Merge branch 'graphviz' of https://github.com/biomass-dev/biomass int…

…o graphviz
biomass-dev · Jun 22, 2022 · 8425db7 · 8425db7
2 parents 61bda09 + 55c05af
commit 8425db7
Show file tree

Hide file tree

Showing 3 changed files with 31 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -36,6 +36,8 @@ $ pip install biomass
 
 BioMASS supports Python 3.7 or newer.
 
+:ledger: **Note: You will need to manually install [Graphviz](https://www.graphviz.org) (version 2.42 or later).**
+
 ## References
 
 - Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. _Cancers_ **12**, 2878 (2020). https://doi.org/10.3390/cancers12102878

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -3,28 +3,46 @@ Installation
 
 BioMASS supports Python 3.7 or newer.
 
+
 PyPI
 ----
 
 Install BioMASS from PyPI using::
 
    pip install biomass
 
-Development version
--------------------
+.. Note::
+    You will need to manually install `Graphviz <https://www.graphviz.org>`_ (version 2.42 or later).
 
-If you want the latest development version, install from GitHub using::
+Linux (Ubuntu and Debian)
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
-   pip install git+https://github.com/biomass-dev/biomass
+.. code-block::
+
+    $ sudo apt-get install graphviz graphviz-dev
+
+Linux (Fedora and Red Hat)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You may need to replace ``dnf`` with ``yum`` in the example below.
 
-Docker
-------
+.. code-block::
+    
+    $ sudo dnf install graphviz graphviz-devel
 
-BioMASS is also available through docker::
+macOS
+^^^^^
 
-   docker pull jnicolaus/biomass:latest
+Use the Homebrew package manager.
 
+.. code-block::
 
-or through singularity::
+    $ brew install graphviz
+
+Development version
+-------------------
+
+If you want the latest development version, install from GitHub using::
+
+   pip install git+https://github.com/biomass-dev/biomass
 
-   singularity pull docker://jnicolaus/biomass:latest
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,7 @@
 matplotlib>=3.0
 numpy>=1.17
 pandas>=0.24
+pygraphviz
 scipy>=1.6 # integrate.simps was renamed to integrate.simpson (v1.6.0)
 seaborn>=0.11.2
 tqdm>=4.50.2