sclab 0.1.7__tar.gz → 0.1.8__tar.gz

{sclab-0.1.7 → sclab-0.1.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sclab
-Version: 0.1.7
+Version: 0.1.8
 Summary: sclab
 Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
 Requires-Python: >=3.10,<3.13
@@ -16,7 +16,7 @@ Requires-Dist: ipywidgets
 Requires-Dist: itables
 Requires-Dist: numpy<2.2
 Requires-Dist: pandas
-Requires-Dist: plotly
+Requires-Dist: plotly<6.0
 Requires-Dist: scanpy
 Requires-Dist: scikit-learn
 Requires-Dist: scikit-misc
@@ -53,23 +53,29 @@ pip install sclab
 Open a Jupyter Notebook and run the following:
 
 ```python
+from IPython.display import display
 from sclab import SCLabDashboard
+from sclab.examples.processor_steps import QC, Preprocess, PCA, Neighbors, UMAP, Cluster
 import scanpy as sc
-from IPython.display import display
 
 # Load your data
 adata = sc.read_10x_h5("your_data.h5")
 
 # Create dashboard
 dashboard = SCLabDashboard(adata, name="My Analysis")
+# Add desired processing steps to the interface
+dashboard.pr.add_steps({"Processing": [QC, Preprocess, PCA, Neighbors, UMAP, Cluster]})
 
 # Display dashboard
 display(dashboard)
 
 # The dashboard provides easy access to components:
-dashboard.ds  # Dataset (wrapper for AnnData)
-dashboard.pl  # Plotter
-dashboard.pr  # Processor
+# dashboard.ds  # Dataset (wrapper for AnnData)
+# dashboard.pl  # Plotter
+# dashboard.pr  # Processor
+
+# the resulting AnnData object is found within the dataset object:
+# dashboard.ds.adata
 ```
 
 ## Components
@@ -129,10 +135,10 @@ This project is licensed under the BSD 3-Clause License - see the [LICENSE](LICE
 If you use SCLab in your research, please cite:
 
 ```bibtex
-@software{sclab2024,
+@software{sclab2025,
   author = {Arriojas, Argenis},
   title = {SCLab: Interactive Single-Cell Analysis Toolkit},
-  year = {2024},
+  year = {2025},
   publisher = {GitHub},
   url = {https://github.com/umbibio/sclab}
 }

{sclab-0.1.7 → sclab-0.1.8}/README.md

@@ -22,23 +22,29 @@ pip install sclab
 Open a Jupyter Notebook and run the following:
 
 ```python
+from IPython.display import display
 from sclab import SCLabDashboard
+from sclab.examples.processor_steps import QC, Preprocess, PCA, Neighbors, UMAP, Cluster
 import scanpy as sc
-from IPython.display import display
 
 # Load your data
 adata = sc.read_10x_h5("your_data.h5")
 
 # Create dashboard
 dashboard = SCLabDashboard(adata, name="My Analysis")
+# Add desired processing steps to the interface
+dashboard.pr.add_steps({"Processing": [QC, Preprocess, PCA, Neighbors, UMAP, Cluster]})
 
 # Display dashboard
 display(dashboard)
 
 # The dashboard provides easy access to components:
-dashboard.ds  # Dataset (wrapper for AnnData)
-dashboard.pl  # Plotter
-dashboard.pr  # Processor
+# dashboard.ds  # Dataset (wrapper for AnnData)
+# dashboard.pl  # Plotter
+# dashboard.pr  # Processor
+
+# the resulting AnnData object is found within the dataset object:
+# dashboard.ds.adata
 ```
 
 ## Components
@@ -98,10 +104,10 @@ This project is licensed under the BSD 3-Clause License - see the [LICENSE](LICE
 If you use SCLab in your research, please cite:
 
 ```bibtex
-@software{sclab2024,
+@software{sclab2025,
   author = {Arriojas, Argenis},
   title = {SCLab: Interactive Single-Cell Analysis Toolkit},
-  year = {2024},
+  year = {2025},
   publisher = {GitHub},
   url = {https://github.com/umbibio/sclab}
 }

{sclab-0.1.7 → sclab-0.1.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "sclab"
-version = "0.1.7"
+version = "0.1.8"
 description = "sclab"
 readme = "README.md"
 authors = [
@@ -21,7 +21,7 @@ dependencies = [
     "itables",
     "numpy<2.2",
     "pandas",
-    "plotly",
+    "plotly<6.0",
     "scanpy",
     "scikit-learn",
     "scikit-misc",
@@ -53,4 +53,7 @@ dev = [
     "ruff>=0.9.4",
     "nox>=2024.1.29",
     "pytest>=8.3.4",
+    "mkdocs>=1.6.1",
+    "mkdocs-material>=9.6.3",
+    "mkdocs-jupyter>=0.25.1",
 ]

{sclab-0.1.7 → sclab-0.1.8}/src/sclab/__init__.py

@@ -4,4 +4,4 @@ __all__ = [
     "SCLabDashboard",
 ]
 
-__version__ = "0.1.7"
+__version__ = "0.1.8"

{sclab-0.1.7 → sclab-0.1.8}/src/sclab/dataset/_dataset.py

@@ -336,7 +336,7 @@ class SCLabDataset(EventClient):
         self.broker.publish("dset_selected_rows_change", value)
 
     @property
-    def selected_rows_mask(self) -> NDArray[np.bool]:
+    def selected_rows_mask(self) -> NDArray[np.bool_]:
         return self.metadata.index.isin(self.selected_rows)
 
     @property