create sanitized release

Cargo.toml

@@ -36,9 +36,9 @@ categories = ["command-line-utilities", "science"]
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
 cc = "1.2.10"
-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 = "0.4.0" }
+seq_geom_parser = { version = "0.3.0" }
+seq_geom_xform = { version = "0.4.0" }
+roers = { version = "0.4.0" }
 anyhow = "^1.0"
 clap = { version = "4.5.27", features = [
   "derive",
@@ -89,7 +89,7 @@ regex = { version = "1.11.1", default-features = false, features = [
 ] }
 tempfile = "3.15.0"
 ureq = { version = "3.0.0-rc5", features = ["json"] }
-af-anndata = { version = "0.2.0", git = "https://github.com/COMBINE-lab/af-anndata" }
+af-anndata = { version = "0.2.0"}
 
 [profile.release]
 lto = "thin"

Cargo.toml.cs_orig

@@ -0,0 +1,125 @@
+[package]
+name = "simpleaf"
+version = "0.19.0"
+edition = "2021"
+authors = [
+  "Rob Patro <[email protected]>",
+  "Dongze He <[email protected]>",
+  "Noor Pratap Singh <[email protected]>",
+]
+description = "A rust framework to make using alevin-fry and alevin-fry-ATAC even simpler."
+license-file = "LICENSE"
+readme = "README.md"
+repository = "https://github.com/COMBINE-lab/simpleaf"
+homepage = "https://simpleaf.readthedocs.io"
+#documentation = "https://fry.readthedocs.io/en/latest/"
+include = [
+  "/src/*.rs",
+  "/src/utils/*.rs",
+  "/src/utils/af_utils/*.rs",
+  "/src/atac/*.rs",
+  "/src/simpleaf_commands/*.rs",
+  "/Cargo.toml",
+  "/Cargo.lock",
+  "/README.md",
+  "/LICENSE",
+]
+keywords = [
+  "single-cell",
+  "preprocessing",
+  "RNA-seq",
+  "single-nucleus",
+  "ATAC-seq",
+]
+categories = ["command-line-utilities", "science"]
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[dependencies]
+cc = "1.2.10"
+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 = "0.4.0" }
+anyhow = "^1.0"
+clap = { version = "4.5.27", features = [
+  "derive",
+  "cargo",
+  "deprecated",
+  "wrap_help",
+  "help",
+  "usage",
+  "error-context",
+] }
+cmd_lib = "^1.9.5"
+tracing = "0.1.41"
+tracing-subscriber = { version = "0.3.19", default-features = true, features = [
+  "env-filter",
+] }
+semver = "^1.0.25"
+serde = { version = "1.0.217", features = ["derive"] }
+serde_json = "1.0.137"
+time = { version = "^0.3.37", features = [
+  "macros",
+  "formatting",
+  "parsing",
+  "serde",
+  "serde-human-readable",
+] }
+which = "7.0.1"
+jrsonnet-evaluator = "0.5.0-pre95"
+jrsonnet-cli = "0.5.0-pre95"
+jrsonnet-parser = "0.5.0-pre95"
+thiserror = "2.0.11"
+phf = { version = "0.11.3", features = ["macros"] }
+chrono = "0.4.39"
+tabled = "0.17.0"
+csv = "1.3.1"
+strum = { version = "0.26.3", features = ["derive", "phf"] }
+strum_macros = "0.26.4"
+niffler = { version = "2.7.0", default-features = false, features = [
+  "gz_zlib-ng",
+] }
+#git = "https://github.com/rob-p/niffler", branch = "master", version = "2.6.0", default-features = false, features = [
+#"gz_zlib-ng-compat",
+#] }
+#niffler = { version = "2.6.0", default-features = false, features = ["gz"] }
+blake3 = { version = "1.5.5", features = ["mmap", "serde"] }
+regex = { version = "1.11.1", default-features = false, features = [
+  "perf",
+  "std",
+] }
+tempfile = "3.15.0"
+ureq = { version = "3.0.0-rc5", features = ["json"] }
+af-anndata = { version = "0.2.0", git = "https://github.com/COMBINE-lab/af-anndata" }
+
+[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 = "0.21.1"
+# 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 = true
+# Path that installers should place binaries in
+install-path = "CARGO_HOME"
+
+[workspace.metadata.dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"