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Replace the hand-built master.toml system with workspace deps (#529)
* Replaces all dep specs with workspace deps. * Deletes master.toml and everything relating to it.
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‎Cargo.lock

-32
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‎Cargo.toml

+114
Original file line numberDiff line numberDiff line change
@@ -61,3 +61,117 @@ split-debuginfo = "unpacked"
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# and then cargo b worked. This seemed to speed up loading by 5-10%, but that did not seem
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# like enough to justify using zld. It might be worth trying again later, as it is being
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# improved.
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[workspace.dependencies]
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align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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anyhow = "1"
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ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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arboard = "2"
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assert_cmd = "2"
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async-trait = "0.1"
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attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] }
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base64 = "0.13"
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binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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bio = "0.39"
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bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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byteorder = "1"
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bytes = "1"
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chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
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clipboard = "0.5"
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cocoa = "0.24"
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core-foundation = "0.9"
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core-graphics = "0.22"
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crc = "2"
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debruijn = "0.3"
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dirs = "4"
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dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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edit-distance = "2"
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enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_denovo = { path = "../enclone_denovo" }
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enclone_help = { path = "../enclone_help" }
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enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_server_proto = { path = "../enclone_server_proto" }
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enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_tail = { path = "../enclone_tail" }
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enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_version = { path = "../enclone_version" }
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equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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evalexpr = "7"
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expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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file-lock = "2"
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flate2 = "1"
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float-ord = "0.3"
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fontdb = "0.7"
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fs_extra = "1"
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git = "https://github.com/10xGenomics/hdf5-rust.git"
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graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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hdf5 = { git = "https://github.com/10XGenomics/hdf5-rust.git", branch = "conda_nov2021", features = ["conda"], default-features = false }
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home = "0.5"
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hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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image = { version = "0.23", features = ["jpeg", "png", "jpeg_rayon"], default-features = false }
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include_dir = { version = "0.6", features = ["search"] }
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io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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itertools = "0.10"
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jpeg-decoder = "0.2"
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kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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lazy_static = "1"
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libc = "0.2"
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log = "0.4"
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lz4 = "1"
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mach = "0.3"
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ndarray = "0.15"
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nix = { version = "0.27", features = ["signal"] }
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num-traits = "0.2"
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objc = "0.2"
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pager = "0.16"
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palette = "0.6"
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perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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permutation = "0.4"
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petgraph = "0.6"
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plotters = { version = "0.3", default_features = false, features = ["svg_backend", "point_series"] }
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png-decoder = "0.1"
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pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
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procfs = { version = "0.12", default_features = false }
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# prost: enclone will compile without the std and prost-derive features, but other things
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# (such as enclone_proto) break.
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prost = { version = "0.9", default_features = false, features = ["std", "prost-derive"] }
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prost-build = "0.9"
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qd = { git = "https://github.com/Barandis/qd" }
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rand = "0.8"
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rand_chacha = "0.3"
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rayon = "1"
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resvg = { version = "0.19", default-features = false }
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regex = { version = "1", default-features = false, features = ["std", "perf"] }
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serde = "1"
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serde_derive = "1"
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serde_json = "1"
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sha2 = "0.10"
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stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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statrs = "0.15"
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stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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superslice = "1"
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tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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tar = "0.4"
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thiserror = "1"
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tilde-expand = "0.1"
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tiny-skia = "0.6"
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tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] }
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tokio-stream = { version = "0.1", default-features = false, features = ["net"] }
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tonic = { version = "0.6", default-features = false, features = ["transport", "codegen", "prost"] }
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tonic-build = { version = "0.6", default-features = false, features = ["transport", "prost"] }
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triple_accel = "0.4"
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users = "0.11"
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usvg = { version = "0.19", features = ["text"] }
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# vdj_ann = "0.4"
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vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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whoami = "1"
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yaml-rust = "0.4"

‎enclone_build/Cargo.toml

+7-7
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@ edition = "2021"
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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]
9-
chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
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itertools = "0.10"
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pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
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string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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chrono.workspace = true
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itertools.workspace = true
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pretty_trace.workspace = true
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string_utils.workspace = true
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enclone_core.workspace = true
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[build-dependencies]
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chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
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string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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chrono.workspace = true
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string_utils.workspace = true

‎enclone_com/Cargo.toml

+5-10
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@@ -16,16 +16,11 @@ edition = "2018"
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license-file = "LICENSE.txt"
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publish = false
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# Please do not edit crate versions within this file. Instead edit the file master.toml
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# in the root of the enclone repo.
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[dependencies]
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bytes = "1"
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enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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lazy_static = "1"
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pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
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string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] }
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vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_core.workspace = true
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pretty_trace.workspace = true
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string_utils.workspace = true
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tokio.workspace = true
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vdj_ann.workspace = true
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‎enclone_denovo/Cargo.toml

+14-26
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@@ -16,29 +16,17 @@ edition = "2018"
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publish = false
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[dependencies]
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amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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bio = "0.39"
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debruijn = "0.3"
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equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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itertools = "0.10"
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kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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# poa_hmm = { git = "https://github.com/ban-m/partial_order_alignment.git" }
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perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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permutation = "0.4"
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petgraph = "0.6"
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pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
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rayon = "1"
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regex = { version = "1", default-features = false, features = ["std", "perf"] }
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serde_json = "1"
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stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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superslice = "1"
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tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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amino.workspace = true
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binary_vec_io.workspace = true
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bio.workspace = true
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debruijn.workspace = true
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fasta_tools.workspace = true
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io_utils.workspace = true
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itertools.workspace = true
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perf_stats.workspace = true
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pretty_trace.workspace = true
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rayon.workspace = true
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string_utils.workspace = true
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superslice.workspace = true
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vdj_ann_ref.workspace = true
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vector_utils.workspace = true

‎enclone_exec/Cargo.toml

+26-29
Original file line numberDiff line numberDiff line change
@@ -16,46 +16,43 @@ edition = "2018"
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license-file = "LICENSE.txt"
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publish = false
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# Please do not edit crate versions within this file. Instead edit the file master.toml
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# in the root of the enclone repo.
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[[bin]]
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name = "enclone"
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path = "src/bin/enclone.rs"
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[dependencies]
27-
chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
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enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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chrono.workspace = true
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enclone_core.workspace = true
2927
enclone_main = { path = "../enclone_main" }
3028
enclone_testlist = { path = "../enclone_testlist" }
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flate2 = "1"
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home = "0.5"
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io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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itertools = "0.10"
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nix = { version = "0.27", features = ["signal"] }
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pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
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serde_json = "1"
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string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] }
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vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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flate2.workspace = true
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io_utils.workspace = true
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itertools.workspace = true
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nix.workspace = true
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pretty_trace.workspace = true
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serde_json.workspace = true
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string_utils.workspace = true
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tokio.workspace = true
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vector_utils.workspace = true
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[dev-dependencies]
43-
ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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anyhow = "1"
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attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] }
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enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
40+
ansi_escape.workspace = true
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anyhow.workspace = true
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attohttpc.workspace = true
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enclone_vars.workspace = true
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enclone_proto.workspace = true
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enclone_ranger.workspace = true
4946
enclone_tools = { path = "../enclone_tools" }
50-
flate2 = "1"
51-
fs_extra = "1"
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itertools = "0.10"
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perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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rayon = "1"
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serde_json = "1"
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sha2 = "0.10"
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stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
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yaml-rust = "0.4"
47+
flate2.workspace = true
48+
fs_extra.workspace = true
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itertools.workspace = true
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perf_stats.workspace = true
51+
rayon.workspace = true
52+
serde_json.workspace = true
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sha2.workspace = true
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stats_utils.workspace = true
55+
yaml-rust.workspace = true
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[features]
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default = []

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