Merge branch 'latest' into try-skipmers

.github/workflows/rust.yml

@@ -273,11 +273,11 @@ jobs:
 
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: "1.65.0"
+          toolchain: "1.66.0"
           override: true
 
       - name: check if README matches MSRV defined here
-        run: grep '1.65.0' src/core/README.md
+        run: grep '1.66.0' src/core/README.md
 
       - name: Check if it builds properly
         uses: actions-rs/cargo@v1

src/core/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "sourmash"
 version = "0.17.1"
-authors = ["Luiz Irber <[email protected]>", "N. Tessa Pierce-Ward <[email protected]>"]
+authors = ["Luiz Irber <[email protected]>", "N. Tessa Pierce-Ward <[email protected]>", "C. Titus Brown <[email protected]>"]
 description = "tools for comparing biological sequences with k-mer sketches"
 repository = "https://github.com/sourmash-bio/sourmash"
 keywords = ["minhash", "bioinformatics"]
@@ -11,7 +11,7 @@ edition = "2021"
 readme = "README.md"
 autoexamples = false
 autobins = false
-rust-version = "1.65.0"
+rust-version = "1.66.0"
 
 [lib]
 name = "sourmash"
@@ -109,6 +109,6 @@ wasm-bindgen-test = "0.3.42"
 
 ### These crates don't compile on wasm
 [target.'cfg(not(target_arch = "wasm32"))'.dependencies]
-rocksdb = { version = "0.21.0", optional = true }
+rocksdb = { version = "0.22.0", optional = true }
 [target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies]
 criterion = "0.5.1"

src/core/README.md

@@ -38,4 +38,4 @@ Development happens on github at
 
 ## Minimum supported Rust version
 
-Currently the minimum supported Rust version is 1.65.0.
+Currently the minimum supported Rust version is 1.66.0.

src/core/src/collection.rs

@@ -409,8 +409,8 @@ mod test {
         // no sigs should remain
         assert_eq!(cl.len(), 6);
         for (_idx, rec) in cl.iter() {
-            // need to pass select again here so we actually downsample
-            let this_sig = cl.sig_from_record(rec).unwrap().select(&selection).unwrap();
+            dbg!("record scaled is: {}", rec.scaled());
+            let this_sig = cl.sig_from_record(rec).unwrap();
             let this_mh = this_sig.minhash().unwrap();
             assert_eq!(this_mh.scaled(), 2000);
         }
@@ -440,7 +440,7 @@ mod test {
         filename.push("../../tests/test-data/prot/hp.zip");
         // create Selection object
         let mut selection = Selection::default();
-        selection.set_scaled(100);
+        selection.set_scaled(200);
         selection.set_moltype(HashFunctions::Murmur64Hp);
         // load sigs into collection + select compatible signatures
         let cl = Collection::from_zipfile(&filename)
@@ -450,10 +450,9 @@ mod test {
         // count collection length
         assert_eq!(cl.len(), 2);
         for (idx, _rec) in cl.iter() {
-            // need to pass select again here so we actually downsample
-            let this_sig = cl.sig_for_dataset(idx).unwrap().select(&selection).unwrap();
+            let this_sig = cl.sig_for_dataset(idx).unwrap();
             let this_mh = this_sig.minhash().unwrap();
-            assert_eq!(this_mh.scaled(), 100);
+            assert_eq!(this_mh.scaled(), 200);
         }
     }
 

src/core/src/manifest.rs

@@ -259,8 +259,13 @@ impl Manifest {
 }
 
 impl Select for Manifest {
+    // select only records that satisfy selection conditions; also update
+    // scaled value to match.
     fn select(self, selection: &Selection) -> Result<Self> {
-        let rows = self.records.iter().filter(|row| {
+        let Manifest { mut records } = self;
+
+        // TODO: with num as well?
+        records.retain_mut(|row| {
             let mut valid = true;
             valid = if let Some(ksize) = selection.ksize() {
                 row.ksize == ksize
@@ -279,7 +284,12 @@ impl Select for Manifest {
             };
             valid = if let Some(scaled) = selection.scaled() {
                 // num sigs have row.scaled = 0, don't include them
-                valid && row.scaled != 0 && row.scaled <= scaled
+                let v = valid && row.scaled != 0 && row.scaled <= scaled;
+                // if scaled is set, update!
+                if v {
+                    row.scaled = scaled
+                };
+                v
             } else {
                 valid
             };
@@ -291,41 +301,7 @@ impl Select for Manifest {
             valid
         });
 
-        Ok(Manifest {
-            records: rows.cloned().collect(),
-        })
-
-        /*
-        matching_rows = self.rows
-        if ksize:
-            matching_rows = ( row for row in matching_rows
-                              if row['ksize'] == ksize )
-        if moltype:
-            matching_rows = ( row for row in matching_rows
-                              if row['moltype'] == moltype )
-        if scaled or containment:
-            if containment and not scaled:
-                raise ValueError("'containment' requires 'scaled' in Index.select'")
-
-            matching_rows = ( row for row in matching_rows
-                              if row['scaled'] and not row['num'] )
-        if num:
-            matching_rows = ( row for row in matching_rows
-                              if row['num'] and not row['scaled'] )
-
-        if abund:
-            # only need to concern ourselves if abundance is _required_
-            matching_rows = ( row for row in matching_rows
-                              if row['with_abundance'] )
-
-        if picklist:
-            matching_rows = ( row for row in matching_rows
-                              if picklist.matches_manifest_row(row) )
-
-        # return only the internal filenames!
-        for row in matching_rows:
-            yield row
-        */
+        Ok(Manifest { records })
     }
 }
 
@@ -567,6 +543,19 @@ mod test {
         selection.set_scaled(100);
         let scaled100 = manifest.select(&selection).unwrap();
         assert_eq!(scaled100.len(), 6);
+
+        // check that 'scaled' is updated
+        let manifest = collection.manifest().clone();
+        selection = Selection::default();
+        selection.set_scaled(400);
+        let scaled400 = manifest.select(&selection).unwrap();
+        assert_eq!(scaled400.len(), 6);
+        let max_scaled = scaled400
+            .iter()
+            .map(|r| r.scaled())
+            .max()
+            .expect("no records?!");
+        assert_eq!(*max_scaled, 400);
     }
 
     #[test]

src/core/src/selection.rs

@@ -125,7 +125,7 @@ impl Selection {
             abund: Some(row.with_abundance()),
             moltype: Some(row.moltype()),
             num: None,
-            scaled: None,
+            scaled: Some(*row.scaled()),
             containment: None,
             picklist: None,
         })