From f4a038fecf9bc7cb55394f5a5cc83191b6cb7734 Mon Sep 17 00:00:00 2001
From: "N. Tessa Pierce-Ward" <ntpierce@gmail.com>
Date: Mon, 6 May 2024 17:35:54 -0700
Subject: [PATCH] upd zip

---
 Cargo.lock          | 97 +++++++++++++++++++++++++++++++++++++++++++--
 Cargo.toml          |  2 +-
 src/directsketch.rs |  6 +--
 3 files changed, 98 insertions(+), 7 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index ffb1959..1e7d860 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -73,6 +73,15 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "arbitrary"
+version = "1.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7d5a26814d8dcb93b0e5a0ff3c6d80a8843bafb21b39e8e18a6f05471870e110"
+dependencies = [
+ "derive_arbitrary",
+]
+
 [[package]]
 name = "autocfg"
 version = "1.2.0"
@@ -398,6 +407,28 @@ dependencies = [
  "memchr",
 ]
 
+[[package]]
+name = "derive_arbitrary"
+version = "1.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "67e77553c4162a157adbf834ebae5b415acbecbeafc7a74b0e886657506a7611"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.60",
+]
+
+[[package]]
+name = "displaydoc"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "487585f4d0c6655fe74905e2504d8ad6908e4db67f744eb140876906c2f3175d"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.60",
+]
+
 [[package]]
 name = "either"
 version = "1.11.0"
@@ -1207,6 +1238,27 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "num_enum"
+version = "0.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "02339744ee7253741199f897151b38e72257d13802d4ee837285cc2990a90845"
+dependencies = [
+ "num_enum_derive",
+]
+
+[[package]]
+name = "num_enum_derive"
+version = "0.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "681030a937600a36906c185595136d26abfebb4aa9c65701cefcaf8578bb982b"
+dependencies = [
+ "proc-macro-crate",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.60",
+]
+
 [[package]]
 name = "object"
 version = "0.32.2"
@@ -1427,6 +1479,15 @@ dependencies = [
  "num-integer",
 ]
 
+[[package]]
+name = "proc-macro-crate"
+version = "3.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6d37c51ca738a55da99dc0c4a34860fd675453b8b36209178c2249bb13651284"
+dependencies = [
+ "toml_edit",
+]
+
 [[package]]
 name = "proc-macro-error"
 version = "1.0.4"
@@ -2258,6 +2319,23 @@ dependencies = [
  "tracing",
 ]
 
+[[package]]
+name = "toml_datetime"
+version = "0.6.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3550f4e9685620ac18a50ed434eb3aec30db8ba93b0287467bca5826ea25baf1"
+
+[[package]]
+name = "toml_edit"
+version = "0.21.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6a8534fd7f78b5405e860340ad6575217ce99f38d4d5c8f2442cb5ecb50090e1"
+dependencies = [
+ "indexmap",
+ "toml_datetime",
+ "winnow",
+]
+
 [[package]]
 name = "tower"
 version = "0.4.13"
@@ -2671,6 +2749,15 @@ version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0"
 
+[[package]]
+name = "winnow"
+version = "0.5.40"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f593a95398737aeed53e489c785df13f3618e41dbcd6718c6addbf1395aa6876"
+dependencies = [
+ "memchr",
+]
+
 [[package]]
 name = "winreg"
 version = "0.52.0"
@@ -2707,14 +2794,18 @@ checksum = "cfe53a6657fd280eaa890a3bc59152892ffa3e30101319d168b781ed6529b049"
 
 [[package]]
 name = "zip"
-version = "0.6.6"
+version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261"
+checksum = "57c07d35c02b10a0884b033b17edb61a4d7bc443ef9a12636bb8cd2e8b8ab5ca"
 dependencies = [
- "byteorder",
+ "arbitrary",
  "crc32fast",
  "crossbeam-utils",
+ "displaydoc",
  "flate2",
+ "indexmap",
+ "num_enum",
+ "thiserror",
 ]
 
 [[package]]
diff --git a/Cargo.toml b/Cargo.toml
index d8093df..b966f6f 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -16,7 +16,7 @@ sourmash = { version = "0.13.1", features=["branchwater"]}
 serde_json = "1.0.116"
 niffler = "2.4.0"
 needletail = "0.5.1"
-zip = { version = "0.6", default-features = false, features = ["deflate"] }
+zip = { version = "1.2.0", default-features = false, features = ["deflate"] }
 simple-error = "0.3.0"
 anyhow = "1.0.82"
 camino = "1.1.6"
diff --git a/src/directsketch.rs b/src/directsketch.rs
index 5b87273..99b67c4 100644
--- a/src/directsketch.rs
+++ b/src/directsketch.rs
@@ -299,12 +299,12 @@ async fn dl_sketch_accession(
     Ok((sigs, failed))
 }
 
-fn write_sig(
+fn write_sig<T: zip::write::FileOptionExtension>(
     sig: &Signature,
     md5sum_occurrences: &mut HashMap<String, usize>,
     manifest_rows: &mut Vec<Record>,
     zip_f: &mut ZipWriter<std::fs::File>,
-    zip_options: zip::write::FileOptions,
+    zip_options: zip::write::FileOptions<T>,
 ) -> Result<()> {
     let md5sum_str = sig.md5sum();
     let count = md5sum_occurrences.entry(md5sum_str.clone()).or_insert(0);
@@ -377,7 +377,7 @@ pub async fn download_and_sketch(
     let outpath: PathBuf = output_sigs.into();
     let mut zip_f = ZipWriter::new(std::fs::File::create(&outpath)?);
     // zip options
-    let options = zip::write::FileOptions::default()
+    let options = zip::write::SimpleFileOptions::default()
         .compression_method(zip::CompressionMethod::Stored)
         .large_file(true);