simspace 0.3.0__tar.gz → 0.3.2__tar.gz

{simspace-0.3.0/simspace.egg-info → simspace-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: simspace
-Version: 0.3.0
+Version: 0.3.2
 Summary: SimSpace: a comprehensive in-silico spatial omics data simulation framework
 Author: Tianxiao Zhao
 License: MIT
@@ -26,10 +26,12 @@ Dynamic: requires-python
 [![Docs](https://readthedocs.org/projects/simspace/badge/?version=latest)](https://simspace.readthedocs.io/en/latest/)
 [![PyPI](https://img.shields.io/pypi/v/simspace.svg)](https://pypi.org/project/simspace/)
 
-**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
+**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model. 
 
 ![SimSpace Workflow](images/overview.png)
 
+For full figure reproduction (all analyses and scripts) for the SimSpace manuscript, see: https://github.com/TianxiaoNYU/simspace-reproducibility
+
 ## 📦 Installation
 
 To install the latest version of SimSpace, we recommend using conda to setup the environment:
@@ -90,12 +92,10 @@ The documentation includes:
 To get started with SimSpace, we provide detailed tutorials covering both reference-based and reference-free simulation modes.
 
 - **Step-by-step tutorials** can be found in [`tutorials.md`](./tutorials.md)
-- **Executable notebook examples** are located in the [`examples/`](./examples/) directory
+- **Executable notebooks** are located in the [`tutorials/`](./tutorials/) directory
 
 These resources walk through how to configure and run simulations as well as visualize outputs.
 
-To reproduce the figures in the manuscript, one can find the scripts at [`examples/figures.ipynb`](./examples/figures.ipynb).
-
 ## 🚀 Quick Start
 
 Here’s a basic example to simulate a 2D tissue with 3 spatial niches and 8 cell types:
@@ -131,6 +131,4 @@ Developed by Tianxiao Zhao at NYU Grossman School of Medicine. Should you have a
 
 ## 🔗 References
 If you use SimSpace in your work, please cite the work on BioRxiv:
-[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587v1)
-
-
+[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)

{simspace-0.3.0 → simspace-0.3.2}/README.md

@@ -3,10 +3,12 @@
 [![Docs](https://readthedocs.org/projects/simspace/badge/?version=latest)](https://simspace.readthedocs.io/en/latest/)
 [![PyPI](https://img.shields.io/pypi/v/simspace.svg)](https://pypi.org/project/simspace/)
 
-**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
+**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model. 
 
 ![SimSpace Workflow](images/overview.png)
 
+For full figure reproduction (all analyses and scripts) for the SimSpace manuscript, see: https://github.com/TianxiaoNYU/simspace-reproducibility
+
 ## 📦 Installation
 
 To install the latest version of SimSpace, we recommend using conda to setup the environment:
@@ -67,12 +69,10 @@ The documentation includes:
 To get started with SimSpace, we provide detailed tutorials covering both reference-based and reference-free simulation modes.
 
 - **Step-by-step tutorials** can be found in [`tutorials.md`](./tutorials.md)
-- **Executable notebook examples** are located in the [`examples/`](./examples/) directory
+- **Executable notebooks** are located in the [`tutorials/`](./tutorials/) directory
 
 These resources walk through how to configure and run simulations as well as visualize outputs.
 
-To reproduce the figures in the manuscript, one can find the scripts at [`examples/figures.ipynb`](./examples/figures.ipynb).
-
 ## 🚀 Quick Start
 
 Here’s a basic example to simulate a 2D tissue with 3 spatial niches and 8 cell types:
@@ -108,6 +108,4 @@ Developed by Tianxiao Zhao at NYU Grossman School of Medicine. Should you have a
 
 ## 🔗 References
 If you use SimSpace in your work, please cite the work on BioRxiv:
-[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587v1)
-
-
+[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)

{simspace-0.3.0 → simspace-0.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "simspace"
-version = "0.3.0"
+version = "0.3.2"
 description = "SimSpace: a comprehensive in-silico spatial omics data simulation framework"
 readme = "README.md"
 requires-python = ">=3.10"

{simspace-0.3.0 → simspace-0.3.2}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setup(
     name="simspace",
-    version="0.3.0",
+    version="0.3.2",
     description="SimSpace: a comprehensive in-silico spatial omics data simulation framework",
     long_description=long_description,
     long_description_content_type="text/markdown",

{simspace-0.3.0 → simspace-0.3.2}/simspace/optimize.py

@@ -13,7 +13,7 @@ warnings.filterwarnings('ignore')
 ## Define the Fitness Function, which do the simulation first and then calculate the fitness value
 #### The fitness value is the distance between the simulation result and the experimental data
 def _get_spatial_statistics(simulation, n_state):
-    simulation.columns = ['celltype', 'x', 'y', 'celltype_ranked']
+    simulation.columns = ['celltype', 'x', 'y', 'niche', 'celltype_ranked']
     tmp = simulation[simulation['celltype'] == -1].index
     simulation = simulation.drop(tmp)
     simulation = simulation.reset_index(drop=True)

{simspace-0.3.0 → simspace-0.3.2}/simspace/plot.py

@@ -46,8 +46,8 @@ def spatial_pie(
     fig.set_size_inches(figure_size)
     fig.set_dpi(dpi)
     ax.set_aspect('equal')
-    ax.set_xlim(-(SimSpace.size[0]/100*2), SimSpace.size[0] + (SimSpace.size[0]/100*2))
-    ax.set_ylim(-(SimSpace.size[1]/100*2), SimSpace.size[1] + (SimSpace.size[1]/100*2))
+    ax.set_xlim(-(SimSpace.shape[0]/100*2), SimSpace.shape[0] + (SimSpace.shape[0]/100*2))
+    ax.set_ylim(-(SimSpace.shape[1]/100*2), SimSpace.shape[1] + (SimSpace.shape[1]/100*2))
     ax.set_xticks([])
     ax.set_yticks([])
     ax.set_title('Convolved SimSpace Dataset')

{simspace-0.3.0 → simspace-0.3.2/simspace.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: simspace
-Version: 0.3.0
+Version: 0.3.2
 Summary: SimSpace: a comprehensive in-silico spatial omics data simulation framework
 Author: Tianxiao Zhao
 License: MIT
@@ -26,10 +26,12 @@ Dynamic: requires-python
 [![Docs](https://readthedocs.org/projects/simspace/badge/?version=latest)](https://simspace.readthedocs.io/en/latest/)
 [![PyPI](https://img.shields.io/pypi/v/simspace.svg)](https://pypi.org/project/simspace/)
 
-**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model.
+**SimSpace** is a Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization. Designed for benchmarking spatial analysis methods, SimSpace enables generation of synthetic datasets that preserve spatial autocorrelation, cell-cell interactions, and spatial proximities using a Markov Random Field (MRF) model. 
 
 ![SimSpace Workflow](images/overview.png)
 
+For full figure reproduction (all analyses and scripts) for the SimSpace manuscript, see: https://github.com/TianxiaoNYU/simspace-reproducibility
+
 ## 📦 Installation
 
 To install the latest version of SimSpace, we recommend using conda to setup the environment:
@@ -90,12 +92,10 @@ The documentation includes:
 To get started with SimSpace, we provide detailed tutorials covering both reference-based and reference-free simulation modes.
 
 - **Step-by-step tutorials** can be found in [`tutorials.md`](./tutorials.md)
-- **Executable notebook examples** are located in the [`examples/`](./examples/) directory
+- **Executable notebooks** are located in the [`tutorials/`](./tutorials/) directory
 
 These resources walk through how to configure and run simulations as well as visualize outputs.
 
-To reproduce the figures in the manuscript, one can find the scripts at [`examples/figures.ipynb`](./examples/figures.ipynb).
-
 ## 🚀 Quick Start
 
 Here’s a basic example to simulate a 2D tissue with 3 spatial niches and 8 cell types:
@@ -131,6 +131,4 @@ Developed by Tianxiao Zhao at NYU Grossman School of Medicine. Should you have a
 
 ## 🔗 References
 If you use SimSpace in your work, please cite the work on BioRxiv:
-[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587v1)
-
-
+[Zhao T, Zhang K, Hollenberg M, Zhou W, Fenyo D. SimSpace: a comprehensive in-silico spatial omics data simulation framework. bioRxiv. 2025:2025.07.18.665587.](https://www.biorxiv.org/content/10.1101/2025.07.18.665587)