documentation update

Author: Lazareva

.github/workflows/publish-to-pypi.yml

@@ -1,9 +1,9 @@
 name: Publish Python Package
 
 on:
-  push:
-    branches:
-      - master  # or your preferred branch
+  release:
+    types:
+      - created  # This workflow will run when a new release is created
 
 jobs:
   build:
@@ -26,10 +26,15 @@ jobs:
       run: |
         python setup.py sdist bdist_wheel
 
-    - name: Publish to PyPI
-      env:
-        TWINE_USERNAME: "__token__"
-        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      run: |
-        python -m pip install --upgrade twine
-        twine upload dist/*
+    # - name: Publish to PyPI
+    #   env:
+    #     TWINE_USERNAME: "__token__"
+    #     TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+    #   run: |
+    #     python -m pip install --upgrade twine
+    #     twine upload dist/*
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@v1.8.10
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

docs/faq/index.md

@@ -0,0 +1,38 @@
+
+---
+layout: default
+title: FAQ
+nav_order: 4
+---
+
+# FAQ
+- **Q:** What if I want to map only cell states, but not clones?
+- **A:** In therory, spaceTree can be used with any type of labels that can be transfered from scRNA-seq to spatial data. In practice, a way to achive that at the moment requirs a few modifications to the tutorial:
+
+1) Currently the format of `data` object is fixed, but you can assign a dummy label to `clone` column in `adata.obs` by assigning roughlhly 50% of the cells to clone '0' and the rest to 'diploid'.
+
+2) When you define the model, you need to set `map_enteties` to 'type' instead of 'both'. E.g.:
+```python
+model = GATLightningModule_sampler(data_param=data, weight_type=weight_type, map_enteties='type')
+```
+3) Instead of running `get_results_calibrated()`, you can use `get_results_type(pred, data, node_encoder_rev, node_encoder_ct, activation='softmax')` to get the results for cell types only. 
+
+- **Q:** What if I want to map only clones, but not cell types?
+
+- **A:** In therory, spaceTree can be used with any type of labels that can be transfered from scRNA-seq to spatial data. In practice, a way to achive that at the moment requirs a few modifications to the tutorial:
+
+1) Currently the format of `data` object is fixed, but you can assign a dummy label to 'cell_type' column in `adata_ref.obs` by assigning roughlhly 50% of the cells to dummy_cell_type1 and the rest to 'dummy_cell_type2' (or use any other names).
+
+2) When you define the model, you need to set `map_enteties` to 'clone' instead of 'both'. E.g.:
+```python
+model = GATLightningModule_sampler(data_param=data, weight_clone=weight_clone, map_enteties='clone')
+```
+3) Instead of running `get_results_calibrated()`, you can use `get_results_clone(pred, data, node_encoder_rev, node_encoder_cl, activation='softmax')` to get the results for clones only. 
+
+- **Q:** What if I want to map a different type of labels, e.g. cell types and cell cycle phases?
+- **A:** In therory, spaceTree can be used with any type of labels that can be transfered from scRNA-seq to spatial data. In practice, due to due to the fixed format of clonal labels, you might have to represent cell cycle phases as clones: e.g. "diploid","0","1", etc.
+
+- **Q:** What if I want to use more than 2 sets of labels?
+- **A:** Right now we do not support more than 2 sets of labels. However, if you feel confident in your programming skills, you can modify the code of model and the evaluation functions to support more than 2 sets of labels.
+
+

docs/index.md

@@ -19,6 +19,9 @@ Welcome to the official documentation for spaceTree! Here, you will find tutoria
     1. [Cell state and clone mapping to 10x Visium with SpaceTree](tutorials/cell-state-clone-mapping.md)
     2. [Cell state and clone mapping to 10x Xenium with SpaceTree](tutorials/cell-state-clone-mapping-xenium.md)
     3. [Visium HD data tips and tricks](tutorials/visium-hd.md)
+3. [FAQ](faq/index.md)
+4. [API Reference](api/index.md)
+5. [Citation](#citation)
 
 ## Installation <a name="installation"></a>
 ### pytorch & pytorch geometric dependencies <a name="dependency"></a>
@@ -80,3 +83,9 @@ If you need help defining clones based on your own scRNA-seq data, you can use t
 
 For the sake of the Visium and Xenium tutorials, we also show how we ran the clone inference based on inferCNVpy [here](https://github.com/PMBio/spaceTree/blob/master/notebooks/infercnv_run.ipynb)
 
+## Citiation <a name="citation"></a>
+If you use spaceTree in your research, please cite our paper:
+
+```
+To be added 
+```