Add tskit::SizeType (#192)

* tsk_id_t and tsk_size_t removed from prelude.
* tsk_id_t and tsk_size_t no longer publicly exported from lib.rs
* Public API now returns SizeType instead of tsk_size_t

Closes #181

Author: molpopgen

src/_macros.rs

@@ -46,13 +46,15 @@ macro_rules! unsafe_tsk_column_access {
 
 macro_rules! unsafe_tsk_ragged_column_access {
     ($i: expr, $lo: expr, $hi: expr, $array: expr, $offset_array: expr, $offset_array_len: expr) => {{
-        if $i < $lo || $i >= ($hi as tsk_id_t) {
+        use std::convert::TryFrom;
+        let i = crate::SizeType::try_from($i)?;
+        if $i < $lo || i >= $hi {
             Err(TskitError::IndexError {})
         } else if $offset_array_len == 0 {
             Ok(None)
         } else {
             let start = unsafe { *$offset_array.offset($i as isize) };
-            let stop = if $i < ($hi as tsk_id_t) {
+            let stop = if i < $hi {
                 unsafe { *$offset_array.offset(($i + 1) as isize) }
             } else {
                 $offset_array_len as tsk_size_t
@@ -70,13 +72,15 @@ macro_rules! unsafe_tsk_ragged_column_access {
     }};
 
     ($i: expr, $lo: expr, $hi: expr, $array: expr, $offset_array: expr, $offset_array_len: expr, $output_id_type: expr) => {{
-        if $i < $lo || $i >= ($hi as tsk_id_t) {
+        use std::convert::TryFrom;
+        let i = crate::SizeType::try_from($i)?;
+        if $i < $lo || i >= $hi {
             Err(TskitError::IndexError {})
         } else if $offset_array_len == 0 {
             Ok(None)
         } else {
             let start = unsafe { *$offset_array.offset($i as isize) };
-            let stop = if $i < ($hi as tsk_id_t) {
+            let stop = if i < $hi {
                 unsafe { *$offset_array.offset(($i + 1) as isize) }
             } else {
                 $offset_array_len as tsk_size_t
@@ -99,13 +103,15 @@ macro_rules! unsafe_tsk_ragged_column_access {
 #[allow(unused_macros)]
 macro_rules! unsafe_tsk_ragged_char_column_access {
     ($i: expr, $lo: expr, $hi: expr, $array: expr, $offset_array: expr, $offset_array_len: expr) => {{
-        if $i < $lo || $i >= ($hi as tsk_id_t) {
+        use std::convert::TryFrom;
+        let i = crate::SizeType::try_from($i)?;
+        if $i < $lo || i >= $hi {
             Err(TskitError::IndexError {})
         } else if $offset_array_len == 0 {
             Ok(None)
         } else {
             let start = unsafe { *$offset_array.offset($i as isize) };
-            let stop = if $i < ($hi as tsk_id_t) {
+            let stop = if i < $hi {
                 unsafe { *$offset_array.offset(($i + 1) as isize) }
             } else {
                 $offset_array_len as tsk_size_t
@@ -299,6 +305,14 @@ macro_rules! impl_id_traits {
             }
         }
 
+        impl std::convert::TryFrom<$idtype> for crate::SizeType {
+            type Error = crate::TskitError;
+
+            fn try_from(value: $idtype) -> Result<Self, Self::Error> {
+                crate::SizeType::try_from(value.0)
+            }
+        }
+
         impl PartialEq<$crate::tsk_id_t> for $idtype {
             fn eq(&self, other: &$crate::tsk_id_t) -> bool {
                 self.0 == *other
@@ -325,6 +339,35 @@ macro_rules! impl_id_traits {
     };
 }
 
+macro_rules! impl_size_type_comparisons_for_row_ids {
+    ($idtype: ty) => {
+        impl PartialEq<$idtype> for crate::SizeType {
+            fn eq(&self, other: &$idtype) -> bool {
+                self.0 == other.0 as crate::bindings::tsk_size_t
+            }
+        }
+
+        impl PartialEq<crate::SizeType> for $idtype {
+            fn eq(&self, other: &crate::SizeType) -> bool {
+                (self.0 as crate::bindings::tsk_size_t) == other.0
+            }
+        }
+
+        impl PartialOrd<$idtype> for crate::SizeType {
+            fn partial_cmp(&self, other: &$idtype) -> Option<std::cmp::Ordering> {
+                self.0
+                    .partial_cmp(&(other.0 as crate::bindings::tsk_size_t))
+            }
+        }
+
+        impl PartialOrd<crate::SizeType> for $idtype {
+            fn partial_cmp(&self, other: &crate::SizeType) -> Option<std::cmp::Ordering> {
+                (self.0 as crate::bindings::tsk_size_t).partial_cmp(&other.0)
+            }
+        }
+    };
+}
+
 /// Convenience macro to handle implementing
 /// [`crate::metadata::MetadataRoundtrip`]
 #[macro_export]

src/edge_table.rs

@@ -1,6 +1,6 @@
 use crate::bindings as ll_bindings;
 use crate::metadata;
-use crate::{tsk_id_t, tsk_size_t, TskitError};
+use crate::{tsk_id_t, TskitError};
 use crate::{EdgeId, NodeId};
 
 /// Row of an [`EdgeTable`]
@@ -25,7 +25,12 @@ impl PartialEq for EdgeTableRow {
 }
 
 fn make_edge_table_row(table: &EdgeTable, pos: tsk_id_t) -> Option<EdgeTableRow> {
-    if pos < table.num_rows() as tsk_id_t {
+    use std::convert::TryFrom;
+    // panic is okay here, as we are handling a bad
+    // input value before we first call this to
+    // set up the iterator
+    let p = crate::SizeType::try_from(pos).unwrap();
+    if p < table.num_rows() {
         let rv = EdgeTableRow {
             id: pos.into(),
             left: table.left(pos).unwrap(),
@@ -78,8 +83,8 @@ impl<'a> EdgeTable<'a> {
     }
 
     /// Return the number of rows
-    pub fn num_rows(&'a self) -> tsk_size_t {
-        self.table_.num_rows
+    pub fn num_rows(&'a self) -> crate::SizeType {
+        self.table_.num_rows.into()
     }
 
     /// Return the ``parent`` value from row ``row`` of the table.
@@ -147,6 +152,10 @@ impl<'a> EdgeTable<'a> {
     ///
     /// [`TskitError::IndexError`] if `r` is out of range.
     pub fn row<E: Into<EdgeId> + Copy>(&self, r: E) -> Result<EdgeTableRow, TskitError> {
-        table_row_access!(r.into().0, self, make_edge_table_row)
+        let ri = r.into();
+        if ri < 0 {
+            return Err(crate::TskitError::IndexError);
+        }
+        table_row_access!(ri.0, self, make_edge_table_row)
     }
 }

src/error.rs

@@ -5,6 +5,9 @@ use thiserror::Error;
 
 #[derive(Error, Debug)]
 pub enum TskitError {
+    /// Returned when conversion attempts fail
+    #[error("range error: {}", *.0)]
+    RangeError(&'static str),
     /// Used when bad input is encountered.
     #[error("we received {} but expected {}",*got, *expected)]
     ValueError { got: String, expected: String },

src/individual_table.rs

@@ -49,7 +49,12 @@ pub struct IndividualTable<'a> {
 }
 
 fn make_individual_table_row(table: &IndividualTable, pos: tsk_id_t) -> Option<IndividualTableRow> {
-    if pos < table.num_rows() as tsk_id_t {
+    use std::convert::TryFrom;
+    // panic is okay here, as we are handling a bad
+    // input value before we first call this to
+    // set up the iterator
+    let p = crate::SizeType::try_from(pos).unwrap();
+    if p < table.num_rows() {
         let rv = IndividualTableRow {
             id: pos.into(),
             flags: table.flags(pos).unwrap(),
@@ -96,8 +101,8 @@ impl<'a> IndividualTable<'a> {
     }
 
     /// Return the number of rows
-    pub fn num_rows(&'a self) -> ll_bindings::tsk_size_t {
-        self.table_.num_rows
+    pub fn num_rows(&'a self) -> crate::SizeType {
+        self.table_.num_rows.into()
     }
 
     /// Return the flags for a given row.
@@ -181,6 +186,10 @@ impl<'a> IndividualTable<'a> {
         &self,
         r: I,
     ) -> Result<IndividualTableRow, TskitError> {
-        table_row_access!(r.into().0, self, make_individual_table_row)
+        let ri = r.into();
+        if ri < 0 {
+            return Err(crate::TskitError::IndexError);
+        }
+        table_row_access!(ri.0, self, make_individual_table_row)
     }
 }

src/lib.rs

@@ -102,8 +102,9 @@ pub use bindings::TSK_NODE_IS_SAMPLE;
 
 // re-export types, too
 pub use bindings::tsk_flags_t;
-pub use bindings::tsk_id_t;
-pub use bindings::tsk_size_t;
+
+use bindings::tsk_id_t;
+use bindings::tsk_size_t;
 
 /// A node ID
 ///
@@ -116,7 +117,7 @@ pub use bindings::tsk_size_t;
 ///
 /// ```
 /// use tskit::NodeId;
-/// use tskit::tsk_id_t;
+/// use tskit::bindings::tsk_id_t;
 ///
 /// let x: tsk_id_t = 1;
 /// let y: NodeId = NodeId::from(x);
@@ -137,7 +138,7 @@ pub use bindings::tsk_size_t;
 ///
 /// ```
 /// use tskit::NodeId;
-/// use tskit::tsk_id_t;
+/// use tskit::bindings::tsk_id_t;
 ///
 /// fn interesting<N: Into<NodeId>>(x: N) -> NodeId {
 ///     x.into()
@@ -226,6 +227,112 @@ impl_id_traits!(MutationId);
 impl_id_traits!(MigrationId);
 impl_id_traits!(EdgeId);
 
+impl_size_type_comparisons_for_row_ids!(NodeId);
+impl_size_type_comparisons_for_row_ids!(EdgeId);
+impl_size_type_comparisons_for_row_ids!(SiteId);
+impl_size_type_comparisons_for_row_ids!(MutationId);
+impl_size_type_comparisons_for_row_ids!(PopulationId);
+impl_size_type_comparisons_for_row_ids!(MigrationId);
+
+/// Wraps `tsk_size_t`
+///
+/// This type plays the role of C's `size_t` in the `tskit` C library.
+///
+/// # Examples
+///
+/// ```
+/// let s = tskit::SizeType::from(1 as tskit::bindings::tsk_size_t);
+/// let mut t: tskit::bindings::tsk_size_t = s.into();
+/// assert!(t == s);
+/// assert!(t == 1);
+/// let u = tskit::SizeType::from(s);
+/// assert!(u == s);
+/// t += 1;
+/// assert!(t > s);
+/// assert!(s < t);
+/// ```
+///
+/// #[repr(transparent)]
+#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
+pub struct SizeType(tsk_size_t);
+
+impl std::fmt::Display for SizeType {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        write!(f, "SizeType({})", self.0)
+    }
+}
+
+impl From<tsk_size_t> for SizeType {
+    fn from(value: tsk_size_t) -> Self {
+        Self(value)
+    }
+}
+
+impl From<SizeType> for tsk_size_t {
+    fn from(value: SizeType) -> Self {
+        value.0
+    }
+}
+
+impl From<SizeType> for usize {
+    fn from(value: SizeType) -> Self {
+        value.0 as usize
+    }
+}
+
+impl From<usize> for SizeType {
+    fn from(value: usize) -> Self {
+        Self(value as tsk_size_t)
+    }
+}
+
+impl std::convert::TryFrom<tsk_id_t> for SizeType {
+    type Error = crate::TskitError;
+
+    fn try_from(value: tsk_id_t) -> Result<Self, Self::Error> {
+        match value >= 0 {
+            true => Ok(Self(value as crate::bindings::tsk_size_t)),
+            false => Err(crate::TskitError::RangeError(stringify!(value.0))),
+        }
+    }
+}
+
+impl std::convert::TryFrom<SizeType> for tsk_id_t {
+    type Error = crate::TskitError;
+
+    fn try_from(value: SizeType) -> Result<Self, Self::Error> {
+        if value.0 > tsk_id_t::MAX as tsk_size_t {
+            Err(TskitError::RangeError(stringify!(value.0)))
+        } else {
+            Ok(value.0 as tsk_id_t)
+        }
+    }
+}
+
+impl PartialEq<SizeType> for tsk_size_t {
+    fn eq(&self, other: &SizeType) -> bool {
+        *self == other.0
+    }
+}
+
+impl PartialEq<tsk_size_t> for SizeType {
+    fn eq(&self, other: &tsk_size_t) -> bool {
+        self.0 == *other
+    }
+}
+
+impl PartialOrd<tsk_size_t> for SizeType {
+    fn partial_cmp(&self, other: &tsk_size_t) -> Option<std::cmp::Ordering> {
+        self.0.partial_cmp(other)
+    }
+}
+
+impl PartialOrd<SizeType> for tsk_size_t {
+    fn partial_cmp(&self, other: &SizeType) -> Option<std::cmp::Ordering> {
+        self.partial_cmp(&other.0)
+    }
+}
+
 // tskit defines this via a type cast
 // in a macro. bindgen thus misses it.
 // See bindgen issue 316.

src/metadata.rs

@@ -164,6 +164,7 @@
 //!   into `Python` via the `tskit` `Python API`.
 
 use crate::bindings::{tsk_id_t, tsk_size_t};
+use crate::SizeType;
 use thiserror::Error;
 
 #[cfg(feature = "derive")]
@@ -233,8 +234,8 @@ impl EncodedMetadata {
         }
     }
 
-    pub(crate) fn len(&self) -> tsk_size_t {
-        self.encoded.len() as tsk_size_t
+    pub(crate) fn len(&self) -> SizeType {
+        self.encoded.len().into()
     }
 }
 
@@ -344,8 +345,8 @@ mod tests {
         let enc = EncodedMetadata::new(&f).unwrap();
         let p = enc.as_ptr();
         let mut d = vec![];
-        for i in 0..enc.len() {
-            d.push(unsafe { *p.add(i as usize) as u8 });
+        for i in 0..usize::from(enc.len()) {
+            d.push(unsafe { *p.add(i) as u8 });
         }
         let df = F::decode(&d).unwrap();
         assert_eq!(f.x, df.x);
@@ -378,8 +379,8 @@ mod test_serde {
         let enc = EncodedMetadata::new(&f).unwrap();
         let p = enc.as_ptr();
         let mut d = vec![];
-        for i in 0..enc.len() {
-            d.push(unsafe { *p.add(i as usize) as u8 });
+        for i in 0..usize::from(enc.len()) {
+            d.push(unsafe { *p.add(i) as u8 });
         }
         let df = F::decode(&d).unwrap();
         assert_eq!(f.x, df.x);