v1.7.0

v1.7.0

Author: dbdimitrov

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.6.1
+current_version = 1.7.0
 commit = True
 tag = True
 

CHANGELOG.md

@@ -1,5 +1,18 @@
 # 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`.
+- Added Python 3.13 support in classifiers. #216
+- Added Installation instructions in `installation.md`. #217
+- Properly check if a passed (cell type) labels in plotting are a string #220
+- Fixed an issue where MetalinksDB download would fail due to User-Agent restrictions.
+
 ## 1.6.1 (28.09.2025)
 
 - Comply with AnnData CSR matrix changes

docs/index.md

@@ -6,6 +6,7 @@
 :hidden: true
 :maxdepth: 2
 
+installation.md
 api.md
 changelog.md
 contributing.md

docs/installation.md

@@ -0,0 +1,48 @@
+# 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

docs/notebooks/basic_usage.ipynb

@@ -494,6 +494,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "804d2c01",
    "metadata": {},
    "source": [
     "## By default, LIANA+ uses **human gene symbols**. See the documentation and the [Prior Knowledge vignette](https://liana-py.readthedocs.io/en/latest/notebooks/prior_knowledge.html) for details and instructions for homology conversion.\n"
@@ -1737,7 +1738,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "liana311",
+   "display_name": "liana_squidpy",
    "language": "python",
    "name": "python3"
   },
@@ -1751,7 +1752,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.13"
+   "version": "3.10.15"
   }
  },
  "nbformat": 4,

docs/notebooks/index.md

@@ -13,4 +13,5 @@ targeted.ipynb
 liana_c2c.ipynb
 mofacellular.ipynb
 mofatalk.ipynb
+inflow_score.ipynb
 ```

docs/notebooks/inflow_score.ipynb

@@ -4,7 +4,7 @@ requires = [ "hatchling" ]
 
 [project]
 name = "liana"
-version = "1.6.1"
+version = "1.7.0"
 description = "LIANA+: a one-stop-shop framework for cell-cell communication"
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -22,14 +22,14 @@ authors = [
   { name = "Jovan Tanevski"},
   { name = "Ricardo Omar Ramirez Flores"},
   { name = "Julio Saez-Rodriguez"},
-
 ]
 requires-python = ">=3.10,<3.14"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
   "anndata>=0.7.4",
@@ -52,7 +52,7 @@ optional-dependencies.dev = [
 ]
 
 optional-dependencies.extras = [
-  "decoupler>=1.6.1",
+  "decoupler>=2.0.0",
   "omnipath>=1.0.6",
   "pydeseq2>=0.3.5",
   "cell2cell",

pyproject.toml

@@ -1,4 +1,4 @@
-__version__ = '1.6.1'
+__version__ = '1.7.0'
 
 from liana import method as mt, plotting as pl, resource as rs, multi as mu, utils as ut, testing
 

src/liana/__init__.py

@@ -202,6 +202,32 @@
 mask_negatives
     Whether to mask negative-negative (low-low) or uncategorized interactions."""
 
+_spatial_kwargs = """
+spatial_kwargs
+    Keyword arguments passed to `liana.utils.spatial_pair_proximity()` for computing
+    spatial proximity weights. Default is None, which uses default values
+    (bandwidth=250, kernel='gaussian', trim_fraction=0.1)."""
+
+_kernel = """
+kernel
+    Kernel function used to generate connectivity/proximity weights.
+    It controls the shape of the connectivity weights.
+    The following options are available: ['gaussian', 'exponential', 'linear', 'misty_rbf']."""
+
+_coordinates = """
+coordinates
+    Spatial coordinates (e.g., in µm) with shape (n_cells, n_dimensions)."""
+
+_bandwidth = """
+bandwidth
+    Denotes signaling length and controls the maximum distance at which two spots/cells are considered.
+    Corresponds to the units in which spatial coordinates are expressed."""
+
+_contact_bandwidth = """
+contact_bandwidth
+    Bandwidth for contact proximity calculation and distance threshold for contact interactions.
+    If None, contact proximity is not calculated. Default is None."""
+
 
 # Plot docstrings
 _liana_res = """\
@@ -353,5 +379,10 @@
     cmap=_cmap,
     figure_size=_figure_size,
     return_fig=_return_fig,
+    spatial_kwargs=_spatial_kwargs,
+    bandwidth=_bandwidth,
+    contact_bandwidth=_contact_bandwidth,
+    kernel=_kernel,
+    coordinates=_coordinates,
 
 )