Merge pull request #24 from KVSlab/dokken/turtle-envs

Add Dockerfile, environment.yml and dependencies to setup.py

Author: johannesring

.github/workflows/test_turtle.yml

@@ -15,16 +15,16 @@ on:
     - cron: "0 8 * * *"
 jobs:
   check-code:
-
     runs-on: ubuntu-22.04
-    container: quay.io/fenicsproject/stable:latest
+    # Runs against FEniCS main branch built the 08-12-2022
+    container: ghcr.io/scientificcomputing/fenics:2022-12-08
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v3
+      
 
       - name: "Install code"
         run: python3 setup.py install
-
       - name: Run tests
         run: |
           python3 -m pytest

docker/Dockerfile

@@ -0,0 +1,27 @@
+FROM condaforge/mambaforge 
+
+
+WORKDIR /tmp/
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install ssh (missing dependency to run conda envs)
+RUN apt-get update && \
+    apt-get install -y ssh build-essential
+
+# Upgrade mamba
+RUN mamba upgrade -y mamba
+
+# Copy environment and requirements files into docker env
+COPY . turtleFSI
+
+# Update environment file with new environment name
+RUN mamba env update --file ./turtleFSI/environment.yml --name dockerenv
+SHELL ["mamba", "run", "-n", "dockerenv", "/bin/bash", "-c"]
+
+RUN python3 -m pip install ./turtleFSI pytest
+
+# Test turtleFSI
+RUN python3 -m pytest ./turtleFSI/tests
+
+RUN echo "source activate dockerenv" > ~/.bashrc

environment.yml

@@ -0,0 +1,12 @@
+
+name: turtleFSI
+channels:
+  - conda-forge
+dependencies:
+  - fenics-dolfin
+  - python=3.10
+  - pip
+  - git
+  - scipy
+  - pip:
+    - cppimport

setup.py

@@ -3,7 +3,8 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-DEPENDENCIES = ['configargparse']
+DEPENDENCIES = ['configargparse', "fenics-dolfin",
+                "scipy", "cppimport", "numpy"]
 TEST_DEPENDENCIES = ['pytest']
 
 VERSION = "1.5"
@@ -38,8 +39,9 @@
               "turtleFSI.problems",
               "turtleFSI.utils"],
     package_dir={"turtleFSI": "turtleFSI"},
-    package_data = {"turtleFSI": ["utils/probe/*.h",
-                                  "utils/probe/*.cpp"]},
-    include_package_data = True,
-    entry_points={'console_scripts': ['turtleFSI=turtleFSI.run_turtle:main']}
+    package_data={"turtleFSI": ["utils/probe/*.h",
+                                "utils/probe/*.cpp"]},
+    include_package_data=True,
+    entry_points={'console_scripts': ['turtleFSI=turtleFSI.run_turtle:main']},
+
 )