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Cargo.toml
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Cargo.toml
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[workspace]
resolver = '2'
members = [
"packages/*",
]
exclude = [
"packages/3rdparty",
]
[workspace.package]
name = "nextclade"
version = "3.6.0"
description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. Library module."
repository = "https://github.com/nextstrain/nextclade"
documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
homepage = "https://clades.nextstrain.org/"
edition = "2021"
license = "MIT"
publish = false
authors = ["Nextstrain team"]
[workspace.dependencies]
assert2 = "=0.3.11"
atty = "=0.2.14"
auto_ops = "=0.3.0"
bio = "=1.3.1"
bio-types = "=1.0.0"
bzip2 = { version = "=0.4.4", features = ["static"] }
chrono = { version = "=0.4.26", default-features = false, features = ["clock", "std", "wasmbind"] }
clap = { version = "=4.4.2", features = ["derive", "color", "unicode", "unstable-styles"] }
clap-markdown = "=0.1.3"
clap_complete = "=4.4.1"
clap_complete_fig = "=4.4.0"
color-eyre = "=0.6.2"
comfy-table = "=7.0.1"
console_error_panic_hook = "=0.1.7"
criterion = { version = "=0.5.1", features = ["html_reports"] }
crossbeam = "=0.8.2"
crossbeam-channel = "=0.5.8"
csv = "=1.2.2"
ctor = "=0.2.2"
derive_more = "=0.99.17"
dotenv = "=0.15.0"
dotenv_codegen = "=0.15.0"
edit-distance = "=2.1.0"
either = "=1.8.1"
env_logger = "=0.10.0"
eyre = "=0.6.8"
flate2 = "=1.0.26"
gcollections = "=1.5.0"
getrandom = { version = "=0.2.10", features = ["js"] }
indexmap = { version = "=1.9.3", features = ["serde"] }
intervallum = "=1.4.0"
itertools = "=0.11.0"
js-sys = { version = "=0.3.64", features = [] }
lazy_static = "=1.4.0"
log = "=0.4.19"
maplit = "=1.0.2"
multimap = "=0.8.3"
num = "=0.4.0"
num-traits = "=0.2.15"
num_cpus = "=1.16.0"
optfield = "=0.3.0"
ordered-float = { version = "=3.9.1", features = ["rand", "serde", "schemars"] }
owo-colors = "=3.5.0"
pretty_assertions = "=1.3.0"
rayon = "=1.7.0"
regex = "=1.8.4"
reqwest = { version = "=0.11.18", default-features = false, features = ["blocking", "deflate", "gzip", "brotli", "socks", "rustls-tls"] }
rstest = "=0.17.0"
rstest_reuse = "=0.5.0"
schemars = { version = "=0.8.12", features = ["chrono", "either", "enumset", "indexmap"] }
semver = { version = "=1.0.17", features = ["serde"] }
serde = { version = "=1.0.164", features = ["derive"] }
serde-wasm-bindgen = { version = "=0.5.0" }
serde_json = { version = "=1.0.99", features = ["preserve_order", "indexmap", "unbounded_depth"] }
serde_repr = "=0.1.12"
serde_stacker = { version = "=0.1.8" }
serde_yaml = "=0.9.22"
strsim = "=0.10.0"
strum = "=0.25.0"
strum_macros = "=0.25.0"
tinytemplate = "=1.2.1"
traversal = "=0.1.2"
url = { version = "=2.4.0", features = ["serde"] }
urlencoding = "=2.1.2"
validator = { version = "=0.16.1", features = ["derive"] }
wasm-bindgen = { version = "=0.2.87", features = ["serde-serialize"] }
wasm-logger = "=0.2.0"
web-sys = { version = "=0.3.64", features = ["console"] }
xz2 = { version = "=0.1.7", features = ["static"] }
zip = { version = "=0.6.6", default-features = false, features = ["aes-crypto", "deflate", "time"] }
zstd = { version = "=0.12.3", features = ["zstdmt"] }
[workspace.lints.rust]
# Lint groups
# https://doc.rust-lang.org/rustc/lints/groups.html
deprecated_in_future = "warn"
future_incompatible = "warn"
nonstandard_style = "warn"
rust_2018_idioms = "warn"
rust_2021_compatibility = "warn"
trivial_numeric_casts = "warn"
# Disable some of the lints enabled by default
# https://doc.rust-lang.org/rustc/lints/listing/warn-by-default.html
elided_lifetimes_in_paths = "allow"
# Enable lints not enabled by default
# https://doc.rust-lang.org/rustc/lints/listing/allowed-by-default.html
absolute_paths_not_starting_with_crate = "warn"
explicit_outlives_requirements = "warn"
ffi_unwind_calls = "warn"
keyword_idents = "warn"
let_underscore_drop = "warn"
macro_use_extern_crate = "warn"
meta_variable_misuse = "warn"
missing_abi = "warn"
non_ascii_idents = "warn"
rust_2021_incompatible_closure_captures = "warn"
rust_2021_incompatible_or_patterns = "warn"
rust_2021_prefixes_incompatible_syntax = "warn"
rust_2021_prelude_collisions = "warn"
single_use_lifetimes = "warn"
trivial_casts = "warn"
unit_bindings = "warn"
unsafe_code = "warn"
unsafe_op_in_unsafe_fn = "warn"
unused_lifetimes = "warn"
unused_macro_rules = "warn"
unused_qualifications = "warn"
unused_tuple_struct_fields = "warn"
variant_size_differences = "warn"
# missing_copy_implementations = "warn"
# missing_debug_implementations = "warn"
[workspace.lints.clippy]
# https://rust-lang.github.io/rust-clippy/stable/
# This is a strict (sometimes too much) Clippy setup.
# We go bold and enable all Clippy lints, then disable the ones that we don't need.
# This has an advantage that when upgrading Rust and Clippy, we receive new lints automatically.
all = { level = "warn", priority = -2 }
pedantic = { level = "warn", priority = -1 }
blanket_clippy_restriction_lints = "allow"
restriction = { level = "warn", priority = -1 }
nursery = { level = "warn", priority = -1 }
# Disable some of the Clippy lints
absolute_paths = "allow"
allow_attributes = "allow"
arithmetic_side_effects = "allow"
as_conversions = "allow"
assign_op_pattern = "allow"
bool_to_int_with_if = "allow"
cast_lossless = "allow"
cast_possible_truncation = "allow"
cast_possible_wrap = "allow"
cast_precision_loss = "allow"
cast_sign_loss = "allow"
cognitive_complexity = "allow"
comparison_chain = "allow"
default_numeric_fallback = "allow"
deref_by_slicing = "allow"
doc_markdown = "allow"
else_if_without_else = "allow"
exhaustive_enums = "allow"
exhaustive_structs = "allow"
expect_used = "allow"
float_arithmetic = "allow"
if_not_else = "allow"
impl_trait_in_params = "allow"
implicit_hasher = "allow"
implicit_return = "allow"
inconsistent_digit_grouping = "allow"
indexing_slicing = "allow"
integer_division = "allow"
iter_nth_zero = "allow"
large_digit_groups = "allow"
len_zero = "allow"
let_underscore_must_use = "allow"
manual_string_new = "allow"
match_same_arms = "allow"
min_ident_chars = "allow"
missing_assert_message = "allow"
missing_docs_in_private_items = "allow"
missing_errors_doc = "allow"
missing_inline_in_public_items = "allow"
missing_panics_doc = "allow"
missing_trait_methods = "allow"
mod_module_files = "allow"
module_inception = "allow"
module_name_repetitions = "allow"
modulo_arithmetic = "allow"
must_use_candidate = "allow"
needless_for_each = "allow"
needless_raw_string_hashes = "allow"
needless_raw_strings = "allow"
new_without_default = "allow"
non_ascii_literal = "allow"
option_if_let_else = "allow"
panic = "allow"
panic_in_result_fn = "allow"
pattern_type_mismatch = "allow"
print_stderr = "allow"
print_stdout = "allow"
pub_use = "allow"
pub_with_shorthand = "allow"
question_mark_used = "allow"
self_named_module_files = "allow"
semicolon_inside_block = "allow"
semicolon_outside_block = "allow"
separated_literal_suffix = "allow"
shadow_reuse = "allow"
shadow_same = "allow"
shadow_unrelated = "allow"
should_implement_trait = "allow"
similar_names = "allow"
single_call_fn = "allow"
single_char_lifetime_names = "allow"
std_instead_of_alloc = "allow"
std_instead_of_core = "allow"
struct_field_names = "allow"
suboptimal_flops = "allow"
too_many_arguments = "allow"
too_many_lines = "allow"
type_repetition_in_bounds = "allow"
unnecessary_wraps = "allow"
unreachable = "allow"
unreadable_literal = "allow"
unsafe_derive_deserialize = "allow"
unused_self = "allow"
unused_unit = "allow"
unwrap_in_result = "allow"
unwrap_used = "allow"
use_debug = "allow"
use_self = "allow"
useless_transmute = "allow"
wildcard_enum_match_arm = "allow"
[workspace.lints.rustdoc]
broken_intra_doc_links = "warn"
bare_urls = "warn"