From 324c4fb973ae9fe7744f4d1748f8bf3b3aa368f0 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 29 Jul 2024 23:26:06 +0000
Subject: [PATCH] create sanitized release

---
 Cargo.toml         |  4 +-
 Cargo.toml.cs_orig | 92 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+), 2 deletions(-)
 create mode 100644 Cargo.toml.cs_orig

diff --git a/Cargo.toml b/Cargo.toml
index 05410cc..ee8c725 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -31,7 +31,7 @@ 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 = "0.1.0" }
+seqcol_rs = { version = "0.1.0" }
 anyhow = "1.0.86"
 bio-types = { version = "1.0.3", features = ["serde"] }
 clap = { version = "4.5.11", features = ["derive"] }
@@ -55,7 +55,7 @@ path-tools = "0.1.0"
 atomic_float = "1.0.0"
 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 = "0.1.0" }
+kders = { version = "0.1.0" }
 
 [[bin]]
 name = "oarfish"
diff --git a/Cargo.toml.cs_orig b/Cargo.toml.cs_orig
new file mode 100644
index 0000000..05410cc
--- /dev/null
+++ b/Cargo.toml.cs_orig
@@ -0,0 +1,92 @@
+[package]
+name = "oarfish"
+version = "0.5.0"
+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 = "0.1.0" }
+anyhow = "1.0.86"
+bio-types = { version = "1.0.3", features = ["serde"] }
+clap = { version = "4.5.11", features = ["derive"] }
+coitrees = "0.4.0"
+noodles-bam = "0.65.0"
+noodles-gtf = "0.30.0"
+noodles-sam = "0.62.0"
+num-format = "0.4.4"
+tabled = "0.15.0"
+tracing = "0.1.40"
+tracing-subscriber = {version="0.3.18", features=["env-filter"]}
+typed-builder = "0.19.1"
+rayon = "1.10"
+statrs = "0.17"
+csv = "1.3"
+ndarray = "0.15"
+serde = { version = "1", features = ["derive"] }
+itertools = "0.13.0"
+serde_json = "1.0.121"
+path-tools = "0.1.0"
+atomic_float = "1.0.0"
+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 = "0.1.0" }
+
+[[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 = "0.19.1"
+# 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"]
+# Publish jobs to run in CI
+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"