Fixing readthedocs

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: docs/source/requirements.txt

LICENSE.txt

@@ -0,0 +1,19 @@
+Corresponding SPDX licence
+BSD 3-Clause "New" or "Revised" License
+Licence ID
+BSD-3-Clause
+
+
+Licence text
+Copyright (c) 2019-2023, Chintaluri et al.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -1,8 +1,26 @@
 include LICENSE.txt
 include README.rst
-graft data
+include kcsd/data/gang_7x7_200/electrode_positions/elcoord_x_y_z
+include kcsd/data/gang_7x7_200/LFP/myLFP
+include kcsd/data/gang_7x7_200/morphology/*
+include kcsd/data/ball_and_stick_8/electrode_positions/elcoord_x_y_z
+include kcsd/data/ball_and_stick_8/LFP/myLFP
+include kcsd/data/ball_and_stick_8/morphology/*
+include kcsd/data/ball_and_stick_16/electrode_positions/elcoord_x_y_z
+include kcsd/data/ball_and_stick_16/LFP/myLFP
+include kcsd/data/ball_and_stick_16/morphology/*
+include kcsd/data/ball_and_stick_128/electrode_positions/elcoord_x_y_z
+include kcsd/data/ball_and_stick_128/LFP/myLFP
+include kcsd/data/ball_and_stick_128/morphology/*
+include kcsd/data/Y_shaped_neuron/electrode_positions/elcoord_x_y_z
+include kcsd/data/Y_shaped_neuron/LFP/myLFP
+include kcsd/data/Y_shaped_neuron/morphology/*
+include kcsd/data/Simple_with_branches/electrode_positions/elcoord_x_y_z
+include kcsd/data/Simple_with_branches/LFP/myLFP
+include kcsd/data/Simple_with_branches/morphology/*
+include kcsd/data/morphology/*
+include kcsd/data/sinsyn.mod
 graft figures
-graft doc
-graft tests
-graft validation
-global-exclude *.py[cod] __pycache__ *.so
+graft docs
+graft tutorials
+global-exclude *.py[cod] __pycache__ *.so *.pdf *.npz *.png *.npy

README.rst

@@ -1,7 +1,11 @@
 Kernel Current Source Density
 =============================
 
-This 2.0 version of kCSD inverse method proposed in python3
+This 2.0 version of kCSD method.
+
+Only supported for python 3.
+
+
 
 Relevant Papers
 ---------------
@@ -41,11 +45,12 @@ More information on the tutorials is provided here `Tutorials!`_
 
 .. _Tutorials!: /docs/source/TUTORIALS.rst
 
-To have these tutorials and saved on your desktop, you will also need jupyter-notebook installed
+You can also save these tutorials on your desktop, for this you will
+need to install jupyter-notebook. Do this by
 
 ..  code-block:: bash
 
-		 pip install jupyterlab
+		 pip install jupyter notebook
 
 
 Figures
@@ -83,7 +88,7 @@ Also included here are authors and their contributions, citation policy, contact
 
 Earlier Stable versions
 -----------------------
-Please see git tags for earlier versions
+Please see git tags for earlier versions. These are not available as packages unfortunately.
 
 - v1.2 corresponds to the first time kCSD-python released as a python package
 - v1.0 corresponds to the version with the test cases written inside tests folder

docs/source/conf.py

@@ -52,8 +52,8 @@
 
 # General information about the project.
 project = 'kCSD-python'
-copyright = '2019, Chintaluri et.al'
-author = 'Chintaluri et.al'
+copyright = '2019-2023, Chintaluri et al'
+author = 'Chintaluri et al'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the