diff --git a/Cargo.lock b/Cargo.lock
index 576f94d5..326be4ed 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -86,7 +86,7 @@ version = "0.69.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a00dc851838a2120612785d195287475a3ac45514741da670b735818822129a0"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags",
  "cexpr",
  "clang-sys",
  "itertools",
@@ -103,12 +103,6 @@ dependencies = [
  "which",
 ]
 
-[[package]]
-name = "bitflags"
-version = "1.3.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
-
 [[package]]
 name = "bitflags"
 version = "2.5.0"
@@ -548,7 +542,7 @@ version = "0.38.32"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "65e04861e65f21776e67888bfbea442b3642beaa0138fdb1dd7a84a52dffdb89"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags",
  "errno",
  "libc",
  "linux-raw-sys",
@@ -672,7 +666,7 @@ dependencies = [
  "anyhow",
  "bincode",
  "bindgen",
- "bitflags 1.3.2",
+ "bitflags",
  "cc",
  "clap",
  "delegate",
diff --git a/Cargo.toml b/Cargo.toml
index 6a176b58..20de16cf 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -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}
diff --git a/src/sys/flags.rs b/src/sys/flags.rs
index cf55bb3d..92b40900 100644
--- a/src/sys/flags.rs
+++ b/src/sys/flags.rs
@@ -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)
     }
 }
 
diff --git a/tests/example_flags.rs b/tests/example_flags.rs
index c37101ad..c973db40 100644
--- a/tests/example_flags.rs
+++ b/tests/example_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());