add installation

Author: dbdimitrov

CHANGELOG.md

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 # Changelog
 
+## 1.7.0 (07.01.2026)
+
+- Inflow implementation and tutorial #221 by @AtheerAS
+- Global specificity calculation #221 by @AtheerAS
+-  The integration of spatial proximity weighting into scoring and permutation-based p-value calculations, new user-facing parameters for spatial analysis, and enhancements to the documentation to reflect these features. #222. The main cell-cell communication pipeline (`liana_pipe`) and scoring methods now support spatial proximity weighting. This includes new arguments (`spatial_key`, `spatial_kwargs`) and logic to compute and merge spatial proximity scores into LR (ligand-receptor) results, and to adjust permutation-based p-value calculations accordingly. (`src/liana/method/sc/_liana_pipe.py`)
+- Expanded docstrings and parameter documentation to cover new spatial analysis arguments, including detailed descriptions of spatial proximity options and kernel/bandwidth settings.
+- Updated the notebook index and documentation to reference new spatial analysis notebooks, such as `inflow_score.ipynb`.
+- Bumped the package version to 1.7.0 across configuration files, and updated dependencies for `decoupler` and `cvxpy-base` to `>=1.7.0`.
+- Added Python 3.13 support in classifiers. #216
+- Added Installation instructions in `installation.md`. #217
+
 ## 1.6.1 (28.09.2025)
 
 - Comply with AnnData CSR matrix changes

docs/index.md

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 :hidden: true
 :maxdepth: 2
 
+installation.md
 api.md
 changelog.md
 contributing.md

docs/installation.md

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+# Installation
+
+## Basic Installation
+
+Install LIANA using pip:
+
+```bash
+pip install liana
+```
+
+## Conda Installation
+
+```bash
+conda install bioconda::liana
+```
+
+## Installation with Extras
+
+LIANA offers optional dependencies for extended functionality:
+
+### All Extras
+
+Install all optional dependencies:
+
+```bash
+pip install 'liana[extras]'
+```
+
+This includes additional packages for:
+- Multi-view analysis (decoupler, muon, mofax, mofapy2)
+- Database access (omnipath)
+- Differential expression (pydeseq2)
+- Pathway analysis (gseapy)
+- Optimization (corneto, cvxpy-base, PySCIPOpt)
+- And more (cell2cell, kneed)
+
+### Development Installation From Source
+
+```bash
+git clone https://github.com/saezlab/liana-py.git
+cd liana-py
+pip install -e '.[dev]'
+```
+
+## Requirements
+
+- Python 3.10 or higher (up to 3.13)
+- Core dependencies: anndata, mudata, scanpy, numba, pandas, and others are installed automatically