removed pyparsing dependency and moved plotting into separate file

README.md

@@ -117,13 +117,17 @@ Then go ahead and execute `ozzy.py`:
 ```
 
 ## Version
+v0.9 -- code cleanup
+    * removed networkx dependency
+    * moved plotting libraries and functions into a separate file to avoid automatic import.
+
 v0.8 -- beta status
-  * now using logging
-  * python >= 3.7 only
-  * improved header documentation
-  * using entry_points for crnsimulator script
-  * set defaultrate = 1 (new postprocessing strandard)
-  * new commandline arguments: labels, labels-strict
-  * support the constant concentration flag
+    * now using logging
+    * python >= 3.7 only
+    * improved header documentation
+    * using entry_points for crnsimulator script
+    * set defaultrate = 1 (new postprocessing strandard)
+    * new commandline arguments: labels, labels-strict
+    * support the constant concentration flag
 
 [oscillator.crn]: <https://github.com/bad-ants-fleet/crnsimulator/blob/master/tests/crns/oscillator.crn>

crnsimulator/__init__.py

@@ -1,13 +1,12 @@
 """
-Simulate formal Chemical Reaction Networks using ODEs (library interface).
+Simulate formal chemical reaction networks using ODEs (library interface).
 """
 
-__version__ = "v0.8"
+__version__ = "v0.9"
 
 import logging
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 from crnsimulator.crn_parser import parse_crn_string, parse_crn_file
 from crnsimulator.reactiongraph import ReactionGraph
 from crnsimulator.solver import writeODElib, get_integrator
-from crnsimulator.odelib_template import ode_plotter

crnsimulator/crn_parser.py

@@ -8,12 +8,10 @@
 Test using tests/test_crn_parser.py.
 """
 
-from pyparsing import (Word, Literal, Group, Suppress, Combine, Optional,
+from pyparsing import (Word, Literal, Group, Suppress, Combine, Optional, ParseException,
                        alphas, nums, alphanums, delimitedList, StringStart, StringEnd, LineEnd,
                        ZeroOrMore, OneOrMore, pythonStyleComment, ParseElementEnhance)
 
-from pyparsing import ParseException
-
 class CRNParseError(Exception):
     pass
 
@@ -203,3 +201,4 @@ def parse_crn_string(data, process = True, **kwargs):
     else:
         return crn_document.parseString(data).asList()
 
+

crnsimulator/odelib_template.py

@@ -1,17 +1,16 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 """
 A template file to simulate a specific system of Ordinary Differential Equations (ODEs).
 
 ... or an autogenerated script from the *crnsimulator* Python package.
 
 Note: If this file is executable, it is *autogenerated*.
     This means it contains a system of hardcoded ODEs together with some
-    default parameters. It may be helfpul to teak e.g.  the ode_plotter
-    function, but beware that this file may be overwritten by the next
-    execution of the `crnsimulator` executable. 
-    For heavy edits, is recommended to edit the source directly at:
-    "crnsimulator.odelib_template" or provide your own template file.
-    Alternatively, use the option --output to prevent the loss of your edits.
+    default parameters. While it may be tempting to tweak some functions,
+    beware that this file may be overwritten by the next execution of the
+    `crnsimulator` executable.  Edits should be done at the source file:
+    "crnsimulator.odelib_template.py" or you can provide an alternative
+    template file. Use the option --output to avoid overwriting this file.
 
 Usage: 
     python #<&>FILENAME<&># --help
@@ -22,96 +21,11 @@
 
 import argparse
 import numpy as np
-import matplotlib.pyplot as plt
 from scipy.integrate import odeint
 
-import seaborn as sns
-sns.set(style="darkgrid", font_scale=1, rc={"lines.linewidth": 2.0})
-
 class ODETemplateError(Exception):
     pass
 
-
-def ode_plotter(name, t, ny, svars, log = False, labels = None,
-        xlim = None, ylim = None, plim = None, labels_strict = False):
-    """ Plots the ODE trajectories.
-
-    Args:
-      name (str): Name of the outputfile including extension (e.g. *.pdf)
-      t (list[flt]) : time units plotted on the x-axis.
-      ny (list[list[flt]]) : a list of trajectories plotted on the y-axis.
-      svars (list[str]): A list of names for every trajectory in ny
-      log (bool,optional): Plot data on a logarithmic time scale
-      labels (set(),optional): Define species that appear labelled in the plot
-      xlim ((float,float), optional): matplotlib xlim.
-      ylim ((float,float), optional): matplotlib ylim.
-      plim (float, optional): Minimal occupancy to plot a trajectory. Defaults to None.
-      labels_strict (bool, optional): Only print labels that were specified using labels.
-
-    Prints:
-      A file containing the plot (Format *.pdf, *.png, etc.)
-
-    Returns:
-      [str]: Name of the file containing the plot
-    """
-    fig, ax = plt.subplots(1, 1, figsize=(8, 4.5))
-
-    # b : blue.
-    # g : green.
-    # r : red.
-    # c : cyan.
-    # m : magenta.
-    # y : yellow.
-    # k : black.
-    mycolors = ['blue', 
-                'red', 
-                'green', 
-                'orange', 
-                'maroon', 
-                'springgreen', 
-                'cyan', 
-                'magenta', 
-                'yellow']
-    mycolors += list('kkkkkkkkkkk')
-
-    if labels:
-        i = 0
-        for e, y in enumerate(ny):
-            if svars[e] in labels:
-                ax.plot(t, y, '-', label=svars[e], color=mycolors[i])
-                i = i + 1 if i < len(mycolors) - 1 else 0
-            elif not labels_strict:
-                ax.plot(t, y, '--', lw=0.1, color='gray', zorder=1)
-    else:
-        for e, y in enumerate(ny):
-            if plim is None or max(y) > plim:
-                ax.plot(t, y, '-', label=svars[e])
-            else:
-                ax.plot(t, y, '--', lw=0.1, color='gray', zorder=1)
-
-    plt.title(name)
-    if xlim:
-        plt.xlim(xlim)
-    # plt.xticks(np.arange(0, 61, step=20))
-
-    if ylim:
-        plt.ylim(ylim)
-    # plt.yticks(np.arange(0, 51, step=10))
-
-    ax.set_xlabel('Time', fontsize=16)
-    ax.set_ylabel('Concentration', fontsize=16)
-    if log:
-        ax.set_xscale('log')
-    else:
-        ax.set_xscale('linear')
-
-    plt.legend(loc='upper right')
-    fig.tight_layout()
-    plt.savefig(name)
-    plt.close()
-    return name
-
-
 rates = {
     #<&>RATES<&>#
 }
@@ -289,6 +203,7 @@ def integrate(args, setlogger = False):
             print(' '.join(map("{:.9e}".format, i)))
 
     if args.pyplot:
+        from crnsimulator.plotting import ode_plotter
         plotfile = ode_plotter(args.pyplot, time, ny, svars,
                                log=True if args.t_log else False,
                                labels=set(args.labels),

crnsimulator/plotting.py

@@ -0,0 +1,84 @@
+
+import matplotlib.pyplot as plt
+import seaborn as sns
+sns.set(style="darkgrid", font_scale=1, rc={"lines.linewidth": 2.0})
+
+def ode_plotter(name, t, ny, svars, log = False, labels = None,
+        xlim = None, ylim = None, plim = None, labels_strict = False):
+    """ Plots the ODE trajectories.
+
+    Args:
+      name (str): Name of the outputfile including extension (e.g. *.pdf)
+      t (list[flt]) : time units plotted on the x-axis.
+      ny (list[list[flt]]) : a list of trajectories plotted on the y-axis.
+      svars (list[str]): A list of names for every trajectory in ny
+      log (bool,optional): Plot data on a logarithmic time scale
+      labels (set(),optional): Define species that appear labelled in the plot
+      xlim ((float,float), optional): matplotlib xlim.
+      ylim ((float,float), optional): matplotlib ylim.
+      plim (float, optional): Minimal occupancy to plot a trajectory. Defaults to None.
+      labels_strict (bool, optional): Only print labels that were specified using labels.
+
+    Prints:
+      A file containing the plot (Format *.pdf, *.png, etc.)
+
+    Returns:
+      [str]: Name of the file containing the plot
+    """
+    fig, ax = plt.subplots(1, 1, figsize=(8, 4.5))
+
+    # b : blue.
+    # g : green.
+    # r : red.
+    # c : cyan.
+    # m : magenta.
+    # y : yellow.
+    # k : black.
+    mycolors = ['blue', 
+                'red', 
+                'green', 
+                'orange', 
+                'maroon', 
+                'springgreen', 
+                'cyan', 
+                'magenta', 
+                'yellow']
+    mycolors += list('kkkkkkkkkkk')
+
+    if labels:
+        i = 0
+        for e, y in enumerate(ny):
+            if svars[e] in labels:
+                ax.plot(t, y, '-', label=svars[e], color=mycolors[i])
+                i = i + 1 if i < len(mycolors) - 1 else 0
+            elif not labels_strict:
+                ax.plot(t, y, '--', lw=0.1, color='gray', zorder=1)
+    else:
+        for e, y in enumerate(ny):
+            if plim is None or max(y) > plim:
+                ax.plot(t, y, '-', label=svars[e])
+            else:
+                ax.plot(t, y, '--', lw=0.1, color='gray', zorder=1)
+
+    plt.title(name)
+    if xlim:
+        plt.xlim(xlim)
+    # plt.xticks(np.arange(0, 61, step=20))
+
+    if ylim:
+        plt.ylim(ylim)
+    # plt.yticks(np.arange(0, 51, step=10))
+
+    ax.set_xlabel('Time', fontsize=16)
+    ax.set_ylabel('Concentration', fontsize=16)
+    if log:
+        ax.set_xscale('log')
+    else:
+        ax.set_xscale('linear')
+
+    plt.legend(loc='upper right')
+    fig.tight_layout()
+    plt.savefig(name)
+    plt.close()
+    return name
+