Merge pull request #2 from lzj1769/develop

Develop

.gitignore

@@ -2,3 +2,8 @@ test/*
 test_old/
 Tutorial/*.h5
 pychromvar/__pycache__
+docs/source/notebooks/*.csv
+docs/source/notebooks/*.h5
+docs/source/notebooks/.ipynb_checkpoints/*
+docs/source/notebooks/*.fa
+docs/source/notebooks/*.fa.fai

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/source/requirements.txt

README.md

@@ -1,5 +1,6 @@
 [![Stars](https://img.shields.io/github/stars/lzj1769/pychromVAR?logo=GitHub&color=yellow)](https://github.com/lzj1769/pychromVAR/stargazers)
 [![PyPI](https://img.shields.io/pypi/v/pychromvar?logo=PyPI)](https://pypi.org/project/pychromvar/)
+[![Docs](https://readthedocs.org/projects/pychromvar/badge/?version=latest)](https://pychromvar.readthedocs.io)
 
 # pychromVAR 
 
@@ -17,6 +18,6 @@ pip install pychromvar
 
 # Tutorial
 
-You can find [here](https://github.com/lzj1769/pychromVAR/blob/main/tutorial/tutorial.ipynb) a tutorial how to use pychromVAR combined with Muon to analysis multimodal single-cell PBMC data.
+You can find [here](https://pychromvar.readthedocs.io/en/latest/notebooks/multimodal_pbmc_3k.html) a tutorial how to use pychromVAR combined with Muon to analysis multimodal single-cell PBMC data.
 
 

docs/source/_static/css/custom.css

@@ -0,0 +1,11 @@
+.wy-side-nav-search a img.logo {
+  height: 200px;
+}
+
+.wy-side-nav-search {
+    background-color: transparent
+}
+
+.wy-nav-content {
+    max-width: 1200px;
+}

docs/source/conf.py

@@ -2,6 +2,8 @@
 
 import os
 import sys
+from datetime import datetime
+
 sys.path.insert(0, os.path.abspath('../..'))
 
 
@@ -25,6 +27,7 @@ def get_version(rel_path: str) -> str:
 author = 'Zhijian Li'
 release = get_version("../../pychromvar/__init__.py")
 version = get_version("../../pychromvar/__init__.py")
+copyright = f"{datetime.now():%Y}, {author}"
 
 # -- General configuration
 
@@ -59,14 +62,12 @@ def get_version(rel_path: str) -> str:
 )
 html_context = dict(
     display_github=True,  # Integrate GitHub
-    github_user='saezlab',  # Username
-    github_repo='decoupler-py',  # Repo name
-    github_version='master',  # Version
+    github_user='lzj1769',  # Username
+    github_repo='pychromVAR',  # Repo name
+    github_version='develop',  # Version
     conf_py_path='/docs/source/',  # Path in the checkout to the docs root
 )
 html_show_sphinx = False
-html_logo = 'logo.png'
-html_favicon = 'logo.png'
 html_css_files = [
     'css/custom.css',
 ]

docs/source/index.rst

@@ -1,2 +1,30 @@
-pychromVAR - A python package for chromVAR
-==============================================================
+pychromVAR
+==============================================================
+
+pychromVAR is a python package for inferring transcription factor binding variability from 
+scATAC-seq data by implmenting the algorithm proposed in 
+`chromVAR <https://github.com/GreenleafLab/chromVAR>`__. 
+It is built on `anndata <https://anndata.readthedocs.io/en/latest/>`__ and 
+`mudata <https://mudata.readthedocs.io/en/latest/>`__ therefore can work seamlessly 
+with `scanpy <https://scanpy.readthedocs.io/en/stable/>`__ and
+`muon <https://muon.readthedocs.io/en/latest/>`__ pipeline.
+
+For more methdological detials, please refer to the original `paper <https://www.nature.com/articles/nmeth.4401>`__.
+
+.. toctree::
+   :caption: mail
+   :maxdepth: 1
+   :hidden:
+
+   installation
+
+.. toctree::
+   :caption: notebooks
+   :maxdepth: 1
+   :hidden:
+
+   notebooks/run_chromVAR
+   notebooks/compare_with_chromVAR
+   notebooks/multimodal_pbmc_3k
+
+

docs/source/installation.rst

@@ -0,0 +1,12 @@
+Installation
+============
+
+**pychromVAR** requires Python version >= 3 to run.
+
+PyPI
+----
+**pychromVAR** is also available on PyPI:
+
+.. code-block:: console
+
+   pip install pychromvar