From 6a24f4783f9f7b893bd57182a3050f0b14a0d1fb Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:44:29 +0000
Subject: [PATCH] create sanitized release

---
 Cargo.toml         |  6 ++--
 Cargo.toml.cs_orig | 85 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 88 insertions(+), 3 deletions(-)
 create mode 100644 Cargo.toml.cs_orig

diff --git a/Cargo.toml b/Cargo.toml
index a4c8473..39beed7 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -32,9 +32,9 @@ categories = ["command-line-utilities", "science"]
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
-seq_geom_parser = { git = "https://github.com/COMBINE-lab/seq_geom_parser", branch = "dev", version = "0.3.0" }
-seq_geom_xform = { git = "https://github.com/COMBINE-lab/seq_geom_xform", branch = "dev", version = "0.4.0" }
-roers = { git = "https://github.com/COMBINE-lab/roers", branch = "main", version = "0.3.0" }
+seq_geom_parser = { version = "0.3.0" }
+seq_geom_xform = { version = "0.4.0" }
+roers = { version = "0.3.0" }
 anyhow = "^1.0"
 clap = { version = "4.5.9", features = ["derive", "cargo", "deprecated", "wrap_help", "help", "usage", "error-context"] } 
 cmd_lib = "^1.9.4"
diff --git a/Cargo.toml.cs_orig b/Cargo.toml.cs_orig
new file mode 100644
index 0000000..a4c8473
--- /dev/null
+++ b/Cargo.toml.cs_orig
@@ -0,0 +1,85 @@
+[package]
+name = "simpleaf"
+version = "0.17.2"
+edition = "2021"
+authors = [
+  "Rob Patro <rob@cs.umd.edu>",
+  "Dongze He <dhe17@umd.edu>",
+]
+description = "A rust framework to make using alevin-fry even simpler."
+license-file = "LICENSE"
+readme = "README.md"
+repository = "https://github.com/COMBINE-lab/simpleaf"
+homepage = "https://github.com/COMBINE-lab/simpleaf"
+#documentation = "https://alevin-fry.readthedocs.io/en/latest/"
+include = [
+  "/src/*.rs",
+  "/src/utils/*.rs",
+  "/src/simpleaf_commands/*.rs",
+  "/Cargo.toml",
+  "/Cargo.lock",
+  "/README.md",
+  "/LICENSE",
+]
+keywords = [
+  "single-cell",
+  "preprocessing",
+  "RNA-seq",
+  "single-nucleus",
+  "RNA-velocity",
+]
+categories = ["command-line-utilities", "science"]
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[dependencies]
+seq_geom_parser = { git = "https://github.com/COMBINE-lab/seq_geom_parser", branch = "dev", version = "0.3.0" }
+seq_geom_xform = { git = "https://github.com/COMBINE-lab/seq_geom_xform", branch = "dev", version = "0.4.0" }
+roers = { git = "https://github.com/COMBINE-lab/roers", branch = "main", version = "0.3.0" }
+anyhow = "^1.0"
+clap = { version = "4.5.9", features = ["derive", "cargo", "deprecated", "wrap_help", "help", "usage", "error-context"] } 
+cmd_lib = "^1.9.4"
+tracing = "0.1.40"
+tracing-subscriber = { version = "0.3.18", default-features = true, features = ["env-filter"] }
+semver = "^1.0.23"
+serde = {version = "1.0.204", features = ["derive"]}
+serde_json = "1.0.120"
+time = {version = "^0.3.36", features = ["macros", "formatting", "parsing", "serde", "serde-human-readable"]}
+which = "^6.0.1"
+jrsonnet-evaluator = "0.5.0-pre95"
+jrsonnet-cli = "0.5.0-pre95"
+jrsonnet-parser = "0.5.0-pre95"
+thiserror = "1.0"
+phf = { version = "0.11.2", features = ["macros"] }
+chrono = "0.4.38"
+tabled = "0.15.0"
+csv = "1.3.0"
+minreq = { version = "2.11.2", features = ["serde", "serde_json", "https", "json-using-serde"] }
+strum = { version = "0.26.3", features = ["derive", "phf"] }
+strum_macros = "0.26.4"
+
+[profile.release]
+lto = "thin"
+opt-level = 3
+
+# 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 = "0.18.0"
+# 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 = true
+
+[workspace.metadata.dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"