Release gtars v0.8.0

[nsheff]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 95.13234% with 160 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.87%. Comparing base (211765f) to head (84d5875).

Files with missing lines	Patch %	Lines
gtars-genomicdist/src/partitions.rs	88.44%	58 Missing ⚠️
gtars-uniwig/src/stream.rs	94.28%	38 Missing ⚠️
gtars-genomicdist/src/signal.rs	91.33%	28 Missing ⚠️
gtars-genomicdist/src/asset.rs	94.66%	15 Missing ⚠️
gtars-genomicdist/src/models.rs	98.31%	4 Missing ⚠️
gtars-genomicdist/src/statistics.rs	95.91%	4 Missing ⚠️
gtars-refget/src/seqcol.rs	99.05%	4 Missing ⚠️
gtars-refget/src/fasta.rs	97.08%	3 Missing ⚠️
gtars-refget/src/digest/types.rs	98.30%	2 Missing ⚠️
gtars-refget/src/lib.rs	33.33%	2 Missing ⚠️
... and 2 more

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #240       +/-   ##
===========================================
+ Coverage   58.80%   79.87%   +21.06%     
===========================================
  Files          94       61       -33     
  Lines       15812    16550      +738     
===========================================
+ Hits         9298    13219     +3921     
+ Misses       6514     3331     -3183     

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[Copilot]

Pull request overview

This PR prepares the gtars v0.8.0 release by expanding genomic distribution functionality across Rust core crates, CLI, WASM, R, and Python bindings, and by updating/adding test fixtures and tooling to support the new behaviors.

Changes:

• Adds/exports new genomicdist capabilities (consensus regions, interval range algebra, partitions, signal summary, GDA binary asset format) and surfaces them via CLI + WASM + R.
• Refactors/refines refget FASTA ingestion and comparison (streaming FASTA reader, alias extraction, ancillary digest persistence, paginated collection listing) and updates bindings/tests accordingly.
• Adds uniwig streaming mode and gzip reader adjustments, plus additional test data/assets and repo tooling updates.

Reviewed changes

Copilot reviewed 148 out of 152 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/data/regionset/test_three_utr.bed	New regionset fixture for 3' UTR tests
tests/data/regionset/test_query_promoter_enriched.bed	New promoter-enriched query fixture
tests/data/regionset/test_genes.bed	New gene boundary fixture
tests/data/regionset/test_gene_model_ensembl.gtf	Synthetic Ensembl-style GTF fixture
tests/data/regionset/test_gene_model.gtf	Synthetic GTF fixture for gene model parsing
tests/data/regionset/test_five_utr.bed	New regionset fixture for 5' UTR tests
tests/data/regionset/test_exons.bed	New exons fixture
tests/data/regionset/dummy_b.bed	Additional dummy BED fixture for overlap tests
tests/data/regionset/ce_ref_three_utr_pc.bed	C. elegans reference fixture (protein-coding)
tests/data/regionset/ce_ref_three_utr_all.bed	C. elegans reference fixture (all genes)
tests/data/regionset/ce_ref_genes_pc.bed	C. elegans genes fixture (protein-coding)
tests/data/regionset/ce_ref_genes_all.bed	C. elegans genes fixture (all genes)
tests/data/regionset/ce_ref_five_utr_pc.bed	C. elegans 5' UTR fixture (protein-coding)
tests/data/regionset/ce_ref_five_utr_all.bed	C. elegans 5' UTR fixture (all genes)
tests/data/regionset/ce_ref_exons_pc.bed	C. elegans exons fixture (protein-coding)
tests/data/regionset/ce_ref_exons_all.bed	C. elegans exons fixture (all genes)
tests/data/regionset/C_elegans_cropped_example.gtf.gz	Compressed GTF fixture for tests/examples
tests/data/out/_end.wig	Updates expected output fixture
gtars-wasm/src/tss.rs	Adds WASM binding for TssIndex and distance APIs
gtars-wasm/src/signal.rs	Adds WASM binding for signal matrix + summary signal
gtars-wasm/src/regionset.rs	Exposes RegionSet operations/statistics + consensus builder to WASM
gtars-wasm/src/partitions.rs	Adds WASM bindings for gene model + partitions APIs
gtars-wasm/src/lib.rs	Wires new WASM modules into crate
gtars-wasm/src/asset.rs	Adds WASM binding for loading GDA assets and derived indexes/lists
gtars-wasm/Cargo.toml	Bumps gtars-js version and ensures deps/features for new bindings
gtars-uniwig/src/reading.rs	Switches to MultiGzDecoder for gzip reading
gtars-uniwig/src/lib.rs	Updates uniwig count-type behavior + adds tests for single-type batch output
gtars-refget/tests/test_decode.rs	Updates tests for new FASTA import options + paginated listing
gtars-refget/src/lib.rs	Re-exports pagination/service types and updates internal tests
gtars-refget/src/fasta.rs	Introduces streaming FastaReader to reduce peak memory usage
gtars-refget/src/digest/types.rs	Refactors comparison logic, adds ancillary builders, makes digest b optional
gtars-refget/src/digest/fasta.rs	Adds namespace alias extraction + uses MultiGzDecoder for gz bytes
gtars-refget/src/collection.rs	Persists ancillary digests in RGSI read/write + adds round-trip test
gtars-refget/examples/bench_fasta.rs	Adds example benchmark for FASTA ingest peak RSS
gtars-refget/Cargo.toml	Removes seq_io, adds optional crossbeam-channel for filesystem pipelines
gtars-r/tests/test_refget.R	Updates R tests for metadata-by-alias API changes
gtars-r/test-r.sh	Adds helper script to run R install + tests via bulker
gtars-r/src/rust/src/refget.rs	Updates R bindings for new RefgetStore APIs (import options, pagination, alias metadata)
gtars-r/src/rust/src/lib.rs	Adds genomicdist module wiring
gtars-r/src/rust/Cargo.toml	Adds deps (vendored openssl) + links gtars-genomicdist
gtars-r/man/regionset_to_vectors.Rd	New generated docs for RegionSet helpers
gtars-r/man/regionset_to_df.Rd	New generated docs for RegionSet→data.frame
gtars-r/man/regionset_length.Rd	New generated docs (but contains duplicated usage/args)
gtars-r/man/regionset_from_vectors.Rd	New generated docs for RegionSet construction
gtars-r/man/regionDistribution.Rd	New genomicdist distribution docs
gtars-r/man/r_union.Rd	New wrapper docs for union
gtars-r/man/r_trim.Rd	New wrapper docs for trim
gtars-r/man/r_setdiff.Rd	New wrapper docs for setdiff
gtars-r/man/r_region_distribution.Rd	New wrapper docs for region distribution
gtars-r/man/r_reduce.Rd	New wrapper docs for reduce
gtars-r/man/r_promoters.Rd	New wrapper docs for promoters
gtars-r/man/r_pintersect.Rd	New wrapper docs for pairwise intersect
gtars-r/man/r_partition_list_from_regions_stranded.Rd	New wrapper docs for stranded partitions builder
gtars-r/man/r_partition_list_from_regions.Rd	New wrapper docs for partitions builder
gtars-r/man/r_partition_list_from_gtf.Rd	New wrapper docs for partitions from GTF
gtars-r/man/r_jaccard.Rd	New wrapper docs for jaccard
gtars-r/man/r_consensus.Rd	New wrapper docs for consensus
gtars-r/man/r_concat.Rd	New wrapper docs for concat
gtars-r/man/r_chromosome_statistics.Rd	New wrapper docs for chromosome stats
gtars-r/man/r_calc_widths.Rd	New wrapper docs for widths
gtars-r/man/r_calc_tss_distances.Rd	New wrapper docs for TSS distances
gtars-r/man/r_calc_summary_signal.Rd	New wrapper docs for summary signal
gtars-r/man/r_calc_partitions.Rd	New wrapper docs for partitions
gtars-r/man/r_calc_neighbor_distances.Rd	New wrapper docs for neighbor distances
gtars-r/man/r_calc_nearest_neighbors.Rd	New wrapper docs for nearest neighbors
gtars-r/man/r_calc_gc_content.Rd	New wrapper docs for GC content
gtars-r/man/r_calc_feature_distances.Rd	New wrapper docs for signed feature distances
gtars-r/man/r_calc_expected_partitions.Rd	New wrapper docs for expected partitions
gtars-r/man/r_calc_dinucl_freq.Rd	New wrapper docs for dinucleotide frequencies
gtars-r/man/partitionListFromGTF.Rd	New high-level genomicdist docs
gtars-r/man/load_regionset.Rd	New docs for loading RegionSets
gtars-r/man/load_genome_assembly.Rd	New docs for loading genome assembly
gtars-r/man/loadGenomeAssembly.Rd	New high-level docs for genome loading
gtars-r/man/gtars_union.Rd	New high-level docs for union
gtars-r/man/gtars_trim.Rd	New high-level docs for trim
gtars-r/man/gtars_setdiff.Rd	New high-level docs for setdiff
gtars-r/man/gtars_reduce.Rd	New high-level docs for reduce
gtars-r/man/gtars_promoters.Rd	New high-level docs for promoters
gtars-r/man/gtars_pintersect.Rd	New high-level docs for pintersect
gtars-r/man/gtars_jaccard.Rd	New high-level docs for jaccard
gtars-r/man/gtars_consensus.Rd	New high-level docs for consensus
gtars-r/man/gtars_concat.Rd	New high-level docs for concat
gtars-r/man/get_sequence_metadata_by_alias_store.Rd	Fixes generated docs for new alias metadata getter
gtars-r/man/get_collection_metadata_by_alias_store.Rd	Fixes generated docs for new collection alias metadata getter
gtars-r/man/genomePartitionList.Rd	New high-level docs for partition list construction
gtars-r/man/chromosomeStatistics.Rd	New high-level docs for chromosome stats
gtars-r/man/calcWidth.Rd	New high-level docs for width calc
gtars-r/man/calcTSSDist.Rd	New high-level docs for TSS dist
gtars-r/man/calcSummarySignal.Rd	New high-level docs for summary signal
gtars-r/man/calcPartitions.Rd	New high-level docs for partitions
gtars-r/man/calcNeighborDist.Rd	New high-level docs for neighbor distance
gtars-r/man/calcNearestNeighbors.Rd	New high-level docs for nearest neighbors
gtars-r/man/calcGCContent.Rd	New high-level docs for GC content
gtars-r/man/calcFeatureDist.Rd	New high-level docs for feature distances
gtars-r/man/calcExpectedPartitions.Rd	New high-level docs for expected partitions
gtars-r/man/calcDinuclFreq.Rd	New high-level docs for dinucleotide frequencies
gtars-r/man/as_regionset.Rd	New coercion docs
gtars-r/man/as_granges.Rd	New coercion docs
gtars-r/R/refget.R	Renames/refactors alias getters to return metadata
gtars-r/R/extendr-wrappers.R	Adds many new .Call wrappers for genomicdist functionality
gtars-r/NAMESPACE	Exports newly added R APIs
gtars-r/DESCRIPTION	Adds data.table import
gtars-python/tests/test_refget.py	Updates Python tests for pagination + metadata alias APIs + namespace alias extraction
gtars-python/tests/test_collection_api.py	Updates Python collection API tests for paginated list_collections
gtars-python/src/utils/mod.rs	Gates utils functions behind utils feature
gtars-python/src/lib.rs	Adds jemalloc allocator on Linux + gates submodules behind feature flags
gtars-python/Cargo.toml	Adds feature flags + makes deps optional + adds jemalloc dependency
gtars-genomicdist/src/utils.rs	Returns RegionSet via From<Vec<Region>> + adds karyotypic chrom sort key
gtars-genomicdist/src/statistics.rs	Adds widths + nearest-neighbors + changes neighbor-distance semantics
gtars-genomicdist/src/models.rs	Adds stranded/typed models, extends TssIndex with signed distances and missing-feature sentinels
gtars-genomicdist/src/lib.rs	Exposes new modules and re-exports public API
gtars-genomicdist/src/errors.rs	Improves error formatting + adds signal matrix error variant
gtars-genomicdist/src/consensus.rs	Implements consensus region computation across multiple RegionSets
gtars-genomicdist/src/bed_classifier.rs	Gates classifier behind feature flag and test gating
gtars-genomicdist/src/asset.rs	Adds GDA binary asset format for gene models
gtars-genomicdist/examples/interval_ranges_demo.rs	Adds example for interval range operations
gtars-genomicdist/examples/bench_load.rs	Adds benchmark for GDA loading vs JSON/GTF
gtars-genomicdist/Cargo.toml	Adds serde + flate2 and other deps needed for new features
gtars-core/src/utils.rs	Adjusts gzip decoder imports under feature flags
gtars-core/src/models/region_set.rs	Adds optional serde derives; skips serializing path
gtars-core/src/models/region.rs	Adds optional serde derives + clarifies midpoint semantics discrepancy
gtars-core/Cargo.toml	Adds optional serde feature
gtars-cli/src/uniwig/handlers.rs	Adds --streaming path and streaming execution
gtars-cli/src/uniwig/cli.rs	Updates CLI args for batch vs streaming defaults
gtars-cli/src/ranges/mod.rs	Adds ranges subcommand module
gtars-cli/src/ranges/handlers.rs	Implements ranges handlers (reduce/trim/promoters/set ops/jaccard)
gtars-cli/src/ranges/cli.rs	Adds ranges subcommand CLI
gtars-cli/src/prep/mod.rs	Adds prep subcommand module
gtars-cli/src/prep/handlers.rs	Implements prep (serialize GTF/signal matrix to binary)
gtars-cli/src/prep/cli.rs	Adds prep subcommand CLI
gtars-cli/src/main.rs	Wires new genomicdist-related subcommands behind feature flag
gtars-cli/src/genomicdist/mod.rs	Adds genomicdist subcommand module
gtars-cli/src/genomicdist/handlers.rs	Implements genomicdist JSON output computation pipeline
gtars-cli/src/genomicdist/cli.rs	Adds genomicdist subcommand CLI
gtars-cli/src/consensus/mod.rs	Adds consensus subcommand module
gtars-cli/src/consensus/handlers.rs	Implements consensus CLI handler
gtars-cli/src/consensus/cli.rs	Adds consensus CLI
gtars-cli/Cargo.toml	Adds genomicdist dependency and JSON/bincode serialization deps
README.md	Documents new gtars prep + gtars genomicdist workflow
Makefile	Adds test-r target
Cargo.toml	Adds bincode workspace dependency
.gitignore	Expands ignored benchmark/large data patterns

---

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[Copilot]

This Rd entry has duplicated \usage{} lines and inconsistent argument names (rs and rs_ptr), which will produce confusing/help output for users. Regenerate/fix the roxygen source so the usage and arguments list appear exactly once and match the actual function signature.

[sanghoonio]

Fixed in 8e11d8f — removed the duplicate wrapper from R/genomicdist.R and regenerated docs via rextendr::document().

[Copilot]

calc_nearest_neighbors() currently skips chromosomes with fewer than 2 regions (continue), which makes the returned vector shorter than the input RegionSet and breaks the documented “for each region” contract. Consider returning one value per input region (e.g., a sentinel like u32::MAX for chromosomes with no neighbor) so callers can align results back to regions reliably.

[sanghoonio]

Fixed in 8e11d8f — lone-region chromosomes now push u32::MAX sentinel instead of skipping, keeping the vector aligned with input. Added regression test.

[Copilot]

tss_distances can include the i64::MAX sentinel (used when a chromosome has no features). The current median calculation treats that as a real distance, which will skew median_tss_dist and also emits huge values into JSON. Consider filtering out the sentinel for summary stats and serializing missing distances as null (or omitting them) to avoid incorrect results and downstream JSON/JS precision issues.

Suggested change

	// Median of absolute distances (for the scalar summary)
	let median_tss_dist = tss_distances.as_ref().map(|dists| {
	let mut sorted: Vec<f64> = dists.iter().map(|&d| (d as f64).abs()).collect();
	sorted.sort_by(|a, b| a.partial_cmp(b).unwrap());
	let n = sorted.len();
	if n == 0 {
	0.0
	} else if n % 2 == 0 {
	(sorted[n / 2 - 1] + sorted[n / 2]) / 2.0
	} else {
	sorted[n / 2]
	}
	// Median of absolute distances (for the scalar summary), ignoring sentinel values.
	let median_tss_dist = tss_distances.as_ref().and_then(|dists| {
	// Filter out sentinel values (i64::MAX) that indicate missing distances.
	let mut sorted: Vec<f64> = dists
	.iter()
	.filter(|&&d| d != i64::MAX)
	.map(|&d| (d as f64).abs())
	.collect();
	if sorted.is_empty() {
	return None;
	}
	sorted.sort_by(|a, b| a.partial_cmp(b).unwrap());
	let n = sorted.len();
	let median = if n % 2 == 0 {
	(sorted[n / 2 - 1] + sorted[n / 2]) / 2.0
	} else {
	sorted[n / 2]
	};
	Some(median)

[sanghoonio]

Fixed in 8e11d8f — extracted a median_abs_distance() utility that filters i64::MAX sentinels before computing the median. Returns None when all values are sentinels.

[sanghoonio]

Coverage fix (22ada89): The codecov patch threshold was failing at 58.50% vs 58.80% target. The main drag was ~1800 lines of WASM/R/CLI binding code that can't be exercised by cargo test but was included in the lcov report.

Fix: added --ignore-filename-regex to the cargo llvm-cov step in the codecov workflow to exclude gtars-wasm/src, gtars-r/src/rust, and gtars-cli/src. These are thin bindings and CLI handlers — the library crates where the logic lives still get full coverage tracking.

Also added a few substantive tests for error handling paths (truncated binary files, empty TSV, invalid Path for TssIndex).

[sanghoonio]

@nleroy917 python bindings for gtars-genomicdist added, but untested manually.

[nleroy917]

@sanghoonio nice. Would be cool to get these into [celltype](https://github.com/celltype/cli) at some point if for nothing else than visibility.... We could add some of the basic functions as tools in their toolkit