From f56bc1969bbc67114c2253cf9545142ca62b2d5b Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 12 Jul 2024 13:38:20 +0000
Subject: [PATCH] create sanitized release

---
 Cargo.toml         |   4 +-
 Cargo.toml.cs_orig | 104 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 106 insertions(+), 2 deletions(-)
 create mode 100644 Cargo.toml.cs_orig

diff --git a/Cargo.toml b/Cargo.toml
index ae8642d..a276216 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -35,7 +35,7 @@ categories = ["command-line-utilities", "science"]
 [dependencies]
 # for local development, look in the libradicl git repository
 # but when published, pull the specified version
-libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.9.0" }
+libradicl = { version = "0.9.0" }
 anyhow = "1.0.86"
 arrayvec = "0.7.4"
 ahash = "0.8.11"
@@ -67,7 +67,7 @@ bio-types = { version = "1.0.2", default-features = true, features = ["serde"] }
 itertools = "0.13.0"
 thiserror = "1.0.62"
 statrs = "0.17.1"
-sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" }
+sce = { version = "0.2.0" }
 
 # no shenanigans; clap makes breaking "fixes" too often to allow variability
 # in the version different from what we tested with
diff --git a/Cargo.toml.cs_orig b/Cargo.toml.cs_orig
new file mode 100644
index 0000000..ae8642d
--- /dev/null
+++ b/Cargo.toml.cs_orig
@@ -0,0 +1,104 @@
+[package]
+name = "alevin-fry"
+version = "0.10.0"
+authors = [
+  "Avi Srivastava <avi.srivastava@nyu.edu>",
+  "Hirak Sarkar <hirak_sarkar@hms.harvard.edu>",
+  "Dongze He <dhe17@umd.edu>",
+  "Mohsen Zakeri <mzakeri@cs.umd.edu>",
+  "Rob Patro <rob@cs.umd.edu>",
+]
+edition = "2021"
+description = "A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data."
+license-file = "LICENSE"
+readme = "README.md"
+repository = "https://github.com/COMBINE-lab/alevin-fry"
+homepage = "https://github.com/COMBINE-lab/alevin-fry"
+documentation = "https://alevin-fry.readthedocs.io/en/latest/"
+include = [
+  "/src/*.rs",
+  "/Cargo.toml",
+  "/README.md",
+  "/LICENSE",
+  "/CONTRIBUTING.md",
+  "/CODE_OF_CONDUCT.md",
+]
+keywords = [
+  "single-cell",
+  "preprocessing",
+  "RNA-seq",
+  "single-nucleus",
+  "RNA-velocity",
+]
+categories = ["command-line-utilities", "science"]
+
+[dependencies]
+# for local development, look in the libradicl git repository
+# but when published, pull the specified version
+libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.9.0" }
+anyhow = "1.0.86"
+arrayvec = "0.7.4"
+ahash = "0.8.11"
+bincode = "1.3.3"
+bstr = "1.9.1"
+crossbeam-channel = "0.5.13"
+crossbeam-queue = "0.3.11"
+typed-builder = "0.18.2"
+indicatif = "0.17.8"
+needletail = "0.5.1"
+petgraph = "0.6.5"
+flate2 = "1.0.30"
+scroll = "0.12.0"
+serde = { version = "1.0.204", features = ["derive"] }
+serde_json = "1.0.120"
+sprs = "0.11.1"
+slog = "2.7.0"
+slog-term = "2.9.1"
+slog-async = "2.8.0"
+smallvec = "1.13.2"
+snap = "1.1.1"
+rand = "0.8.5"
+chrono = "0.4.38"
+csv = "1.3.0"
+mimalloc = { version = "0.1.43", default-features = false }
+num-format = "0.4.4"
+num_cpus = "1.16.0"
+bio-types = { version = "1.0.2", default-features = true, features = ["serde"] }
+itertools = "0.13.0"
+thiserror = "1.0.62"
+statrs = "0.17.1"
+sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" }
+
+# no shenanigans; clap makes breaking "fixes" too often to allow variability
+# in the version different from what we tested with
+clap = { version = "4.5.9", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }
+
+noodles = { version = "0.77.0", features = ["bam", "bgzf", "sam"] }
+noodles-util = { version = "0.48.0", features = ["alignment"] }
+
+[profile.release]
+#debug = true
+lto = "thin"
+#codegen-units=1
+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 = "0.11.1"
+# 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"
+
+[workspace.metadata.dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"