From 2f81fa037176a382027f43278a2a66ca7eb54a94 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 28 Nov 2024 02:37:25 +0000
Subject: [PATCH] create sanitized release

---
 Cargo.toml         |   4 +-
 Cargo.toml.cs_orig | 113 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 115 insertions(+), 2 deletions(-)
 create mode 100644 Cargo.toml.cs_orig

diff --git a/Cargo.toml b/Cargo.toml
index afe5300..f991414 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -26,7 +26,7 @@ categories = ["command-line-utilities", "science"]
 # See more keys and their definitions 
 # at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
-seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.3" }
+seqcol_rs = { version = "0.1.3" }
 anyhow = "1.0.93"
 bstr = "1.11.0"
 bio-types = { version = "1.0.4", features = ["serde"] }
@@ -56,7 +56,7 @@ arrow2 = { version = "0.18.0", features = [
   "io_parquet_zstd",
   "io_parquet_snappy",
 ] }
-kders = { git = "https://github.com/COMBINE-lab/kde-rs.git", branch = "dev", version = "0.1.1" }
+kders = { version = "0.1.1" }
 noodles-bgzf = { version = "0.33.0" }
 crossbeam = { version = "0.8.4", features = [
   "crossbeam-queue",
diff --git a/Cargo.toml.cs_orig b/Cargo.toml.cs_orig
new file mode 100644
index 0000000..afe5300
--- /dev/null
+++ b/Cargo.toml.cs_orig
@@ -0,0 +1,113 @@
+[package]
+name = "oarfish"
+version = "0.6.5"
+edition = "2021"
+authors = [
+  "Zahra Zare Jousheghani <zzare@umd.edu>",
+  "Noor Pratap Singh <npsingh@umd.edu>",
+  "Rob Patro <rob@cs.umd.edu>",
+]
+description = "A fast, accurate and versatile tool for long-read transcript quantification."
+license-file = "LICENSE"
+readme = "README.md"
+repository = "https://github.com/COMBINE-lab/oarfish"
+homepage = "https://COMBINE-lab.github.io/oarfish"
+include = [
+  "/src/*.rs",
+  "/src/util/*.rs",
+  "/Cargo.toml",
+  "/Cargo.lock",
+  "/README.md",
+  "/LICENSE",
+]
+keywords = ["RNA-seq", "quantification", "long-read", "transcriptomics"]
+categories = ["command-line-utilities", "science"]
+
+# See more keys and their definitions 
+# at https://doc.rust-lang.org/cargo/reference/manifest.html
+[dependencies]
+seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.3" }
+anyhow = "1.0.93"
+bstr = "1.11.0"
+bio-types = { version = "1.0.4", features = ["serde"] }
+clap = { version = "4.5.21", features = ["derive"] }
+noodles-bam = "0.70.0"
+noodles-sam = "0.66.0"
+num-format = "0.4.4"
+lz4 = "1.28.0"
+either = "1.13.0"
+tabled = "0.17.0"
+tracing = "0.1.41"
+tracing-subscriber = { version = "0.3.18", features = ["env-filter"] }
+typed-builder = "0.20.0"
+rayon = "1.10"
+statrs = "0.17"
+csv = "1.3"
+serde = { version = "1", features = ["derive"] }
+itertools = "0.13.0"
+serde_json = "1.0.133"
+path-tools = "0.1.0"
+atomic_float = "1.1.0"
+sendable-swapvec = "0.4.3"
+rand = "0.8.5"
+arrow2 = { version = "0.18.0", features = [
+  "io_parquet",
+  "io_parquet_gzip",
+  "io_parquet_zstd",
+  "io_parquet_snappy",
+] }
+kders = { git = "https://github.com/COMBINE-lab/kde-rs.git", branch = "dev", version = "0.1.1" }
+noodles-bgzf = { version = "0.33.0" }
+crossbeam = { version = "0.8.4", features = [
+  "crossbeam-queue",
+  "crossbeam-channel",
+] }
+sprs = "0.11.2"
+
+# alternative sources for dev
+minimap2-sys = { version = "0.1.20" } #, git = "https://github.com/jguhlin/minimap2-rs.git", branch = "main" }
+minimap2 = { version = "0.1.21" }     #, git = "https://github.com/jguhlin/minimap2-rs.git", branch = "main" }
+
+needletail = "0.6.0"
+indicatif = "0.17.9"
+rustc-hash = "2.0.0"
+
+[[bin]]
+name = "oarfish"
+path = "src/main.rs"
+
+[profile.release]
+debug-assertions = false
+lto = "thin"
+panic = "abort"
+
+# The profile that 'cargo dist' will build with
+[profile.dist]
+inherits = "release"
+lto = "thin"
+
+# Config for 'cargo dist'
+[workspace.metadata.dist]
+# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax)
+cargo-dist-version = "0.21.1"
+# CI backends to support
+ci = "github"
+# The installers to generate for each app
+installers = ["shell"]
+# Target platforms to build apps for (Rust target-triple syntax)
+targets = [
+  "aarch64-apple-darwin",
+  "x86_64-apple-darwin",
+  "x86_64-unknown-linux-gnu",
+]
+# Which actions to run on pull requests
+pr-run-mode = "plan"
+# Whether to install an updater program
+install-updater = false
+# Path that installers should place binaries in
+install-path = "CARGO_HOME"
+
+[workspace.metadata.dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"
+# don't have linux arm builders on GitHub yet
+# aarch64-unknown-linux-gnu = "buildjet-8vcpu-ubuntu-2204-arm"