v1.0.0 Release

[alexsweeten]

ModDotPlot v1.0.0
A major performance, plotting, and packaging update.
Highlights:

• Faster, lower-memory dotplot generation with native ntHash, indexed FASTA streaming, multiprocessing, memory limits, and reusable sketch caching.
• Expanded comparative plotting: pair manifests, region selection, multi-sequence grids, --grid-only, configurable sequence order, and strand-direction plots.
• Improved static plots, BED annotations, custom palettes, vector output, Cooler export, and reproducibility summaries.
• BEDPE files can now be loaded alongside JSON configuration files, with clearer input validation and error messages.
• Supports Python 3.10–3.14 with a smaller core dependency set.
• Interactive mode is now deprecated, explicitly invoked with moddotplot interactive, and installed through the optional interactive extra.
• Substantially expanded automated testing and cross-platform CI coverage.

[Copilot]

Copilot review overview

🟡 Changes recommended

Interactive BEDPE export transposes coordinates, and self-identity Cooler export lacks coverage for invalid duplicate bins.

Review effort: Balanced
Findings: 1 · 1

Open (2)

• Transpose heatmap matrix before exporting coordinates · New
• Fix duplicate bins in self-export cooler matrices · New

What changed in this PR

Prepares ModDotPlot 1.0.0 with native performance improvements, expanded plotting, optional interactive dependencies, packaging updates, and broader automated coverage.

Changes:

• Adds native sparse rendering, annotations, direction plots, caching, and reproducibility summaries.
• Modernizes packaging, dependency extras, CI, and PyPI publishing.
• Expands tests across algorithms, FASTA access, plotting, CLI behavior, and native hashing.

File	Description
THIRD_PARTY_LICENSES.md	Adds ColorBrewer licensing.
tests/​test_static_customization.py	Tests static plot customization.
tests/​test_sparse_containment.py	Tests sparse containment calculations.
tests/​test_sketch_cache.py	Tests sketch caching and release.
tests/​test_plot_summary.py	Tests reproducibility summaries.
tests/​test_plot_fonts.py	Tests font sizing and fallback.
tests/​test_packaging_metadata.py	Validates package and workflow metadata.
tests/​test_optional_dependencies.py	Tests optional dependency behavior.
tests/​test_nthash.py	Validates native ntHash results.
tests/​test_native_sequence_sketches.py	Tests native sequence sketching.
tests/​test_native_render.py	Tests native rendering primitives.
tests/​test_native_full_plot.py	Tests full native plots.
tests/​test_modimizer_vectorization.py	Tests vectorized modimizer generation.
tests/​test_issue53_memory_safe_plotting.py	Covers memory-safe sparse plotting.
tests/​test_interactive_parser.py	Tests interactive CLI parsing.
tests/​test_interactive_export.py	Tests interactive BEDPE export.
tests/​test_interactive_annotations.py	Tests interactive annotation tracks.
tests/​test_grid.py	Tests multi-sequence grids.
tests/​test_fasta_parser.py	Tests streamed and indexed FASTA access.
tests/​test_entrypoints.py	Tests module entry points.
tests/​test_direction_plot.py	Tests strand-direction plots.
tests/​test_direction_cli.py	Tests direction CLI integration.
tests/​test_cli_integration.py	Adds end-to-end CLI coverage.
tests/​test_annotation_track.py	Tests BED annotation rendering.
tests/​test_algorithms.py	Expands algorithm regression coverage.
src/​moddotplot/​plot_summary.py	Generates plot summaries.
src/​moddotplot/​optional_dependencies.py	Provides optional dependency errors.
src/​moddotplot/​native_render.py	Implements sparse Matplotlib rendering.
src/​moddotplot/​interactive.py	Updates interactive plotting and export.
src/​moddotplot/​const.py	Updates version and direction colors.
src/​moddotplot/​annotations.py	Adds shared BED parsing.
src/​moddotplot/​__main__.py	Lazily loads and quiets the CLI.
setup.py	Builds the native extension.
setup.cfg	Configures licenses and stable ABI wheels.
pyproject.toml	Updates metadata and dependencies.
LICENSE.ntHash	Adds ntHash’s license.
CITATION.cff	Converts citation metadata to CFF.
.gitignore	Adds Python build exclusions.
.github/​workflows/​publish-to-pypi.yml	Reworks release publishing.
.github/​workflows/​ci.yml	Adds cross-version CI.
.github/​workflows/​black.yml	Removes the superseded formatting workflow.

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.