Merge pull request #1 from vivarium-collective/process-setup

feat: added deps to requirements and configured setup file

.github/workflows/pytest.yml

@@ -7,24 +7,24 @@ on:
     branches: [master]
   pull_request:
     branches: [master]
+  workflow_dispatch:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10']
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v2
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; else pip install -e .; fi
+      - name: Test with pytest
+        run: |
+          pytest -v

.gitignore

@@ -0,0 +1,3 @@
+*.egg
+*.egg-info
+/idea 

pytest.ini

@@ -2,6 +2,6 @@
 python_files = *.py
 addopts = --doctest-modules --strict-markers
 # TODO: Replace `template` when you change the folder name.
-testpaths = template
+testpaths = vivarium_tellurium
 markers =
     slow: indicates slow tests (deselect with '-m "not slow"')

requirements.txt

@@ -11,4 +11,6 @@
 #   pip install -r requirements.txt
 #
 
--e .
+vivarium-core
+tellurium
+pytest  

setup.py

@@ -1,35 +1,30 @@
-import os
-import glob
-import setuptools
-from distutils.core import setup
+# import os
+from setuptools import setup
 
 with open("README.md", 'r') as readme:
     long_description = readme.read()
 
 setup(
-    name='',  # TODO: Put your package name here.
+    name='vivarium-tellurium',
     version='0.0.1',
     packages=[
-        # TODO: Replace 'template' with the name of your folder.
-        'template',
-        'template.processes',
-        'template.composites',
-        'template.experiments',
+        'vivarium_tellurium',
+        'vivarium_tellurium.composites',
+        'vivarium_tellurium.experiments',
+        'vivarium_tellurium.library',
+        'vivarium_tellurium.processes',
     ],
-    author='',  # TODO: Put your name here.
-    author_email='',  # TODO: Put your email here.
-    url='',  # TODO: Put your project URL here.
-    license='',  # TODO: Choose a license.
-    entry_points={
-        'console_scripts': []},
-    short_description='',  # TODO: Describe your project briefely.
+    author='Eran Agmon, Alexander Patrie',
+    author_email='',
+    url='https://github.com/vivarium-collective/vivarium-tellurium',
+    license='',
+    description='A Vivarium interface for Tellurium',
     long_description=long_description,
     long_description_content_type='text/markdown',
-    package_data={},
     include_package_data=True,
     install_requires=[
-        'vivarium-core>=1.0.0',
+        'vivarium-core',
+        'tellurium',
         'pytest',
-        # TODO: Add other dependencies.
     ],
-)
+)

vivarium_tellurium/composites/template_composite.py

@@ -0,0 +1,113 @@
+"""
+==================
+Template Composite
+==================
+
+This is a toy composite that loads in two template processes and combines them.
+"""
+
+# TODO: Delete this file before publishing your project.
+
+from vivarium.core.engine import Engine, pp
+from vivarium.core.composer import Composer
+from vivarium.library.pretty import format_dict
+from vivarium.processes.injector import Injector
+
+from vivarium_tellurium.processes.tellurium_process import Template
+
+
+class TemplateComposer(Composer):
+
+    defaults = {
+        'template1': {
+            'parameter1': 2.0,
+        },
+        'template2': {
+            'parameter1': 5.0,
+        },
+    }
+
+    def __init__(self, config=None):
+        super().__init__(config)
+
+    def generate_processes(self, config):
+        template1 = Template(self.config['template1'])
+        template2 = Template(self.config['template2'])
+
+        return {
+            'template1': template1,
+            'template2': template2,
+        }
+
+    def generate_topology(self, config):
+        return {
+            'template1': {
+                'internal': ('internal_1',),
+                'external': ('external_shared', ),
+            },
+            'template2': {
+                'internal': ('internal_2',),
+                'external': ('external_shared', ),
+            },
+        }
+
+
+def test_template_composite():
+    '''Run a simulation of the composite.
+
+    Returns:
+        The simulation output.
+    '''
+
+    # 1.) Declare the initial state, mirroring the ports structure. May be passed as a parsable argument.
+    initial_state = {
+        'internal_1': {
+            'A': 0.0
+        },
+        'internal_2': {
+            'A': 10.0
+        },
+        'external_shared': {
+            'A': 1.0
+        },
+    }
+
+    # 2.) Create the simulation run parameters for the simulator
+    config = {
+        'template1': {
+            'parameter1': 4.0,
+        },
+        'template2': {
+            'parameter1': 4.0,
+        }
+    }
+
+    # 3.) Initialize the composer by passing in a config dict
+    template_composer = TemplateComposer(config)
+
+    # 4.) Generate a composite by calling the Composers' generate method
+    template_composite = template_composer.generate()
+
+    # 5.) Feed the compsite instance you just created to the vivarium Engine
+    sim = Engine(
+        composite=template_composite,
+        initial_state=initial_state
+    )
+
+    # 6.) Call update with that sim object, which calls the next_update method in the implementation you created above using total_time
+    total_time = 3
+    sim.update(
+        interval=total_time
+    )
+
+    # 7.) Get the data which is emitted from the sim object.
+    data = sim.emitter.get_timeseries()
+
+    # 7a.) Observe the data which is return from running the process:
+    print(f'RESULTS: {pp(data)}')
+    return data
+
+
+# run module with python template/processes/template_composite.py
+if __name__ == '__main__':
+    test_template_composite()