Enable running biomass without Graphviz (#162)

* Enable running biomass without Graphviz

* Don't check pygraphviz in dynamic_plot

* Remove _check_pygraphviz

* Update installation

* Remove Graphviz from requirements

* Bump version to 0.9.1

.github/workflows/build.yml

@@ -27,7 +27,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install .[graph]
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

README.md

@@ -36,8 +36,6 @@ $ 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

biomass/graph.py

@@ -5,9 +5,6 @@
 from types import ModuleType
 from typing import List, Literal, Optional
 
-import pygraphviz as pgv
-from pyvis.network import Network
-
 
 class NetworkGraph(object):
     """
@@ -52,6 +49,8 @@ def __init__(self, path: str, biomass_model: ModuleType):
         self.viz = biomass_model.Visualization()
         self.rxn = biomass_model.ReactionNetwork()
 
+        self.graph = None
+
     @property
     def path(self) -> str:
         return self._path
@@ -129,7 +128,7 @@ def to_graph(self) -> None:
         """Constructs a directed graph of the model.
         Using the pygraphviz library a directed graph of the model is constructed by parsing the equations from
         ode.py/reaction_network.py. Equations will be split at the equal sign and an edge is added between the species on the
-        lefthand side to all species on the righthand side. Self references will not be considered.
+        lefthand side to all species on the right hand side. Self references will not be considered.
 
         Raises
         ------
@@ -141,6 +140,11 @@ def to_graph(self) -> None:
         UserWarning
             If species equations are detected outside of the ODE section.
         """
+        try:
+            import pygraphviz as pgv
+        except ImportError:
+            print("pygraphviz is required to run this function.")
+
         use_flux = False
         try:
             if len(self.rxn.flux(0, self.ival(), self.pval())) > 0:
@@ -218,9 +222,7 @@ def static_plot(
         Creates graph with dot layout in pdf file format. Nodes will be rectangular and colored bisque, edges will have no arrows indicating direction.
 
         """
-        try:
-            _ = self.graph
-        except AttributeError:
+        if self.graph is None:
             self.to_graph()
         if gviz_prog not in (available_layout := ["neato", "dot", "twopi", "circo", "fdp", "nop"]):
             raise ValueError(
@@ -267,8 +269,11 @@ def dynamic_plot(
         Creates interactive graph. Controls for physics, manipulation and interaction will be available.
         """
         try:
-            _ = self.graph
-        except AttributeError:
+            from pyvis.network import Network
+        except ImportError:
+            print("pyvis is required to run this function.")
+
+        if self.graph is None:
             self.to_graph()
         if os.path.splitext(file_name)[1] != ".html":
             file_name = file_name + ".html"

biomass/version.py

@@ -1,2 +1,2 @@
 """BioMASS library version"""
-__version__ = "0.9.0"
+__version__ = "0.9.1"

docs/installation.rst

@@ -12,32 +12,8 @@ Install BioMASS from PyPI using::
    pip install biomass
 
 .. Note::
-    You will need to manually install `Graphviz <https://www.graphviz.org>`_ (version 2.42 or later).
-
-Linux (Ubuntu and Debian)
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. 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.
-
-.. code-block::
-    
-    $ sudo dnf install graphviz graphviz-devel
-
-macOS
-^^^^^
-
-Use the Homebrew package manager.
-
-.. code-block::
-
-    $ brew install graphviz
+    If you wish to use `graph visualization functions <https://biomass-core.readthedocs.io/en/latest/graph_visualization.html>`_, install biomass via ``pip install biomass[graph]``.
+    In that case you will need to manually install `Graphviz <https://www.graphviz.org>`_ (version 2.42 or later).
 
 Development version
 -------------------

requirements.txt

@@ -1,8 +1,6 @@
 matplotlib>=3.0
 numpy>=1.17
 pandas>=0.24
-pygraphviz>=1.9
-pyvis>=0.2.1
 scipy>=1.6 # integrate.simps was renamed to integrate.simpson (v1.6.0)
 seaborn>=0.11.2
 tqdm>=4.50.2

setup.py

@@ -61,6 +61,10 @@ def setup_package():
         packages=find_packages(exclude=["tests", "docs"]),
         install_requires=get_install_requires(),
         extras_require={
+            "graph": [
+                "pygraphviz>=1.9",
+                "pyvis>=0.2.1",
+            ],
             "dev": [
                 "black>=20.8b1",
                 "flake8",