Run cargo machete --fix

enclone_com/Cargo.toml

@@ -20,10 +20,7 @@ publish = false
 # in the root of the enclone repo.
 
 [dependencies]
-bytes = "1"
 enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-lazy_static = "1"
 pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
 string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] }

enclone_denovo/Cargo.toml

@@ -20,25 +20,14 @@ amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main"
 binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 bio = "0.39"
 debruijn = "0.3"
-equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 itertools = "0.10"
-kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 # poa_hmm = { git = "https://github.com/ban-m/partial_order_alignment.git" }
 perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-permutation = "0.4"
-petgraph = "0.6"
 pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
 rayon = "1"
-regex = { version = "1", default-features = false, features = ["std", "perf"] }
-serde_json = "1"
-stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 superslice = "1"
-tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }

enclone_exec/Cargo.toml

@@ -29,7 +29,6 @@ enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch =
 enclone_main = { path = "../enclone_main" }
 enclone_testlist = { path = "../enclone_testlist" }
 flate2 = "1"
-home = "0.5"
 io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 itertools = "0.10"
 nix = { version = "0.27", features = ["signal"] }

enclone_paper/Cargo.toml

@@ -31,7 +31,6 @@ flate2 = "1"
 io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 itertools = "0.10"
 perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-plotters = { version = "0.3", default_features = false, features = ["svg_backend", "point_series"] }
 rand_chacha = "0.3"
 rayon = "1"
 pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}

enclone_tail/Cargo.toml

@@ -25,9 +25,7 @@ publish = false
 align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 crc = "2"
-debruijn = "0.3"
 enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
@@ -43,9 +41,6 @@ plotters = { version = "0.3", default_features = false, features = ["svg_backend
 pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
 rayon = "1"
 resvg = { version = "0.19", default-features = false }
-serde = "1"
-serde_derive = "1"
-serde_json = "1"
 stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 superslice = "1"

enclone_tools/Cargo.toml

@@ -22,7 +22,6 @@ publish = false
 [dependencies]
 amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] }
 binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
@@ -38,15 +37,12 @@ evalexpr = "7"
 expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 flate2 = "1"
-fs_extra = "1"
 io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 itertools = "0.10"
 lz4 = "1"
 perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
 pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
-rand_chacha = "0.3"
 rayon = "1"
-regex = { version = "1", default-features = false, features = ["std", "perf"] }
 serde_json = "1"
 statrs = "0.15"
 tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }