Updated README with Troubleshooting section, added notebook n10 about…

… importing a network from sif file and exporting it in bnet format.
sysbio-curie · Oct 28, 2024 · 396065d · 396065d
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diff --git a/README.rst b/README.rst
@@ -65,6 +65,23 @@ For the latest development version, you can still clone the repository and insta
 
 This will give you the latest version of `NeKo` (not officially released, so be aware there could be some bugs) along with the necessary external dependencies.
 
+Troubleshooting
+---------------
+
+If during the installation you encounter problems with the installation of Graphviz, you could be missing basic Graphiz installation on your machine.
+You can install it on Linux system with the following command:
+
+.. code-block:: bash
+
+    sudo apt-get install python3-dev graphviz libgraphviz-dev
+
+or on Mac system:
+
+.. code-block:: bash
+
+    brew install python3-dev graphviz libgraphviz-dev
+
+For more details visit: https://graphviz.org/download/
 
 Documentation
 -------------

diff --git a/docs/src/contents.rst b/docs/src/contents.rst
@@ -31,6 +31,7 @@ Contents
    notebooks/7_tissue_mapping
    notebooks/8_Compare_networks
    notebooks/9-Recreating_famous_pathways
+   notebooks/10_Import_and_complete_a_network
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/src/index.rst b/docs/src/index.rst
@@ -26,7 +26,7 @@ All the dependencies are listed in the pyproject.toml file. To install the packa
 
 CURRENT FEATURES:
 
-version 0.9.1
+version 0.9.6
 --------------
 
 - Network creation and manipulation: The package allows for the creation of a network of nodes and edges, with various methods for enrichment analysis. This includes adding and removing nodes and edges, loading a network from a SIF (Simple Interaction Format) file, and adding paths to the edge list of the network.