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create sanitized release
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2 files changed

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‎Cargo.toml‎

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@@ -36,9 +36,9 @@ categories = ["command-line-utilities", "science"]
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# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
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[dependencies]
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cc = "1.2.16"
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seq_geom_parser = { git = "https://github.com/COMBINE-lab/seq_geom_parser", branch = "dev", version = "0.3.0" }
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seq_geom_xform = { git = "https://github.com/COMBINE-lab/seq_geom_xform", branch = "dev", version = "0.4.0" }
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roers = { git = "https://github.com/COMBINE-lab/roers", branch = "main", version = "0.4.0" }
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seq_geom_parser = { version = "0.3.0" }
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seq_geom_xform = { version = "0.4.0" }
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roers = { version = "0.4.0" }
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anyhow = "^1.0"
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clap = { version = "4.5.31", features = [
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"derive",
@@ -84,7 +84,7 @@ regex = { version = "1.11.1", default-features = false, features = [
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] }
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tempfile = "3.17.1"
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ureq = { version = "3.0.8", features = ["json"] }
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af-anndata = { version = "0.3.2", git = "https://github.com/COMBINE-lab/af-anndata" }
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af-anndata = { version = "0.3.2"}
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[profile.release]
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lto = "thin"

‎Cargo.toml.cs_orig‎

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[package]
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name = "simpleaf"
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version = "0.19.4"
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edition = "2021"
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authors = [
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"Rob Patro <rob@cs.umd.edu>",
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"Dongze He <dhe17@umd.edu>",
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"Noor Pratap Singh <npsingh@umd.edu>",
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]
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description = "A rust framework to make using alevin-fry and alevin-fry-ATAC even simpler."
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license-file = "LICENSE"
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readme = "README.md"
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repository = "https://github.com/COMBINE-lab/simpleaf"
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homepage = "https://simpleaf.readthedocs.io"
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#documentation = "https://fry.readthedocs.io/en/latest/"
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include = [
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"/src/*.rs",
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"/src/utils/*.rs",
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"/src/utils/af_utils/*.rs",
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"/src/atac/*.rs",
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"/src/simpleaf_commands/*.rs",
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"/Cargo.toml",
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"/Cargo.lock",
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"/README.md",
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"/LICENSE",
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]
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keywords = [
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"single-cell",
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"preprocessing",
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"RNA-seq",
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"single-nucleus",
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"ATAC-seq",
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]
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categories = ["command-line-utilities", "science"]
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# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
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[dependencies]
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cc = "1.2.16"
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seq_geom_parser = { git = "https://github.com/COMBINE-lab/seq_geom_parser", branch = "dev", version = "0.3.0" }
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seq_geom_xform = { git = "https://github.com/COMBINE-lab/seq_geom_xform", branch = "dev", version = "0.4.0" }
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roers = { git = "https://github.com/COMBINE-lab/roers", branch = "main", version = "0.4.0" }
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anyhow = "^1.0"
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clap = { version = "4.5.31", features = [
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"derive",
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"cargo",
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"deprecated",
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"wrap_help",
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"help",
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"usage",
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"error-context",
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] }
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cmd_lib = "^1.9.5"
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tracing = "0.1.41"
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tracing-subscriber = { version = "0.3.19", default-features = true, features = [
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"env-filter",
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] }
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semver = "^1.0.25"
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serde = { version = "1.0.218", features = ["derive"] }
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serde_json = "1.0.140"
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time = { version = "^0.3.37", features = [
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"macros",
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"formatting",
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"parsing",
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"serde",
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"serde-human-readable",
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] }
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which = "7.0.2"
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jrsonnet-evaluator = "0.5.0-pre95"
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jrsonnet-cli = "0.5.0-pre95"
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jrsonnet-parser = "0.5.0-pre95"
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thiserror = "2.0.12"
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phf = { version = "0.11.3", features = ["macros"] }
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chrono = "0.4.40"
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tabled = "0.17.0"
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csv = "1.3.1"
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strum = { version = "0.26.3", features = ["derive", "phf"] }
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strum_macros = "0.26.4"
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niffler = { version = "3.0.0", default-features = false, features = ["gz"] }
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flate2 = { version = "1.1.0", default-features = false, features = ["zlib-ng"] }
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blake3 = { version = "1.6.1", features = ["mmap", "serde"] }
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regex = { version = "1.11.1", default-features = false, features = [
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"perf",
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"std",
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] }
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tempfile = "3.17.1"
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ureq = { version = "3.0.8", features = ["json"] }
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af-anndata = { version = "0.3.2", git = "https://github.com/COMBINE-lab/af-anndata" }
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[profile.release]
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lto = "thin"
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opt-level = 3
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# The profile that 'cargo dist' will build with
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[profile.dist]
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inherits = "release"
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lto = "thin"
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# Config for 'cargo dist'
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[workspace.metadata.dist]
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# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax)
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cargo-dist-version = "0.21.1"
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# CI backends to support
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ci = "github"
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# The installers to generate for each app
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installers = ["shell"]
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# Target platforms to build apps for (Rust target-triple syntax)
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targets = [
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"aarch64-apple-darwin",
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"x86_64-apple-darwin",
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"x86_64-unknown-linux-gnu",
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]
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# Which actions to run on pull requests
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pr-run-mode = "plan"
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# Whether to install an updater program
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install-updater = true
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# Path that installers should place binaries in
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install-path = "CARGO_HOME"
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[workspace.metadata.dist.github-custom-runners]
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aarch64-apple-darwin = "macos-14"

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