Cargo.toml

[workspace]
resolver = "2"
members = [
  "fastqrab",
  "fastqrab-config",
  "fastqrab-dna",
  "fastqrab-io",
  "fastqrab-steps"
]
exclude = ["dev/fuzz/fastq_parser"]

[workspace.package]
version = "0.9.1"
authors = ["Florian Finkernagel <finkernagel@imt.uni-marburg.de>"]
edition = "2024"
rust-version = "1.93.1"
description = "The fast, reliable multitool of FASTQ processing"
readme = "README.md"
homepage = "https://tyberiusprime.github.io/fastqrab/"
repository = "https://github.com/TyberiusPrime/fastqrab"
license = "MIT"
keywords = ["bioinformatics", "fastq", "sequencing"]
categories = [
  "command-line-utilities",
  "science::bioinformatics",
  "science::bioinformatics::genomics"
]
exclude = [
  ".claude/",
  ".github/",
  "AGENTS.md",
  "CLAUDE.md",
  "bacon.toml",
  "benchmarks/",
  "cookbooks/*/input/",
  "cookbooks/*/reference_output/",
  "dev/",
  "docs/",
  "experiments/",
  "test_cases/",
]

[workspace.dependencies]
anyhow = { version = "1.0.89", default-features = false }
bio = "3.0"
bitvec = "1.0.1"
bstr = { version = "1.12.0", default-features = false, features = ["alloc"] }
bytes = { version = "1.11.1"}  # https://github.com/advisories/GHSA-434x-w66g-qw3r
clap = { version = "4.5", default-features = false, features = ["error-context", "help", "std", "suggestions", "usage"] }
clap_complete = "4.5"
crossbeam = "0.8.4"
csv = "1.3.1"
disjoint = "0.8.0"
enum_dispatch = "0.3.13"
ex = "0.1.3"
fasteval = "0.2"
flate2 = { version = "1", default-features = false }
gzp = { version = "2.0", default-features = false, features = ["deflate_zlib"] }
hamming-resonate = { version = "0.4.0" }
human-panic = { version = "2.0.2", default-features = false }
indexmap = { version = "2.9.0", default-features = false, features = ["serde"] }
json_value_merge = "2.0.1"
libc = "0.2"
log = "0.4.28"
memchr = { version = "2.7.4", default-features = false }
mimalloc = "0.1"
mutants = "0.0.3"
noodles = { version = "0.108.0", features = ["bam", "bgzf", "csi", "sam"] }
noodles-core = "0.19.0"
num_cpus = "1.16"
rand = { version = "0.9.4", default-features = false }
rand_chacha = { version = "0.9", default-features = false }
rayon = "1.10"
regex = "1.11.1"
rustc-hash = "2.1"
scalable_cuckoo_filter = "0.5.1"
schemars = { version = "1.1.0", default-features = false, features = ["preserve_order", "schemars_derive"] }
serde = { version = "1.0.228", default-features = false }
serde_json = "1.0.132"
sha2 = { version = "0.10.8", default-features = false }
smallvec = "1.15.1"
stringpod = { version = "0.3.0" }
tempfile = { version = "3.13.0", default-features = false }
toml = { version = "0.9.5", default-features = false, features = ["parse", "serde"] }
toml_edit = "0.24"
toml-pretty-deser = { version = "0.4.0" }
triple_accel = "0.4.0"
typed_floats = "1.0.7"
union-find-rs = "0.2.1"
zstd = { version = "0.13.2", default-features = false }

fastqrab-config = { path = "fastqrab-config", version = "0.9.0" }
fastqrab-dna = { path = "fastqrab-dna", version = "0.9.0" }
fastqrab-io = { path = "fastqrab-io", version = "0.9.0" }
fastqrab-steps = { path = "fastqrab-steps", version = "0.9.0" }

rusty-rapidgzip = { version = "0.2.1" }

[workspace.lints.clippy]
get_unwrap = "warn"
# I want it that way when I write it that way
if-not-else = "allow"
indexing_slicing = "allow"  # we do this 200+ times, and there's usually no recovering anyway..
panic = "allow"
# unchecked_time_subtraction = "warn" # pedantic
panic_in_result_fn = "allow"  # we use panic to ensure invariants are being kept / uncover true bugs
# Don't Panic - prevent panics from unwraps and unsafe slicing or indexing
string_slice = "warn"
todo = "warn"
unimplemented = "warn"
unreachable = "allow"  # we use this to document invariants
unwrap_in_result = "allow"
unwrap_used = "deny"
# Optional - see post for caveats
# expect_used = "warn"
# arithmetic_side_effects = "warn"

assertions_on_result_states = "warn"
# Don't Fail Silently - prevent dropped futures and swallowed errors
let_underscore_future = "warn"
let_underscore_must_use = "allow"
map_err_ignore = "warn"
unused_result_ok = "warn"

# Don't Do Bad Async Stuff - prevent deadlocks and concurrency bugs
await_holding_lock = "warn"
await_holding_refcell_ref = "warn"
if_let_mutex = "warn"  # only relevant on editions before 2024
# large_futures = "warn" # pedantic

# Don't Do Unsafe Things with Memory
mem_forget = "warn"
multiple_unsafe_ops_per_block = "allow"
undocumented_unsafe_blocks = "warn"
unnecessary_safety_comment = "warn"
unnecessary_safety_doc = "warn"

# Don't Do Potentially Incorrect Things with Numbers
# float_cmp = "warn" pedantic
float_cmp_const = "warn"
lossy_float_literal = "warn"
# cast_sign_loss = "warn" pedantic
# invalid_upcast_comparisons = "warn" # pedantic
# Optional - these effectively force you to document numeric invariants
# cast_possible_wrap = "warn"
# cast_precision_loss = "warn"
# cast_possible_truncation = "warn"

dbg_macro = "warn"
debug_assert_with_mut_call = "warn"
# iter_not_returning_iterator = "warn" # pedantic
# expl_impl_clone_on_copy = "warn" # pedantic
infallible_try_from = "warn"
# Don't Do Bad Things That are Easy to Avoid
rc_mutex = "warn"

# Don't `allow` Your Way Around These Lints - every suppression must be
# a deliberate #[expect(..., reason = "…")] rather than a silent #[allow]
allow_attributes = "warn"
allow_attributes_without_reason = "warn"

# manually apply the pedantic group
# from https://rust-lang.github.io/rust-clippy/stable/?groups=pedantic

assigning_clones = "deny"
bool_to_int_with_if = "deny"
borrow_as_ptr = "deny"
case_sensitive_file_extension_comparisons = "deny"
cast_lossless = "deny"
cast_possible_truncation = "deny"
cast_possible_wrap = "deny"
cast_precision_loss = "deny"
cast_ptr_alignment = "deny"
cast_sign_loss = "deny"
checked_conversions = "deny"
cloned_instead_of_copied = "deny"
collapsible_else_if = "deny"
comparison_chain = "deny"
copy_iterator = "deny"
# decimal_bitwise_operands = "deny"
default_trait_access = "allow"  # I like Default::default()
doc_broken_link = "deny"
doc_comment_double_space_linebreaks = "deny"
doc_link_with_quotes = "deny"
doc_markdown = "deny"
# duration_suboptimal_units = "deny"
elidable_lifetime_names = "deny"
empty_enums = "deny"
enum_glob_use = "deny"
expl_impl_clone_on_copy = "deny"
explicit_deref_methods = "deny"
explicit_into_iter_loop = "deny"
explicit_iter_loop = "deny"
filter_map_next = "deny"
flat_map_option = "deny"
float_cmp = "deny"
fn_params_excessive_bools = "deny"
format_collect = "deny"
format_push_string = "deny"
from_iter_instead_of_collect = "deny"
if_not_else = "deny"
ignore_without_reason = "deny"
ignored_unit_patterns = "deny"
implicit_clone = "deny"
implicit_hasher = "deny"
inconsistent_struct_constructor = "deny"
index_refutable_slice = "deny"
inefficient_to_string = "deny"
inline_always = "deny"
into_iter_without_iter = "deny"
invalid_upcast_comparisons = "deny"
ip_constant = "deny"
items_after_statements = "deny"
iter_filter_is_ok = "deny"
iter_filter_is_some = "deny"
iter_not_returning_iterator = "deny"
iter_without_into_iter = "deny"
large_digit_groups = "deny"
large_futures = "deny"
large_stack_arrays = "deny"
large_types_passed_by_value = "deny"
linkedlist = "deny"
macro_use_imports = "deny"
manual_assert = "deny"
# manual_ilog2 = "deny"
manual_instant_elapsed = "deny"
manual_is_power_of_two = "deny"
manual_is_variant_and = "deny"
manual_let_else = "deny"
manual_midpoint = "deny"
manual_string_new = "allow"  # I don't care about "".to_string vs String::new()
many_single_char_names = "deny"
map_unwrap_or = "deny"
match_bool = "deny"
match_same_arms = "deny"
match_wild_err_arm = "deny"
match_wildcard_for_single_variants = "deny"
maybe_infinite_iter = "deny"
mismatching_type_param_order = "deny"
missing_errors_doc = "allow"  # idc
missing_fields_in_debug = "deny"
missing_panics_doc = "deny"
must_use_candidate = "deny"
mut_mut = "deny"
naive_bytecount = "deny"
needless_bitwise_bool = "deny"
needless_continue = "deny"
needless_for_each = "deny"
needless_pass_by_value = "deny"
needless_raw_string_hashes = "deny"
no_effect_underscore_binding = "deny"
no_mangle_with_rust_abi = "deny"
non_std_lazy_statics = "deny"
option_as_ref_cloned = "deny"
option_option = "deny"
ptr_as_ptr = "deny"
ptr_cast_constness = "deny"
# ptr_offset_by_literal = "deny"
pub_underscore_fields = "deny"
range_minus_one = "deny"
range_plus_one = "deny"
redundant_closure_for_method_calls = "deny"
redundant_else = "allow"  # it's our style
ref_as_ptr = "deny"
ref_binding_to_reference = "deny"
ref_option = "deny"
ref_option_ref = "deny"
return_self_not_must_use = "deny"
same_functions_in_if_condition = "deny"
# same_length_and_capacity = "deny"
self_only_used_in_recursion = "deny"
semicolon_if_nothing_returned = "deny"
should_panic_without_expect = "deny"
similar_names = "deny"
single_char_pattern = "deny"
single_match_else = "allow"  # that's my style.
stable_sort_primitive = "deny"
str_split_at_newline = "deny"
string_add_assign = "deny"
struct_excessive_bools = "allow"
struct_field_names = "deny"
too_many_lines = "allow"
transmute_ptr_to_ptr = "deny"
trivially_copy_pass_by_ref = "deny"
unchecked_time_subtraction = "deny"
unicode_not_nfc = "deny"
uninlined_format_args = "deny"
unnecessary_box_returns = "deny"
unnecessary_debug_formatting = "deny"
unnecessary_join = "deny"
unnecessary_literal_bound = "deny"
unnecessary_semicolon = "deny"
# unnecessary_trailing_comma = "deny"
unnecessary_wraps = "deny"
unnested_or_patterns = "deny"
unreadable_literal = "deny"
unsafe_derive_deserialize = "deny"
unused_async = "deny"
unused_self = "deny"
used_underscore_binding = "deny"
used_underscore_items = "deny"
verbose_bit_mask = "deny"
wildcard_imports = "deny"
zero_sized_map_values = "deny"

# reduce to minimal necessary debug information in dev profile.
# use debugging profile for full.
[profile.dev]
debug = "line-tables-only"

[profile.dev.package."*"]
opt-level = 3
debug = false

[profile.dev.package.schemars]
opt-level = 3
debug = false

[profile.dev.package.schemars_derive]
opt-level = 3
debug = false

[profile.dev.package.toml-pretty-deser]
opt-level = 3
debug = false

[profile.dev.package.toml-pretty-deser-macros]
opt-level = 3
debug = false

[profile.dev.build-override]
opt-level = 3

[profile.release]
debug = 1

[profile.debugging]
inherits = "dev"
debug = true

[profile.mutants]
inherits = "test"
debug = "none"