feat: update checkpoint

Dockerfile

@@ -17,7 +17,7 @@ COPY ./biosimulator_processes /app/biosimulator_processes
 COPY composer-notebooks /app/notebooks
 
 # copy files
-COPY toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
+COPY pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
 COPY ./scripts/enter-lab.sh /usr/local/bin/enter-lab.sh
 # COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 

biosimulator_processes/steps/ode_simulation.py

@@ -0,0 +1,39 @@
+import abc
+from process_bigraph import Step
+
+
+class OdeSimulation(Step, abc.ABC):
+    config_schema = {
+        'sbml_filepath': 'string',
+        'n_steps': 'integer',
+        'step_size': 'float',
+        'duration': {
+            '_type': 'string',
+            '_default': 10}
+    }
+
+    def __init__(self, config=None, core=None):
+        super().__init__(config, core)
+
+    @abc.abstractmethod
+    def inputs(self):
+        pass
+
+    @abc.abstractmethod
+    def outputs(self):
+        pass
+
+    def update(self, inputs):
+        pass
+
+    @abc.abstractmethod
+    def set_species_list(self):
+        pass
+
+    @abc.abstractmethod
+    def set_global_parameters(self):
+        pass
+
+    @abc.abstractmethod
+    def set_reactions(self):
+        pass

demos/process_comparison_demo.ipynb

@@ -6,8 +6,8 @@
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2024-05-16T13:31:17.318214Z",
-     "start_time": "2024-05-16T13:31:17.134520Z"
+     "end_time": "2024-05-25T01:45:34.475186Z",
+     "start_time": "2024-05-25T01:45:33.943192Z"
     }
    },
    "source": [
@@ -57,7 +57,9 @@
   {
    "metadata": {},
    "cell_type": "markdown",
-   "source": "### Demonstrate a simple example with sample output data for a sample timestep manually",
+   "source": [
+    "### Demonstrate a simple example with sample output data for a sample timestep manually"
+   ],
    "id": "a4e8dec81b3796f1"
   },
   {
@@ -188,7 +190,9 @@
   {
    "metadata": {},
    "cell_type": "markdown",
-   "source": "### Now, perform this analysis over an interation of real ode simulator composite data",
+   "source": [
+    "### Now, perform this analysis over an interation of real ode simulator composite data"
+   ],
    "id": "76a710e75081e93d"
   },
   {
@@ -338,7 +342,12 @@
     }
    },
    "cell_type": "code",
-   "source": "",
+   "source": [
+    "from biosimulator_processes.processes.instance import generate_ode_process_instance\n",
+    "\n",
+    "\n",
+    "\n"
+   ],
    "id": "84f8b41e67dba682",
    "execution_count": 17,
    "outputs": []

toml → pyproject.toml

@@ -7,37 +7,36 @@ readme = "README.md"
 packages = [{include = "biosimulator_processes"}, {include = "test_suite"}]
 
 [tool.poetry.dependencies]
-python = ">=3.10"
+python = "^3.11"
 zarr = "*"
 termcolor = "*"
 jupyterlab = "*"
 bigraph-schema = "*"
-process-bigraph = "^0.0.17"
+process-bigraph = "*"
 bigraph-viz = "*"
 bigraph-builder = "*"
 numpy = "*"
 copasi-basico = "*"
 cobra = "*"
 tellurium = "*"
 amici = "*"
-# smoldyn = {version = ">=2.72", optional = true}
-python-libsbml = "^5.20.2"
-docker = ">=7.0"
-python-libnuml = "^1.1.6"
-notebook = "^7.1.1"
+# smoldyn = {version = "*", optional = true}
+python-libsbml = "*"
+docker = "*"
+python-libnuml = "*"
+notebook = "*"
 toml = "*"
 pyyaml = "*"
 pydantic = "*"
-seaborn = "^0.13.2"
-# psutil = "^5.9.8"
+seaborn = "*"
 
 [tool.poetry.extras]
 smoldyn = ["smoldyn"]
 # simulariumio = "*"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "*"
-mypy = ">=1.8.0"
+mypy = "*"
 flake8 = "*"
 twine = "*"
 

setup.py

@@ -59,7 +59,7 @@
         "bigraph-builder",
         "python-libsbml",  # ==5.20.2",
         "docker>=7.0",
-        "toml",
+        "pyproject.toml",
         "python-libnuml==1.1.6",  # ">=1.0.0"
         "seaborn"
     ],