refactor: use chrono for provenance time stamps (#728)

Author: molpopgen

Cargo.lock

@@ -23,11 +23,11 @@ codegen-units=1
 thiserror = "1.0"
 libc = "0.2.155"
 streaming-iterator = "0.1.5"
-humantime = {version = "2.1.0", optional = true}
 serde = {version = "1.0.203", features = ["derive"], optional = true}
 serde_json = {version = "1.0.120", optional = true}
 bincode = {version = "1.3.1", optional = true}
 tskit-derive = {version = "0.2.0", path = "tskit-derive", optional = true}
+chrono = { version = "0.4.40", default-features = false, features = ["now", "std"] , optional = true}
 
 [dev-dependencies]
 anyhow = {version = "1.0.86"}
@@ -38,9 +38,6 @@ serde_json = {version = "1.0.120"}
 bincode = "1.3.1"
 rand = "0.8.3"
 rand_distr = "0.4.0"
-humantime = {version = "2.1.0"}
-# chrono is out (for now) due to security issues
-# chrono = "0.4.19"
 
 [build-dependencies]
 bindgen = "0.69.4"
@@ -49,7 +46,7 @@ pkg-config = "0.3"
 
 [features]
 bindings = []
-provenance = ["humantime"]
+provenance = ["chrono"]
 derive = ["tskit-derive", "serde", "serde_json", "bincode"]
 
 [package.metadata.docs.rs]

Cargo.toml

@@ -45,7 +45,7 @@ impl ProvenanceTable {
                 "empty provenance record".to_owned(),
             ));
         }
-        let timestamp = humantime::format_rfc3339(std::time::SystemTime::now()).to_string();
+        let timestamp = chrono::Utc::now().to_string();
         let rv = unsafe {
             tsk_provenance_table_add_row(
                 self.as_mut(),

src/sys/provenance_table.rs

@@ -1047,7 +1047,7 @@ impl TableCollection {
     /// specification.
     /// This formatting approach has been the most straightforward method
     /// for supporting round trips to/from a [`crate::provenance::ProvenanceTable`].
-    /// The implementations used here use the [`humantime`](https://docs.rs/humantime/latest/humantime/) crate.
+    /// The implementations used here use the [`chrono`](https://docs.rs/chrono/latest/chrono/) crate.
     ///
     /// # Parameters
     ///
@@ -1076,9 +1076,9 @@ impl TableCollection {
     /// let timestamp = prov_ref.timestamp(0).unwrap();
     /// assert_eq!(timestamp, row_0.timestamp);
     ///
-    /// // You can get the `humantime::Timestamp` object back from the `String`:
+    /// // You can get the `chrono` object back from the `String`:
     /// use core::str::FromStr;
-    /// let timestamp_string = humantime::Timestamp::from_str(&timestamp).unwrap();
+    /// let timestamp_string = chrono::DateTime::<chrono::Utc>::from_str(&timestamp).unwrap();
     ///
     /// // Provenance transfers to the tree sequences
     /// let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();

src/table_collection.rs

@@ -431,7 +431,7 @@ impl TreeSequence {
     /// specification.
     /// This formatting approach has been the most straightforward method
     /// for supporting round trips to/from a [`crate::provenance::ProvenanceTable`].
-    /// The implementations used here use the [`humantime`](https://docs.rs/humantime/latest/humantime/) crate.
+    /// The implementations used here use the [`chrono`](https://docs.rs/chrono/latest/chrono/) crate.
     ///
     /// # Parameters
     ///
@@ -453,7 +453,7 @@ impl TreeSequence {
     /// let timestamp = prov_ref.timestamp(0).unwrap();
     /// assert_eq!(timestamp, row_0.timestamp);
     /// use core::str::FromStr;
-    /// let dt_utc = humantime::Timestamp::from_str(&timestamp).unwrap();
+    /// let dt_utc = chrono::DateTime::<chrono::Utc>::from_str(&timestamp).unwrap();
     /// println!("utc = {}", dt_utc);
     /// # }
     /// ```
@@ -464,7 +464,7 @@ impl TreeSequence {
                 expected: "provenance record".to_string(),
             });
         }
-        let timestamp = humantime::format_rfc3339(std::time::SystemTime::now()).to_string();
+        let timestamp = chrono::Utc::now().to_string();
         let rv = unsafe {
             ll_bindings::tsk_provenance_table_add_row(
                 &mut (*self.inner.as_ref().tables).provenances,