204 add separate equal cost range mode that ignores geometric tsm constraints

[sebschmi]

No description provided.

[Copilot]

Pull request overview

This PR introduces a new “TSM uncertainty range” concept (renaming the previous equal-cost range), adds a mode to extend ranges while ignoring geometry-related cost, and updates the CLI/visualisation + bindings accordingly, alongside a coordinated major version bump across the workspace.

Changes:

• Replace “equal-cost range” with TSMUncertaintyRange across core alignment, SVG rendering, and Python types.
• Add TSMUncertaintyRangeExtensionMode with EqualCostIgnoreGeometry and expose it via --ts-uncertainty-range-extension-mode.
• Bump workspace crate versions to 6.0.0 and update dependent crate constraints/lockfile.

Reviewed changes

Copilot reviewed 32 out of 33 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tsalign/src/show.rs	Renames CLI flag/type for SVG range rendering to uncertainty ranges.
tsalign/src/align/template_switch_distance_type_selectors.rs	Adds CLI selector for uncertainty-range extension mode and plumbs it into align call.
tsalign/src/align.rs	Exposes --ts-uncertainty-range-extension-mode on the align CLI.
tsalign/Cargo.toml	Bumps package/dependency versions to 6.0.0.
tsalign-tests/Cargo.toml	Bumps test crate version to 6.0.0.
test_files/twin_equal_cost_ignore_geometry.sh	Adds a repro script comparing equal-cost vs ignore-geometry outputs.
test_files/twin_equal_cost_ignore_geometry.fa	Adds a small input FASTA for the repro script.
seed_chain/Cargo.toml	Bumps seed_chain + generic_a_star dependency version to 6.0.0.
python_bindings/src/lib.rs	Updates binding to pass the new extension mode argument.
python_bindings/python/tsalign/_types.py	Renames parsed field from equal_cost_range to uncertainty_range.
python_bindings/Cargo.toml	Bumps Python binding crate + deps to 6.0.0.
lib_tsshow/src/ts_arrangement/template_switch.rs	Renames stored range field/type to uncertainty range.
lib_tsshow/src/ts_arrangement/source.rs	Updates optional-source modelling to track “increases_inner” for uncertainty rendering.
lib_tsshow/src/ts_arrangement/inner.rs	Extends inner arrangement to represent increasing/decreasing uncertainty segments.
lib_tsshow/src/ts_arrangement.rs	Threads uncertainty range mode through arrangement and adds helpers for rendering bounds.
lib_tsshow/src/svg.rs	Implements updated uncertainty range rendering + legend changes.
lib_tsshow/Cargo.toml	Bumps lib_tsshow + lib_tsalign dependency version to 6.0.0.
lib_tsalign/src/tests.rs	Updates internal tests to pass the new extension mode argument.
lib_tsalign/src/a_star_aligner/template_switch_distance/display.rs	Renames display formatting from equal-cost range to uncertainty range.
lib_tsalign/src/a_star_aligner/template_switch_distance/alignment_type/tsm_uncertainty_range.rs	Adds new TSMUncertaintyRange + extension mode enum.
lib_tsalign/src/a_star_aligner/template_switch_distance/alignment_type/equal_cost_range.rs	Removes old EqualCostRange type.
lib_tsalign/src/a_star_aligner/template_switch_distance/alignment_type.rs	Switches AlignmentType entrance payload to uncertainty range.
lib_tsalign/src/a_star_aligner/template_switch_distance.rs	Re-exports new types and initializes uncertainty ranges as invalid.
lib_tsalign/src/a_star_aligner/configurable_a_star_align/tests.rs	Updates tests to include new parameter.
lib_tsalign/src/a_star_aligner/configurable_a_star_align.rs	Extends aligner API to accept uncertainty-range extension mode.
lib_tsalign/src/a_star_aligner/alignment_result/alignment/template_switch_specifics.rs	Adds cost computation variants to support “ignore geometry” cost comparisons.
lib_tsalign/src/a_star_aligner/alignment_result.rs	Renames/extends postprocessing to compute uncertainty ranges with mode parameter.
lib_tsalign/src/a_star_aligner.rs	Plumbs extension mode through top-level A* align API and logs chosen behavior.
lib_tsalign/Cargo.toml	Bumps lib_tsalign + deps to 6.0.0.
lib_ts_chainalign/src/chain_align.rs	Renames range type in chained alignment entrance events.
lib_ts_chainalign/Cargo.toml	Bumps lib_ts_chainalign + deps to 6.0.0.
generic_a_star/Cargo.toml	Bumps generic_a_star version to 6.0.0.
Cargo.lock	Updates lockfile versions for the workspace bump.

Suppressed comments (3)

lib_tsshow/src/ts_arrangement/source.rs:1044

• SourceChar::make_copy() turns OptionalSource into Source, which drops the optional/uncertainty-range state (including increases_inner). This likely breaks uncertainty-range visualisation when optional chars are copied (e.g., due to TS copy-depth rendering). Preserve OptionalSource and carry increases_inner through when making a copy.

This issue also appears on line 1067 of the same file.

            } => Self::Source {
                column: *column,
                lower_case: false,
                copy_depth: Some(copy_depth.map(|copy_depth| copy_depth + 1).unwrap_or(0)),
            },

lib_tsshow/src/ts_arrangement/source.rs:1071

• SourceChar::make_visible_copy() also turns OptionalSource into Source, dropping uncertainty-range metadata (increases_inner) and removing optional styling. Preserve OptionalSource when copying so the SVG can keep rendering optional chars correctly.

            } => Self::Source {
                column: *column,
                lower_case: false,
                copy_depth: Some(copy_depth.map(|copy_depth| copy_depth + 1).unwrap_or(0)),
            },

lib_tsshow/src/svg.rs:285

• Similarly, the commented-out SP4 shift logic should be removed or turned into an explicit TODO. As-is it reads like partially reverted logic and makes future maintenance harder.

        /*let descendant_sp4 = if config.uncertainty_range_mode == UncertaintyRangeMode::Full {
            descendant_sp4 + usize::try_from(uncertainty_range.max_end).unwrap()
        } else {
            descendant_sp4
        };*/

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