Major updates: v2.0

Author: serjisa

.gitignore

@@ -0,0 +1,72 @@
+# --- Python Bytecode and Caches ---
+# These are generated by the Python interpreter
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Type checker cache
+.mypy_cache/
+
+# --- Virtual Environments ---
+# Never commit your environment
+venv/
+env/
+.venv/
+.env/
+virtualenv/
+
+# --- Build and Distribution Artifacts ---
+# These are generated when you package your library
+build/
+dist/
+sdist/
+*.egg-info/
+.eggs/
+*.whl
+*.tar.gz
+
+# setuptools cache
+.setuptools-cache
+
+# --- Testing and Coverage ---
+# Caches and reports from testing tools
+.pytest_cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+nosetests.xml
+# tox environments
+.tox/
+
+# --- IDE and Editor Specific ---
+# User-specific settings for various editors
+.idea/
+.vscode/
+*.sublime-project
+*.sublime-workspace
+*.swp
+*.swo
+*~
+
+# --- Operating System Files ---
+# Junk files from macOS, Windows, and Linux
+.DS_Store
+._*
+Thumbs.db
+ehthumbs.db
+
+# --- Secrets and Local Config ---
+# NEVER commit secrets, API keys, or local settings
+.env
+*.env
+local_settings.py
+config.local.ini
+
+# --- Logs ---
+*.log
+
+# --- Docs Build Artifacts ---
+docs/build/
+docs/source/API/
+docs/_build/

README.md

@@ -46,14 +46,4 @@ on the following systems:
 ## Documentation and tutorials
 
 Please visit [documentation web-site](https://sclitr.readthedocs.io/en/latest/) to check out API description and a few
-tutorials with analysis.
-
-An example with the dataset from [Weinreb et al., 2020](https://www.science.org/doi/10.1126/science.aaw3381) is available on
-[Google Colab](https://colab.research.google.com/github/kharchenkolab/scLiTr/blob/main/docs/source/Basic_usage.ipynb)
-(takes about 45 minutes on the CPU, of which approximately 30 minutes are clone2vec latent representation construction).
-
-## clones2cells
-
-For interactive exploration of clonal and gene expression embeddings together we recommend using
-our simple tool [clones2cells](https://github.com/serjisa/clones2cells_app).
-
+tutorials with analysis.

docs/requirements.txt

@@ -1,16 +1,21 @@
 sphinx
-sphinx-rtd-theme
 nbsphinx
 ipywidgets
 numpydoc
+scanpydoc
+sphinx-autodoc-typehints
 tqdm
 numpy
 pandas
+scipy
+seaborn
+matplotlib
 pynndescent
 scanpy
 scikit-learn
 torch
 mpltern
 catboost
 geosketch
+fastglmpca
 textalloc