From 69fd38bed0db859786a4f55c6b16f14a46f8746c Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 11 Oct 2024 09:57:03 -0400
Subject: [PATCH 01/11] update to next sourmash release

---
 Cargo.lock        | 5 ++---
 Cargo.toml        | 3 ++-
 src/manysearch.rs | 1 +
 src/utils.rs      | 2 +-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index f4acf157..968f5cea 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1548,9 +1548,8 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 
 [[package]]
 name = "sourmash"
-version = "0.15.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a73bae93170d8d0f816e18b6a630d76e134b90958850985ee2f0fb2f641d4de"
+version = "0.16.0"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#9b9fc5a4d40521e14390766fb6ffde4c6921062c"
 dependencies = [
  "az",
  "byteorder",
diff --git a/Cargo.toml b/Cargo.toml
index 7935aa38..7dbc99cf 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -12,7 +12,8 @@ crate-type = ["cdylib"]
 pyo3 = { version = "0.22.3", features = ["extension-module", "anyhow"] }
 rayon = "1.10.0"
 serde = { version = "1.0.210", features = ["derive"] }
-sourmash = { version = "0.15.2", features = ["branchwater"] }
+#sourmash = { version = "0.15.2", features = ["branchwater"] }
+sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "refactor_rs_downsample", features = ["branchwater"] }
 serde_json = "1.0.128"
 niffler = "2.4.0"
 log = "0.4.22"
diff --git a/src/manysearch.rs b/src/manysearch.rs
index d343493d..199af8b5 100644
--- a/src/manysearch.rs
+++ b/src/manysearch.rs
@@ -219,6 +219,7 @@ fn downsample_and_inflate_abundances(
     // avoid downsampling if we can
     if against_scaled != query_scaled {
         let against_ds = against
+            .clone()
             .downsample_scaled(query.scaled())
             .expect("cannot downsample sketch");
         (abunds, sum_weighted) = query.inflated_abundances(&against_ds)?;
diff --git a/src/utils.rs b/src/utils.rs
index 33f78316..f0a81d5f 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -478,7 +478,7 @@ pub fn load_sketches_above_threshold(
             if let Ok(against_sig) = against_collection.sig_from_record(against_record) {
                 if let Some(against_mh) = against_sig.minhash() {
                     // downsample against_mh, but keep original md5sum
-                    let against_mh_ds = against_mh.downsample_scaled(query.scaled()).unwrap();
+                    let against_mh_ds = against_mh.clone().downsample_scaled(query.scaled()).unwrap();
                     if let Ok(overlap) = against_mh_ds.count_common(query, false) {
                         if overlap >= threshold_hashes {
                             let result = PrefetchResult {

From ee580b683ae9f5564b5c48c8e70cda4586c8fbe9 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 11 Oct 2024 10:04:16 -0400
Subject: [PATCH 02/11] cargo fmt

---
 src/utils.rs | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/utils.rs b/src/utils.rs
index f0a81d5f..a702378f 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -478,7 +478,10 @@ pub fn load_sketches_above_threshold(
             if let Ok(against_sig) = against_collection.sig_from_record(against_record) {
                 if let Some(against_mh) = against_sig.minhash() {
                     // downsample against_mh, but keep original md5sum
-                    let against_mh_ds = against_mh.clone().downsample_scaled(query.scaled()).unwrap();
+                    let against_mh_ds = against_mh
+                        .clone()
+                        .downsample_scaled(query.scaled())
+                        .unwrap();
                     if let Ok(overlap) = against_mh_ds.count_common(query, false) {
                         if overlap >= threshold_hashes {
                             let result = PrefetchResult {

From 981405166f6e4c341242357db28c1b58beddbe5e Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 11 Oct 2024 15:53:16 -0400
Subject: [PATCH 03/11] upd sourmash

---
 Cargo.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.lock b/Cargo.lock
index 968f5cea..7e2264f7 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#9b9fc5a4d40521e14390766fb6ffde4c6921062c"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#79afb857967d5f48393341a77e43ea27ab3caf22"
 dependencies = [
  "az",
  "byteorder",

From d27b03e8e677a6b96d866ea2c89208dcc7135aa4 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 11 Oct 2024 16:38:32 -0400
Subject: [PATCH 04/11] correct numbers

---
 Cargo.lock                               | 2 +-
 src/python/tests/test_fastmultigather.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 7e2264f7..7b1eb621 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#79afb857967d5f48393341a77e43ea27ab3caf22"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ddcb049e99749f1d16c414e0fdb2d06d55a38db7"
 dependencies = [
  "az",
  "byteorder",
diff --git a/src/python/tests/test_fastmultigather.py b/src/python/tests/test_fastmultigather.py
index f485b7f0..653b0ba5 100644
--- a/src/python/tests/test_fastmultigather.py
+++ b/src/python/tests/test_fastmultigather.py
@@ -959,7 +959,7 @@ def test_indexed_full_output(runtmp):
     # check a few columns
     average_ani = set(df['average_containment_ani'])
     avg_ani = set([round(x, 4) for x in average_ani])
-    assert avg_ani == {0.8502, 0.8584, 0.8602}
+    assert avg_ani == {0.9221, 0.9306, 0.9316} # @CTB check against py gather
 
     f_unique_weighted = set(df['f_unique_weighted'])
     f_unique_weighted = set([round(x, 4) for x in f_unique_weighted])
@@ -967,7 +967,7 @@ def test_indexed_full_output(runtmp):
 
     unique_intersect_bp = set(df['unique_intersect_bp'])
     unique_intersect_bp = set([round(x,4) for x in unique_intersect_bp])
-    assert unique_intersect_bp == {44000, 18000, 22000}
+    assert unique_intersect_bp == {4400000, 1800000, 2200000}
 
 
 def test_nonindexed_full_vs_sourmash_gather(runtmp):

From e35111a7d2a6a5c510a23b04f8bb091a4ca30e76 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 12 Oct 2024 06:08:38 -0400
Subject: [PATCH 05/11] upd sourmash

---
 Cargo.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.lock b/Cargo.lock
index 7b1eb621..da608df5 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ddcb049e99749f1d16c414e0fdb2d06d55a38db7"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#6eb86a390c53fc243bf65dd38fab3d1712c9f579"
 dependencies = [
  "az",
  "byteorder",

From 4778862e9def28528a7e9cc65d8d75c6ec2dc9f0 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 12 Oct 2024 06:24:42 -0400
Subject: [PATCH 06/11] upd sourmash

---
 Cargo.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.lock b/Cargo.lock
index da608df5..f1218059 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#6eb86a390c53fc243bf65dd38fab3d1712c9f579"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#62f03eb3de8f4b05307efad74f321ced04de40f1"
 dependencies = [
  "az",
  "byteorder",

From a0e02efb86ad084e1fcd18585a5f71253ca105ad Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 13 Oct 2024 07:19:58 -0400
Subject: [PATCH 07/11] upd sourmash

---
 Cargo.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.lock b/Cargo.lock
index f1218059..a56788cf 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#62f03eb3de8f4b05307efad74f321ced04de40f1"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#e4e5555fd81a9a8677bbe065cf7f528270b01fed"
 dependencies = [
  "az",
  "byteorder",

From 9b448c8a873e9fde1bc4cb84f441863078677eb9 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 13 Oct 2024 07:29:52 -0400
Subject: [PATCH 08/11] use new try_into() and eliminate several clone()s

---
 src/utils.rs | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/src/utils.rs b/src/utils.rs
index a702378f..0b7df6c9 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -476,28 +476,30 @@ pub fn load_sketches_above_threshold(
             let mut results = Vec::new();
             // Load against into memory
             if let Ok(against_sig) = against_collection.sig_from_record(against_record) {
-                if let Some(against_mh) = against_sig.minhash() {
-                    // downsample against_mh, but keep original md5sum
-                    let against_mh_ds = against_mh
-                        .clone()
-                        .downsample_scaled(query.scaled())
-                        .unwrap();
-                    if let Ok(overlap) = against_mh_ds.count_common(query, false) {
-                        if overlap >= threshold_hashes {
-                            let result = PrefetchResult {
-                                name: against_record.name().to_string(),
-                                md5sum: against_mh.md5sum(),
-                                minhash: against_mh_ds.clone(),
-                                location: against_record.internal_location().to_string(),
-                                overlap,
-                            };
-                            results.push(result);
-                        }
+                let against_filename = against_sig.filename();
+                let against_mh: KmerMinHash = against_sig.try_into().expect("cannot get sketch");
+                let against_md5 = against_mh.md5sum(); // keep original md5sum
+
+                let against_mh_ds = against_mh
+                    .downsample_scaled(query.scaled())
+                    .expect("cannot downsample sketch");
+
+                // good? ok, store as candidate from prefetch.
+                if let Ok(overlap) = against_mh_ds.count_common(query, false) {
+                    if overlap >= threshold_hashes {
+                        let result = PrefetchResult {
+                            name: against_record.name().to_string(),
+                            md5sum: against_md5,
+                            minhash: against_mh_ds,
+                            location: against_record.internal_location().to_string(),
+                            overlap,
+                        };
+                        results.push(result);
                     }
                 } else {
                     eprintln!(
                         "WARNING: no compatible sketches in path '{}'",
-                        against_sig.filename()
+                        against_filename
                     );
                     let _i = skipped_paths.fetch_add(1, atomic::Ordering::SeqCst);
                 }

From 18a363e4adb120fbe43b77ec41fc5158c414107b Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 13 Oct 2024 10:45:13 -0400
Subject: [PATCH 09/11] upd sourmash

---
 Cargo.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.lock b/Cargo.lock
index a56788cf..14c16762 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1549,7 +1549,7 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#e4e5555fd81a9a8677bbe065cf7f528270b01fed"
+source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ceaea393d95b3b85575b51c20784d3b9442da149"
 dependencies = [
  "az",
  "byteorder",

From be4c39c682f0a2a6ea3aed2a8aadf3b3072b764c Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 15 Oct 2024 14:41:44 -0400
Subject: [PATCH 10/11] update to sourmash r0.16.0 :tada:

---
 Cargo.lock | 31 ++++++++++++++++---------------
 Cargo.toml |  3 +--
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 37308eaf..87c0d5e4 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -713,9 +713,9 @@ dependencies = [
 
 [[package]]
 name = "js-sys"
-version = "0.3.70"
+version = "0.3.72"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1868808506b929d7b0cfa8f75951347aa71bb21144b7791bae35d9bccfcfe37a"
+checksum = "6a88f1bda2bd75b0452a14784937d796722fdebfe50df998aeb3f0b7603019a9"
 dependencies = [
  "wasm-bindgen",
 ]
@@ -1549,7 +1549,8 @@ checksum = "bceb57dc07c92cdae60f5b27b3fa92ecaaa42fe36c55e22dbfb0b44893e0b1f7"
 [[package]]
 name = "sourmash"
 version = "0.16.0"
-source = "git+https://github.com/sourmash-bio/sourmash.git?branch=refactor_rs_downsample#ceaea393d95b3b85575b51c20784d3b9442da149"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "596f20eac8896a06ca65889399ea6f408deeba375aa44c4a2efb3b46e31a02c0"
 dependencies = [
  "az",
  "byteorder",
@@ -1802,9 +1803,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5"
+checksum = "128d1e363af62632b8eb57219c8fd7877144af57558fb2ef0368d0087bddeb2e"
 dependencies = [
  "cfg-if",
  "once_cell",
@@ -1813,9 +1814,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b"
+checksum = "cb6dd4d3ca0ddffd1dd1c9c04f94b868c37ff5fac97c30b97cff2d74fce3a358"
 dependencies = [
  "bumpalo",
  "log",
@@ -1828,9 +1829,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf"
+checksum = "e79384be7f8f5a9dd5d7167216f022090cf1f9ec128e6e6a482a2cb5c5422c56"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -1838,9 +1839,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836"
+checksum = "26c6ab57572f7a24a4985830b120de1594465e5d500f24afe89e16b4e833ef68"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1851,15 +1852,15 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.93"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484"
+checksum = "65fc09f10666a9f147042251e0dda9c18f166ff7de300607007e96bdebc1068d"
 
 [[package]]
 name = "web-sys"
-version = "0.3.70"
+version = "0.3.72"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0"
+checksum = "f6488b90108c040df0fe62fa815cbdee25124641df01814dd7282749234c6112"
 dependencies = [
  "js-sys",
  "wasm-bindgen",
diff --git a/Cargo.toml b/Cargo.toml
index 8491762f..2c40a4de 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -12,8 +12,7 @@ crate-type = ["cdylib"]
 pyo3 = { version = "0.22.4", features = ["extension-module", "anyhow"] }
 rayon = "1.10.0"
 serde = { version = "1.0.210", features = ["derive"] }
-#sourmash = { version = "0.15.2", features = ["branchwater"] }
-sourmash = { git = "https://github.com/sourmash-bio/sourmash.git", branch = "refactor_rs_downsample", features = ["branchwater"] }
+sourmash = { version = "0.16.0", features = ["branchwater"] }
 serde_json = "1.0.128"
 niffler = "2.4.0"
 log = "0.4.22"

From b7d1f5308ce6a8143596330ef4a6372e23334e27 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 15 Oct 2024 14:44:30 -0400
Subject: [PATCH 11/11] fix mambaforge -> miniforge

---
 .github/workflows/build-test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
index 51041d65..c9fac079 100644
--- a/.github/workflows/build-test.yml
+++ b/.github/workflows/build-test.yml
@@ -29,7 +29,6 @@ jobs:
         auto-update-conda: true
         python-version: 3.12
         channels: conda-forge,bioconda
-        miniforge-variant: Mambaforge
         miniforge-version: latest
         use-mamba: true
         mamba-version: "*"