AMS-BP 0.2.0__tar.gz → 0.3.0__tar.gz

{ams_bp-0.2.0 → ams_bp-0.3.0}/.github/workflows/pages.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10.13"]
+        python-version: ["3.12"]
 
     steps:
       - uses: actions/checkout@v4

{ams_bp-0.2.0 → ams_bp-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.2.0
+Version: 0.3.0
 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
@@ -9,7 +9,7 @@ Maintainer-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
 License-File: LICENSE
 Keywords: SMS
 Requires-Python: >=3.12
-Requires-Dist: boundedfbm>=0.2.0
+Requires-Dist: boundedfbm>=0.4.0
 Requires-Dist: jsonschema>=4.23.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pydantic>=2.9.2
@@ -155,7 +155,17 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
+```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 ## Advanced Usage
 
 ### Using AMS-BP as a Library
@@ -187,7 +197,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 > A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
 
 ## High Priority Features
-1. Irregular cell shapes with motion models
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
 2. Stimulated Emission models
 3. STORM workflow examples
 4. CTRW motion models

{ams_bp-0.2.0 → ams_bp-0.3.0}/README.md

@@ -133,7 +133,17 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
+```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 ## Advanced Usage
 
 ### Using AMS-BP as a Library
@@ -165,7 +175,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 > A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
 
 ## High Priority Features
-1. Irregular cell shapes with motion models
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
 2. Stimulated Emission models
 3. STORM workflow examples
 4. CTRW motion models

{ams_bp-0.2.0 → ams_bp-0.3.0}/docs/API_Documentation/configio/configmodels.md

@@ -5,6 +5,7 @@ The configuration models module defines Pydantic BaseModel classes for validatin
 
 ## Models
 
+
 ### CellParameters
 Defines the physical parameters of the cell being simulated.