refactor: bump bitflags to 2.5.x (#630)

BREAKING CHANGE: flags types expose breaking changes in
bitflags public API

Author: molpopgen

Cargo.lock

@@ -20,7 +20,7 @@ codegen-units=1
 thiserror = "1.0"
 libc = "0.2.154"
 streaming-iterator = "0.1.5"
-bitflags = "1.2.1"
+bitflags = "2.5.0"
 humantime = {version = "2.1.0", optional = true}
 serde = {version = "1.0.199", features = ["derive"], optional = true}
 serde_json = {version = "1.0.114", optional = true}

Cargo.toml

@@ -71,7 +71,7 @@ bitflags! {
     /// assert!(flags.contains(SimplificationOptions::FILTER_POPULATIONS));
     /// assert!(flags.contains(SimplificationOptions::FILTER_SITES));
     /// ```
-    #[derive(Default)]
+    #[derive(Default, Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct SimplificationOptions: RawFlags {
         /// Default behavior
@@ -229,7 +229,7 @@ bitflags! {
     /// assert!(f.contains(TableClearOptions::CLEAR_TS_METADATA_SCHEMA));
     /// assert!(f.contains(TableClearOptions::CLEAR_PROVENANCE);
     /// ```
-    #[derive(Default)]
+    #[derive(Default, Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TableClearOptions : RawFlags {
         /// Default behavior.
@@ -302,7 +302,7 @@ bitflags! {
     /// assert!(f.contains(TableEqualityOptions::IGNORE_PROVENANCE));
     /// assert!(f.contains(TableEqualityOptions::IGNORE_METADATA));
     /// ```
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TableEqualityOptions : RawFlags {
         /// Default behavior.
@@ -351,7 +351,7 @@ bitflags! {
     /// let f = TableSortOptions::default().no_check_integrity();
     /// assert_eq!(f, TableSortOptions::NO_CHECK_INTEGRITY);
     /// ```
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TableSortOptions : RawFlags {
         /// Default behavior.
@@ -379,7 +379,7 @@ bitflags! {
     /// let f = IndividualTableSortOptions::default();
     /// assert_eq!(f, IndividualTableSortOptions::NONE);
     /// ```
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct IndividualTableSortOptions : RawFlags {
         /// Default behavior.
@@ -416,7 +416,7 @@ bitflags! {
     /// let f = TreeFlags::default().no_sample_counts();
     /// assert_eq!(f, TreeFlags::NO_SAMPLE_COUNTS);
     /// ```
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TreeFlags: RawFlags {
         /// Default behavior.
@@ -460,7 +460,7 @@ bitflags! {
     /// when outputting a [`crate::TableCollection`], then
     /// call [`crate::TableCollection::build_index`] prior to calling
     /// [`crate::TableCollection::dump`].
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TableOutputOptions : RawFlags {
         const NONE = 0;
@@ -491,7 +491,7 @@ bitflags! {
     /// assert_eq!(f, TreeSequenceFlags::BUILD_INDEXES);
     /// ```
     ///
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TreeSequenceFlags: RawFlags {
         /// Default behavior
@@ -572,7 +572,7 @@ bitflags! {
     /// let f = TableIntegrityCheckFlags::default().check_trees();
     /// assert_eq!(f, TableIntegrityCheckFlags::CHECK_TREES);
     /// ```
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct TableIntegrityCheckFlags: RawFlags {
         /// Default behavior is a set of basic checks
@@ -656,7 +656,7 @@ bitflags! {
     /// let f = NodeFlags::default().mark_sample();
     /// assert_eq!(f, NodeFlags::IS_SAMPLE);
     /// ```
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     pub struct NodeFlags : RawFlags {
         /// Default (empty)
@@ -696,7 +696,7 @@ impl NodeFlags {
 }
 
 bitflags! {
-    #[derive(Default)]
+    #[derive(Default,Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
     #[repr(transparent)]
     /// Individual flags
     pub struct IndividualFlags : RawFlags {
@@ -736,19 +736,13 @@ impl_from_for_flag_types!(TableOutputOptions);
 
 impl From<RawFlags> for NodeFlags {
     fn from(flags: RawFlags) -> Self {
-        // Safety: node flags can contain user-defined values.
-        // It is an error on the user's part to define flags
-        // in the first 16 bits, as per the C API docs.
-        unsafe { Self::from_bits_unchecked(flags) }
+        Self::from_bits_retain(flags)
     }
 }
 
 impl From<RawFlags> for IndividualFlags {
     fn from(flags: RawFlags) -> Self {
-        // Safety: node flags can contain user-defined values.
-        // It is an error on the user's part to define flags
-        // in the first 16 bits, as per the C API docs.
-        unsafe { Self::from_bits_unchecked(flags) }
+        Self::from_bits_retain(flags)
     }
 }
 

src/sys/flags.rs

@@ -14,7 +14,7 @@ fn clip_invalid_flags() {
     assert!(simplification_flags.is_valid());
 
     // You can skip the unsetting of invalid bits...
-    let simplification_flags = unsafe { SimplificationOptions::from_bits_unchecked(f) };
+    let simplification_flags = SimplificationOptions::from_bits_retain(f);
 
     // ... and use this function to check.
     assert!(!simplification_flags.is_valid());