Merge pull request #51 from justinlaughlin/dokken/CI-example1

Add Example 1 to CI

.github/workflows/test_fenics_stubs.yml

@@ -16,15 +16,21 @@ on:
 jobs:
   check-code:
     runs-on: ubuntu-22.04
-    # Runs against FEniCS main branch built the 12-12-2022
-    container: ghcr.io/scientificcomputing/fenics:2022-12-12
+    # Runs against FEniCS main branch built the 16-01-2023
+    container: ghcr.io/scientificcomputing/fenics:2023-01-16
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v3
 
       - name: "Install code"
         run: python3 -m pip install --no-binary=h5py .[dev]
-      - name: Run tests
+
+      - name: Run example 1
         run: |
-          cd tests/
-          python3 -m pytest .
+          cd examples/example1/
+          python3 example1_driver.py
+
+      # - name: Run tests
+      #   run: |
+      #     cd tests/
+      #     python3 -m pytest .

README.md

@@ -17,7 +17,7 @@ Although FEniCS is a core dependency, because it has many different versions (20
 
 ```bash
 # create a container using DOLFIN built on ubuntu 22.04 with Python 3.10
-jgl:~$ docker run -ti --init ghcr.io/scientificcomputing/fenics:2022-12-12
+jgl:~$ docker run -ti --init ghcr.io/scientificcomputing/fenics:2023-01-16
 # pip install stubs from within the container
 root@jgl:~$ python3 -m pip install fenics-stubs
 ```

examples/example1/example1_driver.py

@@ -2,14 +2,18 @@
 # STUBS driver script example
 # =============================================================================================
 # Imports
-import stubs
-import dolfin as d
 import os
 
+import dolfin as d
+
+import example1_model
+
+import stubs
+
+
 # =============================================================================================
 # Load model
 # =============================================================================================
-import example1_model
 pc, sc, cc, rc = example1_model.make_model()
 
 # =============================================================================================

examples/example1/example1_model.py

@@ -15,12 +15,13 @@
 
 Roughly, this model is similar to an IP3 pulse at the PM, leading to Ca2+ release at the ER
 """
-# Imports
-import stubs
-from stubs.common import empty_sbmodel, sbmodel_from_locals
-from stubs.model_assembly import Parameter, Species, Compartment, Reaction, parse_expr
+
 import sympy as sym
 
+import stubs
+from stubs.common import sbmodel_from_locals
+from stubs.model_assembly import Compartment, Parameter, Reaction, Species
+
 # Aliases - base units
 unit          = stubs.unit # unit registry
 uM            = unit.uM