AMS-BP 0.4.0__tar.gz → 0.4.22__tar.gz

{ams_bp-0.4.0 → ams_bp-0.4.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.4.0
+Version: 0.4.22
 Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
 Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
 Project-URL: Source code, https://github.com/joemans3/AMS_BP
@@ -63,31 +63,29 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](./src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
 
 ### ***PyPi***
 
-1. Run:
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
 ```bash
 pip install AMS_BP
 ```
 
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -111,10 +109,10 @@ In addition to the CLI and programmatic API, AMS-BP comes with a graphical inter
 ### Main GUI Features
 The GUI provides the following tools from a single interface:
 
-**Create Configuration File** — Launches the visual configuration builder
-**Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
-**Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
-**Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
 ### Launch the GUI
 To start the GUI, run:
@@ -123,23 +121,7 @@ To start the GUI, run:
 
 run_AMS_BP gui
 ```
-#### Configuration Builder
-Clicking "Create Configuration File" opens a template selector where you can choose a preconfigured simulation (with preview images), and then visually edit all configuration options through dedicated tabs.
-
-Each section of the configuration is editable via structured UI forms, with contextual help and validation. Tabs include:
-
-- Global/Cell/Molecule/Condensate/Fluorophore parameters
-- Laser and optical configuration
-- Camera and channel settings
-- Experiment setup (e.g., z-stack vs time-series)
-Once ready, click "Preview Configuration TOML" to inspect the final file, and "Save" to export.
-
-#### Running Simulations from GUI
-Clicking "Run Simulation from Config" lets you select any .toml configuration file. A real-time log viewer shows progress, and outputs are saved in a structured AMS_runs/run_*/ directory.
-
-#### Sharing Logs
-Run into an issue? Use the packge logs button to select the logs corresponding to the simulation you just ran, save them and send them over to us! It will help you diagnose the issue!
-
+For detailed walkthrough see the [GUI Documentation](./src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:

{ams_bp-0.4.0 → ams_bp-0.4.22}/README.md

@@ -37,31 +37,29 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](./src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
 
 ### ***PyPi***
 
-1. Run:
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
 ```bash
 pip install AMS_BP
 ```
 
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -85,10 +83,10 @@ In addition to the CLI and programmatic API, AMS-BP comes with a graphical inter
 ### Main GUI Features
 The GUI provides the following tools from a single interface:
 
-**Create Configuration File** — Launches the visual configuration builder
-**Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
-**Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
-**Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
 ### Launch the GUI
 To start the GUI, run:
@@ -97,23 +95,7 @@ To start the GUI, run:
 
 run_AMS_BP gui
 ```
-#### Configuration Builder
-Clicking "Create Configuration File" opens a template selector where you can choose a preconfigured simulation (with preview images), and then visually edit all configuration options through dedicated tabs.
-
-Each section of the configuration is editable via structured UI forms, with contextual help and validation. Tabs include:
-
-- Global/Cell/Molecule/Condensate/Fluorophore parameters
-- Laser and optical configuration
-- Camera and channel settings
-- Experiment setup (e.g., z-stack vs time-series)
-Once ready, click "Preview Configuration TOML" to inspect the final file, and "Save" to export.
-
-#### Running Simulations from GUI
-Clicking "Run Simulation from Config" lets you select any .toml configuration file. A real-time log viewer shows progress, and outputs are saved in a structured AMS_runs/run_*/ directory.
-
-#### Sharing Logs
-Run into an issue? Use the packge logs button to select the logs corresponding to the simulation you just ran, save them and send them over to us! It will help you diagnose the issue!
-
+For detailed walkthrough see the [GUI Documentation](./src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:

{ams_bp-0.4.0 → ams_bp-0.4.22}/src/AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.4.0"
+__version__ = "0.4.22"

ams_bp-0.4.22/src/AMS_BP/gui/README.md

@@ -0,0 +1,81 @@
+# AMS-BP GUI
+
+The AMS-BP GUI provides a user-friendly interface for constructing and validating configuration files for the AMS-BP fluorescence microscopy simulation framework. It integrates simulation execution, configuration design, log packaging, and data visualization in one cohesive window.
+
+## Overview
+
+This GUI supports:
+
+- A template-based configuration builder for quick setup.
+- A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
+- Interactive help sections for each tab.
+- Simulation execution using prebuilt configs.
+- Napari integration for visualization of resulting microscopy data.
+- Packaging of simulation logs for easy sharing.
+
+## Launching the GUI
+
+```bash
+run_AMS_BP gui
+```
+## GUI Structure
+
+### Main Window
+The main window (MainWindow) acts as the launchpad for:
+
+- Configuration Builder — Launches a template selector and opens a full editor.
+- Run Simulation from Config — Lets you pick a .toml file and start the simulation.
+- Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
+- Package Logs for Sharing — Archives a run_* folder into a .zip.
+
+#### Configuration Editor
+Once a template is selected, the ConfigEditor is launched. It contains:
+
+- A dropdown navigation system replacing traditional tabs.
+- A floating tab counter and preview/save buttons.
+- A help button per section (reads *.md files from help_docs/).
+- Live validation using internal config models (convertconfig.py).
+
+##### Tabs & Widgets
+Each configuration section is implemented as a modular PyQt widget, including:
+
+- GlobalConfigWidget
+- CellConfigWidget
+- MoleculeConfigWidget
+- FluorophoreConfigWidget
+- CondensateConfigWidget
+- LaserConfigWidget
+- ExperimentConfigWidget
+- ...and more
+
+Each widget supports:
+
+- get_data() → Extract validated dictionary data
+- set_data(data: dict) → Load existing config into the UI
+- validate() → Validate using backend logic
+- get_help_path() → Load the corresponding markdown help page
+
+####  Running a Simulation
+
+Once you've completed the config file setup via the GUI:
+
+- Click "Preview Configuration TOML" to confirm contents.
+- Click "Ready to Save Configuration" and choose a .toml path.
+- Return to the main window, click "Run Simulation from Config".
+- Simulation will launch in a background thread and print logs to a live window.
+- Once done, results will be saved in a run_*/ folder.
+
+#### Viewing Results
+
+- Click "Visualize Microscopy Data (Napari)"
+- Select any .tif, .tiff, .nd2, or .zarr file
+
+The data will be loaded into a new Napari viewer session
+
+#### Packaging Logs
+
+To share or archive a completed simulation:
+
+- Click "Package Logs for Sharing".
+- Select the run_* folder you want.
+- Choose a destination for the .zip file.

{ams_bp-0.4.0 → ams_bp-0.4.22}/uv.lock

@@ -12,7 +12,7 @@ wheels = [
 
 [[package]]
 name = "ams-bp"
-version = "0.3.1"
+version = "0.4.0"
 source = { editable = "." }
 dependencies = [
     { name = "boundedfbm" },

ams_bp-0.4.0/src/AMS_BP/gui/README.md

@@ -1,77 +0,0 @@
-# AMS-BP GUI
-
-The AMS-BP GUI provides a user-friendly interface for constructing and validating configuration files for the AMS-BP fluorescence microscopy simulation framework. It integrates simulation execution, configuration design, log packaging, and data visualization in one cohesive window.
-
-## Overview
-
-This GUI supports:
-
-A template-based configuration builder for quick setup.
-A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
-Interactive help sections for each tab.
-Simulation execution using prebuilt configs.
-Napari integration for visualization of resulting microscopy data.
-Packaging of simulation logs for easy sharing.
-
-## Launching the GUI
-
-```bash
-run_AMS_BP gui
-```
-## GUI Structure
-
-### Main Window
-The main window (MainWindow) acts as the launchpad for:
-
-Configuration Builder — Launches a template selector and opens a full editor.
-Run Simulation from Config — Lets you pick a .toml file and start the simulation.
-Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
-Package Logs for Sharing — Archives a run_* folder into a .zip.
-#### Configuration Editor
-Once a template is selected, the ConfigEditor is launched. It contains:
-
-A dropdown navigation system replacing traditional tabs.
-A floating tab counter and preview/save buttons.
-A help button per section (reads *.md files from help_docs/).
-Live validation using internal config models (convertconfig.py).
-##### Tabs & Widgets
-Each configuration section is implemented as a modular PyQt widget, including:
-
-GlobalConfigWidget
-CellConfigWidget
-MoleculeConfigWidget
-FluorophoreConfigWidget
-CondensateConfigWidget
-LaserConfigWidget
-ExperimentConfigWidget
-...and more
-Each widget supports:
-
-get_data() → Extract validated dictionary data
-set_data(data: dict) → Load existing config into the UI
-validate() → Validate using backend logic
-get_help_path() → Load the corresponding markdown help page
-
-####  Running a Simulation
-
-Once you've completed the config file setup via the GUI:
-
-Click "Preview Configuration TOML" to confirm contents.
-Click "Ready to Save Configuration" and choose a .toml path.
-Return to the main window, click "Run Simulation from Config".
-Simulation will launch in a background thread and print logs to a live window.
-Once done, results will be saved in a run_*/ folder.
-
-#### Viewing Results
-
-Click "Visualize Microscopy Data (Napari)"
-Select any .tif, .tiff, .nd2, or .zarr file
-The data will be loaded into a new Napari viewer session
-
-#### Packaging Logs
-
-To share or archive a completed simulation:
-
-Click "Package Logs for Sharing".
-Select the run_* folder you want.
-Choose a destination for the .zip file.

{ams_bp-0.4.0 → ams_bp-0.4.22}/src/AMS_BP/gui/widgets/molecule_config_widget.py

@@ -235,6 +235,9 @@ class MoleculeConfigWidget(QWidget):
             }
             self.molecule_type_widgets[i].set_data(type_data)
 
+    def get_help_path(self) -> Path:
+        return Path(__file__).parent.parent / "help_docs" / "molecule_help.md"
+
 
 class MoleculeTypeWidget(QWidget):
     def __init__(self, type_index):
@@ -709,6 +712,3 @@ class TransitionMatrixWidget(QWidget):
         for i in range(size):
             for j in range(min(size, len(matrix[i]))):
                 self.spinboxes[i][j].setValue(matrix[i][j])
-
-    def get_help_path(self) -> Path:
-        return Path(__file__).parent.parent / "help_docs" / "molecule_help.md"