pub mod args;
mod batch;
mod cache;
mod dataset;
mod debug;
mod diff;
mod doctor;
pub mod handlers;
mod package;
mod package_args;
mod package_convert;
mod package_convert_layout;
mod package_init;
mod package_skeleton;
mod package_skeleton_files;
mod pipeline;
mod pipeline_config;
mod pipeline_lock;
mod pipeline_output;
pub(crate) mod tokenizer_convert;
mod workflow;
pub use args::{
    BatchCommand, CacheCommand, Cli, Command, DatasetCommand, FastaCommand, KindArg, PaddingArg,
    SeqCommand, ServiceCommand, TokenizerCommand, TokenizerProfileArg,
};
pub(crate) use batch::run_batch_command;
pub(crate) use cache::run_cache_command;
pub(crate) use dataset::run_dataset_command;
pub(crate) use debug::run_debug;
pub(crate) use diff::run_diff;
pub(crate) use doctor::build_doctor_report;
pub use handlers::run;
pub(crate) use package::run_package_command;
pub use package_args::{
    PackageCommand, PackageConvertArgs, PackageConvertProjectArgs, PackageInitArgs,
};
pub(crate) use package_convert::run_package_convert;
pub(crate) use package_init::{run_package_convert_project, run_package_init};
pub(crate) use pipeline::{run_pipeline, PipelineRunOptions};
pub(crate) use workflow::run_workflow;
