API Reference¶

Hifuku is organized as a pipeline of composable modules. The typical call order for a survey is shown below; see the individual pages for full signatures and behavior.

TaxonTable ──► read_tree ──► nj_tree ──► AnchorTriangle.from_anchors
                │                                   │
                └──► load_alignment                 │  (chart + CBS/RF metric)
                           │                        ▼
                     log_likelihood ◄────── SurveyRun.execute
                     (CPU or GPU)                    │
                                              run_survey (driver)
                                                     │
                                        CpuBackend / CudaBackend
                                                     │
                                              EliteArchive
                                                     │
                        ┌────────────────────────────┴───────────────┐
                        │                                            │
          elevation_map / z_fidelity_map              split_coordinates ──► distances
                                                                     │
                                                    mds / ordinate ──► faithfulness

    chart_table ──► ChartTable.select ──► assign_genes ──► SurveyPlan
    (before a survey)

Modules¶

Module	Key exports
`hifuku.taxa`	`TaxonTable`, `AlignmentIndex`
`hifuku.alignment`	`Alignment`, `load_alignment`
`hifuku.tree_io`	`HifukuTree`, `read_tree`
`hifuku.substitution`	`EigenDecomp`, `jc69`, `gtr`
`hifuku.pruning`	`log_likelihood`
`hifuku.gpu_pruning`	`log_likelihood_gpu`
`hifuku.moves`	`nni_move`, `spr_move`, `branch_scale_move`, `branch_slide_move`
`hifuku.nj`	`nj_tree`
`hifuku.metric`	`CBSMetric`, `compute_normalizers`
`hifuku.anchor_triangle`	`AnchorTriangle`, `TreeMetric`, `barycentric`
`hifuku.archive`	`run_archive`, `EliteArchive`, `locate_tree`
`hifuku.gpu_walk`	`run_archive_gpu`, `evaluate_gpu`
`hifuku.params`	`ArchiveParams`, `GpuParams`
`hifuku.backend`	`Backend`, `Capabilities`, `Stats`, `RunContext`
`hifuku.driver`	`run_survey`, `ArchiveResult`
`hifuku.monitor`	`bind_monitor`, `Checkpoint`
`hifuku.analysis2d`	`elevation_map`, `z_fidelity_map`
`hifuku.charts`	`ChartTable`, `chart_table`, `assign_genes`, `smacof`
`hifuku.ordination`	`split_coordinates`, `distances`, `mds`, `faithfulness`
`hifuku.survey_io`	`SurveyPlan`, `SurveyRun`, `SurveyTask`, `Survey`, `Ordination`