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Breaking changes: major reorganization of netneurotools #140

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Nov 18, 2024
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5caf537
Initial reorg
liuzhenqi77 May 10, 2024
e8bb7e3
Fix examples
liuzhenqi77 May 10, 2024
8e320e7
Fix netneurotools.datasets
liuzhenqi77 May 14, 2024
8479622
Lots of fixes
liuzhenqi77 May 14, 2024
d55443c
Fix style
liuzhenqi77 May 14, 2024
148aee8
Fix package data
liuzhenqi77 May 14, 2024
09b9c92
Fix doctests
liuzhenqi77 May 14, 2024
0321994
Add test for custom colormaps
liuzhenqi77 May 22, 2024
a4747f2
Fix doc config
liuzhenqi77 May 22, 2024
63b5106
Refactor datasets module
liuzhenqi77 May 22, 2024
16bf5ff
Fix tests
liuzhenqi77 May 22, 2024
4eda1a0
Fix style
liuzhenqi77 May 22, 2024
32335f7
Fix tests
liuzhenqi77 May 22, 2024
9f06f93
Fix style
liuzhenqi77 May 22, 2024
9123745
Fix pyproject.toml
liuzhenqi77 Nov 5, 2024
3a16eca
Fix error
liuzhenqi77 Nov 5, 2024
1420d85
Fix numpy changes
liuzhenqi77 Nov 5, 2024
fd3b03d
[MNT] Update redocs/requirements.txt
liuzhenqi77 Nov 8, 2024
5cd7d0e
Merge branch 'master' of github.com:netneurolab/netneurotools into br…
liuzhenqi77 Nov 8, 2024
2d68c5c
Update README.rst
liuzhenqi77 Nov 8, 2024
c41dc01
Update README.rst to streamline content and improve clarity
liuzhenqi77 Nov 8, 2024
6f11e8d
Refactor dataset download functions to improve readability
liuzhenqi77 Nov 12, 2024
ae086b4
Add new datasets and update project fetching functions
liuzhenqi77 Nov 12, 2024
f03d97a
Add curated datasets for fsaverage, fsLR, and CIVET
liuzhenqi77 Nov 15, 2024
63a22c5
Add pyvista plotter
liuzhenqi77 Nov 15, 2024
82b5926
Improve pyvista import handling
liuzhenqi77 Nov 15, 2024
b1ade67
Improve PyVista import handling and error reporting
liuzhenqi77 Nov 15, 2024
abc386e
Mark test as expected failures
liuzhenqi77 Nov 15, 2024
388f7fc
Refactor test_fetch.py
liuzhenqi77 Nov 16, 2024
0ed21fe
Rename datasets and update URL handling for GitHub archives
liuzhenqi77 Nov 16, 2024
068a07c
Fix typo in API documentation
liuzhenqi77 Nov 18, 2024
0d47815
Update documentation to reflect transition from PySurfer to Pyvista f…
liuzhenqi77 Nov 18, 2024
7e55153
Add transforms module for datasets
liuzhenqi77 Nov 18, 2024
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
docs/generated/
docs/auto_examples/
docs/modules/
docs/sg_execution_times.rst

# Byte-compiled / optimized / DLL files
__pycache__/
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4 changes: 3 additions & 1 deletion MANIFEST.in
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
include README.rst LICENSE environment.yml requirements.txt
recursive-include netneurotools/data *
include versioneer.py
include netneurotools/datasets/datasets.json
include netneurotools/datasets/references.json
include netneurotools/datasets/netneurotools.bib
60 changes: 34 additions & 26 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -26,53 +26,60 @@ netneurotools: Tools for network neuroscience
|

This toolbox is a collection of functions written in Python that get frequent
usage in the `Network Neuroscience Lab <netneurolab.github.io/>`_, housed in
usage in the `Network Neuroscience Lab <https://netneurolab.github.io/>`_, housed in
the `Brain Imaging Centre <https://www.mcgill.ca/bic/home>`_ at
`McGill University <https://www.mcgill.ca/>`_.

.. _installation:

Installation
------------

Install directly from PyPi with :code:`pip install netneurotools` or install the main branch with

.. code-block:: bash

git clone https://github.com/netneurolab/netneurotools.git
cd netneurotools
pip install .

.. _features:

Features
--------

* Network neuroscience metrics: up-to-date and optimized
Netneurotools provides a wide range of tools for network neuroscience research.

* Network communication
* Null networks
* A range of useful datasets fetchers

* Brain plotting functions: easy to use and customize
* Network construction: empirical and surrogate

* Surface visualization
`plot_fsaverage <https://netneurotools.readthedocs.io/en/latest/generated/netneurotools.plotting.plot_fsaverage.html>`_
and `plot_fslr <https://netneurotools.readthedocs.io/en/latest/generated/netneurotools.plotting.plot_fslr.html>`_
* 3D point brain `plot_point_brain <https://netneurotools.readthedocs.io/en/latest/generated/netneurotools.plotting.plot_point_brain.html>`_
* Sorted communities `plot_mod_heatmap <https://netneurotools.readthedocs.io/en/latest/generated/netneurotools.plotting.plot_mod_heatmap.html>`_
* Network (graph) metrics calculation: up-to-date and optimized

* Statistics functions
* Brain and network visualization

* Dominance analysis `get_dominance_stats <https://netneurotools.readthedocs.io/en/latest/generated/netneurotools.stats.get_dominance_stats.html>`_
* Optimized statistics routines

* Fetchers for common datasets
* Convenient interface for external tools

* Utilities for working with FreeSurfer and CIVET
* And much more!


Check out our `documentation <https://netneurotools.readthedocs.io/en/latest>`_
for more information!


.. _installation:

Installation
------------

You can install directly from PyPi with :code:`pip install netneurotools`.

This package is under active development. We recommend installing the latest version
with

.. code-block:: bash

pip install git+https://github.com/netneurolab/netneurotools.git


If you are looking for the earlier version of the toolbox before the recent breaking changes,
you can install it with

.. code-block:: bash

pip install git+https://github.com/netneurolab/[email protected]


.. _development:

Development
Expand All @@ -85,6 +92,7 @@ you've found a bug, are experiencing a problem, or have a question, create a
new `issue <https://github.com/netneurolab/netneurotools/issues>`_ with some
information about it and one of our team members will do our best to help you.


.. _licensing:

License Information
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26 changes: 0 additions & 26 deletions dev_environment.yml

This file was deleted.

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