Refactor all examples into examples/ (#85)

Author: molpopgen

.github/workflows/tests.yml

@@ -30,14 +30,14 @@ jobs:
         with:
           toolchain: ${{ matrix.rust }}
           override: true
-      - run: cargo check
+      - name: cargo check
+        run: cargo check
+      - name: cargo check examples
+        run: cargo check --examples
       - name: run tests
         run: |
             cargo test
             cargo test --examples
-      - name: check examples
-        working-directory: tskit_rust_examples
-        run: cargo check
 
   build-osx:
     runs-on: macos-latest
@@ -55,14 +55,14 @@ jobs:
         with:
           toolchain: ${{ matrix.rust }}
           override: true
-      - run: cargo check
+      - name: cargo check
+        run: cargo check
+      - name: cargo check examples
+        run: cargo check --examples
       - name: run tests
         run: |
             cargo test
             cargo test --examples
-      - name: check examples
-        working-directory: tskit_rust_examples
-        run: cargo check
 
   fmt:
     name: rust fmt
@@ -92,10 +92,5 @@ jobs:
           toolchain: stable
           override: true
       - run: rustup component add clippy
-      - run: |
-          cargo clippy -- -D warnings
-      - run: |
-          cargo clippy --tests -- -D warnings
-      - name: Run clippy on the examples
-        working-directory: tskit_rust_examples
-        run: cargo clippy -- -D warnings
+      - name: clippy (all targets)
+        run: cargo clippy --all-targets -- -D warnings

Cargo.toml

@@ -18,10 +18,21 @@ streaming-iterator = "0.1.5"
 bitflags = "1.2.1"
 
 [dev-dependencies]
+clap = "~2.27.0"
 serde = {version = "1.0.118", features = ["derive"]}
 bincode = "1.3.1"
 
 [build-dependencies]
 bindgen = "0.57.0"
 cc = { version = "1.0", features = ["parallel"] }
 pkg-config = "0.3"
+
+[[example]]
+name = "mutation_metadata_bincode"
+
+[[example]]
+name = "mutation_metadata_std"
+
+# Not run during tests
+[[example]]
+name = "tree_traversals"

examples/mutation.rs

@@ -1,8 +1,12 @@
 use tskit::metadata;
-use tskit::*;
-mod mutation;
+use tskit::TableAccess;
 
-use mutation::Mutation;
+#[derive(serde::Serialize, serde::Deserialize, Debug)]
+pub struct Mutation {
+    pub effect_size: f64,
+    pub dominance: f64,
+    pub origin_time: i32,
+}
 
 // Implement the metadata trait for our mutation
 // type.  Will will use the standard library for the implementation
@@ -17,10 +21,34 @@ impl metadata::MetadataRoundtrip for Mutation {
     }
 }
 
-make_mutation_metadata_run!();
+pub fn run() {
+    let mut tables = tskit::TableCollection::new(1000.).unwrap();
+    // The simulation generates a mutation:
+    let m = Mutation {
+        effect_size: -0.235423,
+        dominance: 0.5,
+        origin_time: 1,
+    };
+
+    // The mutation's data are included as metadata:
+    tables
+        .add_mutation_with_metadata(0, 0, 0, 0.0, None, Some(&m))
+        .unwrap();
+
+    // Decoding requres 2 unwraps:
+    // 1. The first is to handle errors.
+    // 2. The second is b/c metadata are optional,
+    //    so a row may return None.
+    let decoded = tables.mutations().metadata::<Mutation>(0).unwrap().unwrap();
+
+    // Check that we've made the round trip:
+    assert_eq!(decoded.origin_time, 1);
+    assert!((m.effect_size - decoded.effect_size).abs() < f64::EPSILON);
+    assert!((m.dominance - decoded.dominance).abs() < f64::EPSILON);
+}
 
 #[test]
-fn run_bincode() {
+fn run_test() {
     run();
 }
 

examples/mutation_metadata_bincode.rs

@@ -1,8 +1,37 @@
 use tskit::metadata;
-use tskit::*;
-mod mutation;
+use tskit::TableAccess;
 
-use mutation::Mutation;
+pub struct Mutation {
+    pub effect_size: f64,
+    pub dominance: f64,
+    pub origin_time: i32,
+}
+
+pub fn run() {
+    let mut tables = tskit::TableCollection::new(1000.).unwrap();
+    // The simulation generates a mutation:
+    let m = Mutation {
+        effect_size: -0.235423,
+        dominance: 0.5,
+        origin_time: 1,
+    };
+
+    // The mutation's data are included as metadata:
+    tables
+        .add_mutation_with_metadata(0, 0, 0, 0.0, None, Some(&m))
+        .unwrap();
+
+    // Decoding requres 2 unwraps:
+    // 1. The first is to handle errors.
+    // 2. The second is b/c metadata are optional,
+    //    so a row may return None.
+    let decoded = tables.mutations().metadata::<Mutation>(0).unwrap().unwrap();
+
+    // Check that we've made the round trip:
+    assert_eq!(decoded.origin_time, 1);
+    assert!((m.effect_size - decoded.effect_size).abs() < f64::EPSILON);
+    assert!((m.dominance - decoded.dominance).abs() < f64::EPSILON);
+}
 
 impl metadata::MetadataRoundtrip for Mutation {
     fn encode(&self) -> Result<Vec<u8>, metadata::MetadataError> {
@@ -26,10 +55,8 @@ impl metadata::MetadataRoundtrip for Mutation {
     }
 }
 
-make_mutation_metadata_run!();
-
 #[test]
-fn run_std() {
+fn run_test() {
     run();
 }