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Merged
wiheto merged 1 commit into from
Dec 11, 2025
Merged

Add temporal spectral community detection #94

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6 changes: 5 additions & 1 deletion .gitnore → .gitignore
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@@ -1,4 +1,3 @@
117 lines (94 sloc) 1.32 KB
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
Expand Down Expand Up @@ -29,5 +28,10 @@ share/python-wheels/

# Sphinx documentation
docs/_build/
docs/api/

# IDE/editor metadata
.vscode/

# macOS Finder artifacts
teneto/__MACOSX/
9 changes: 3 additions & 6 deletions docs/conf.py
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Expand Up @@ -18,7 +18,7 @@
# -- Project information -----------------------------------------------------

project = 'teneto'
copyright = '2018-2021, William Hedley Thompson'
copyright = '2018-2025, William Hedley Thompson'
author = 'William Hedley Thompson'

version = "../teneto/_version.py"
Expand All @@ -45,7 +45,6 @@
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'matplotlib.sphinxext.only_directives',
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@wiheto wiheto Dec 1, 2025

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Not sure why this being removed? Was it redundant?

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@JacobH140 JacobH140 Dec 2, 2025

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Yes, I believe it is redundant, and indeed removed as of Matplotlib 3.0. I had to drop the extension to build the docs.

'matplotlib.sphinxext.plot_directive',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
Expand All @@ -56,7 +55,7 @@
'sphinx.ext.viewcode',
'sphinx.ext.githubpages',
'sphinx.ext.napoleon',
'm2r',
'myst_parser',
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@wiheto wiheto Dec 1, 2025

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Whats the purpose of adding this in the documents?

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@JacobH140 JacobH140 Dec 2, 2025

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m2r is no longer supported; Sphinx currently recommends myst_parser instead.

'sphinx_automodapi.automodapi',
'sphinx.ext.autosectionlabel',
'nbsphinx',
Expand All @@ -79,7 +78,7 @@
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
language = 'en'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
Expand Down Expand Up @@ -200,5 +199,3 @@
numpydoc_show_class_members = False
# MOCK MODULESS
autodoc_mock_imports = ['tables', 'scikit-learn', 'joblib', 'nilearn', 'NiftiLabelsMasker']


4 changes: 2 additions & 2 deletions docs/requirements.txt
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Expand Up @@ -5,10 +5,10 @@ pybids>=0.11.1
#python-igraph>=0.7.1
#louvain >= 0.6.1
statsmodels>=0.8.0
m2r>=0.2.1
myst-parser>=2.0
nbsphinx>=0.4.2
sphinx-automodapi>=0.9
networkx>=2.0
python-louvain>=0.13
matplotlib==2.2.0
matplotlib>=3.8
templateflow>=0.6.2
7 changes: 7 additions & 0 deletions docs/teneto.communitydetection.rst
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@@ -1,6 +1,13 @@
teneto.communitydetection
=================================

Spectral
----------------------------------------

.. automodule:: teneto.communitydetection.spectral
:members:
:show-inheritance:

Louvain
----------------------------------------

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1 change: 1 addition & 0 deletions requirements.txt
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Expand Up @@ -9,3 +9,4 @@ statsmodels>=0.8.0
networkx>=2.0
python-louvain>=0.13
tables>=3.4.4
scikit-learn>=1.0
3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -20,7 +20,8 @@
'pandas>=0.21',
'scipy>=1.4.1',
'numpy>=1.19.5',
'templateflow>=0.6.2'],
'templateflow>=0.6.2',
'scikit-learn>=1.0'],
description='Temporal network tools',
packages=find_packages(),
author='William Hedley Thompson',
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14 changes: 10 additions & 4 deletions teneto/communitydetection/__init__.py
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@@ -1,6 +1,12 @@
"""Import of community detection"""
"""Community detection convenience imports."""
from teneto.communitydetection.louvain import *
from teneto.communitydetection.tctc import tctc
#from teneto.communitydetection.louvain import find_tctc
__all__ = ['tctc', 'temporal_louvain',
'make_consensus_matrix', 'make_temporal_consensus', ]
from teneto.communitydetection.spectral import temporal_spectral

__all__ = [
"tctc",
"temporal_louvain",
"make_consensus_matrix",
"make_temporal_consensus",
"temporal_spectral",
]
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