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Anne Hartebrodt
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add autogenerated documentation
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‎.github/workflows/static.yaml‎

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- name: Install dependencies
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run: |
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pip install sphinx sphinx-rtd-theme # Add any other extensions here
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# If you have a requirements.txt, use: pip install -r requirements.txt
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pip install sphinx sphinx-rtd-theme
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pip install . # This installs your package so Sphinx can import it
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- name: Build Sphinx Documentation
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run: |

‎docs/source/conf.py‎

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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../../')) # Adjust path to point to your app root
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project = 'Netmap'
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copyright = '2025, Anne Hartebrodt, Mhaned Oubounyt'
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author = 'Anne Hartebrodt, Mhaned Oubounyt'
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release = 'Jan, 2026'
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = []
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.napoleon', # Highly recommended for Google/NumPy style docstrings
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'sphinx_rtd_theme',
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]
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templates_path = ['_templates']
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exclude_patterns = []

‎docs/source/modules.rst‎

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netmap
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======
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.. toctree::
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:maxdepth: 4
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netmap

‎docs/source/netmap.downstream.rst‎

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netmap.downstream package
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=========================
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Submodules
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----------
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netmap.downstream.clustering module
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-----------------------------------
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.. automodule:: netmap.downstream.clustering
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.downstream.downstreammain module
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---------------------------------------
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.. automodule:: netmap.downstream.downstreammain
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.downstream.edge\_selection module
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----------------------------------------
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.. automodule:: netmap.downstream.edge_selection
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.downstream.final\_downstream module
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------------------------------------------
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.. automodule:: netmap.downstream.final_downstream
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.downstream.gene\_clustering module
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-----------------------------------------
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.. automodule:: netmap.downstream.gene_clustering
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: netmap.downstream
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/source/netmap.masking.rst‎

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netmap.masking package
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======================
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Submodules
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----------
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netmap.masking.external module
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------------------------------
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.. automodule:: netmap.masking.external
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.masking.internal module
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------------------------------
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.. automodule:: netmap.masking.internal
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: netmap.masking
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/source/netmap.model.rst‎

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netmap.model package
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====================
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Submodules
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----------
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netmap.model.nbautoencoder module
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---------------------------------
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.. automodule:: netmap.model.nbautoencoder
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.model.standardautoencoder module
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---------------------------------------
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.. automodule:: netmap.model.standardautoencoder
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.model.train\_model module
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--------------------------------
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.. automodule:: netmap.model.train_model
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.model.zinbautoencoder module
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-----------------------------------
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.. automodule:: netmap.model.zinbautoencoder
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: netmap.model
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/source/netmap.rst‎

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netmap package
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==============
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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netmap.downstream
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netmap.masking
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netmap.model
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netmap.utils
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Submodules
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----------
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netmap.model\_concept module
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----------------------------
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.. automodule:: netmap.model_concept
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.netmap module
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--------------------
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.. automodule:: netmap.netmap
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: netmap
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/source/netmap.utils.rst‎

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netmap.utils package
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====================
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Submodules
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----------
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netmap.utils.data\_utils module
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-------------------------------
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.. automodule:: netmap.utils.data_utils
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.utils.misc module
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------------------------
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.. automodule:: netmap.utils.misc
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.utils.netmap\_config module
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----------------------------------
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.. automodule:: netmap.utils.netmap_config
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:members:
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:show-inheritance:
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:undoc-members:
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netmap.utils.tf\_utils module
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-----------------------------
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.. automodule:: netmap.utils.tf_utils
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: netmap.utils
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:members:
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:show-inheritance:
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:undoc-members:

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