Merge branch 'latest' into plant-db

doc/support.md

@@ -81,6 +81,13 @@ you upgrade within a major sourmash release (barring bug fixes!). Moreover,
 if you rely on a feature introduced in v3.3.0, that feature will not break
 in v3.4.0, but will also not be backported to version 3.2.0.
 
+### Output file formats
+
+In particular, the CSV output file formats are guaranteed to be stable
+within major versions, with one caveat: we may add or rearrange
+columns between releases.  You should use column headers/column names
+to parse CSV files, and not depend on column order.
+
 ### Python API
 
 We intend to guarantee the Python API at the top level, i.e.

include/sourmash.h

@@ -49,6 +49,7 @@ enum SourmashErrorCode {
   SOURMASH_ERROR_CODE_NIFFLER_ERROR = 100005,
   SOURMASH_ERROR_CODE_CSV_ERROR = 100006,
   SOURMASH_ERROR_CODE_ROCKS_DB_ERROR = 100007,
+  SOURMASH_ERROR_CODE_ZIP_ERROR = 100008,
 };
 typedef uint32_t SourmashErrorCode;
 

src/core/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sourmash"
-version = "0.17.2"
+version = "0.18.0"
 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"

src/core/src/errors.rs

@@ -90,6 +90,9 @@ pub enum SourmashError {
     #[cfg(feature = "branchwater")]
     #[error(transparent)]
     RocksDBError(#[from] rocksdb::Error),
+
+    #[error(transparent)]
+    ZipError(#[from] piz::result::ZipError),
 }
 
 #[derive(Debug, Error)]
@@ -140,6 +143,7 @@ pub enum SourmashErrorCode {
     NifflerError = 100_005,
     CsvError = 100_006,
     RocksDBError = 100_007,
+    ZipError = 100_008,
 }
 
 #[cfg(not(all(target_arch = "wasm32", target_os = "unknown")))]
@@ -179,6 +183,8 @@ impl SourmashErrorCode {
             #[cfg(not(target_arch = "wasm32"))]
             #[cfg(feature = "branchwater")]
             SourmashError::RocksDBError { .. } => SourmashErrorCode::RocksDBError,
+
+            SourmashError::ZipError { .. } => SourmashErrorCode::ZipError,
         }
     }
 }

src/core/src/storage/mod.rs

@@ -403,22 +403,22 @@ impl ZipStorage {
         let zip_file = File::open(location.as_ref())?;
         let mapping = unsafe { memmap2::Mmap::map(&zip_file)? };
 
-        let mut storage = ZipStorageBuilder {
+        let mut storage = ZipStorageTryBuilder {
             mapping: Some(mapping),
             archive_builder: |mapping: &Option<memmap2::Mmap>| {
-                piz::ZipArchive::new(mapping.as_ref().unwrap()).unwrap()
+                piz::ZipArchive::new(mapping.as_ref().unwrap())
             },
             metadata_builder: |archive: &piz::ZipArchive| {
-                archive
+                Ok(archive
                     .entries()
                     .iter()
                     .map(|entry| (entry.path.as_os_str(), entry))
-                    .collect()
+                    .collect())
             },
             subdir: None,
             path: Some(location.as_ref().into()),
         }
-        .build();
+        .try_build()?;
 
         let subdir = find_subdirs(storage.borrow_archive())?;
         storage.with_mut(|fields| *fields.subdir = subdir);