From 67174666005bd144582f90d054cf7b2acc504f41 Mon Sep 17 00:00:00 2001
From: Austin Richardson <accounts@agdr.org>
Date: Fri, 5 Jan 2024 19:54:22 -0800
Subject: [PATCH 1/3] Increase capnproto size limit

Bump limit for Mash

Make Clippy happy

Fix comment. Decrease limit
---
 README.md                     | 10 ++++++++++
 cli/Cargo.toml                |  2 +-
 lib/src/serialization/json.rs |  1 -
 lib/src/serialization/mash.rs |  6 +++++-
 lib/src/serialization/mod.rs  |  6 +++++-
 5 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index ff92c60..1ac20f7 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,17 @@ This repository provides a library and command-line interface that reimplements
 You may build Finch from source, which requires Rust >= `1.49`. Rust's Cargo package manager (see [rustup](https://www.rustup.rs) for Cargo installation instructions) can automatically build and install Finch with `cargo install finch_cli`.
 If you require python bindings, you must take extra steps (see [python support](#python-support)). Alternatively, [download a prebuilt binary](https://github.com/onecodex/finch-rs/releases) or install from [PyPi](https://pypi.org/project/finch-sketch/) `pip install finch-sketch`.
 
+### Building ###
+
+To compile from source:
+
+```sh
+# from finch-rs
+cargo +nightly-2023-06-28 build --release
+```
+
 ### Example Usage ###
+
 To get started, we first compute sketches for several FASTA or FASTQ files. These sketches are compact, sampled representations of the underlying genomic data, and what allow `finch` to rapidly estimate distances between datasets. Sketching files uses the `finch sketch` command:
 
 ```
diff --git a/cli/Cargo.toml b/cli/Cargo.toml
index 7eacc26..a4fe088 100644
--- a/cli/Cargo.toml
+++ b/cli/Cargo.toml
@@ -16,7 +16,7 @@ path = "src/main.rs"
 
 [dependencies]
 clap = "2.33.0"
-finch = "0.6"
+finch = { path = "../lib" }
 serde_json = "1"
 anyhow = "1"
 
diff --git a/lib/src/serialization/json.rs b/lib/src/serialization/json.rs
index 61402bc..56fcf89 100644
--- a/lib/src/serialization/json.rs
+++ b/lib/src/serialization/json.rs
@@ -9,7 +9,6 @@ use serde::{Deserialize, Serialize};
 use crate::bail;
 use crate::errors::FinchResult;
 use crate::filtering::FilterParams;
-pub use crate::serialization::mash::{read_mash_file, write_mash_file};
 use crate::serialization::Sketch;
 use crate::sketch_schemes::{KmerCount, SketchParams};
 
diff --git a/lib/src/serialization/mash.rs b/lib/src/serialization/mash.rs
index 761d084..1790456 100644
--- a/lib/src/serialization/mash.rs
+++ b/lib/src/serialization/mash.rs
@@ -58,7 +58,11 @@ pub fn write_mash_file(file: &mut dyn Write, sketches: &[Sketch]) -> FinchResult
 }
 
 pub fn read_mash_file(file: &mut dyn BufRead) -> FinchResult<Vec<Sketch>> {
-    let options = *message::ReaderOptions::new().traversal_limit_in_words(Some(1024 * 1024 * 1024));
+    let options = *message::ReaderOptions::new().traversal_limit_in_words(
+        // measured in words
+        // 1 word = 8 bytes
+        Some(2 * 1024 * 1024 * 1024),
+    );
     let reader = capnp_serialize::read_message(file, options)?;
     let mash_data: min_hash::Reader = reader.get_root::<min_hash::Reader>()?;
 
diff --git a/lib/src/serialization/mod.rs b/lib/src/serialization/mod.rs
index 19ccb37..6b0dee1 100644
--- a/lib/src/serialization/mod.rs
+++ b/lib/src/serialization/mod.rs
@@ -171,7 +171,11 @@ pub fn write_finch_file(file: &mut dyn Write, sketches: &[Sketch]) -> FinchResul
 }
 
 pub fn read_finch_file(file: &mut dyn BufRead) -> FinchResult<Vec<Sketch>> {
-    let options = *message::ReaderOptions::new().traversal_limit_in_words(Some(1024 * 1024 * 1024));
+    let options = *message::ReaderOptions::new().traversal_limit_in_words(
+        // measured in words
+        // 1 word = 8 bytes
+        Some(2 * 1024 * 1024 * 1024),
+    );
     let reader = capnp_serialize::read_message(file, options)?;
     let cap_data: multisketch::Reader = reader.get_root::<multisketch::Reader>()?;
     let cap_sketches = cap_data.get_sketches()?;

From e6e4d4d791293d1dd35f46b817c7edead47b8fd2 Mon Sep 17 00:00:00 2001
From: Austin Richardson <accounts@agdr.org>
Date: Fri, 5 Jan 2024 20:08:23 -0800
Subject: [PATCH 2/3] Update install instructions

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 1ac20f7..50784db 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@ To compile from source:
 
 ```sh
 # from finch-rs
-cargo +nightly-2023-06-28 build --release
+cargo +stable build --release
 ```
 
 ### Example Usage ###

From 92d3b7c82122c55b2f54ecaa7f6bc99338417cbd Mon Sep 17 00:00:00 2001
From: Austin Richardson <accounts@agdr.org>
Date: Mon, 8 Jan 2024 08:43:15 -0800
Subject: [PATCH 3/3] Revert change

---
 cli/Cargo.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cli/Cargo.toml b/cli/Cargo.toml
index a4fe088..7eacc26 100644
--- a/cli/Cargo.toml
+++ b/cli/Cargo.toml
@@ -16,7 +16,7 @@ path = "src/main.rs"
 
 [dependencies]
 clap = "2.33.0"
-finch = { path = "../lib" }
+finch = "0.6"
 serde_json = "1"
 anyhow = "1"