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Cargo.toml
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Cargo.toml
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[workspace]
members = [
"enclone_denovo",
"enclone_exec",
"enclone_help",
"enclone_main",
"enclone_paper",
"enclone_tail",
"enclone_tools",
"enclone_version",
"enclone_build",
"enclone_testlist",
]
resolver = "2"
# ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
# dev mode profile: setting lto = true or lto = "thin" or codegen-units = 1 or even
# codegen-units = 5 all speed up execution (as measured by our cycle count test), by up to
# about 10%, but they all have at least some effect on compile time, and it doesn't seem worth it
[profile.dev]
debug = 1
opt-level = 3
split-debuginfo = "unpacked"
# ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
[profile.release]
debug = 1
lto = true
codegen-units = 1
overflow-checks = true
# ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
[profile.test]
debug = 1
opt-level = 3
split-debuginfo = "unpacked"
# Cautionary note. We set package versions in enclone_versions, but it's not clear that
# this is a sound practice, particularly in the case where a crate outside the enclone repo
# depends on a crate in the enclone repo. Such an external crate sees "*" and it's not clear
# what is done with that.
# ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
# We attempted to speed up loading on the Mac using zld,
# https://github.com/michaeleisel/zld. First we downloaded the current release at
# https://github.com/michaeleisel/zld/releases/tag/1.3.2, and then added these lines
# (without the #) to .cargo/config:
# [target.x86_64-apple-darwin]
# rustflags = ["-C", "link-arg=-fuse-ld=/Users/david.jaffe/bin/zld"]
# To get this to work, we had to install Xcode 12.4, by going to the apple developers site.
# For the particular version of macOS we have, the later versions of Xcode wouldn't work.
# To complete the installation, we did
# sudo xcode-select -s /path/to/Xcode.app
# 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"] }
backtrace = "0.3"
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_process = { 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"
martian-filetypes = { git = "https://github.com/martian-lang/martian-rust", branch = "master" }
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"
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_types = { 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" }
whoami = "1"
yaml-rust = "0.4"