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mark functions to create borroed tables as unsafe #724

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Merged
molpopgen merged 1 commit into from
Mar 7, 2025
Merged

mark functions to create borroed tables as unsafe #724

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9 changes: 8 additions & 1 deletion src/edge_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,14 @@ impl EdgeTable {
Ok(Self { table_ })
}

pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
edges: *mut ll_bindings::tsk_edge_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(edges).unwrap();
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9 changes: 8 additions & 1 deletion src/individual_table.rs
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Expand Up @@ -183,7 +183,14 @@ impl Iterator for IndividualTableIterator {
}

impl IndividualTable {
pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
individuals: *mut ll_bindings::tsk_individual_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(individuals).unwrap();
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9 changes: 8 additions & 1 deletion src/migration_table.rs
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Expand Up @@ -211,7 +211,14 @@ pub struct MigrationTable {
}

impl MigrationTable {
pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
migrations: *mut ll_bindings::tsk_migration_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(migrations).unwrap();
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9 changes: 8 additions & 1 deletion src/mutation_table.rs
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Expand Up @@ -207,7 +207,14 @@ pub struct MutationTable {
}

impl MutationTable {
pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
mutations: *mut ll_bindings::tsk_mutation_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(mutations).unwrap();
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9 changes: 8 additions & 1 deletion src/node_table.rs
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Expand Up @@ -439,7 +439,14 @@ impl NodeTable {
Ok(Self { table_ })
}

pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
nodes: *mut ll_bindings::tsk_node_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(nodes).unwrap();
Expand Down
9 changes: 8 additions & 1 deletion src/population_table.rs
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Expand Up @@ -157,7 +157,14 @@ pub struct PopulationTable {
}

impl PopulationTable {
pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
populations: *mut ll_bindings::tsk_population_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(populations).unwrap();
Expand Down
9 changes: 8 additions & 1 deletion src/provenance.rs
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Expand Up @@ -154,7 +154,14 @@ pub struct ProvenanceTable {
}

impl ProvenanceTable {
pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
provenances: *mut ll_bindings::tsk_provenance_table_t,
) -> Result<Self, crate::TskitError> {
let ptr = std::ptr::NonNull::new(provenances).unwrap();
Expand Down
9 changes: 8 additions & 1 deletion src/site_table.rs
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Expand Up @@ -176,7 +176,14 @@ pub struct SiteTable {
}

impl SiteTable {
pub(crate) fn new_from_table(
// # Safety
//
// * this fn must NEVER by part of the public API
// * all returned values must only be visible to the public API
// by REFERENCE (& or &mut)
// * the input ptr must not be NULL
// * the input ptr must point to an initialized table
pub(crate) unsafe fn new_from_table(
sites: *mut ll_bindings::tsk_site_table_t,
) -> Result<Self, TskitError> {
let ptr = std::ptr::NonNull::new(sites).unwrap();
Expand Down
60 changes: 40 additions & 20 deletions src/table_collection.rs
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Expand Up @@ -100,16 +100,24 @@ impl TableCollection {
/// ```
pub fn new<P: Into<Position>>(sequence_length: P) -> Result<Self, TskitError> {
let mut inner = LLTableCollection::new(sequence_length.into().into())?;
let edges = crate::EdgeTable::new_from_table(inner.edges_mut())?;
let nodes = crate::NodeTable::new_from_table(inner.nodes_mut())?;
let sites = crate::SiteTable::new_from_table(inner.sites_mut())?;
let mutations = crate::MutationTable::new_from_table(inner.mutations_mut())?;
let individuals = crate::IndividualTable::new_from_table(inner.individuals_mut())?;
let populations = crate::PopulationTable::new_from_table(inner.populations_mut())?;
let migrations = crate::MigrationTable::new_from_table(inner.migrations_mut())?;
// SAFETY: all the casts to *mut Foo are coming in via an implicit
// cast from &mut Foo, which means that the ptr cannot be NULL.
// Further, successful creation of LLTableCollection means
// that tables are initialized.
// Finally, none of these variables will be pub directly other than
// by reference.
let edges = unsafe { crate::EdgeTable::new_from_table(inner.edges_mut())? };
let nodes = unsafe { crate::NodeTable::new_from_table(inner.nodes_mut())? };
let sites = unsafe { crate::SiteTable::new_from_table(inner.sites_mut())? };
let mutations = unsafe { crate::MutationTable::new_from_table(inner.mutations_mut())? };
let individuals =
unsafe { crate::IndividualTable::new_from_table(inner.individuals_mut())? };
let populations =
unsafe { crate::PopulationTable::new_from_table(inner.populations_mut())? };
let migrations = unsafe { crate::MigrationTable::new_from_table(inner.migrations_mut())? };
#[cfg(feature = "provenance")]
let provenances =
crate::provenance::ProvenanceTable::new_from_table(inner.provenances_mut())?;
unsafe { crate::provenance::ProvenanceTable::new_from_table(inner.provenances_mut())? };
Ok(Self {
inner,
idmap: vec![],
Expand All @@ -127,16 +135,24 @@ impl TableCollection {

pub(crate) fn new_from_ll(lltables: LLTableCollection) -> Result<Self, TskitError> {
let mut inner = lltables;
let edges = crate::EdgeTable::new_from_table(inner.edges_mut())?;
let nodes = crate::NodeTable::new_from_table(inner.nodes_mut())?;
let sites = crate::SiteTable::new_from_table(inner.sites_mut())?;
let mutations = crate::MutationTable::new_from_table(inner.mutations_mut())?;
let individuals = crate::IndividualTable::new_from_table(inner.individuals_mut())?;
let populations = crate::PopulationTable::new_from_table(inner.populations_mut())?;
let migrations = crate::MigrationTable::new_from_table(inner.migrations_mut())?;
// SAFETY: all the casts to *mut Foo are coming in via an implicit
// cast from &mut Foo, which means that the ptr cannot be NULL.
// Further, successful creation of LLTableCollection means
// that tables are initialized.
// Finally, none of these variables will be pub directly other than
// by reference.
let edges = unsafe { crate::EdgeTable::new_from_table(inner.edges_mut())? };
let nodes = unsafe { crate::NodeTable::new_from_table(inner.nodes_mut())? };
let sites = unsafe { crate::SiteTable::new_from_table(inner.sites_mut())? };
let mutations = unsafe { crate::MutationTable::new_from_table(inner.mutations_mut())? };
let individuals =
unsafe { crate::IndividualTable::new_from_table(inner.individuals_mut())? };
let populations =
unsafe { crate::PopulationTable::new_from_table(inner.populations_mut())? };
let migrations = unsafe { crate::MigrationTable::new_from_table(inner.migrations_mut())? };
#[cfg(feature = "provenance")]
let provenances =
crate::provenance::ProvenanceTable::new_from_table(inner.provenances_mut())?;
unsafe { crate::provenance::ProvenanceTable::new_from_table(inner.provenances_mut())? };
Ok(Self {
inner,
idmap: vec![],
Expand Down Expand Up @@ -1740,10 +1756,14 @@ impl TableCollection {
}

// convert sys version of tables to non-sys version of tables
let new_edges = EdgeTable::new_from_table(new_edges.as_mut())?;
let new_migrations = MigrationTable::new_from_table(new_migrations.as_mut())?;
let new_mutations = MutationTable::new_from_table(new_mutations.as_mut())?;
let new_sites = SiteTable::new_from_table(new_sites.as_mut())?;
// SAFETY: all the casts to *mut Foo are coming in via an implicit
// cast from &mut Foo, which means that the ptr cannot be NULL.
// Further, all input tables are initialized.
// Finally, none of these variables will be every be pub.
let new_edges = unsafe { EdgeTable::new_from_table(new_edges.as_mut())? };
let new_migrations = unsafe { MigrationTable::new_from_table(new_migrations.as_mut())? };
let new_mutations = unsafe { MutationTable::new_from_table(new_mutations.as_mut())? };
let new_sites = unsafe { SiteTable::new_from_table(new_sites.as_mut())? };

// replace old tables with new tables
tables.set_edges(&new_edges).map(|_| ())?;
Expand Down
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