Replace all crate deps with workspace deps.

Cargo.toml

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

enclone_build/Cargo.toml

@@ -6,12 +6,12 @@ edition = "2021"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
-itertools = "0.10"
-pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+chrono.workspace = true
+itertools.workspace = true
+pretty_trace.workspace = true
+string_utils.workspace = true
+enclone_core.workspace = true
 
 [build-dependencies]
-chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+chrono.workspace = true
+string_utils.workspace = true

enclone_com/Cargo.toml

@@ -20,9 +20,9 @@ publish = false
 # in the root of the enclone repo.
 
 [dependencies]
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-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"] }
-vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone_core.workspace = true
+pretty_trace.workspace = true
+string_utils.workspace = true
+tokio.workspace = true
+vdj_ann.workspace = true
 

enclone_denovo/Cargo.toml

@@ -16,18 +16,17 @@ edition = "2018"
 publish = false
 
 [dependencies]
-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"
-fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-itertools = "0.10"
-# poa_hmm = { git = "https://github.com/ban-m/partial_order_alignment.git" }
-perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
-rayon = "1"
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-superslice = "1"
-vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+amino.workspace = true
+binary_vec_io.workspace = true
+bio.workspace = true
+debruijn.workspace = true
+fasta_tools.workspace = true
+io_utils.workspace = true
+itertools.workspace = true
+perf_stats.workspace = true
+pretty_trace.workspace = true
+rayon.workspace = true
+string_utils.workspace = true
+superslice.workspace = true
+vdj_ann_ref.workspace = true
+vector_utils.workspace = true

enclone_exec/Cargo.toml

@@ -24,37 +24,37 @@ name = "enclone"
 path = "src/bin/enclone.rs"
 
 [dependencies]
-chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+chrono.workspace = true
+enclone_core.workspace = true
 enclone_main = { path = "../enclone_main" }
 enclone_testlist = { path = "../enclone_testlist" }
-flate2 = "1"
-io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-itertools = "0.10"
-nix = { version = "0.27", features = ["signal"] }
-pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
-serde_json = "1"
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] }
-vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+flate2.workspace = true
+io_utils.workspace = true
+itertools.workspace = true
+nix.workspace = true
+pretty_trace.workspace = true
+serde_json.workspace = true
+string_utils.workspace = true
+tokio.workspace = true
+vector_utils.workspace = true
 
 [dev-dependencies]
-ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-anyhow = "1"
-attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] }
-enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+ansi_escape.workspace = true
+anyhow.workspace = true
+attohttpc.workspace = true
+enclone_vars.workspace = true
+enclone_proto.workspace = true
+enclone_ranger.workspace = true
 enclone_tools = { path = "../enclone_tools" }
-flate2 = "1"
-fs_extra = "1"
-itertools = "0.10"
-perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-rayon = "1"
-serde_json = "1"
-sha2 = "0.10"
-stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-yaml-rust = "0.4"
+flate2.workspace = true
+fs_extra.workspace = true
+itertools.workspace = true
+perf_stats.workspace = true
+rayon.workspace = true
+serde_json.workspace = true
+sha2.workspace = true
+stats_utils.workspace = true
+yaml-rust.workspace = true
 
 [features]
 default = []

enclone_help/Cargo.toml

@@ -20,12 +20,12 @@ publish = false
 # in the root of the enclone repo.
 
 [dependencies]
-ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-itertools = "0.10"
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+ansi_escape.workspace = true
+enclone_core.workspace = true
+io_utils.workspace = true
+itertools.workspace = true
+string_utils.workspace = true
+tables.workspace = true
 enclone_build = {path = "../enclone_build"}
 
 

enclone_main/Cargo.toml

@@ -20,32 +20,29 @@ publish = false
 # in the root of the enclone repo.
 
 [dependencies]
-dirs = "4"
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+dirs.workspace = true
+enclone_core.workspace = true
 enclone_help = { path = "../enclone_help" }
-enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone_print.workspace = true
+enclone_proto.workspace = true
+enclone_stuff.workspace = true
 enclone_tail = { path = "../enclone_tail" }
 enclone_build = { path = "../enclone_build" }
-enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone_vars.workspace = true
+enclone.workspace = true
+enclone_args.workspace = true
 enclone_testlist = { path = "../enclone_testlist" }
-expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-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" }
-pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
-rayon = "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" }
-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" }
-
-
-hdf5 = {git = "https://github.com/10XGenomics/hdf5-rust.git", branch = "conda_nov2021", features = ["conda"], default-features = false }
-# hdf5-sys = {git = "https://github.com/10XGenomics/hdf5-rust.git", branch = "conda_nov2021"}
+expr_tools.workspace = true
+io_utils.workspace = true
+itertools.workspace = true
+perf_stats.workspace = true
+pretty_trace.workspace = true
+rayon.workspace = true
+serde_json.workspace = true
+stats_utils.workspace = true
+string_utils.workspace = true
+tables.workspace = true
+vdj_ann.workspace = true
+vdj_ann_ref.workspace = true
+vector_utils.workspace = true
+hdf5.workspace = true

enclone_paper/Cargo.toml

@@ -22,21 +22,21 @@ publish = false
 # To keep compile time down, this file should *not* access the enclone crate.
 
 [dependencies]
-bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-debruijn = "0.3"
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+bio_edit.workspace = true
+debruijn.workspace = true
+enclone_core.workspace = true
 enclone_tail = { path = "../enclone_tail" }
 enclone_testlist = { path = "../enclone_testlist" }
-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" }
-rand_chacha = "0.3"
-rayon = "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" }
-tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-triple_accel = "0.4"
-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" }
+flate2.workspace = true
+io_utils.workspace = true
+itertools.workspace = true
+perf_stats.workspace = true
+rand_chacha.workspace = true
+rayon.workspace = true
+pretty_trace.workspace = true
+string_utils.workspace = true
+tables.workspace = true
+triple_accel.workspace = true
+vdj_ann.workspace = true
+vdj_ann_ref.workspace = true
+vector_utils.workspace = true