create sanitized release

Cargo.toml.cs_orig

@@ -0,0 +1,127 @@
+[package]
+authors = [
+  "Avi Srivastava <asrivastava@wistar.org>",
+  "Hirak Sarkar <hiraksarkar.cs@gmail.com>",
+  "Dongze He <dhe17@umd.edu>.zakeri@gmail.com>",
+  "Noor Pratap Singh <npsingh@umd.edu>",
+  "Rob Patro <rob@cs.umd.edu>",
+]
+name = "alevin-fry"
+version = "0.11.1"
+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",
+  "/src/atac/*.rs",
+  "/Cargo.toml",
+  "/README.md",
+  "/LICENSE",
+  "/CONTRIBUTING.md",
+  "/CODE_OF_CONDUCT.md",
+]
+keywords = [
+  "single-cell",
+  "preprocessing",
+  "RNA-seq",
+  "ATAC-seq",
+  "single-nucleus",
+]
+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 = "0.10.0" }
+libradicl = { version = "0.10.0" }
+anyhow = "1.0.95"
+arrayvec = "0.7.6"
+ahash = "0.8.11"
+bincode = "1.3.3"
+bstr = "1.11.1"
+crossbeam-channel = "0.5.14"
+crossbeam-queue = "0.3.12"
+typed-builder = "0.20.0"
+indicatif = "0.17.9"
+needletail = "0.6.1"
+petgraph = "0.6.5"
+flate2 = "1.0.35"
+scroll = "0.12.0"
+serde = { version = "1.0.216", features = ["derive"] }
+serde_json = "1.0.134"
+sprs = "0.11.2"
+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 = "0.4.39"
+csv = "1.3.1"
+mimalloc = { version = "0.1.43", default-features = false }
+num-format = "0.4.4"
+num_cpus = "1.16.0"
+bio-types = { version = "1.0.4", default-features = true, features = ["serde"] }
+itertools = "0.13.0"
+thiserror = "2.0.9"
+statrs = "0.18.0"
+#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
+clap = { version = "4.5.23", features = [
+  "derive",
+  "wrap_help",
+  "cargo",
+  "help",
+  "usage",
+  "string",
+  "error-context",
+] }
+
+noodles = { version = "0.85.0", features = ["bam", "bgzf", "sam"] }
+dashmap = { version = "6.1.0", features = ["serde", "inline"] }
+nalgebra = "0.33.2"
+niffler = { version = "2.6.0", default-features = false, features = [
+  "gz",
+  "gz_cloudflare_zlib",
+] }
+
+[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 'dist'
+[workspace.metadata.dist]
+# The preferred dist version to use in CI (Cargo.toml SemVer syntax)
+cargo-dist-version = "0.25.1"
+# 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"
+# Path that installers should place binaries in
+install-path = "CARGO_HOME"
+# Whether to install an updater program
+install-updater = true
+
+[workspace.metadata.dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"