biopro-sdk 1.0.0__tar.gz

biopro_sdk-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: biopro-sdk
+Version: 1.0.0
+Summary: Software Development Kit and CLI for BioPro desktop plugins.
+Author: Kalaimaran Balasothy
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: cryptography>=41.0.0
+Requires-Dist: PyQt6>=6.5.0
+
+# 🔌 BioPro SDK
+
+The Software Development Kit (SDK) and Command-Line Interface (CLI) for building, validating, and signing plugins for the **BioPro** desktop scientific suite.
+
+---
+
+## 🚀 Key Features
+
+- **Decoupled Architecture**: Build and test PyQt6-based scientific plugins independently of the main desktop app.
+- **Fail-Safe Dynamic Theme Fallbacks**: Visual components automatically load custom HSL-tailored colors when running standalone inside CI/CD test gates or external visualizers.
+- **Merkle-Tree Cryptographic Integrity**: Built-in Ed25519 signing and verification tools to secure user environments against remote execution and tampering.
+- **PyPI-Ready Packaging**: Complete declarative `pyproject.toml` config, built to publish natively under the `biopro-sdk` package.
+
+---
+
+## 🛠️ Installation
+
+Install the SDK directly into your plugin's virtual environment:
+
+```bash
+pip install biopro-sdk
+```
+
+*(Or during development, install in editable mode):*
+```bash
+git clone https://github.com/KalaimaranB/BioPro-SDK.git
+cd BioPro-SDK
+pip install -e .
+```
+
+---
+
+## 📦 Creating a Custom BioPro Plugin
+
+To build a valid plugin, implement the `BioProPlugin` interface and declare your entrypoints.
+
+### 1. `manifest.json`
+Every plugin must include a manifest file in its root directory:
+```json
+{
+  "id": "my_custom_plugin",
+  "name": "My Custom Plugin",
+  "version": "1.0.0",
+  "author": "Dr. Kalaimaran",
+  "description": "High-performance scientific analysis plugin.",
+  "category": "analysis",
+  "min_core_version": "1.0.0",
+  "entrypoint": "plugin:MyPluginClass"
+}
+```
+
+### 2. `plugin.py`
+```python
+from PyQt6.QtWidgets import QWidget, QVBoxLayout, QLabel
+from biopro_sdk.core.interfaces import BioProPlugin
+from biopro_sdk.ui import PrimaryButton
+
+class MyPluginClass(BioProPlugin):
+    """A professional-grade BioPro plugin."""
+
+    def initialize(self) -> None:
+        self.logger.info("Initializing custom plugin...")
+
+    def create_panel(self, parent=None) -> QWidget:
+        panel = QWidget(parent)
+        layout = QVBoxLayout(panel)
+        
+        title = QLabel("Welcome to Custom Analysis Panel")
+        btn = PrimaryButton("Execute Step")
+        
+        layout.addWidget(title)
+        layout.addWidget(btn)
+        return panel
+```
+
+---
+
+## 🛡️ Cryptographic Trust Architecture
+
+BioPro implements a professional-grade **Chain of Trust** to protect laboratory environments:
+
+```
+[ Root Authority ] (Hardcoded Core Key)
+       │
+       ▼ (signs)
+[ Developer Key ] (Dev Certificate)
+       │
+       ▼ (signs)
+[ Plugin Manifest ] (Ed25519 Signature + Merkle-Tree Hashes)
+```
+
+### 1. Generate Your Cryptographic Identity
+```bash
+biopro-sdk setup-identity
+```
+- Local Private Key: `~/.biopro/dev_private_key.pem`
+- Developer Certificate: `~/.biopro/dev_cert.bin`
+
+### 2. Sign Your Plugin payload
+Calculates Merkle-hashes for all your files recursively, excludes development directories automatically, updates `manifest.json`, and writes `signature.bin`:
+```bash
+biopro-sdk sign <path/to/plugin>
+```
+
+### 3. Modularity Compliance Check
+Verify your plugin matches QA and security standards:
+```bash
+biopro-sdk evaluate <path/to/plugin>
+```
+
+---
+
+## 📘 Standalone Preview Support
+Since the SDK decouples all theme components from the desktop core using robust try-except fallbacks, you can instantiate and preview components standalone in development:
+
+```python
+import sys
+from PyQt6.QtWidgets import QApplication
+from biopro_sdk.ui import PrimaryButton, WizardPanel
+
+app = QApplication(sys.argv)
+widget = WizardPanel()  # Renders beautifully even without the main app!
+widget.show()
+sys.exit(app.exec())
+```
+
+---
+
+## 📄 License
+This project is licensed under the MIT License.

biopro_sdk-1.0.0/README.md

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+# 🔌 BioPro SDK
+
+The Software Development Kit (SDK) and Command-Line Interface (CLI) for building, validating, and signing plugins for the **BioPro** desktop scientific suite.
+
+---
+
+## 🚀 Key Features
+
+- **Decoupled Architecture**: Build and test PyQt6-based scientific plugins independently of the main desktop app.
+- **Fail-Safe Dynamic Theme Fallbacks**: Visual components automatically load custom HSL-tailored colors when running standalone inside CI/CD test gates or external visualizers.
+- **Merkle-Tree Cryptographic Integrity**: Built-in Ed25519 signing and verification tools to secure user environments against remote execution and tampering.
+- **PyPI-Ready Packaging**: Complete declarative `pyproject.toml` config, built to publish natively under the `biopro-sdk` package.
+
+---
+
+## 🛠️ Installation
+
+Install the SDK directly into your plugin's virtual environment:
+
+```bash
+pip install biopro-sdk
+```
+
+*(Or during development, install in editable mode):*
+```bash
+git clone https://github.com/KalaimaranB/BioPro-SDK.git
+cd BioPro-SDK
+pip install -e .
+```
+
+---
+
+## 📦 Creating a Custom BioPro Plugin
+
+To build a valid plugin, implement the `BioProPlugin` interface and declare your entrypoints.
+
+### 1. `manifest.json`
+Every plugin must include a manifest file in its root directory:
+```json
+{
+  "id": "my_custom_plugin",
+  "name": "My Custom Plugin",
+  "version": "1.0.0",
+  "author": "Dr. Kalaimaran",
+  "description": "High-performance scientific analysis plugin.",
+  "category": "analysis",
+  "min_core_version": "1.0.0",
+  "entrypoint": "plugin:MyPluginClass"
+}
+```
+
+### 2. `plugin.py`
+```python
+from PyQt6.QtWidgets import QWidget, QVBoxLayout, QLabel
+from biopro_sdk.core.interfaces import BioProPlugin
+from biopro_sdk.ui import PrimaryButton
+
+class MyPluginClass(BioProPlugin):
+    """A professional-grade BioPro plugin."""
+
+    def initialize(self) -> None:
+        self.logger.info("Initializing custom plugin...")
+
+    def create_panel(self, parent=None) -> QWidget:
+        panel = QWidget(parent)
+        layout = QVBoxLayout(panel)
+        
+        title = QLabel("Welcome to Custom Analysis Panel")
+        btn = PrimaryButton("Execute Step")
+        
+        layout.addWidget(title)
+        layout.addWidget(btn)
+        return panel
+```
+
+---
+
+## 🛡️ Cryptographic Trust Architecture
+
+BioPro implements a professional-grade **Chain of Trust** to protect laboratory environments:
+
+```
+[ Root Authority ] (Hardcoded Core Key)
+       │
+       ▼ (signs)
+[ Developer Key ] (Dev Certificate)
+       │
+       ▼ (signs)
+[ Plugin Manifest ] (Ed25519 Signature + Merkle-Tree Hashes)
+```
+
+### 1. Generate Your Cryptographic Identity
+```bash
+biopro-sdk setup-identity
+```
+- Local Private Key: `~/.biopro/dev_private_key.pem`
+- Developer Certificate: `~/.biopro/dev_cert.bin`
+
+### 2. Sign Your Plugin payload
+Calculates Merkle-hashes for all your files recursively, excludes development directories automatically, updates `manifest.json`, and writes `signature.bin`:
+```bash
+biopro-sdk sign <path/to/plugin>
+```
+
+### 3. Modularity Compliance Check
+Verify your plugin matches QA and security standards:
+```bash
+biopro-sdk evaluate <path/to/plugin>
+```
+
+---
+
+## 📘 Standalone Preview Support
+Since the SDK decouples all theme components from the desktop core using robust try-except fallbacks, you can instantiate and preview components standalone in development:
+
+```python
+import sys
+from PyQt6.QtWidgets import QApplication
+from biopro_sdk.ui import PrimaryButton, WizardPanel
+
+app = QApplication(sys.argv)
+widget = WizardPanel()  # Renders beautifully even without the main app!
+widget.show()
+sys.exit(app.exec())
+```
+
+---
+
+## 📄 License
+This project is licensed under the MIT License.

biopro_sdk-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "biopro-sdk"
+version = "1.0.0"
+description = "Software Development Kit and CLI for BioPro desktop plugins."
+readme = "README.md"
+requires-python = ">=3.11"
+authors = [
+    { name = "Kalaimaran Balasothy" }
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "cryptography>=41.0.0",
+    "PyQt6>=6.5.0",
+]
+
+[project.scripts]
+biopro-sdk = "biopro_sdk.sdk_cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]

biopro_sdk-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

biopro_sdk-1.0.0/src/biopro_sdk/__init__.py

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+"""BioPro SDK — Complete plugin development framework.
+
+Provides everything needed to build plugins:
+
+Core Components:
+    - PluginBase: Main plugin class to inherit from
+    - PluginState: State management with undo/redo
+    - PluginSignals: Standard signals for communication
+    - AnalysisBase: Abstract analysis logic class
+    - AnalysisWorker: Background worker for threads
+
+UI Components:
+    - PrimaryButton, SecondaryButton, DangerButton: Semantic buttons
+    - ModuleCard, HeaderLabel: Styled components
+    - WizardStep, WizardPanel: Multi-step interface framework
+
+Utilities:
+    - Dialogs: File, message, and input dialogs
+    - I/O: JSON and configuration management
+    - Validation: Input validation helpers
+
+Contrib (Optional):
+    - Image utilities: Common image processing functions
+
+Example:
+    >>> from biopro_sdk.core import PluginBase, PluginState
+    >>> from biopro_sdk.ui import PrimaryButton, WizardPanel
+    >>> from biopro_sdk.utils import show_error
+    >>>
+    >>> class MyState(PluginState):
+    ...     image_path: str = ""
+    ...
+    >>> class MyPlugin(PluginBase):
+    ...     def __init__(self, plugin_id: str):
+    ...         super().__init__(plugin_id)
+    ...         self.state = MyState()
+    ...
+    ...     def get_state(self) -> PluginState:
+    ...         return self.state
+    ...
+    ...     def set_state(self, state: PluginState) -> None:
+    ...         self.state = state
+"""
+
+from . import contrib, core, ui, utils
+from .core import (
+    AnalysisBase,
+    AnalysisWorker,
+    PluginBase,
+    PluginSignals,
+    PluginState,
+    PreferenceManagerProtocol,
+    diagnostics,
+)
+from .core.ai import AIAssistant, AIServerManager, ai_manager
+from .core.docs import PluginDocumentation, docs_registry
+from .core.events import CentralEventBus
+from .ui import (
+    DangerButton,
+    HeaderLabel,
+    ModuleCard,
+    PrimaryButton,
+    SecondaryButton,
+    StepIndicator,
+    SubtitleLabel,
+    WizardPanel,
+    WizardStep,
+)
+from .utils import (
+    PluginConfig,
+    PluginPreferenceManager,
+    ask_ok_cancel,
+    ask_yes_no,
+    get_directory,
+    get_double,
+    get_image_path,
+    get_number,
+    get_save_path,
+    get_text,
+    load_json,
+    save_json,
+    show_error,
+    show_info,
+    show_warning,
+    validate_directory_exists,
+    validate_file_exists,
+    validate_non_negative,
+    validate_not_empty,
+    validate_positive,
+    validate_value_range,
+)
+
+__all__ = [
+    # Submodules
+    "core",
+    "ui",
+    "utils",
+    "contrib",
+    # Core
+    "PluginBase",
+    "PluginState",
+    "PluginSignals",
+    "AnalysisBase",
+    "AnalysisWorker",
+    "PreferenceManagerProtocol",
+    "CentralEventBus",
+    "PluginDocumentation",
+    "docs_registry",
+    "AIAssistant",
+    "AIServerManager",
+    "ai_manager",
+    # UI
+    "PrimaryButton",
+    "SecondaryButton",
+    "DangerButton",
+    "ModuleCard",
+    "HeaderLabel",
+    "SubtitleLabel",
+    "StepIndicator",
+    "WizardStep",
+    "WizardPanel",
+    # Utils
+    "get_image_path",
+    "get_save_path",
+    "get_directory",
+    "show_info",
+    "show_warning",
+    "show_error",
+    "ask_yes_no",
+    "ask_ok_cancel",
+    "get_text",
+    "get_number",
+    "get_double",
+    "load_json",
+    "save_json",
+    "PluginConfig",
+    "PluginPreferenceManager",
+    "validate_file_exists",
+    "validate_directory_exists",
+    "validate_value_range",
+    "validate_positive",
+    "validate_non_negative",
+    "validate_not_empty",
+    "diagnostics",
+]

biopro_sdk-1.0.0/src/biopro_sdk/contrib/__init__.py

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+"""BioPro SDK Contrib — Optional utilities to support plugin development.
+
+Image utilities for common analysis operations. Use these to keep plugin
+code DRY and focused on domain-specific logic.
+"""
+
+try:
+    from biopro.shared.analysis.image_utils import (
+        adjust_contrast,
+        auto_detect_inversion,
+        crop_to_content,
+        enhance_for_band_detection,
+        invert_image,
+        load_and_convert,
+        rotate_image,
+    )
+except ImportError:
+    # Standalone fallback: raise ImportError only if called, keeping SDK CLI lightweight
+    def _raise_import_error(*args, **kwargs):
+        raise ImportError("This utility requires 'biopro-core' or 'scikit-image' to be installed.")
+    
+    adjust_contrast = _raise_import_error
+    auto_detect_inversion = _raise_import_error
+    crop_to_content = _raise_import_error
+    enhance_for_band_detection = _raise_import_error
+    invert_image = _raise_import_error
+    load_and_convert = _raise_import_error
+    rotate_image = _raise_import_error
+
+__all__ = [
+    "adjust_contrast",
+    "load_and_convert",
+    "auto_detect_inversion",
+    "invert_image",
+    "enhance_for_band_detection",
+    "rotate_image",
+    "crop_to_content",
+]

biopro_sdk-1.0.0/src/biopro_sdk/core/__init__.py

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+"""BioPro SDK Core — Base classes for plugin development.
+
+Provides:
+- PluginSignals: Standard PyQt6 signals for plugin communication
+- PluginState: Base class for serializable plugin state
+- AnalysisBase: Abstract base for analysis logic
+- AnalysisWorker: Background worker for thread execution
+- PluginBase: Main plugin class to inherit from
+"""
+
+try:
+    from biopro.core.diagnostics import diagnostics
+except ImportError:
+    class MockDiagnostics:
+        def report_error(self, message, exception=None, plugin_id=None, fatal=False):
+            import logging
+            logging.getLogger("biopro_sdk.diagnostics").error(f"[{plugin_id or 'System'}] {message}: {exception or ''}")
+    diagnostics = MockDiagnostics()
+
+from .analysis import AnalysisBase, AnalysisWorker
+from .base import PluginBase
+from .interfaces import BioProPlugin
+from .managed_task import FunctionalTask
+from .preferences import PreferenceManagerProtocol
+from .signals import PluginSignals
+from .state import PluginState
+
+__all__ = [
+    "PluginSignals",
+    "PluginState",
+    "AnalysisBase",
+    "AnalysisWorker",
+    "PluginBase",
+    "FunctionalTask",
+    "BioProPlugin",
+    "PreferenceManagerProtocol",
+    "diagnostics",
+]