DOC update dependencies

Author: TomDLT

README.rst

@@ -65,13 +65,9 @@ The package ``voxelwise_tutorials`` has the following dependencies:
 - `h5py <https://github.com/h5py/h5py>`_
 - `scikit-learn <https://github.com/scikit-learn/scikit-learn>`_
 - `matplotlib <https://github.com/matplotlib/matplotlib>`_
+- `networkx <https://github.com/networkx/networkx>`_
+- `nltk <https://github.com/nltk/nltk>`_
 - `pycortex <https://github.com/gallantlab/pycortex>`_
-
-Each tutorial requires additional packages, as listed in their respective
-documentations, such as:
-
-- `voxelwise_tutorials <https://github.com/gallantlab/voxelwise_tutorials>`_
-  (this repository)
 - `himalaya <https://github.com/gallantlab/himalaya>`_
 - `pymoten <https://github.com/gallantlab/pymoten>`_
 

doc/voxelwise_package.rst

@@ -38,12 +38,9 @@ The package ``voxelwise_tutorials`` has the following dependencies:
 - `h5py <https://github.com/h5py/h5py>`_
 - `scikit-learn <https://github.com/scikit-learn/scikit-learn>`_
 - `matplotlib <https://github.com/matplotlib/matplotlib>`_
+- `networkx <https://github.com/networkx/networkx>`_
+- `nltk <https://github.com/nltk/nltk>`_
 - `pycortex <https://github.com/gallantlab/pycortex>`_
-
-Each tutorial requires additional packages, as listed in their respective
-documentations, such as:
-
-- `voxelwise_tutorials <https://github.com/gallantlab/voxelwise_tutorials>`_ (this helper package)
 - `himalaya <https://github.com/gallantlab/himalaya>`_
 - `pymoten <https://github.com/gallantlab/pymoten>`_
 

setup.py

@@ -11,12 +11,16 @@
         __version__ = match.groups()[0]
 
 requirements = [
-    "h5py",
-    "matplotlib",
     "numpy",
-    "pycortex",
     "scipy",
+    "h5py",
     "scikit-learn>=0.23",
+    "matplotlib",
+    "networkx",
+    "nltk",
+    "pycortex",
+    "himalaya @ git+https://github.com/gallantlab/himalaya@master#egg=himalaya",  # noqa
+    "pymoten @ git+https://github.com/gallantlab/pymoten@master#egg=pymoten",
 ]
 
 if __name__ == "__main__":

tutorials/movies_3T/README.rst

@@ -32,17 +32,8 @@ the scikit-learn terminology, which is explained in great details in the
 **Requirements:**
 This tutorial requires the following Python packages:
 
-- voxelwise_tutorials  (this repository)
-- numpy
-- scipy
-- h5py
-- pycortex
-- scikit-learn
-- matplotlib
-- himalaya
-- jupyter  (optional, to run examples as notebooks)
-- pymoten  (optional, for extracting motion energy)
-- cupy/pytorch  (optional, to use a GPU backend in himalaya)
+- voxelwise_tutorials  (this repository) and its dependencies
+- cupy or pytorch  (optional, to use a GPU backend in himalaya)
 
 **References:**
 

tutorials/movies_4T/README.rst

@@ -26,17 +26,8 @@ publication [5]_, and the CRCNS data set [6]_.
 **Requirements:**
 This tutorial requires the following Python packages:
 
-- voxelwise_tutorials  (this repository)
-- numpy
-- scipy
-- h5py
-- pycortex
-- scikit-learn
-- matplotlib
-- himalaya
-- pymoten
-- jupyter  (optional, to run examples as notebooks)
-- cupy/pytorch  (optional, to use a GPU backend in himalaya)
+- voxelwise_tutorials  (this repository) and its dependencies
+- cupy or pytorch  (optional, to use a GPU backend in himalaya)
 
 **References:**
 

tutorials/notebooks/README.md

@@ -15,18 +15,5 @@ install the `voxelwise_tutorials` package:
     pip install .
 ```
 
-You also need the following dependencies:
-
-- numpy
-- scipy
-- h5py
-- scikit-learn
-- jupyter
-- matplotlib
-- himalaya
-- pycortex  (optional, for using 3D brain viewers)
-- pymoten  (optional, for extracting motion energy)
-- cupy/pytorch (optional, to use a GPU backend in himalaya)
-
 For more info about how to run jupyter notebooks, see
 [the official documentation](https://jupyter-notebook.readthedocs.io/en/stable/).