-        assert!(codelist
-            .entries
-            .iter()
-            .any(|e| e.0 == "A01" && e.1 .0 == Some("Test Disease 1".to_string())));
-        assert!(codelist
-            .entries
-            .iter()
-            .any(|e| e.0 == "B02" && e.1 .0 == Some("Test Disease 2".to_string())));
-        assert!(codelist
-            .entries
-            .iter()
-            .any(|e| e.0 == "C03" && e.1 .0 == Some("Test Disease 3".to_string())));
+        assert!(
+            codelist
+                .entries
+                .iter()
+                .any(|e| e.0 == "A01" && e.1.0 == Some("Test Disease 1".to_string()))
+        );
+        assert!(
+            codelist
+                .entries
+                .iter()
+                .any(|e| e.0 == "B02" && e.1.0 == Some("Test Disease 2".to_string()))
+        );
+        assert!(
+            codelist
+                .entries
+                .iter()
+                .any(|e| e.0 == "C03" && e.1.0 == Some("Test Disease 3".to_string()))
+        );
 
         assert!(!codelist.codelist_options.allow_duplicates);
         assert_eq!(codelist.codelist_options.code_column_name, "code".to_string());

rust/codelist-rs/src/metadata/categorisation_and_usage.rs

@@ -259,7 +259,10 @@ mod tests {
         let mut categorisation_and_usage = test_categorisation_and_usage_all_some();
         let error = categorisation_and_usage.add_license("license1".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "License already exists: Unable to add license license1. Please use update license instead.");
+        assert_eq!(
+            error_string,
+            "License already exists: Unable to add license license1. Please use update license instead."
+        );
         Ok(())
     }
 
@@ -277,7 +280,10 @@ mod tests {
         let mut categorisation_and_usage = test_categorisation_and_usage_all_none();
         let error = categorisation_and_usage.update_license("example".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "License does not exist: Unable to update license example. Please use add license instead.");
+        assert_eq!(
+            error_string,
+            "License does not exist: Unable to update license example. Please use add license instead."
+        );
         Ok(())
     }
 

rust/codelist-rs/src/metadata/purpose_and_context.rs

@@ -285,7 +285,10 @@ mod tests {
         let error =
             purpose_and_context.add_target_audience("Target Audience".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Target audience already exists: Unable to add target audience. Please use update target audience instead.");
+        assert_eq!(
+            error_string,
+            "Target audience already exists: Unable to add target audience. Please use update target audience instead."
+        );
         Ok(())
     }
 
@@ -303,7 +306,10 @@ mod tests {
         let error =
             purpose_and_context.update_target_audience("Target Audience".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Target audience does not exist: Unable to update target audience. Please use add target audience instead.");
+        assert_eq!(
+            error_string,
+            "Target audience does not exist: Unable to update target audience. Please use add target audience instead."
+        );
         Ok(())
     }
 
@@ -340,7 +346,10 @@ mod tests {
         let mut purpose_and_context = create_test_purpose_and_context_all_params_are_some();
         let error = purpose_and_context.add_use_context("Use Context".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Use context already exists: Unable to add use context. Please use update use context instead.");
+        assert_eq!(
+            error_string,
+            "Use context already exists: Unable to add use context. Please use update use context instead."
+        );
         Ok(())
     }
 
@@ -357,7 +366,10 @@ mod tests {
         let mut purpose_and_context = create_test_purpose_and_context_all_params_are_none();
         let error = purpose_and_context.update_use_context("Use Context".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Use context does not exist: Unable to update use context. Please use add use context instead.");
+        assert_eq!(
+            error_string,
+            "Use context does not exist: Unable to update use context. Please use add use context instead."
+        );
         Ok(())
     }
 

rust/codelist-rs/src/metadata/validation_and_review.rs

@@ -395,7 +395,10 @@ mod tests {
         let mut validation_and_review = test_validation_and_review_all_params_are_some_or_true();
         let error = validation_and_review.add_review_date(chrono::Utc::now()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Review date already exists: Unable to add review date. Please use update review date instead.");
+        assert_eq!(
+            error_string,
+            "Review date already exists: Unable to add review date. Please use update review date instead."
+        );
         Ok(())
     }
 
@@ -414,7 +417,10 @@ mod tests {
         let mut validation_and_review = test_validation_and_review_all_params_are_none();
         let error = validation_and_review.update_review_date(chrono::Utc::now()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Review date does not exist: Unable to update review date. Please use add review date instead.");
+        assert_eq!(
+            error_string,
+            "Review date does not exist: Unable to update review date. Please use add review date instead."
+        );
         Ok(())
     }
 
@@ -513,7 +519,10 @@ mod tests {
         let error =
             validation_and_review.add_validation_notes("Validation Notes".to_string()).unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Validation notes already exist: Unable to add validation notes. Please use update validation notes instead.");
+        assert_eq!(
+            error_string,
+            "Validation notes already exist: Unable to add validation notes. Please use update validation notes instead."
+        );
         Ok(())
     }
 
@@ -536,7 +545,10 @@ mod tests {
             .update_validation_notes("Validation Notes".to_string())
             .unwrap_err();
         let error_string = error.to_string();
-        assert_eq!(error_string, "Validation notes do not exist: Unable to update validation notes. Please use add validation notes instead.");
+        assert_eq!(
+            error_string,
+            "Validation notes do not exist: Unable to update validation notes. Please use add validation notes instead."
+        );
         Ok(())
     }