genome-spy-python 0.4.0__tar.gz → 0.5.0__tar.gz

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/.github/workflows/ci.yml

@@ -103,7 +103,7 @@ jobs:
           uv venv --seed --python 3.11 "$RUNNER_TEMP/notebook-env"
           for wheel in "$GITHUB_WORKSPACE"/dist/*.whl; do
             uv pip install --python "$RUNNER_TEMP/notebook-env/bin/python" \
-              "$wheel[arrow]" "anywidget==0.11.0" jupyterlab pandas numpy scipy statsmodels playwright pillow pytest
+              "$wheel[arrow]" "anywidget==0.11.0" jupyterlab pandas numpy scipy statsmodels playwright pillow pytest aiohttp
           done
           "$RUNNER_TEMP/notebook-env/bin/python" -m playwright install --with-deps chromium
       - name: Verify offline HTML from the installed wheel

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/CHANGELOG.md

@@ -5,6 +5,36 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.5.0] - 2026-09-25
+
+### Added
+
+- Compose selection conditions in `gs.when()` with `and`, `or`, and `not`,
+  endpoint projections, and named predicate references. Nested selection
+  handles retain their empty-selection behavior.
+- Add PISA squid and interaction-matrix gallery examples adapted from the
+  official GenomeSpy specifications, with endpoint brushing, conditional link
+  highlighting, and zoom-dependent cell labels.
+
+### Changed
+
+- Reorganize the gallery into 13 categories, separating regulatory model
+  interpretation, read alignments and RNA splicing, sequences and alignments,
+  and interaction examples from the broader browser, annotation, and basic groups.
+- Upgrade GenomeSpy Core, controls, and Inspector from 0.88.1 to 0.89.0.
+  Regenerate support for 2D displacement, bidirectional arrows, debounced
+  expression parameters and transforms, composed selection predicates, and
+  `tickStep` expressions.
+- Upstream interval brushes now use half-open boundaries. View-level scale
+  declarations require explicit `axes` settings to create axes when no
+  positional encoding supplies them.
+
+### Fixed
+
+- Preserve explicitly wrapped `ExprParameter` declarations after upstream
+  split expression parameters into plain, transitioned, and debounced variants.
+- Refresh the bundled runtime build for the relocated upstream font license.
+
 ## [0.4.0] - 2026-09-18
 
 ### Added
@@ -96,6 +126,7 @@ First public alpha release, targeting GenomeSpy Core 0.87.0.
 - Packaged example datasets, documentation, tutorials, and an interactive
   visualization gallery.
 
+[0.5.0]: https://github.com/genome-spy/genome-spy-python/compare/v0.4.0...v0.5.0
 [0.4.0]: https://github.com/genome-spy/genome-spy-python/compare/v0.3.0...v0.4.0
 [0.3.0]: https://github.com/genome-spy/genome-spy-python/compare/v0.2.0...v0.3.0
 [0.2.0]: https://github.com/genome-spy/genome-spy-python/compare/v0.1.0...v0.2.0

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: genome-spy-python
-Version: 0.4.0
+Version: 0.5.0
 Summary: genome-spy-python is a declarative genomics visualization library for Python, built on top of the genome-spy JSON specification.
 Project-URL: Homepage, https://github.com/genome-spy/genome-spy-python
 Project-URL: Documentation, https://genomespy.app/genome-spy-python/

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/_ext/genomespy_gallery.py

@@ -158,6 +158,11 @@ GALLERY_CARD_LABELS = {
         "Zoom-adaptive allele contributions",
         "SPI1 binding-QTL data",
     ),
+    "pisa_squid": ("PISA squid plot", "Drosophila sog enhancer · dm6"),
+    "pisa_interaction_matrix": (
+        "PISA interaction matrix",
+        "Drosophila sog enhancer · dm6",
+    ),
     "cytobands": ("Chromosome ideogram", "Human cytobands · hg38"),
     "copy_number": (
         "Allele-specific copy-number profile",

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/airway_ma_plot.py

@@ -12,7 +12,7 @@ from genome_spy.datasets._airway import airway_differential_expression
 from genome_spy.schema import Scale
 
 META = {
-    "category": "Volcano and MA plots",
+    "category": "Differential analysis",
     "order": 11,
     "height": 420,
     "max_width": 760,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/airway_volcano_plot.py

@@ -12,7 +12,7 @@ from genome_spy.datasets._airway import airway_differential_expression
 from genome_spy.schema import Scale
 
 META = {
-    "category": "Volcano and MA plots",
+    "category": "Differential analysis",
     "order": 10,
     "height": 420,
     "max_width": 760,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/bam_read_alignments.py

@@ -8,7 +8,7 @@ from __future__ import annotations
 import genome_spy as gs
 
 META = {
-    "category": "Genome browser tracks",
+    "category": "Read alignments and RNA splicing",
     "order": 26,
     "height": 600,
     "max_width": 980,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/bam_read_pileup.py

@@ -5,7 +5,7 @@ Load a genomic window from an indexed BAM file and stack its reads by strand.
 
 import genome_spy as gs
 
-META = {"category": "Genome browser tracks", "order": 25, "height": 520}
+META = {"category": "Read alignments and RNA splicing", "order": 25, "height": 520}
 
 # Change the space between read rows without reloading the data.
 lane_height = gs.param(

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/bigbed_ccre_track.py

@@ -9,7 +9,7 @@ from __future__ import annotations
 import genome_spy as gs
 
 META = {
-    "category": "Reference annotation tracks",
+    "category": "Genome annotations",
     "order": 18,
     "height": 180,
     "max_width": 920,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/composing_genome_browser.py

@@ -7,7 +7,7 @@ are imported by URL and aligned under a parent-owned genomic scale and axis.
 import genome_spy as gs
 
 META = {
-    "category": "Genome browser tracks",
+    "category": "Multi-track genome browsers",
     "order": 38,
     "height": 650,
     "max_width": 980,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/coverage_pileup.py

@@ -8,7 +8,7 @@ import pandas as pd
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 31, "height": 420}
+META = {"category": "Basic charts and composition", "order": 31, "height": 420}
 
 data = pd.DataFrame({"start": np.arange(1, 100)})
 

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/cytobands.py

@@ -10,7 +10,7 @@ from __future__ import annotations
 import genome_spy as gs
 
 META = {
-    "category": "Reference annotation tracks",
+    "category": "Genome annotations",
     "order": 5,
     "height": 120,
     "max_width": 920,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/diverging_bars.py

@@ -8,7 +8,7 @@ import pandas as pd
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 30, "height": 340}
+META = {"category": "Basic charts and composition", "order": 30, "height": 340}
 
 data = pd.DataFrame({"x": np.arange(60)})
 chart = (

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/dynseq_adaptive_bqtl.py

@@ -7,7 +7,7 @@ letters to labeled bars as the reader zooms in.
 import genome_spy as gs
 
 META = {
-    "category": "Genome browser tracks",
+    "category": "Regulatory model interpretation",
     "order": 35,
     "height": 300,
     "max_width": 980,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/dynseq_bqtl.py

@@ -7,7 +7,7 @@ over the same base-resolution locus.
 import genome_spy as gs
 
 META = {
-    "category": "Genome browser tracks",
+    "category": "Regulatory model interpretation",
     "order": 34,
     "height": 300,
     "max_width": 980,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/genome_tracks.py

@@ -10,7 +10,7 @@ from __future__ import annotations
 import genome_spy as gs
 
 META = {
-    "category": "Genome browser tracks",
+    "category": "Multi-track genome browsers",
     "order": 10,
     "height": 250,
     "max_width": 920,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/geometric_zoom.py

@@ -8,7 +8,7 @@ import pandas as pd
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 32, "height": 360}
+META = {"category": "Interaction and exploration", "order": 32, "height": 360}
 
 # A fixed seed keeps the noisy wave the same each time.
 rng = np.random.default_rng(42)

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/gff3_gene_annotations.py

@@ -10,7 +10,7 @@ from __future__ import annotations
 import genome_spy as gs
 
 META = {
-    "category": "Reference annotation tracks",
+    "category": "Genome annotations",
     "order": 15,
     "height": 430,
     "max_width": 920,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/heatmap_with_text.py

@@ -8,7 +8,7 @@ import pandas as pd
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 25, "height": 480}
+META = {"category": "Interaction and exploration", "order": 25, "height": 480}
 
 # Create one row for each cell in a 200 × 200 grid.
 grid = pd.DataFrame({"i": np.arange(40000)})

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/independent_scales.py

@@ -5,7 +5,7 @@ Overlay probe measurements and segment means with separate vertical axes.
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 28, "height": 360}
+META = {"category": "Basic charts and composition", "order": 28, "height": 360}
 
 # Keep the upstream tables remote, rather than embedding them in the spec.
 probes = gs.Data(url="https://genomespy.app/docs/data/cnv_chr19_raw.tsv")

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/indexed_fasta_sequence.py

@@ -9,7 +9,7 @@ from __future__ import annotations
 import genome_spy as gs
 
 META = {
-    "category": "Reference annotation tracks",
+    "category": "Sequences, alignments, and logos",
     "order": 22,
     "height": 180,
     "max_width": 920,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/layered_lollipop.py

@@ -8,7 +8,7 @@ import pandas as pd
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 27, "height": 360}
+META = {"category": "Basic charts and composition", "order": 27, "height": 360}
 
 # Generate regularly spaced positions along a sine wave.
 data = pd.DataFrame({"x": np.arange(0, 6.284, 0.39269908169)})

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/link_mark.py

@@ -8,7 +8,7 @@ import genome_spy as gs
 from genome_spy.datasets._grammar import link_data
 
 META = {
-    "category": "Basics",
+    "category": "Basic charts and composition",
     "order": 40,
     "height": 300,
 }

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/multiple_sequence_alignment.py

@@ -8,7 +8,7 @@ import genome_spy as gs
 from genome_spy.schema import Scale
 
 META = {
-    "category": "Reference annotation tracks",
+    "category": "Sequences, alignments, and logos",
     "order": 28,
     "height": 440,
     "max_width": 980,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/p53_sequence_comparison.py

@@ -9,7 +9,7 @@ import genome_spy as gs
 from genome_spy.datasets import load_dataset
 
 META = {
-    "category": "Reference annotation tracks",
+    "category": "Sequences, alignments, and logos",
     "order": 29,
     "height": 850,
     "max_width": 1000,

{genome_spy_python-0.4.0 → genome_spy_python-0.5.0}/docs/examples/penguin_brush.py

@@ -5,7 +5,7 @@ Select penguins in a scatter plot and count the selection by species and sex.
 
 import genome_spy as gs
 
-META = {"category": "Basics", "order": 33, "height": 460}
+META = {"category": "Interaction and exploration", "order": 33, "height": 460}
 
 data = gs.Data(
     url="https://cdn.jsdelivr.net/npm/vega-datasets@2.9.0/data/penguins.json"

genome_spy_python-0.5.0/docs/examples/pisa_interaction_matrix.md

@@ -0,0 +1,48 @@
+Rows show ATAC-seq output positions and columns show input bases around the
+*Drosophila sog* enhancer, following Figure 2d of McAnany et al. Each cell's
+color encodes the signed PISA effect. Accessibility and contribution-score
+margin tracks share the corresponding output and input coordinates.
+
+## What to notice
+
+Positive effects are red and negative effects are blue. Pink and green mark
+values beyond the central diverging scale. The dashed diagonal identifies
+equal input and output coordinates; the pointer ruler helps trace rows and
+columns through the overview. Motif intervals sit near the matrix's bottom edge.
+
+Pan and zoom in both dimensions. Numeric cell values appear when cells are
+large enough to read, and the ruler fades away. The contribution track changes
+from bars to base-colored sequence letters as you zoom in.
+
+## How the chart is built
+
+Python authors a three-cell `gs.concat(..., columns=2)` grid: matrix, right-hand
+accessibility track, and bottom contribution track. Shared index scales align
+each margin with the matrix; each margin's signal scale is excluded from the
+shared genomic resolution.
+
+The example references prepared remote Parquet tables without loading or
+processing them in Python. GenomeSpy loads the tables and executes all
+declarative transforms in the browser. Reactive parameters measure the visible
+domain spans. A collected branch filters labels to stable 10-by-15-base tiles
+intersecting the viewport, and only when cells are readable. The full matrix
+stays visible while this smaller text layer changes. This example uses
+expression parameters rather than selection conditions, so it does not need
+`gs.when()`.
+
+See the [PISA squid plot](pisa_squid) for linked endpoint brushing and the
+[official GenomeSpy matrix example](https://genomespy.app/docs/examples/genomic-data/bpreveal-pisa-matrix/)
+for the original JSON specification.
+
+:::{admonition} Data use and provenance
+:class: note
+
+This example uses a Parquet extract of the dm6 *sog* locus from the
+[supporting data](https://doi.org/10.5281/zenodo.20318019) for McAnany et al.,
+[*Positional interpretation of cis-regulatory code and nucleosome organization
+with deep learning models*](https://doi.org/10.1038/s41467-026-74807-1), prepared
+with the [GenomeSpy recipe](https://github.com/genome-spy/genomespy-dataset-recipes/tree/main/recipes/bpreveal-pisa).
+The extract is distributed under [GPL-2.0-or-later](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html);
+the accessibility model's training data are GEO accession
+[GSE218852](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218852).
+:::