Cleaned up dependencies

README.org

@@ -17,25 +17,25 @@ pip install ./scdemon
 #+END_SRC
 
 
-**** Minimal conda environment:
-
+**** Conda environment:
 #+BEGIN_SRC bash
-conda create -n scdemonpy conda-forge::anndata conda-forge::tqdm conda-forge::pip conda-forge::igraph conda-forge::umap-learn conda::scikit-build
+# Minimal:
+conda create -n scdemonpy -c conda-forge numpy pandas scipy igraph umap-learn leidenalg scanpy seaborn matplotlib
+
+# If you want to run GO enrichment:
+conda install -n scdemonpy -c bioconda gprofiler-official
 #+END_SRC
 
 
-**** Full Dependencies:
+**** Dependencies:
 
 #+BEGIN_SRC bash
-numpy, pandas,
-scipy, tqdm,
-igraph, umap-learn,
-leidenalg, scikit-learn,
-scanpy, anndata,
-seaborn, matplotlib,
-gprofiler-official,
-python-igraph, adjustText,
-numba
+# Core:
+numpy, pandas, scipy, igraph, umap-learn, 
+leidenalg, scanpy, seaborn, matplotlib
+
+# Optional:
+anndata, gprofiler-official, adjustText
 #+END_SRC
 
 
@@ -80,3 +80,6 @@ mod.save_modules(graph_id)
 gpres = sm.get_goterms(mod, graph_id)
 #+END_SRC
 
+
+Cite: Mathys*, Boix*, Akay*, et al., [_Single-cell multiregion dissection of Alzheimer’s disease_](https://www.nature.com/articles/s41586-024-07606-7)
+

docs/source/api/graph.md

@@ -1,4 +1,4 @@
-### Graph
+# Graph
 
 ```{eval-rst}
 .. module:: scdemon.graph

docs/source/api/index.rst

@@ -7,5 +7,4 @@ API
    modules
    graph
    plotting
-   utils
 

docs/source/api/modules.md

@@ -1,4 +1,4 @@
-## Modules
+# Modules
 
 <!-- TODO: Add description of how to use modules objects here -->
 

docs/source/api/plotting.md

@@ -1,4 +1,4 @@
-### Plotting
+# Plotting
 
 ```{eval-rst}
 .. module:: scdemon.plotting

docs/source/example.rst

@@ -1,4 +1,5 @@
 .. _example:
+
 Basic example
 =============
 
@@ -18,6 +19,7 @@ Basic example using one of the :code:`scanpy` datasets:
 
 
 .. TODO: link to modules objects code documentation
+
 Once we have this dataset, we can create an object that handles any modules and graphs derived from it:
 
 .. code-block:: python
@@ -28,6 +30,7 @@ Once we have this dataset, we can create an object that handles any modules and
 
 
 .. TODO: link to graph code documentation
+
 After this, we build a basic gene-gene graph and learn modules on top of it. Any graph we create is an independent :code:`graph` object under the overarching modules object.
 
 .. code-block:: python
@@ -41,6 +44,7 @@ After this, we build a basic gene-gene graph and learn modules on top of it. Any
 
 
 .. TODO: put some of these plots in the documentation
+
 We can also plot these modules in multiple ways:
 
 .. code-block:: python
@@ -54,6 +58,7 @@ We can also plot these modules in multiple ways:
 
 
 .. TODO: link gprofiler
+
 We can also use :code:`gprofiler-official` to annotate these modules with functional terms:
 
 .. code-block:: python

docs/source/usage.rst

@@ -2,6 +2,7 @@ Usage
 =====
 
 .. _installation:
+
 Installation
 ------------
 
@@ -26,19 +27,20 @@ A minimal conda environment for this package includes:
 
 .. code-block:: console
 
-   conda create -n scdemonpy conda-forge::anndata conda-forge::tqdm conda-forge::pip conda-forge::igraph conda-forge::umap-learn conda::scikit-build
+    # Minimal:
+    conda create -n scdemonpy -c conda-forge numpy pandas scipy igraph umap-learn leidenalg scanpy seaborn matplotlib
+
+    # If you want to run GO enrichment:
+    conda install -n scdemonpy -c bioconda gprofiler-official
 
 
 The full list of dependencies is as follows:
 
 .. code-block:: console
 
-    numpy, pandas,
-    scipy, tqdm,
-    igraph, umap-learn,
-    leidenalg, scikit-learn,
-    scanpy, anndata,
-    seaborn, matplotlib,
-    gprofiler-official,
-    igraph, adjustText,
-    numba
+    # Core:
+    numpy, pandas, scipy, igraph, umap-learn, 
+    leidenalg, scanpy, seaborn, matplotlib
+
+    # Optional:
+    anndata, gprofiler-official, adjustText

pyproject.toml

@@ -3,11 +3,6 @@ requires = [
     "setuptools>=60",
     "setuptools-scm>=8.0"]
 
-# [build-system]
-# requires = ["scikit-build-core>=0.3.3"] 
-# build-backend = "scikit_build_core.build"
-# build-backend = "setuptools.build_meta"
-
 [project]
 name = "scdemon"
 version = "0.0.4"
@@ -17,14 +12,10 @@ authors = [{name = "Benjamin James", email = "[email protected]"},
 license = {file = "LICENSE"}
 requires-python = ">=3.7"
 dependencies = [
-    "numpy", "pandas",
-    "scipy", "tqdm",
-    "igraph", "umap-learn",
-    "leidenalg", "scikit-learn",
-    # Added from original modules, can prune:
-    "scanpy", "anndata",
-    "seaborn", "matplotlib",
-    "igraph", "numba"
+    "numpy", "pandas", 
+    "scipy", "igraph", 
+    "umap-learn", "leidenalg", 
+    "scanpy", "seaborn", "matplotlib"
 ]
 
 [project.urls]
@@ -33,10 +24,7 @@ Source = "https://github.com/kellislab/scdemon"
 Home-page = "https://github.com/kellislab/scdemon"
 
 [project.optional-dependencies]
-test = ["adjustText", "gprofiler-official"]
-
-[tool.scikit-build]
-wheel.expand-macos-universal-tags = true
+test = ["adjustText", "gprofiler-official", "anndata"]
 
 [tool.setuptools]
 packages = ["scdemon", 

scdemon/graph/utils_community_detection.py

@@ -2,7 +2,6 @@
 """Utility scripts for community detection."""
 import logging
 import numpy as np
-import leidenalg as la
 
 
 def compute_leiden_partition(graph,
@@ -11,6 +10,7 @@ def compute_leiden_partition(graph,
                              use_weights=False,
                              n_iterations=-1,
                              random_state=1):
+    import leidenalg as la
     # Set up the leidenalg arguments:
     partition_kwargs = {}
     partition_kwargs["n_iterations"] = n_iterations