Rename TSM primary and secondary to descendant and ancestor.

[sebschmi]

No description provided.

[Copilot]

Pull request overview

This PR updates terminology across the project by renaming Template Switch Model (TSM) “primary/secondary” to “descendant/ancestor”, and propagates that rename through configs, documentation, Rust crates, and Python bindings.

Changes:

• Renames TSM-related types/fields/enums across lib_tsalign, lib_tsshow, and lib_ts_chainalign (e.g., TemplateSwitchPrimary/Secondary → TemplateSwitchDescendant/Ancestor, anti_primary_gap → anti_descendant_gap).
• Updates .tsa config keys and examples (ForwardAntiPrimaryGap/ReverseAntiPrimaryGap → ForwardAntiDescendantGap/ReverseAntiDescendantGap).
• Updates README + Python bindings docs/types to reflect the new names and removes unused plain-text alignment stream code in lib_tsshow.

Reviewed changes

Copilot reviewed 37 out of 37 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
test_files/config/small/config.tsa	Renames anti-gap cost function keys to descendant terminology.
test_files/config/range/config.tsa	Renames anti-gap cost function keys to descendant terminology.
test_files/config/no_intra_forward_jump/config.tsa	Renames anti-gap cost function keys to descendant terminology.
test_files/config/experiments/config.tsa	Renames anti-gap cost function keys to descendant terminology.
test_files/config/chainalignn/config.tsa	Renames anti-gap cost function keys to descendant terminology.
test_files/config/chainalign/config.tsa	Renames anti-gap cost function keys to descendant terminology.
test_files/config/bench/config.tsa	Renames anti-gap cost function keys to descendant terminology.
sample_tsa_config/config.tsa	Updates sample config to new anti-gap cost function key names.
README.md	Updates documentation and example config snippet to new key names.
python_bindings/README.md	Updates Python usage examples to new op field names.
python_bindings/python/tsalign/_types.py	Renames parsed alignment op fields to descendant/ancestor and anti_descendant_gap.
lib_tsshow/src/ts_arrangement/template_switch.rs	Renames TemplateSwitch struct fields to descendant/ancestor terminology.
lib_tsshow/src/ts_arrangement/source.rs	Propagates descendant/ancestor rename through TS arrangement construction and helpers.
lib_tsshow/src/ts_arrangement/inner.rs	Updates inner arrangement logic to use ancestor/descendant naming and accessors.
lib_tsshow/src/ts_arrangement/complement.rs	Renames secondary-complement helpers to ancestor-complement.
lib_tsshow/src/ts_arrangement.rs	Updates arrangement APIs and internal fields to ancestor terminology.
lib_tsshow/src/svg.rs	Updates SVG rendering logic to use descendant/ancestor enums and fields.
lib_tsshow/src/plain_text/parse_template_switches.rs	Updates TS parsing offsets/fields to ancestor/descendant names.
lib_tsshow/src/plain_text/alignment_stream.rs	Removes now-unneeded local alignment stream implementation.
lib_tsshow/src/plain_text.rs	Updates plain-text renderer to use new TS field names.
lib_tsshow/src/error.rs	Renames SVG negative-gap error variant/message to anti-descendant terminology.
lib_tsalign/src/config/io.rs	Updates config parser/printer to expect new anti-gap cost function keys.
lib_tsalign/src/config.rs	Renames config fields and helpers to anti_descendant_gap_costs and descendant/ancestor enums.
lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/template_switch_min_length.rs	Propagates renamed identifier fields (descendant/ancestor indices/types).
lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/descendant.rs	Updates descendant strategy trait to use the new descendant enum.
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch.rs	Updates lower-bound logic to use anti_descendant_gap and renamed config fields.
lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch_alignment.rs	Updates generated lower-bound config to new anti-gap cost fields.
lib_tsalign/src/a_star_aligner/template_switch_distance/identifier.rs	Renames core identifier enums/fields from primary/secondary to descendant/ancestor.
lib_tsalign/src/a_star_aligner/template_switch_distance/display.rs	Updates display formatting for renamed TS fields (but still has old labels in places).
lib_tsalign/src/a_star_aligner/template_switch_distance/context.rs	Propagates rename through successor generation and cost evaluation.
lib_tsalign/src/a_star_aligner/template_switch_distance/alignment_type.rs	Renames alignment type fields (descendant/ancestor, anti_descendant_gap).
lib_tsalign/src/a_star_aligner/template_switch_distance.rs	Propagates renamed identifiers/types into node generation.
lib_tsalign/src/a_star_aligner/alignment_result/alignment/template_switch_specifics.rs	Updates TS-specific alignment manipulation to renamed fields.
lib_tsalign/src/a_star_aligner/alignment_result/alignment/stream.rs	Updates alignment stream coordinate tracking to use descendant enum and anti-descendant gap.
lib_ts_chainalign/src/costs/compat.rs	Updates chainalign compat mapping to new anti-descendant cost field.
lib_ts_chainalign/src/chain_align.rs	Updates emitted tsalign alignment ops to new TS field names.
lib_ts_chainalign/src/alignment/ts_kind.rs	Updates ts_kind conversions to new tsalign descendant/ancestor enums.

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