Merge pull request #789 from StochSS/develop

Release v1.7.0

.github/workflows/run-full-tests.yml

@@ -21,6 +21,16 @@ jobs:
       with:
         python-version: ${{ matrix.python-versions }}
 
+    # see: https://github.com/actions/virtual-environments/pull/5729
+    # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
+    # Until this issue can be addressed, downgrade to the previous known working version, v8.1.0.
+    - name: Initialize MinGW dependencies
+      run: |
+        choco install make
+        choco uninstall mingw
+        choco install mingw --version 8.1.0 --force
+      if: matrix.os == 'windows-latest'
+
     - name: Install Python dependencies
       run: | 
         python -m pip install --upgrade pip
@@ -32,4 +42,4 @@ jobs:
         pip install nbformat
         
     - name: Run tests
-      run: coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_tests.py -m develop
+      run: coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_integration_tests.py -m develop

.github/workflows/run-integration-tests.yml

@@ -0,0 +1,42 @@
+name: Run GillesPy2 Integration Tests
+
+on: [push]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+
+    steps:
+    - name: Initialize environment
+      uses: actions/checkout@v2
+
+    - name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+
+    # see: https://github.com/actions/virtual-environments/pull/5729
+    # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
+    # Until this issue can be addressed, downgrade to the previous known working version, v8.1.0.
+    - name: Initialize MinGW dependencies
+      run: |
+        choco install make
+        choco uninstall mingw
+        choco install mingw --version 8.1.0 --force
+      if: matrix.os == 'windows-latest'
+
+    - name: Install Python dependencies
+      run: | 
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install python-libsbml
+        pip install cython
+        pip install coverage
+        pip install nbformat
+        pip install nbconvert
+        
+    - name: Run tests
+      run: coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_integration_tests.py -m develop

.github/workflows/run-system-tests.yml

@@ -0,0 +1,44 @@
+name: Run GillesPy2 System Tests
+
+on:
+  push:
+    branches: [main, develop]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+
+    steps:
+    - name: Initialize environment
+      uses: actions/checkout@v2
+
+    - name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+
+    # see: https://github.com/actions/virtual-environments/pull/5729
+    # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
+    # Until this issue can be addressed, downgrade to the previous known working version, v8.1.0.
+    - name: Initialize MinGW dependencies
+      run: |
+        choco install make
+        choco uninstall mingw
+        choco install mingw --version 8.1.0 --force
+      if: matrix.os == 'windows-latest'
+
+    - name: Install Python dependencies
+      run: | 
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install python-libsbml
+        pip install cython
+        pip install coverage
+        pip install nbformat
+        pip install nbconvert
+        
+    - name: Run tests
+      run: coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_system_tests.py -m develop

.github/workflows/run-tests.yml → .github/workflows/run-unit-tests.yml

@@ -1,4 +1,4 @@
-name: Run GillesPy2 Tests
+name: Run GillesPy2 Unit Tests
 
 on: [push]
 
@@ -18,6 +18,16 @@ jobs:
       with:
         python-version: '3.7'
 
+    # see: https://github.com/actions/virtual-environments/pull/5729
+    # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
+    # Until this issue can be addressed, downgrade to the previous known working version, v8.1.0.
+    - name: Initialize MinGW dependencies
+      run: |
+        choco install make
+        choco uninstall mingw
+        choco install mingw --version 8.1.0 --force
+      if: matrix.os == 'windows-latest'
+
     - name: Install Python dependencies
       run: | 
         python -m pip install --upgrade pip
@@ -29,4 +39,4 @@ jobs:
         pip install nbconvert
         
     - name: Run tests
-      run: coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_tests.py -m develop
+      run: coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_unit_tests.py -m develop

.gitignore

@@ -69,3 +69,5 @@ __pycache__
 .coverage
 htmlcov
 /build
+.idea
+

.travis.yml

@@ -36,7 +36,8 @@ install:
   - pip3 install cython
   - pip3 install coverage
 script:
-  - "coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_tests.py -m develop"
+  - "coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_unit_tests.py -m develop"
+  - "coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_integration_tests.py -m develop"
 deploy:
   # API token stored in env var PYPI_PASSWORD on Travis CI
   provider: pypi

README.md

@@ -2,7 +2,7 @@
 <img src="https://raw.githubusercontent.com/StochSS/GillesPy2/develop/.graphics/gillespy2-logo.png">
 </p>
 
-GillesPy2 is a Python 3 package for stochastic simulation of biochemical systems.  It offers an object-oriented approach for creating mathematical models of biological systems, as well as a variety of methods for performing time simulation of those models.  The methods include the [Gillespie direct method (SSA)](https://en.wikipedia.org/wiki/Gillespie_algorithm), several variant stochastic simulation methods including [tau-leaping](https://en.wikipedia.org/wiki/Tau-leaping), and numerical integration of ODEs.  The solvers support a variety of user environments, with optimized code for C++, [Cython](https://cython.org), and [NumPy](https://numpy.org).  GillesPy2 also supports [SBML](https://en.wikipedia.org/wiki/SBML).
+GillesPy2 is a Python 3 package for stochastic simulation of biochemical systems.  It offers an object-oriented approach for creating mathematical models of biological systems, as well as a variety of methods for performing time simulation of those models.  The methods include the [Gillespie direct method (SSA)](https://en.wikipedia.org/wiki/Gillespie_algorithm), several variant stochastic simulation methods including [tau-Leaping](https://en.wikipedia.org/wiki/Tau-leaping), and numerical integration of ODEs.  The solvers support a variety of user environments, with optimized code for C++, [Cython](https://cython.org), and [NumPy](https://numpy.org).  GillesPy2 also supports [SBML](https://en.wikipedia.org/wiki/SBML).
 
 <table><tr><td><b>
 <img width="20%" align="right" src="https://raw.githubusercontent.com/StochSS/GillesPy2/develop/.graphics/stochss-logo.png">
@@ -70,7 +70,7 @@ GillesPy2 provides simple object-oriented abstractions for defining a model of a
 1. Create a `GillesPy2.Model` containing molecular species, parameters, and reactions (or import it from an [SBML](http://sbml.org) file)
 2. Invoke the model's `.run()` method.
 
-The `run()` method can be customized using keyword arguments to select different solvers, random seed, data return type and more.  For more detailed examples on how to use GillesPy2, please see the [Getting Started](https://github.com/StochSS/GillesPy2/tree/main/examples/StartHere.ipynb) Jupyter notebook contained in the [examples](https://github.com/StochSS/GillesPy2/tree/main/examples) subdirectory.
+The `run()` method can be customized using keyword arguments to select different solvers, random seed, data return type and more.  For more detailed examples on how to use GillesPy2, please see the [Getting Started](https://github.com/StochSS/GillesPy2/tree/main/examples/Start_Here.ipynb) Jupyter notebook contained in the [examples](https://github.com/StochSS/GillesPy2/tree/main/examples) subdirectory.
 
 ### _Simple example to illustrate the use of GillesPy2_
 
@@ -82,43 +82,44 @@ The `run()` method can be customized using keyword arguments to select different
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<i>k<sub>d</sub></i><br>
 </p>
 
-In GillesPy2, a model is expressed as an object having the parent class `Model`.  Components of the model, such as the reactions, molecular species, and characteristics such as the time span for simulation, are all defined within the subclass definition.  The following Python code represents our dimerization model using GillesPy2's facility:
+In GillesPy2, a model is expressed as an object.  Components, such as the reactions, molecular species, and characteristics such as the time span for simulation, are all defined within the model.  The following Python code represents our dimerization model using GillesPy2's facility:
 
 ```python
-class Dimerization(gillespy2.Model):
-    def __init__(self, parameter_values=None):
-        # First call the gillespy2.Model initializer.
-        gillespy2.Model.__init__(self, name='Dimerization')
-
-        # Define parameters for the rates of creation and dissociation.
-        k_c = gillespy2.Parameter(name='k_c', expression=0.005)
-        k_d = gillespy2.Parameter(name='k_d', expression=0.08)
-        self.add_parameter([k_c, k_d])
-
-        # Define variables for the molecular species representing M and D.
-        m = gillespy2.Species(name='monomer', initial_value=30)
-        d = gillespy2.Species(name='dimer',   initial_value=0)
-        self.add_species([m, d])
-
-        # The list of reactants and products for a Reaction object are each a
-        # Python dictionary in which the dictionary keys are Species objects
-        # and the values are stoichiometries of the species in the reaction.
-        r_c = gillespy2.Reaction(name="r_creation", rate=k_c, reactants={m:2}, products={d:1})
-        r_d = gillespy2.Reaction(name="r_dissociation", rate=k_d, reactants={d:1}, products={m:2})
-        self.add_reaction([r_c, r_d])
-
-        # Set the timespan for the simulation.
-        self.timespan(numpy.linspace(0, 100, 101))
+def create_dimerization(parameter_values=None):
+    # First call the gillespy2.Model initializer.
+    model = gillespy2.model(name='Dimerization')
+
+    # Define parameters for the rates of creation and dissociation.
+    k_c = gillespy2.Parameter(name='k_c', expression=0.005)
+    k_d = gillespy2.Parameter(name='k_d', expression=0.08)
+    model.add_parameter([k_c, k_d])
+
+    # Define variables for the molecular species representing M and D.
+    m = gillespy2.Species(name='monomer', initial_value=30)
+    d = gillespy2.Species(name='dimer',   initial_value=0)
+    model.add_species([m, d])
+
+    # The list of reactants and products for a Reaction object are each a
+    # Python dictionary in which the dictionary keys are Species objects
+    # and the values are stoichiometries of the species in the reaction.
+    r_c = gillespy2.Reaction(name="r_creation", rate=k_c, reactants={m:2}, products={d:1})
+    r_d = gillespy2.Reaction(name="r_dissociation", rate=k_d, reactants={d:1}, products={m:2})
+    model.add_reaction([r_c, r_d])
+
+    # Set the timespan for the simulation.
+    tspan = gillespy2.TimeSpan.linspace(t=100, num_points=101)
+    model.timespan(tspan)
+    return model
 ```
 
-Given the class definition above, the model can be simulated by first instantiating the class object, and then invoking the `run()` method on the object.  The following code will run the model 10 times to produce 10 sample trajectories:
+Given the model creation function above, the model can be simulated by first instantiating the model object, and then invoking the run() method on the object. The following code will run the model 10 times to produce 10 sample trajectories:
 
 ```python
-model = Dimerization()
+model = create_dimerization()
 results = model.run(number_of_trajectories=10)
 ```
 
-The results are then stored in a class `Results` object for single trajectories, or a class `Ensemble` object for multiple trajectories.  Results/Ensembles can be plotted with matplotlib using `plot()` or in plotly (offline) using `plotplotly()`.  For additional plotting options such as plotting from a selection of species, or statistical plotting, please see the documentation.:
+The results are then stored in a class `Results` object for single trajectory or for multiple trajectories.  Results can be plotted with matplotlib using `plot()` or in plotly (offline) using `plotplotly()`.  For additional plotting options such as plotting from a selection of species, or statistical plotting, please see the documentation.:
 
 ```python
 results.plot()

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 3660d62a689826af0ef6e8b2cfa373ce
+config: b55ff5dc6e7452417ea83baca6ee686c
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/gillespy2/core/assignmentrule.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.6.9 documentation</title>
+    <title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.6.10 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />
@@ -146,7 +146,8 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
         <span class="bp">self</span><span class="o">.</span><span class="n">formula</span> <span class="o">=</span> <span class="n">formula</span>
 
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</span> <span class="o">+</span> <span class="s1">&#39;: &#39;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">formula</span>
+        <span class="n">var_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">variable</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</span><span class="o">.</span><span class="n">name</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">: Var: </span><span class="si">{</span><span class="n">var_name</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">formula</span><span class="si">}</span><span class="s2">&quot;</span>
 
 <div class="viewcode-block" id="AssignmentRule.sanitized_formula"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.assignmentrule.AssignmentRule.sanitized_formula">[docs]</a>    <span class="k">def</span> <span class="nf">sanitized_formula</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">species_mappings</span><span class="p">,</span> <span class="n">parameter_mappings</span><span class="p">):</span>
         <span class="n">names</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">species_mappings</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">parameter_mappings</span><span class="o">.</span><span class="n">keys</span><span class="p">()),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">),</span>

docs/build/html/_modules/gillespy2/core/cleanup.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.cleanup &#8212; GillesPy2 1.6.9 documentation</title>
+    <title>gillespy2.core.cleanup &#8212; GillesPy2 1.6.10 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />

docs/build/html/_modules/gillespy2/core/events.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.events &#8212; GillesPy2 1.6.9 documentation</title>
+    <title>gillespy2.core.events &#8212; GillesPy2 1.6.10 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />

docs/build/html/_modules/gillespy2/core/functiondefinition.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.6.9 documentation</title>
+    <title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.6.10 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />