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Merged
sebschmi merged 2 commits into from
Jun 5, 2026
Merged

Release #192

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12230f2
chore: Release
sebschmi Jun 5, 2026
ffb40fa
Reduce binary size.
sebschmi Jun 5, 2026
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16 changes: 8 additions & 8 deletions Cargo.lock
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2 changes: 1 addition & 1 deletion generic_a_star/Cargo.toml
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@@ -1,7 +1,7 @@
[package]
name = "generic_a_star"
description = "A generic implementation of the A* algorithm"
version = "3.0.0"
version = "4.0.0"
edition.workspace = true
rust-version.workspace = true
license.workspace = true
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6 changes: 3 additions & 3 deletions lib_ts_chainalign/Cargo.toml
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Expand Up @@ -2,15 +2,15 @@
name = "lib_ts_chainalign"
description = "A chaining-based sequence-to-sequence aligner that accounts for template switches"
authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>"]
version = "3.0.0"
version = "4.0.0"
license.workspace = true
edition.workspace = true
rust-version.workspace = true
repository.workspace = true

[dependencies]
generic_a_star = { version = "3.0.0", path = "../generic_a_star" }
lib_tsalign = { version = "3.0.0", path = "../lib_tsalign" }
generic_a_star = { version = "4.0.0", path = "../generic_a_star" }
lib_tsalign = { version = "4.0.0", path = "../lib_tsalign" }
ndarray = { version = "0.17.1", features = ["serde"] }
num-traits.workspace = true
serde = { workspace = true, features = ["derive"] }
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6 changes: 3 additions & 3 deletions lib_tsalign/Cargo.toml
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Expand Up @@ -2,7 +2,7 @@
name = "lib_tsalign"
description = "A sequence-to-sequence aligner that accounts for template switches"
authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>"]
version = "3.0.0"
version = "4.0.0"
license.workspace = true
edition.workspace = true
rust-version.workspace = true
Expand All @@ -26,9 +26,9 @@ thiserror = "2.0.3"
num-traits.workspace = true
serde = { workspace = true, features = ["derive"], optional = true }
noisy_float = { version = "0.2.0" }
generic_a_star = { version = "3.0.0", path = "../generic_a_star" }
generic_a_star = { version = "4.0.0", path = "../generic_a_star" }
log.workspace = true
rustc-hash = "2.1.1"
seed_chain = { version = "3.0.0", path = "../seed_chain" }
seed_chain = { version = "4.0.0", path = "../seed_chain" }
extend_map = "0.14.3"
template-switch-error-free-inners = "0.1.1"
4 changes: 2 additions & 2 deletions lib_tsshow/Cargo.toml
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Expand Up @@ -3,13 +3,13 @@ name = "lib_tsshow"
description = "A visualiser for template-switch alignments"
license.workspace = true
authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>"]
version = "3.0.0"
version = "4.0.0"
edition.workspace = true
rust-version.workspace = true
repository.workspace = true

[dependencies]
lib_tsalign = { version = "3.0.0", path = "../lib_tsalign" }
lib_tsalign = { version = "4.0.0", path = "../lib_tsalign" }
log.workspace = true
svg = "0.18.0"
resvg = "0.45.0"
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6 changes: 3 additions & 3 deletions python_bindings/Cargo.toml
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Expand Up @@ -6,7 +6,7 @@ authors = [
"Sebastian Schmidt <sebastian.schmidt@helsinki.fi>",
"Jasper Krauter <jasper.krauter@helsinki.fi>",
]
version = "3.0.0"
version = "4.0.0"
edition.workspace = true
rust-version.workspace = true
repository.workspace = true
Expand All @@ -18,10 +18,10 @@ crate-type = ["cdylib"]

[dependencies]
pyo3 = "0.26"
lib_tsalign = { version = "3.0.0", path = "../lib_tsalign", features = [
lib_tsalign = { version = "4.0.0", path = "../lib_tsalign", features = [
"serde",
] }
lib_tsshow = { version = "3.0.0", path = "../lib_tsshow" }
lib_tsshow = { version = "4.0.0", path = "../lib_tsshow" }
serde.workspace = true
pythonize = "0.26"
pyo3-log = "0.13"
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4 changes: 2 additions & 2 deletions seed_chain/Cargo.toml
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Expand Up @@ -3,7 +3,7 @@ name = "seed_chain"
description = "A seeding and generic chaining mechanism for sequence-to-sequence alignment"
license.workspace = true
authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>"]
version = "3.0.0"
version = "4.0.0"
edition.workspace = true
rust-version.workspace = true
repository.workspace = true
Expand All @@ -12,5 +12,5 @@ repository.workspace = true
[dependencies]
compact-genome.workspace = true
log.workspace = true
generic_a_star = { version = "3.0.0", path = "../generic_a_star" }
generic_a_star = { version = "4.0.0", path = "../generic_a_star" }
num-traits.workspace = true
2 changes: 1 addition & 1 deletion tsalign-tests/Cargo.toml
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Expand Up @@ -2,7 +2,7 @@
name = "tsalign-tests"
license.workspace = true
authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>", "Jasper Krauter <jasper.krauter@helsinki.fi>"]
version = "3.0.0"
version = "4.0.0"
edition.workspace = true
rust-version.workspace = true
repository.workspace = true
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23 changes: 18 additions & 5 deletions tsalign/Cargo.toml
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Expand Up @@ -3,18 +3,31 @@ name = "tsalign"
description = "A sequence-to-sequence aligner that accounts for template switches"
license.workspace = true
authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>"]
version = "3.0.0"
version = "4.0.0"
edition.workspace = true
rust-version.workspace = true
repository.workspace = true

[features]
alphabet_dna = []
alphabet_dna_n = []
alphabet_dna_iupac = []
alphabet_rna = []
alphabet_rna_n = []
alphabet_rna_iupac = []

strategy_total_length_none = []
strategy_total_length_maximise = []

default = ["strategy_total_length_maximise", "alphabet_dna", "alphabet_dna_n"]

[dependencies]
generic_a_star = { version = "3.0.0", path = "../generic_a_star" }
lib_tsalign = { version = "3.0.0", path = "../lib_tsalign", features = [
generic_a_star = { version = "4.0.0", path = "../generic_a_star" }
lib_tsalign = { version = "4.0.0", path = "../lib_tsalign", features = [
"serde",
] }
lib_ts_chainalign = { version = "3.0.0", path = "../lib_ts_chainalign" }
lib_tsshow = { version = "3.0.0", path = "../lib_tsshow" }
lib_ts_chainalign = { version = "4.0.0", path = "../lib_ts_chainalign" }
lib_tsshow = { version = "4.0.0", path = "../lib_tsshow" }
clap.workspace = true
compact-genome = { workspace = true, features = ["io"] }
traitsequence.workspace = true
Expand Down
36 changes: 26 additions & 10 deletions tsalign/src/align.rs
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Expand Up @@ -11,16 +11,7 @@ use clap::{
builder::{BoolishValueParser, TypedValueParser},
};
use compact_genome::{
implementation::{
alphabets::{
dna_alphabet::DnaAlphabet, dna_alphabet_or_n::DnaAlphabetOrN,
dna_iupac_nucleic_acid_alphabet::DnaIupacNucleicAcidAlphabet,
rna_alphabet::RnaAlphabet, rna_alphabet_or_n::RnaAlphabetOrN,
rna_iupac_nucleic_acid_alphabet::RnaIupacNucleicAcidAlphabet,
},
vec_sequence::VectorGenome,
vec_sequence_store::VectorSequenceStore,
},
implementation::{vec_sequence::VectorGenome, vec_sequence_store::VectorSequenceStore},
interface::{
alphabet::Alphabet,
sequence::{GenomeSequence, OwnedGenomeSequence},
Expand Down Expand Up @@ -50,6 +41,19 @@ use template_switch_distance_type_selectors::{
align_a_star_template_switch_distance,
};

#[cfg(feature = "alphabet_dna")]
use compact_genome::implementation::alphabets::dna_alphabet::DnaAlphabet;
#[cfg(feature = "alphabet_dna_n")]
use compact_genome::implementation::alphabets::dna_alphabet_or_n::DnaAlphabetOrN;
#[cfg(feature = "alphabet_dna_iupac")]
use compact_genome::implementation::alphabets::dna_iupac_nucleic_acid_alphabet::DnaIupacNucleicAcidAlphabet;
#[cfg(feature = "alphabet_rna")]
use compact_genome::implementation::alphabets::rna_alphabet::RnaAlphabet;
#[cfg(feature = "alphabet_rna_n")]
use compact_genome::implementation::alphabets::rna_alphabet_or_n::RnaAlphabetOrN;
#[cfg(feature = "alphabet_rna_iupac")]
use compact_genome::implementation::alphabets::rna_iupac_nucleic_acid_alphabet::RnaIupacNucleicAcidAlphabet;

use crate::align::{
a_star_chain_ts::align_a_star_chain_ts,
fasta_parser::{parse_pair_fasta_file, parse_single_fasta_file},
Expand Down Expand Up @@ -282,11 +286,17 @@ enum AlignmentMethod {

#[derive(Debug, Clone, Eq, PartialEq, ValueEnum)]
enum InputAlphabet {
#[cfg(feature = "alphabet_dna")]
Dna,
#[cfg(feature = "alphabet_dna_n")]
DnaN,
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#[cfg(feature = "alphabet_rna")]
Rna,
#[cfg(feature = "alphabet_rna_n")]
RnaN,
#[cfg(feature = "alphabet_dna_iupac")]
DnaIupac,
#[cfg(feature = "alphabet_rna_iupac")]
RnaIupac,
}

Expand All @@ -308,11 +318,17 @@ pub fn cli(cli: Cli) -> Result<()> {
}

match cli.alphabet {
#[cfg(feature = "alphabet_dna")]
InputAlphabet::Dna => execute_with_alphabet::<DnaAlphabet>(cli)?,
#[cfg(feature = "alphabet_dna_n")]
InputAlphabet::DnaN => execute_with_alphabet::<DnaAlphabetOrN>(cli)?,
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#[cfg(feature = "alphabet_rna")]
InputAlphabet::Rna => execute_with_alphabet::<RnaAlphabet>(cli)?,
#[cfg(feature = "alphabet_rna_n")]
InputAlphabet::RnaN => execute_with_alphabet::<RnaAlphabetOrN>(cli)?,
#[cfg(feature = "alphabet_dna_iupac")]
InputAlphabet::DnaIupac => execute_with_alphabet::<DnaIupacNucleicAcidAlphabet>(cli)?,
#[cfg(feature = "alphabet_rna_iupac")]
InputAlphabet::RnaIupac => execute_with_alphabet::<RnaIupacNucleicAcidAlphabet>(cli)?,
}

Expand Down
14 changes: 10 additions & 4 deletions tsalign/src/align/template_switch_distance_type_selectors.rs
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Expand Up @@ -29,10 +29,7 @@ use lib_tsalign::{
PreprocessedLookaheadTemplateSwitchMinLengthStrategy,
PreprocessedTemplateSwitchMinLengthStrategy, TemplateSwitchMinLengthStrategy,
},
template_switch_total_length::{
MaxTemplateSwitchTotalLengthStrategy, NoTemplateSwitchTotalLengthStrategy,
TemplateSwitchTotalLengthStrategy,
},
template_switch_total_length::TemplateSwitchTotalLengthStrategy,
},
},
template_switch_distance_a_star_align,
Expand All @@ -41,6 +38,11 @@ use lib_tsalign::{
};
use log::info;

#[cfg(feature = "strategy_total_length_none")]
use lib_tsalign::a_star_aligner::template_switch_distance::strategies::template_switch_total_length::NoTemplateSwitchTotalLengthStrategy;
#[cfg(feature = "strategy_total_length_maximise")]
use lib_tsalign::a_star_aligner::template_switch_distance::strategies::template_switch_total_length::MaxTemplateSwitchTotalLengthStrategy;

use super::Cli;
use crate::util::load_tsa_config;

Expand Down Expand Up @@ -71,7 +73,9 @@ pub enum TemplateSwitchChainingStrategySelector {

#[derive(Clone, ValueEnum)]
pub enum TemplateSwitchTotalLengthStrategySelector {
#[cfg(feature = "strategy_total_length_none")]
None,
#[cfg(feature = "strategy_total_length_maximise")]
Maximise,
}
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Expand Down Expand Up @@ -375,6 +379,7 @@ fn align_a_star_template_switch_select_template_switch_total_length_strategy<
template_switch_count_memory: <TemplateSwitchCount as TemplateSwitchCountStrategy>::Memory,
) {
match cli.ts_total_length_strategy {
#[cfg(feature = "strategy_total_length_none")]
TemplateSwitchTotalLengthStrategySelector::None => {
align_a_star_template_switch_select_template_switch_descendant_strategy::<
_,
Expand All @@ -395,6 +400,7 @@ fn align_a_star_template_switch_select_template_switch_total_length_strategy<
template_switch_count_memory,
)
}
#[cfg(feature = "strategy_total_length_maximise")]
TemplateSwitchTotalLengthStrategySelector::Maximise => {
align_a_star_template_switch_select_template_switch_descendant_strategy::<
_,
Expand Down
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