Doc

.github/workflows/python-package.yml

@@ -1,17 +1,14 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: Python package
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "main", "doc" ] # Added "doc" so you can see if it works before merging!
   pull_request:
     branches: [ "main" ]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -20,22 +17,27 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5 # Updated to v5 (current best practice)
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        python -m pip install git+https://github.com/jsnagai/Nichesphere#subdirectory=nichesphere
-        if [ -f nichesphere/requirements.txt ]; then pip install -r nichesphere/requirements.txt; fi
+        # IMPORTANT: This installs YOUR local code from the current branch
+        pip install -e . 
+        # Check if requirements exist in the new root or docs folder
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
     - name: Lint with flake8
       run: |
-        # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
-        pytest
+        # This tells pytest to look in your new root tests/ folder
+        pytest tests/

.readthedocs.yaml

@@ -16,7 +16,7 @@ build:
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-  configuration: nichesphere/nichesphere/source/conf.py
+  configuration: docs/conf.py
   # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
   # builder: "dirhtml"
   # Fail on all warnings to avoid broken references
@@ -32,4 +32,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-     - requirements: nichesphere/nichesphere/docs/requirements.txt
+     - requirements: docs/requirements.txt

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Ruiz"
+  given-names: "Mayra"
+- family-names: "Nagai"
+  given-names: "James"
+title: "NicheSphere"
+version: 1.0.0
+doi: 10.5281/zenodo.XXXXX  # Update this AFTER you get your DOI from Zenodo
+date-released: 2026-02-24  # Use today's date
+url: "https://github.com/CostaLab/NicheSphere"

README.md

@@ -1,11 +1,13 @@
-<img align="right" src="nichesphere/nichesphere/source/_static/logo.png" alt="Nichesphere Logo" width="200">
+<img align="right" src="docs/_static/logo.png" alt="Nichesphere Logo" width="200">
 
 # NicheSphere
 
-NicheSphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting cell boundaries overlaps for each cell type pair in single cell spatial data (MERFISH , CODEX …).
+[![DOI](https://zenodo.org)](https://doi.org)
 
-It also offers the possibility to look at biological process based differential communication among differential co-localization domains based on Ligand-Receptor pairs expression data, such as results from CrossTalkeR [ref.].
+NicheSphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting nearest neighbors of each type for each cell in single cell spatial data like MERFISH or CODEX.
 
-You can find our documentation and an application example on the Myocardial Infarction atlas data from Kuppe et. al. 2022 here: https://nichesphere.readthedocs.io/en/latest/ 
+It also offers the possibility to look at biological process based differential communication between cell type pairs or differential co-localization domains based on Ligand-Receptor pairs expression data, which can be obtained from diverse cell cell communication tools, such as [CrossTalkeR](https://costalab.github.io/CrossTalkeR/).
+
+You can find our documentation and an application example on the Myocardial Infarction atlas data from Kuppe et. al. 2022 here: https://nichesphere.readthedocs.io/en/latest/ , The data you'll need to run the tutorials is stored in [Zenodo](https://doi.org/10.5281/zenodo.15790389)
 
 

docs/api.rst

@@ -0,0 +1,9 @@
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+
+   coloc
+   comm
+   tl

nichesphere/nichesphere/source/coloc.rst → docs/coloc.rst

@@ -3,6 +3,7 @@ coloc module
 
 Focused on differential co-localization
 
-.. automodule:: coloc
+.. automodule:: nichesphere.coloc
    :members:
+   :undoc-members:
    :show-inheritance:

nichesphere/nichesphere/source/comm.rst → docs/comm.rst

@@ -3,6 +3,7 @@ comm module
 
 Focused on differential communication
 
-.. automodule:: comm
+.. automodule:: nichesphere.comm
    :members:
+   :undoc-members:
    :show-inheritance:

nichesphere/nichesphere/source/conf.py → docs/conf.py

@@ -8,16 +8,17 @@
 
 # Add path to module
 #sys.path.insert(0, os.path.abspath('/home/mayra/source/Nichesphere/nichesphere/nichesphere'))
-sys.path.insert(0, os.path.abspath('../'))
-sys.path.insert(0, os.path.abspath('../../'))
+#sys.path.insert(0, os.path.abspath('../'))
+#sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath('../src'))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'Nichesphere'
-copyright = '2025, Mayra Ruiz'
-author = 'Mayra Ruiz'
-release = '0.1.0'
+project = 'NicheSphere'
+copyright = '2025, Mayra Ruiz, James Nagai'
+author = 'Mayra Ruiz, James Nagai'
+release = '1.0.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration