fix(format): a dataset attribute set again replaces the earlier value

b0a1e4f fixed this for group and root attributes only. Setting a dataset
attribute twice still wrote two attribute messages with one name, and h5py
read back the first value: set_attr("a", 1) then set_attr("a", 2) read as
1, and list(attrs) was ["a", "a"]. DatasetBuilder::set_attr now replaces
the earlier value, compact or dense. Likewise, a hand-set attribute named
like a provenance attribute (_provenance_sha256, ...) is replaced by the
computed one instead of being written next to it and read first.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>

crates/clawhdf5-format/src/file_writer.rs

@@ -1355,7 +1355,10 @@ fn flatten_ds(db: DatasetBuilder, refcount: u32) -> Result<DsFlat, FormatError>
             timestamp: prov.timestamp.clone(),
             source: prov.source.clone(),
         };
-        attrs.extend(p.build_attrs(&raw));
+        // The provenance attributes replace any the caller set by hand.
+        let prov = p.build_attrs(&raw);
+        attrs.retain(|a| prov.iter().all(|b| b.name != a.name));
+        attrs.extend(prov);
     }
     let fill_message = fill_value_message(db.fill_time, db.fill_value.as_deref(), &dt)?;
     Ok(DsFlat {

crates/clawhdf5-format/src/type_builders.rs

@@ -695,8 +695,13 @@ impl DatasetBuilder {
         self
     }
 
+    /// Set attribute `name`. Setting it again replaces the earlier value,
+    /// as `attrs[name] = v` does in h5py.
     pub fn set_attr(&mut self, name: &str, value: AttrValue) -> &mut Self {
-        self.attrs.push((name.to_string(), value));
+        match self.attrs.iter_mut().find(|(n, _)| n == name) {
+            Some(slot) => slot.1 = value,
+            None => self.attrs.push((name.to_string(), value)),
+        }
         self
     }