close

Author: molpopgen

src/sys/flags.rs

@@ -42,6 +42,14 @@ macro_rules! bits {
     };
 }
 
+macro_rules! all {
+    () => {
+        pub fn all() -> Self {
+            Self(RawFlags::MAX)
+        }
+    };
+}
+
 macro_rules! contains {
     () => {
         pub fn contains<I>(&self, bit: I) -> bool
@@ -199,6 +207,7 @@ impl SimplificationOptions {
     => filter_individuals, FILTER_INDIVIDUALS);
 
     bits!();
+    all!();
     contains!();
 }
 
@@ -263,6 +272,7 @@ impl TableClearOptions {
         /// Set [`CLEAR_PROVENANCE`](crate::TableClearOptions::CLEAR_PROVENANCE)
         => clear_provenance, CLEAR_PROVENANCE);
     bits!();
+    all!();
     contains!();
 }
 
@@ -339,6 +349,7 @@ impl TableEqualityOptions {
         /// Set [`IGNORE_TIMESTAMPS`](crate::TableEqualityOptions::IGNORE_TIMESTAMPS)
         => ignore_timestamps, IGNORE_TIMESTAMPS);
     bits!();
+    all!();
     contains!();
 }
 
@@ -376,6 +387,7 @@ impl TableSortOptions {
         /// Set [`NO_CHECK_INTEGRITY`](crate::TableSortOptions::NO_CHECK_INTEGRITY)
         => no_check_integrity, NO_CHECK_INTEGRITY);
     bits!();
+    all!();
     contains!();
 }
 
@@ -398,6 +410,7 @@ impl IndividualTableSortOptions {
     /// Default behavior.
     pub const NONE: RawFlags = 0;
     bits!();
+    all!();
     contains!();
 }
 
@@ -449,6 +462,7 @@ impl TreeFlags {
         /// Set [`NO_SAMPLE_COUNTS`](crate::TreeFlags::NO_SAMPLE_COUNTS)
         => no_sample_counts, NO_SAMPLE_COUNTS);
     bits!();
+    all!();
     contains!();
 }
 
@@ -478,6 +492,7 @@ pub struct TableOutputOptions(RawFlags);
 
 impl TableOutputOptions {
     bits!();
+    all!();
     contains!();
 }
 
@@ -517,6 +532,7 @@ impl TreeSequenceFlags {
         /// Set [`BUILD_INDEXES`](crate::TreeSequenceFlags::BUILD_INDEXES)
         => build_indexes, BUILD_INDEXES);
     bits!();
+    all!();
     contains!();
 }
 
@@ -632,6 +648,7 @@ impl TableIntegrityCheckFlags {
         /// Set [`CHECK_TREES`](crate::TableIntegrityCheckFlags::CHECK_TREES)
         => check_trees, CHECK_TREES);
     bits!();
+    all!();
     contains!();
 }
 
@@ -673,6 +690,7 @@ impl NodeFlags {
     }
 
     bits!();
+    all!();
     contains!();
 
     pub fn toggle(&mut self, bit: tsk_flags_t) {
@@ -708,6 +726,7 @@ impl IndividualFlags {
         true
     }
     bits!();
+    all!();
     contains!();
 }
 

src/table_views.rs

@@ -266,7 +266,7 @@ mod table_views_tests {
         tables.add_node(0, 1.0, -1, -1).unwrap(); // parent
         tables.add_edge(0., 100., 1, 0).unwrap();
         let ts = tables
-            .tree_sequence(crate::TreeSequenceFlags::BUILD_INDEXES)
+            .tree_sequence(crate::TreeSequenceFlags::BUILD_INDEXES.into())
             .unwrap();
         assert_eq!(ts.edges().num_rows(), 1);
         assert_eq!(ts.nodes().num_rows(), 2);

tests/example_flags.rs

@@ -6,18 +6,12 @@ fn clip_invalid_flags() {
     // tskit::SimplificationFlags
     let f: RawFlags = 1000000;
 
-    // Creating flags from this value will unset invalid
-    // bits, meaning the final value != the input value.
+    // Creating flags from this value will retain invalid
+    // bits, meaning the final value == the input value.
     let simplification_flags = SimplificationOptions::from(f);
 
-    assert_ne!(f, simplification_flags.bits());
+    assert_eq!(f, simplification_flags.bits());
     assert!(simplification_flags.is_valid());
-
-    // You can skip the unsetting of invalid bits...
-    let simplification_flags = SimplificationOptions::from_bits_retain(f);
-
-    // ... and use this function to check.
-    assert!(!simplification_flags.is_valid());
 }
 
 fn example_node_flags() {