Release Notes

Table of contents

1. v1.0.1 — pip-install fix
2. v1.0.0 — first stable release
   1. Public surface
   2. Correctness fixes since the pre-1.0 code
   3. browser import is now unambiguous
   4. Testing
3. Upgrade notes

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v1.0.1 — pip-install fix

1.0.0 listed cgranges (Heng Li’s C interval index) as a dependency, but cgranges is not published on PyPI, so pip install genomeblocks failed with No matching distribution found for cgranges.

• cgranges is no longer a pip dependency. When it isn’t importable, genomeblocks now uses a pure-Python interval index with identical overlap results, so pip install genomeblocks works out of the box. Install cgranges (conda, or pip install git+https://github.com/lh3/cgranges) for the fast C path on large sets.

If you installed 1.0.0 from PyPI and hit the error, upgrade: pip install -U genomeblocks.

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v1.0.0 — first stable release

genomeblocks v1.0 is the first release with a frozen public surface, a full synthetic test suite, and complete module documentation. The public API is the set of names re-exported from the top-level package plus the Atlas class:

from genomeblocks import (
    Locus, Exon, CDS, UTR,          # single intervals
    Loci,                            # interval container + set algebra
    Gene, Transcript, Genes,         # gene models / GTF parsing
    Architecture,                    # chromatin-contact graph
    Atlas,                           # GIGGLE-style enrichment
    signal, tmm, compare_heatmap,    # bigWig signal
    scan_motifs, make_genome,        # motif scanning
    browser,                         # region viewer
    coverage,                        # BAM per-base coverage
)

Public surface

The building blocks and their entry points:

Block	Build from	Key methods
Loci	.make(bed), .tile, .from_frame	& \| - ^, slop, sort, merge, nearest, signal, enrich, liftover
Genes	.make(gtf), .make_ucsc	annotations, nearest_genes
Architecture	.make(bedpe)	add_mcool, normalize, annotate, strength, prime_hubs
Atlas	.make(beds)	search, bootstrap, save/load
signal	loci.signal(bigwigs)	tmm, plot_heatmap, compare_heatmap
browser	browser(region, tracks)	mixed bigWig / BAM / bed / bedpe / gene tracks

Correctness fixes since the pre-1.0 code

• Locus ordering across chromosomes. > and >= returned the less-than result across chromosomes, so a > b and b > a could disagree with <. Cross-chromosome comparisons are now consistent. Within-chromosome ordering (and therefore Loci.sort / merge) was already correct.
• Locus is now hashable (by its UID), so a Locus can be used in a set or as a dict key — matching its value-like __eq__.
• Architecture.copy() / subgraph() preserve property types. Types were inferred from a sampled Python value, but graph-tool returns booleans as ints, so bool vertex/edge properties were silently copied as double. Property maps now keep their exact graph-tool value type (and empty graphs keep their properties too).
• Genes.make no longer crashes on a generic UTR feature without a CDS. A non-coding transcript (or a UTR line preceding its CDS) used to raise IndexError; the 5′/3′ inference now falls back safely.
• Signal memory guard checks RAM, not disk. The signal() size check now compares the requested cube against available physical memory (it previously measured free space on /), and raises a clearer MemoryError.

browser import is now unambiguous

The region-viewer drawing code moved from genomeblocks/browser.py to genomeblocks/browserview.py, so the public name browser is always the callable — the old 'module' object is not callable footgun (where a stray import genomeblocks.browser shadowed the function) is gone:

from genomeblocks import browser              # the function
from genomeblocks.browserview import browser  # equivalent

Testing

The suite is fully synthetic — no external genome / bigWig / ChIP-Atlas data — and covers both unit helpers and end-to-end pipelines (a real bigWig written in-test and read back through both signal backends, motif scanning on a planted PWM, Atlas enrichment, a Loci → Genes → Architecture pipeline, and a headless browser() render):

pip install -e ".[test]"
pytest

graph-tool must be importable for the Architecture tests (it is the one conda-only dependency).

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Upgrade notes

There is no prior stable release to migrate from — v1.0 is the baseline. If you were tracking main before the 1.0 tag, note that several exploratory Architecture methods (make_spread, make_clique, cluster, focus, …), the Tags layer, and a handful of Genes helpers were removed in the run-up to 1.0. Use the public surface in the table above.