openms-insight 0.1.0__tar.gz

openms_insight-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Testing
+.coverage
+htmlcov/
+.pytest_cache/
+.mypy_cache/
+
+# Jupyter
+.ipynb_checkpoints/
+
+# Component save files
+*.svcomp
+
+# Node.js
+node_modules/
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Vue/Vite build output
+js-component/dist/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Logs
+*.log

openms_insight-0.1.0/LICENSE

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+--------------------------------------------------------------------------
+                  OpenMS -- Open-Source Mass Spectrometry
+--------------------------------------------------------------------------
+Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
+ETH Zurich, and Freie Universitaet Berlin 2002-present.
+
+This software is released under a three-clause BSD license:
+ * 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 any author or any participating institution
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+For a full list of authors, refer to the git contributions.
+--------------------------------------------------------------------------
+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 ANY OF THE AUTHORS OR THE CONTRIBUTING
+INSTITUTIONS 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.
+

openms_insight-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: openms-insight
+Version: 0.1.0
+Summary: Interactive visualization components for mass spectrometry data in Streamlit
+Project-URL: Homepage, https://github.com/t0mdavid-m/OpenMS-Insight
+Project-URL: Documentation, https://github.com/t0mdavid-m/OpenMS-Insight#readme
+Project-URL: Repository, https://github.com/t0mdavid-m/OpenMS-Insight
+Project-URL: Issues, https://github.com/t0mdavid-m/OpenMS-Insight/issues
+Author: Kohlbacher Lab
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: mass-spectrometry,openms,plotly,proteomics,streamlit,tabulator,visualization,vue
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.9
+Requires-Dist: pandas>=1.5.0
+Requires-Dist: polars>=0.19.0
+Requires-Dist: streamlit>=1.20.0
+Provides-Extra: dev
+Requires-Dist: black>=23.0.0; extra == 'dev'
+Requires-Dist: mypy>=1.0.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# OpenMS-Insight
+
+[![PyPI version](https://badge.fury.io/py/openms-insight.svg)](https://badge.fury.io/py/openms-insight)
+[![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
+
+Interactive visualization components for mass spectrometry data in Streamlit, backed by Vue.js.
+
+## Features
+
+- **Cross-component selection linking** via shared identifiers
+- **Polars LazyFrame support** for efficient data handling
+- **Automatic disk caching** with config-based invalidation
+- **Table component** (Tabulator.js) with filtering, sorting, go-to, pagination
+- **Line plot component** (Plotly.js) with highlighting, annotations, zoom
+- **Heatmap component** (Plotly scattergl) with multi-resolution downsampling
+- **Sequence view component** for peptide/protein visualization
+
+## Installation
+
+```bash
+pip install openms-insight
+```
+
+## Quick Start
+
+```python
+import streamlit as st
+import polars as pl
+from openms_insight import Table, LinePlot, StateManager
+
+# Create state manager for cross-component linking
+state_manager = StateManager()
+
+# Create a table - clicking a row sets the 'item' selection
+table = Table(
+    cache_id="items_table",
+    data=pl.scan_parquet("items.parquet"),
+    interactivity={'item': 'item_id'},
+    column_definitions=[
+        {'field': 'item_id', 'title': 'ID', 'sorter': 'number'},
+        {'field': 'name', 'title': 'Name'},
+    ],
+)
+table(state_manager=state_manager)
+
+# Create a linked plot - filters by the selected 'item'
+plot = LinePlot(
+    cache_id="values_plot",
+    data=pl.scan_parquet("values.parquet"),
+    filters={'item': 'item_id'},
+    x_column='x',
+    y_column='y',
+)
+plot(state_manager=state_manager)
+```
+
+## Cross-Component Linking
+
+Components communicate through **identifiers** using two mechanisms:
+
+- **`filters`**: INPUT - filter this component's data by the selection
+- **`interactivity`**: OUTPUT - set a selection when user clicks
+
+```python
+# Master table: no filters, sets 'spectrum' on click
+master = Table(
+    cache_id="spectra",
+    data=spectra_data,
+    interactivity={'spectrum': 'scan_id'},  # Click -> sets spectrum=scan_id
+)
+
+# Detail table: filters by 'spectrum', sets 'peak' on click
+detail = Table(
+    cache_id="peaks",
+    data=peaks_data,
+    filters={'spectrum': 'scan_id'},        # Filters where scan_id = selected spectrum
+    interactivity={'peak': 'peak_id'},      # Click -> sets peak=peak_id
+)
+
+# Plot: filters by 'spectrum', highlights selected 'peak'
+plot = LinePlot(
+    cache_id="plot",
+    data=peaks_data,
+    filters={'spectrum': 'scan_id'},
+    interactivity={'peak': 'peak_id'},
+    x_column='mass',
+    y_column='intensity',
+)
+```
+
+---
+
+## Components
+
+### Table
+
+Interactive table using Tabulator.js with filtering dialogs, sorting, pagination, and CSV export.
+
+```python
+Table(
+    cache_id="spectra_table",
+    data=pl.scan_parquet("spectra.parquet"),
+    interactivity={'spectrum': 'scan_id'},
+    column_definitions=[
+        {'field': 'scan_id', 'title': 'Scan', 'sorter': 'number'},
+        {'field': 'rt', 'title': 'RT (min)', 'sorter': 'number', 'hozAlign': 'right'},
+        {'field': 'precursor_mz', 'title': 'm/z', 'sorter': 'number'},
+    ],
+    index_field='scan_id',
+    go_to_fields=['scan_id'],
+    default_row=0,
+    pagination=True,
+    page_size=50,
+)
+```
+
+### LinePlot
+
+Stick-style line plot using Plotly.js for mass spectra visualization.
+
+```python
+LinePlot(
+    cache_id="spectrum_plot",
+    data=pl.scan_parquet("peaks.parquet"),
+    filters={'spectrum': 'scan_id'},
+    interactivity={'peak': 'peak_id'},
+    x_column='mass',
+    y_column='intensity',
+    highlight_column='is_annotated',
+    annotation_column='ion_label',
+    title="MS/MS Spectrum",
+    x_label="m/z",
+    y_label="Intensity",
+)
+```
+
+### Heatmap
+
+2D scatter heatmap using Plotly scattergl with multi-resolution downsampling for large datasets (millions of points).
+
+```python
+Heatmap(
+    cache_id="peaks_heatmap",
+    data=pl.scan_parquet("all_peaks.parquet"),
+    x_column='retention_time',
+    y_column='mass',
+    intensity_column='intensity',
+    interactivity={'spectrum': 'scan_id', 'peak': 'peak_id'},
+    min_points=30000,
+    title="Peak Map",
+    x_label="Retention Time (min)",
+    y_label="m/z",
+)
+```
+
+### SequenceView
+
+Peptide/protein sequence visualization with fragment ion matching.
+
+```python
+SequenceView(
+    cache_id="peptide_view",
+    sequence="PEPTIDEK",
+    observed_masses=[147.1, 244.2, 359.3, 456.4],
+    peak_ids=[0, 1, 2, 3],
+    precursor_mass=944.5,
+    interactivity={'peak': 'peak_id'},
+    title="Fragment Coverage",
+)
+```
+
+---
+
+## Shared Component Arguments
+
+All components accept these common arguments:
+
+| Argument | Type | Default | Description |
+|----------|------|---------|-------------|
+| `cache_id` | `str` | **Required** | Unique identifier for disk cache |
+| `data` | `pl.LazyFrame` | `None` | Polars LazyFrame with source data |
+| `filters` | `Dict[str, str]` | `None` | Map identifier -> column for filtering |
+| `interactivity` | `Dict[str, str]` | `None` | Map identifier -> column for click actions |
+| `cache_path` | `str` | `"."` | Base directory for cache storage |
+
+## Rendering
+
+All components are callable. Pass a `StateManager` to enable cross-component linking:
+
+```python
+from openms_insight import StateManager
+
+state_manager = StateManager()
+
+table(state_manager=state_manager, height=300)
+plot(state_manager=state_manager, height=400)
+```
+
+---
+
+## Development
+
+### Building the Vue Component
+
+```bash
+cd js-component
+npm install
+npm run build
+```
+
+### Development Mode
+
+```bash
+cd js-component
+npm run dev
+
+# In another terminal:
+export SVC_DEV_MODE=true
+export SVC_DEV_URL=http://localhost:5173
+streamlit run app.py
+```

openms_insight-0.1.0/README.md

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+# OpenMS-Insight
+
+[![PyPI version](https://badge.fury.io/py/openms-insight.svg)](https://badge.fury.io/py/openms-insight)
+[![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
+
+Interactive visualization components for mass spectrometry data in Streamlit, backed by Vue.js.
+
+## Features
+
+- **Cross-component selection linking** via shared identifiers
+- **Polars LazyFrame support** for efficient data handling
+- **Automatic disk caching** with config-based invalidation
+- **Table component** (Tabulator.js) with filtering, sorting, go-to, pagination
+- **Line plot component** (Plotly.js) with highlighting, annotations, zoom
+- **Heatmap component** (Plotly scattergl) with multi-resolution downsampling
+- **Sequence view component** for peptide/protein visualization
+
+## Installation
+
+```bash
+pip install openms-insight
+```
+
+## Quick Start
+
+```python
+import streamlit as st
+import polars as pl
+from openms_insight import Table, LinePlot, StateManager
+
+# Create state manager for cross-component linking
+state_manager = StateManager()
+
+# Create a table - clicking a row sets the 'item' selection
+table = Table(
+    cache_id="items_table",
+    data=pl.scan_parquet("items.parquet"),
+    interactivity={'item': 'item_id'},
+    column_definitions=[
+        {'field': 'item_id', 'title': 'ID', 'sorter': 'number'},
+        {'field': 'name', 'title': 'Name'},
+    ],
+)
+table(state_manager=state_manager)
+
+# Create a linked plot - filters by the selected 'item'
+plot = LinePlot(
+    cache_id="values_plot",
+    data=pl.scan_parquet("values.parquet"),
+    filters={'item': 'item_id'},
+    x_column='x',
+    y_column='y',
+)
+plot(state_manager=state_manager)
+```
+
+## Cross-Component Linking
+
+Components communicate through **identifiers** using two mechanisms:
+
+- **`filters`**: INPUT - filter this component's data by the selection
+- **`interactivity`**: OUTPUT - set a selection when user clicks
+
+```python
+# Master table: no filters, sets 'spectrum' on click
+master = Table(
+    cache_id="spectra",
+    data=spectra_data,
+    interactivity={'spectrum': 'scan_id'},  # Click -> sets spectrum=scan_id
+)
+
+# Detail table: filters by 'spectrum', sets 'peak' on click
+detail = Table(
+    cache_id="peaks",
+    data=peaks_data,
+    filters={'spectrum': 'scan_id'},        # Filters where scan_id = selected spectrum
+    interactivity={'peak': 'peak_id'},      # Click -> sets peak=peak_id
+)
+
+# Plot: filters by 'spectrum', highlights selected 'peak'
+plot = LinePlot(
+    cache_id="plot",
+    data=peaks_data,
+    filters={'spectrum': 'scan_id'},
+    interactivity={'peak': 'peak_id'},
+    x_column='mass',
+    y_column='intensity',
+)
+```
+
+---
+
+## Components
+
+### Table
+
+Interactive table using Tabulator.js with filtering dialogs, sorting, pagination, and CSV export.
+
+```python
+Table(
+    cache_id="spectra_table",
+    data=pl.scan_parquet("spectra.parquet"),
+    interactivity={'spectrum': 'scan_id'},
+    column_definitions=[
+        {'field': 'scan_id', 'title': 'Scan', 'sorter': 'number'},
+        {'field': 'rt', 'title': 'RT (min)', 'sorter': 'number', 'hozAlign': 'right'},
+        {'field': 'precursor_mz', 'title': 'm/z', 'sorter': 'number'},
+    ],
+    index_field='scan_id',
+    go_to_fields=['scan_id'],
+    default_row=0,
+    pagination=True,
+    page_size=50,
+)
+```
+
+### LinePlot
+
+Stick-style line plot using Plotly.js for mass spectra visualization.
+
+```python
+LinePlot(
+    cache_id="spectrum_plot",
+    data=pl.scan_parquet("peaks.parquet"),
+    filters={'spectrum': 'scan_id'},
+    interactivity={'peak': 'peak_id'},
+    x_column='mass',
+    y_column='intensity',
+    highlight_column='is_annotated',
+    annotation_column='ion_label',
+    title="MS/MS Spectrum",
+    x_label="m/z",
+    y_label="Intensity",
+)
+```
+
+### Heatmap
+
+2D scatter heatmap using Plotly scattergl with multi-resolution downsampling for large datasets (millions of points).
+
+```python
+Heatmap(
+    cache_id="peaks_heatmap",
+    data=pl.scan_parquet("all_peaks.parquet"),
+    x_column='retention_time',
+    y_column='mass',
+    intensity_column='intensity',
+    interactivity={'spectrum': 'scan_id', 'peak': 'peak_id'},
+    min_points=30000,
+    title="Peak Map",
+    x_label="Retention Time (min)",
+    y_label="m/z",
+)
+```
+
+### SequenceView
+
+Peptide/protein sequence visualization with fragment ion matching.
+
+```python
+SequenceView(
+    cache_id="peptide_view",
+    sequence="PEPTIDEK",
+    observed_masses=[147.1, 244.2, 359.3, 456.4],
+    peak_ids=[0, 1, 2, 3],
+    precursor_mass=944.5,
+    interactivity={'peak': 'peak_id'},
+    title="Fragment Coverage",
+)
+```
+
+---
+
+## Shared Component Arguments
+
+All components accept these common arguments:
+
+| Argument | Type | Default | Description |
+|----------|------|---------|-------------|
+| `cache_id` | `str` | **Required** | Unique identifier for disk cache |
+| `data` | `pl.LazyFrame` | `None` | Polars LazyFrame with source data |
+| `filters` | `Dict[str, str]` | `None` | Map identifier -> column for filtering |
+| `interactivity` | `Dict[str, str]` | `None` | Map identifier -> column for click actions |
+| `cache_path` | `str` | `"."` | Base directory for cache storage |
+
+## Rendering
+
+All components are callable. Pass a `StateManager` to enable cross-component linking:
+
+```python
+from openms_insight import StateManager
+
+state_manager = StateManager()
+
+table(state_manager=state_manager, height=300)
+plot(state_manager=state_manager, height=400)
+```
+
+---
+
+## Development
+
+### Building the Vue Component
+
+```bash
+cd js-component
+npm install
+npm run build
+```
+
+### Development Mode
+
+```bash
+cd js-component
+npm run dev
+
+# In another terminal:
+export SVC_DEV_MODE=true
+export SVC_DEV_URL=http://localhost:5173
+streamlit run app.py
+```

openms_insight-0.1.0/openms_insight/__init__.py

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+"""
+Streamlit Vue Components - Interactive visualization components for Streamlit.
+
+This package provides reusable, interactive Streamlit components backed by Vue.js
+visualizations with cross-component selection state management.
+"""
+
+from .core.base import BaseComponent
+from .core.state import StateManager
+from .core.registry import register_component, get_component_class
+from .core.cache import CacheMissError
+
+from .components.table import Table
+from .components.lineplot import LinePlot
+from .components.heatmap import Heatmap
+from .components.sequenceview import SequenceView
+
+__version__ = "0.1.0"
+
+__all__ = [
+    # Core
+    "BaseComponent",
+    "StateManager",
+    "register_component",
+    "get_component_class",
+    "CacheMissError",
+    # Components
+    "Table",
+    "LinePlot",
+    "Heatmap",
+    "SequenceView",
+]

openms_insight-0.1.0/openms_insight/components/__init__.py

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+"""Visualization components."""
+
+from .table import Table
+from .lineplot import LinePlot
+from .heatmap import Heatmap
+
+__all__ = [
+    "Table",
+    "LinePlot",
+    "Heatmap",
+]