Merge pull request #421 from GillesPy2/develop

v.1.5.3

.travis.yml

@@ -1,29 +1,49 @@
-os: linux
-dist: xenial
-language: python
-python: "3.6"
-before_script:
-    - "curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter"
-    - "chmod +x ./cc-test-reporter"
-    - "./cc-test-reporter before-build"
+jobs:
+  allow_failures:
+    - os: windows # This should be removed once tests pass on Windows. 
+  include:
+    - os: linux
+      dist: xenial
+      language: python
+      python: 3.6
+      before_script:
+        - "curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter"
+        - "chmod +x ./cc-test-reporter"
+        - "./cc-test-reporter before-build"
+      after_script:
+        - "coverage xml"
+        - "if [[ \"$TRAVIS_TEST_RESULT\" == 0 ]]; then ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT; fi"
+    - os: linux
+      dist: bionic
+      language: python
+      python: 3.6
+    - os: osx
+      osx_image: xcode9.4   # Python 3.6.5 running on macOS 10.13
+      language: shell       # 'language: python' is an error on Travis CI macOS
+    - os: windows
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.6.0
+        - choco install make
+        - python -m pip install --upgrade pip
+      env: PATH=/c/Python36:/c/Python36/Scripts:$PATH
 install:
-          - pip3 install -r requirements.txt
-          - pip3 install python-libsbml
-          - pip3 install cython
-          - pip3 install coverage
+  - pip3 install --upgrade pip           
+  - pip3 install -r requirements.txt
+  - pip3 install python-libsbml
+  - pip3 install cython
+  - pip3 install coverage
 script:
-    - "coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_tests.py -m develop"
-after_script:
-    - "coverage xml"
-    - "if [[ \"$TRAVIS_TEST_RESULT\" == 0 ]]; then ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT; fi"
+  - "coverage run --source=gillespy2 --omit=gillespy2/solvers/stochkit/* test/run_tests.py -m develop"
 deploy:
   # API token stored in env var PYPI_PASSWORD on Travis CI
   provider: pypi
   distributions: sdist bdist_wheel
   edge: true # opt in to dpl v2
   user: __token__
   on:
+    condition: $TRAVIS_DIST = xenial
     repo: GillesPy2/GillesPy2
     branch: main
     tags: true
-    
+

gillespy2/__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/GillesPy2/GillesPy2
 # =============================================================================
 
-__version__      = '1.5.2'
+__version__      = '1.5.3'
 __title__        = 'GillesPy2'
 __description__  = 'Python interface for Gillespie-style biochemical simulations'
 __url__          = 'https://github.com/GillesPy2/GillesPy2'

gillespy2/core/model.py

@@ -449,6 +449,11 @@ def add_rate_rule(self, rate_rules):
                     raise ModelError('Invalid Rate Rule. Expression must be a non-empty string value')
                 if rate_rules.variable == None:
                     raise ModelError('A GillesPy2 Rate Rule must be associated with a valid variable')
+                if isinstance(rate_rules.variable, str):
+                    v = rate_rules.variable
+                    if v not in self.listOfSpecies and v not in self.listOfParameters:
+                        raise ModelError(
+                            'Invalid variable entered for Rate Rule: {}'.format(rate_rules.name))
 
                 self.listOfRateRules[rate_rules.name] = rate_rules
                 sanitized_rate_rule = RateRule(name='RR{}'.format(len(self._listOfRateRules)))

gillespy2/solvers/cpp/c_base/makefile

@@ -1,16 +1,20 @@
 CC=g++
 CFLAGS=-c -std=c++14 -Wall -O3
-SIMFLAGS = -std=c++14 -Wall -O3
+SIMFLAGS = -L. -std=c++14 -Wall -O3
 DEPS = model.h ssa.h
 OBJ = model.o ssa.o
+.PHONY: all
 
 all: UserSimulation
 
 %.o: %.cpp $(DEPS)
 	$(CC) -c -o $@ $< $(CFLAGS)
 
-UserSimulation: $(OBJ)
-	$(CC) UserSimulation.cpp $(SIMFLAGS) -o $@ $^
+UserSimulation.o:
+	$(CC) -c -o UserSimulation.o UserSimulation.cpp $(CFLAGS)
+
+UserSimulation: $(OBJ) UserSimulation.o
+	$(CC) -o UserSimulation $(OBJ) UserSimulation.o $(SIMFLAGS)
 
 cleanSimulation:
 	rm -f UserSimulation

gillespy2/solvers/cpp/c_base/model.cpp

@@ -82,27 +82,16 @@ namespace Gillespy{
     return os;
   }
 
-  void Simulation :: output_results_buffer(std :: ostream& os){
-    double temp;
-    unsigned char* temp_byte = reinterpret_cast<unsigned char*>(&temp);
-    for(unsigned int i = 0; i < number_timesteps; i++){
-      temp = timeline[i];
-      for(unsigned int byte_i = 0; byte_i < sizeof(double); byte_i++){
-	os << temp_byte[byte_i];
-      }
-      for(unsigned int trajectory = 0; trajectory < number_trajectories; trajectory++){
-	for(unsigned int j = 0; j < model -> number_species; j++){
-	  temp = trajectories[trajectory][i][j];
-	  for(unsigned int byte_i = 0; byte_i < sizeof(double); byte_i++){
-	    os << temp_byte[byte_i];
-	  }
-	}
-      }
+void Simulation :: output_results_buffer(std::ostream& os){
+    for (int i = 0 ; i < number_trajectories; i++){
+        for (int j = 0; j<number_timesteps;j++){
+            os<<timeline[j]<<',';
+            for (int k = 0; k<model->number_species; k++){
+                os<<trajectories[i][j][k]<<',';
+                }
+            }
+         }
+    os<<(int)current_time;
     }
-    temp = current_time;
-	temp_byte = reinterpret_cast<unsigned char*>(&temp);
-    for (unsigned int byte_i=0; byte_i < sizeof(double); byte_i++){
-        os << temp_byte[byte_i];
-    }
-  }
+
 }

gillespy2/solvers/cpp/c_base/model.h

@@ -4,7 +4,7 @@
 #include <string>
 #include <vector>
 #include <iostream>
-#include <math.h>
+#include <cmath>
 
 namespace Gillespy{
 
@@ -24,12 +24,13 @@ namespace Gillespy{
 
   //Represents a model of reactions and species
   struct Model{
+      void update_affected_reactions();
+
     unsigned int number_species;
     std :: unique_ptr<Species[]> species;
     unsigned int number_reactions;
     std :: unique_ptr<Reaction[]> reactions;
     Model(std :: vector<std :: string> species_names, std :: vector<unsigned int> species_populations, std :: vector<std :: string> reaction_names);
-    void update_affected_reactions();
   };
 
   //Interface class to represent container for propensity functions
@@ -43,6 +44,8 @@ namespace Gillespy{
   //Represents simulation return data
   struct Simulation{
     Model* model;
+    ~Simulation();
+
     double* timeline;
     double end_time;
     double current_time;
@@ -53,7 +56,6 @@ namespace Gillespy{
     unsigned int*** trajectories;
     IPropensityFunction *propensity_function;
     Simulation(Model* model, unsigned int number_trajectories, unsigned int number_timesteps, double end_time, IPropensityFunction* propensity_function, int random_seed, double current_time);
-    ~Simulation();
     friend std :: ostream& operator<<(std :: ostream& os, const Simulation& simulation);
     void output_results_buffer(std :: ostream& os);
   };

gillespy2/solvers/cpp/ssa_c_solver.py

@@ -11,7 +11,7 @@
 
 GILLESPY_PATH = os.path.dirname(inspect.getfile(gillespy2))
 GILLESPY_C_DIRECTORY = os.path.join(GILLESPY_PATH, 'solvers/cpp/c_base')
-
+MAKE_FILE = os.path.dirname(os.path.abspath(__file__))+'/c_base/makefile'
 
 def _write_constants(outfile, model, reactions, species, parameter_mappings, resume):
     """
@@ -135,16 +135,21 @@ def __compile(self):
             if self.resume[0].model != self.model:
                 raise gillespyError.ModelError('When resuming, one must not alter the model being resumed.')
             else:
-                built = subprocess.run(["make", "-C", self.output_directory, 'UserSimulation'], stdout=subprocess.PIPE,
-                                       stderr=subprocess.PIPE)
-        else:
-            try:
-                cleaned = subprocess.run(["make", "-C", self.output_directory, 'cleanSimulation'],
-                                         stdout=subprocess.PIPE, stderr=subprocess.PIPE)
                 built = subprocess.run(["make", "-C", self.output_directory, 'UserSimulation'],
-                                       stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-            except KeyboardInterrupt:
-                log.warning("Solver has been interrupted during compile time, unexpected behavior may occur.")
+                    stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        else:
+             try:
+                 cleaned = subprocess.run(
+                     ["make", "-C", self.output_directory, '-f', MAKE_FILE,
+                      'cleanSimulation'],
+                     stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                 built = subprocess.run(
+                     ["make", "-C", self.output_directory, '-f', MAKE_FILE,
+                      'UserSimulation'], stdout=subprocess.PIPE,
+                     stderr=subprocess.PIPE)
+             except KeyboardInterrupt:
+                 log.warning(
+                     "Solver has been interrupted during compile time, unexpected behavior may occur.")
 
         if built.returncode == 0:
             self.__compiled = True
@@ -233,14 +238,16 @@ def run(self=None, model=None, t=20, number_of_trajectories=1, timeout=0,
                         pause = True
                         return_code = 33
 
-            # Parse/return results.
+            # Decode from byte, split by comma into array
+            stdout = stdout.decode('utf-8').split(',')
+            # Parse/return results
+
             if return_code in [0, 33]:
                 trajectory_base, timeStopped = cutils._parse_binary_output(stdout, number_of_trajectories,
-                                                                           number_timesteps, len(model.listOfSpecies),
+                                                                           number_timesteps, len(model.listOfSpecies), stdout,
                                                                            pause=pause)
                 if model.tspan[2] - model.tspan[1] == 1:
                     timeStopped = int(timeStopped)
-
                 # Format results
                 self.simulation_data = []
                 for trajectory in range(number_of_trajectories):

gillespy2/solvers/cpp/variable_ssa_c_solver.py

@@ -11,6 +11,7 @@
 
 GILLESPY_PATH = os.path.dirname(inspect.getfile(gillespy2))
 GILLESPY_C_DIRECTORY = os.path.join(GILLESPY_PATH, 'solvers/cpp/c_base')
+MAKE_FILE = os.path.dirname(os.path.abspath(__file__))+'/c_base/makefile'
 
 
 def _write_variables(outfile, model, reactions, species, parameters, parameter_mappings, resume=None):
@@ -149,16 +150,22 @@ def __compile(self):
             if self.resume[0].model != self.model:
                 raise gillespyError.ModelError('When resuming, one must not alter the model being resumed.')
             else:
-                built = subprocess.run(["make", "-C", self.output_directory, 'UserSimulation'], stdout=subprocess.PIPE,
-                                       stderr=subprocess.PIPE)
+                built = subprocess.run(
+                    ["make", "-C", self.output_directory, 'UserSimulation'],
+                    stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         else:
             try:
-                cleaned = subprocess.run(["make", "-C", self.output_directory, 'cleanSimulation'],
-                                         stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-                built = subprocess.run(["make", "-C", self.output_directory, 'UserSimulation'],
-                                       stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                cleaned = subprocess.run(
+                    ["make", "-C", self.output_directory, '-f', MAKE_FILE,
+                     'cleanSimulation'],
+                    stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                built = subprocess.run(
+                    ["make", "-C", self.output_directory, '-f', MAKE_FILE,
+                     'UserSimulation'], stdout=subprocess.PIPE,
+                    stderr=subprocess.PIPE)
             except KeyboardInterrupt:
-                log.warning("Solver has been interrupted during compile time, unexpected behavior may occur.")
+                log.warning(
+                    "Solver has been interrupted during compile time, unexpected behavior may occur.")
 
         if built.returncode == 0:
             self.__compiled = True
@@ -290,12 +297,14 @@ def run(self=None, model=None, t=20, number_of_trajectories=1, timeout=0,
                     stdout, stderr = simulation.communicate()
                     pause = True
                     return_code = 33
-
+            # Decode from byte, split by comma into array
+            stdout = stdout.decode('utf-8').split(',')
             # Parse/return results.
+
             if return_code in [0, 33]:
                 trajectory_base, timeStopped = cutils._parse_binary_output(stdout, number_of_trajectories,
-                                                                           number_timesteps,
-                                                                           len(model.listOfSpecies), pause=pause)
+                                                                           number_timesteps, len(model.listOfSpecies),
+                                                                           stdout, pause=pause)
                 if model.tspan[2] - model.tspan[1] == 1:
                     timeStopped = int(timeStopped)