add skipmers; update as needed for core changes

Cargo.toml

@@ -12,15 +12,16 @@ crate-type = ["cdylib"]
 pyo3 = { version = "0.23.3", features = ["extension-module","anyhow"], default = ["extension-module"] }
 rayon = "1.10.0"
 serde = { version = "1.0.204", features = ["derive"] }
-sourmash = { version = "0.16.0"}
+#sourmash = { version = "0.18.0"}
+sourmash = {git = "https://github.com/sourmash-bio/sourmash/", branch = "try-skipmers"}
 serde_json = "1.0.132"
 niffler = "2.4.0"
 needletail = "0.5.1"
 async_zip={version="0.0.17", features=["full"]}
 simple-error = "0.3.1"
 anyhow = "1.0.90"
 camino = "1.1.7"
-csv = "1.3.0"
+csv = "1.3.1"
 reqwest = { version = "0.12.8", features = ["json", "stream"] }
 tokio = { version = "1.42.0", features = ["full"] }
 tokio-util = "0.7.11"

environment.yml

@@ -6,8 +6,8 @@ channels:
 dependencies:
   - sourmash>=4.8,<5
   - pip
-  - rust
+  - rust=1.75
   - maturin>=1,<2
   - pytest
   - pandas
-  - compilers
+  - compilers

src/directsketch.rs

@@ -540,34 +540,24 @@ async fn load_existing_zip_batches(outpath: &PathBuf) -> Result<(MultiCollection
         if let Some(file_name) = entry_path.file_name() {
             // Check if the file matches the base zip file or any batched zip file (outpath.zip, outpath.1.zip, etc.)
             if let Some(captures) = zip_file_pattern.captures(file_name) {
-                // Wrap the `from_zipfile` call in `catch_unwind` to prevent panic propagation
-                let result = panic::catch_unwind(|| Collection::from_zipfile(&entry_path));
-                match result {
-                    Ok(Ok(collection)) => {
-                        // Successfully loaded the collection, push to `collections`
+                Collection::from_zipfile(&entry_path)
+                    .and_then(|collection| {
                         collections.push(collection);
 
-                        // Extract the batch number (if it exists) and update the highest_batch
+                        // Extract batch number if it exists
                         if let Some(batch_str) = captures.get(1) {
                             if let Ok(batch_num) = batch_str.as_str().parse::<usize>() {
                                 highest_batch = max(highest_batch, batch_num);
                             }
                         }
-                    }
-                    Ok(Err(e)) => {
-                        // Handle the case where `from_zipfile` returned an error
+                        Ok(()) // Return Ok(()) for the closure
+                    })
+                    .unwrap_or_else(|e| {
                         eprintln!(
-                            "Warning: Failed to load zip file '{}'. Error: {:?}",
+                            "Warning: Failed to load zip file '{}'; skipping. Zipfile Error: {:?}",
                             entry_path, e
                         );
-                        continue; // Skip the file and continue
-                    }
-                    Err(_) => {
-                        // The code inside `from_zipfile` panicked
-                        eprintln!("Warning: Invalid zip file '{}'; skipping.", entry_path);
-                        continue; // Skip the file and continue
-                    }
-                }
+                    });
             }
         }
     }