genome-spy-python 0.1.0__py3-none-any.whl

genome_spy_python-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.5
+Name: genome-spy-python
+Version: 0.1.0
+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/
+Project-URL: Repository, https://github.com/genome-spy/genome-spy-python
+Project-URL: Issues, https://github.com/genome-spy/genome-spy-python/issues
+Author-email: Oskari Lehtonen <oskarilehtonen4@gmail.com>
+License-Expression: MIT AND BSD-3-Clause
+License-File: LICENSE
+License-File: LICENSES/ALTAIR-BSD-3-Clause.txt
+License-File: LICENSES/GALLERY-DATA-MIT.txt
+License-File: THIRD_PARTY_NOTICES.md
+Keywords: anywidget,genome-spy,genomics,jupyter,visualization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Framework :: Jupyter
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.11
+Requires-Dist: anywidget>=0.9.18
+Requires-Dist: jsonschema>=4.26.0
+Requires-Dist: traitlets>=5.14.3
+Provides-Extra: arrow
+Requires-Dist: pyarrow>=18.0.0; extra == 'arrow'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="docs/_static/snaketie.svg" width="180" alt="GenomeSpy for Python logo">
+</p>
+
+<h1 align="center">genome-spy-python</h1>
+
+`genome-spy-python` is a Python interface for
+<a href="https://genomespy.app/" target="_blank" rel="noopener noreferrer">GenomeSpy</a>,
+a grammar for interactive and scalable genomic visualization. It lets Python
+users build GenomeSpy specifications with a declarative, fluent API, serialize
+them to JSON, and display them in Jupyter or Marimo notebooks.
+
+Read the [documentation](https://genomespy.app/genome-spy-python/) for the
+getting-started guide, user guide, examples, and API reference.
+
+<a href="https://altair-viz.github.io/" target="_blank" rel="noopener noreferrer">Altair</a>
+is the project's main source of inspiration. This codebase follows Altair's
+approach of combining schema-backed specification objects with a small
+handwritten Python API for marks, encodings, composition, and rendering. It
+adapts that model to GenomeSpy's genomics-native grammar: locus scales, genomic
+data sources, and coordinated genomic views.
+
+The project is under active development. The current focus is the reusable
+GenomeSpy Core grammar and notebook rendering; GenomeSpy App-specific features
+will come later.
+
+## Installation
+
+The package requires Python 3.11 or newer.
+
+From PyPI:
+
+```bash
+pip install genome-spy-python
+```
+
+From source:
+
+```bash
+pip install uv
+git clone https://github.com/genome-spy/genome-spy-python.git
+cd genome-spy-python
+uv sync
+```
+
+For notebook use, install with Arrow support. This includes PyArrow for
+dataframe transport:
+
+```bash
+pip install "genome-spy-python[arrow]"
+```
+
+See [creating and updating charts in notebooks](docs/user-guide/notebooks.md)
+for supported tables and live updates.
+
+See the [getting-started guide](docs/getting-started.md) for the first example.
+
+## Examples
+
+```python
+import genome_spy as gs
+
+chart = (
+    gs.Chart(
+        [
+            {"x": 1, "y": 4, "group": "A"},
+            {"x": 2, "y": 3, "group": "B"},
+            {"x": 3, "y": 5, "group": "A"},
+        ]
+    )
+    .mark_point(size=80)
+    .encode(
+        x="x:Q",
+        y="y:Q",
+        color="group:N",
+    )
+)
+
+chart
+```
+
+GenomeSpy also has locus-scaled axes for genomic coordinates. This small
+example renders intervals along a region of chromosome 1:
+
+```python
+import genome_spy as gs
+
+intervals = [
+    {"chrom": "chr1", "start": 100, "end": 220, "name": "gene A"},
+    {"chrom": "chr1", "start": 280, "end": 420, "name": "gene B"},
+]
+
+chart = (
+    gs.Chart(intervals)
+    .mark_rect()
+    .encode(
+        x=gs.Locus("chrom", "start"),
+        x2="end:Q",
+        y="name:N",
+        color="name:N",
+    )
+)
+
+chart
+```
+
+Charts can be serialized to a portable GenomeSpy specification or standalone
+HTML:
+
+```python
+chart.to_json()
+chart.save("intervals.html")
+```
+
+### Update data without recreating the chart
+
+For reactive Jupyter or Marimo notebooks, create a widget with an explicitly
+named dataset and replace that dataset as inputs change. The browser keeps the
+existing GenomeSpy instance, so view state such as zoom is preserved.
+
+```python
+chart = (
+    gs.Chart(data={"name": "table"}, datasets={"table": []})
+    .mark_point()
+    .encode(x="x:Q", y="y:Q")
+)
+view = chart.widget()
+
+view.set_dataset("table", updated_dataframe)
+```
+
+See [creating and updating charts in notebooks](docs/user-guide/notebooks.md)
+for the Marimo pattern.
+
+## Contributing
+
+Contributions are welcome. See [CONTRIBUTING.md](CONTRIBUTING.md) for development
+setup, testing, code generation, documentation, gallery, and pull-request
+guidelines.
+
+## References
+
+- <a href="https://genomespy.app/" target="_blank" rel="noopener noreferrer">GenomeSpy</a>
+  — the upstream visualization grammar and JavaScript renderer.
+- <a href="https://altair-viz.github.io/" target="_blank" rel="noopener noreferrer">Altair</a>
+  — a schema-wrapper design reference.
+- <a href="https://gosling-lang.org/" target="_blank" rel="noopener noreferrer">Gos</a>
+  — a related grammar and Python-wrapper design reference for
+  genomics visualization.
+
+Portions of the schema-wrapper implementation and selected tests are adapted
+from Altair under its BSD-3-Clause license. See
+[Third-party notices](THIRD_PARTY_NOTICES.md) for the exact sources and license.

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genome_spy_python-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.32.0
+Root-Is-Purelib: true
+Tag: py3-none-any

genome_spy_python-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Oskari Lehtonen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

genome_spy_python-0.1.0.dist-info/licenses/LICENSES/ALTAIR-BSD-3-Clause.txt

@@ -0,0 +1,27 @@
+Copyright (c) 2015-2025, Vega-Altair Developers
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of vega-altair nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

genome_spy_python-0.1.0.dist-info/licenses/LICENSES/GALLERY-DATA-MIT.txt

@@ -0,0 +1,22 @@
+maftools: Copyright (c) 2018 Anand Mayakonda
+Plotly datasets: Copyright (c) 2019-2024 Plotly Technologies Inc.
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

genome_spy_python-0.1.0.dist-info/licenses/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,42 @@
+# Third-party notices
+
+## Gallery data from maftools and Plotly
+
+`tcga_laml_combined_oncoplot.json.gz` contains prepared TCGA LAML tables from
+maftools revision `015a4cf8c69ba89a55a3fdcea911421509e9a198` (Anand Mayakonda,
+MIT). `p53_sequence_comparison.json.gz` contains p53 sequences and derived
+display tables from Plotly's datasets revision
+`0c447c47b757ad74edecab31f0d72f849d2e67c2` (Plotly Technologies Inc., MIT).
+Source file hashes are retained in the packaged data. The corresponding gallery
+pages describe processing. Copyright notices and terms are included in
+`LICENSES/GALLERY-DATA-MIT.txt`.
+
+## Code adapted from Vega-Altair
+
+Parts of this project are adapted from
+[Vega-Altair](https://github.com/vega/altair), copyright 2015–2025 the
+Vega-Altair Developers, under the BSD-3-Clause license. The complete license
+is in [`LICENSES/ALTAIR-BSD-3-Clause.txt`](LICENSES/ALTAIR-BSD-3-Clause.txt).
+
+The adapted areas are:
+
+- `src/genome_spy/schemapi.py`, a reduced schema-wrapper runtime based on
+  `altair/utils/schemapi.py`;
+- `tools/schemapi/codegen.py`, whose schema-wrapper generation architecture is
+  adapted from Altair's `tools/schemapi/` package and
+  `tools/generate_schema_wrapper.py`;
+- the multifeature penguins and cars strip-plot cases in `tests/test_chart.py`,
+  adapted from Altair's example suite and mark documentation.
+
+Each adapted source location identifies its corresponding upstream source.
+
+## Design references
+
+Altair also informed the separation between generated schema bindings and the
+handwritten chart API, composition operators, channel shorthand, and API
+reference organization. Those areas use project-specific implementations and
+are acknowledged as design references rather than adapted Altair code.
+
+MutGlyph informed the generic scored gene-annotation track used by the
+rainfall and GISTIC examples. The implementation and UCSC-derived data are
+maintained independently in this repository.