Merge pull request #7 from DanShort12/implement_ci

Implement ci

.github/workflows/python.yml

@@ -0,0 +1,35 @@
+name: Python package
+
+on: 
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build_and_test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install plasma source
+      run: |
+        pip install -r requirements-develop.txt
+        python setup.py bdist_wheel
+        python -m pip install --verbose dist/*.whl
+    - name: Run tests
+      run: |
+        pytest tests
+    - name: Upload wheel artifact
+      uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist

CMakeLists.txt

@@ -18,6 +18,26 @@ set(OPENMC_DIR /opt/openmc)
 set(OPENMC_INC_DIR ${OPENMC_DIR}/include)
 set(OPENMC_LIB_DIR ${OPENMC_DIR}/lib)
 
+# Ensure submodules are available and up to date
+find_package(Git QUIET)
+if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
+  # Update submodules as needed
+  option(GIT_SUBMODULE "Check submodules during build" ON)
+  if(GIT_SUBMODULE)
+    message(STATUS "Submodule update")
+    execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
+                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+                    RESULT_VARIABLE GIT_SUBMOD_RESULT)
+    if(NOT GIT_SUBMOD_RESULT EQUAL "0")
+      message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
+    endif()
+  endif()
+endif()
+
+if(NOT EXISTS "${PROJECT_SOURCE_DIR}/pybind11/CMakeLists.txt")
+  message(FATAL_ERROR "The submodules were not downloaded! GIT_SUBMODULE was turned off or failed. Please update submodules and try again.")
+endif()
+
 # Build source_sampling
 list(APPEND source_sampling_SOURCES
   ${SRC_DIR}/source_sampling.cpp
@@ -26,13 +46,15 @@ list(APPEND source_sampling_SOURCES
 
 add_library(source_sampling SHARED ${source_sampling_SOURCES})
 
-find_library(OPENMC_LIB openmc HINTS ${OPENMC_LIB_DIR})
+find_library(OPENMC_LIB openmc HINTS ${OPENMC_LIB_DIR} OPTIONAL)
 
-set_target_properties(source_sampling PROPERTIES PREFIX "")
-set_target_properties(source_sampling PROPERTIES POSITION_INDEPENDENT_CODE ON)
-target_include_directories(source_sampling PUBLIC ${OPENMC_INC_DIR})
-target_include_directories(source_sampling PUBLIC ${OPENMC_DIR}/vendor/pugixml)
-target_link_libraries(source_sampling ${OPENMC_LIB} gfortran)
+if (OPENMC_LIB)
+  set_target_properties(source_sampling PROPERTIES PREFIX "")
+  set_target_properties(source_sampling PROPERTIES POSITION_INDEPENDENT_CODE ON)
+  target_include_directories(source_sampling PUBLIC ${OPENMC_INC_DIR})
+  target_include_directories(source_sampling PUBLIC ${OPENMC_DIR}/vendor/pugixml)
+  target_link_libraries(source_sampling ${OPENMC_LIB} gfortran)
+endif()
 
 # Build plasma_source Python bindings
 list(APPEND plasma_source_pybind_SOURCES

README.md

@@ -1,18 +1,20 @@
 # parametric-plasma-source
 
+![Python package](https://github.com/DanShort12/parametric-plasma-source/workflows/Python%20package/badge.svg)
+
 Python package, C++ source and build files for parametric plasma source for use in fusion neutron transport calculations with OpenMC.
 
 The plasma source is based on a paper by [C. Fausser et al](https://www.sciencedirect.com/science/article/pii/S0920379612000853)
 
-# Installation
+## Installation
 
 ```pip install parametric_plasma_source```
 
-# Usage
+## Usage
 
 The parametric plasma source can be imported an used in Python 3 in the following manner.
 
-```
+```[python]
 from parametric_plasma_source import Plasma
 my_plasma = Plasma(major_radius=6,
                    minor_radius=1.5,
@@ -25,7 +27,7 @@ In the above example the major_radius, minor_radius, elongation and triangularit
 
 There are a number of additional arguments that can be passed to the Plasma class on construction. Units are in SI (e.g. meters not cm)
 
-```
+```[python]
 ion_density_pedistal = 1.09e+20
 ion_density_seperatrix = 3e+19
 ion_density_origin = 1.09e+20

parametric_plasma_source/__init__.py

@@ -1,2 +0,0 @@
-from .plasma import Plasma
-from .plasma_source import PlasmaSource

parametric_plasma_source/plasma_source.cpp

@@ -3,9 +3,6 @@
 #include <cmath>
 #include "plasma_source.hpp"
 #include <stdlib.h>     
-#include "openmc/random_lcg.h"
-
-#define RANDOM openmc::prn()
 
 namespace plasma_source {
 

requirements-develop.txt

@@ -0,0 +1,2 @@
+pytest
+wheel

setup.py

@@ -36,11 +36,11 @@ def build_extension(self, ext):
                       "-DPYTHON_EXECUTABLE=" + sys.executable]
 
         cfg = "Debug" if self.debug else "Release"
-        build_args = ["--config", cfg]
+        build_args = ["--target", "plasma_source"]
+        build_args += ["--config", cfg]
 
         cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
         build_args += ["--", "-j2"]
-        build_args += ["plasma_source"]
 
         env = os.environ.copy()
         env["CXXFLAGS"] = "{} -DVERSION_INFO=\\\"{}\\\"".format(

tests/test_Compile.py

@@ -8,6 +8,8 @@
 
 from parametric_plasma_source.plasma import Plasma
 
+pytest.importorskip("openmc")
+
 class test_object_properties(unittest.TestCase):
 
         def test_compile(self):

tests/test_plasma_source.py

@@ -0,0 +1,96 @@
+"""Tests for the methods in plasma_source."""
+
+import pytest
+
+from parametric_plasma_source.plasma_source import PlasmaSource
+
+plasma_params = {
+    "elongation": 1.557,
+    "ion_density_origin": 1.09e20,
+    "ion_density_peaking_factor": 1,
+    "ion_density_pedistal": 1.09e20,
+    "ion_density_seperatrix": 3e19,
+    "ion_temperature_origin": 45.9,
+    "ion_temperature_peaking_factor": 8.06,
+    "ion_temperature_pedistal": 6.09,
+    "ion_temperature_seperatrix": 0.1,
+    "major_radius": 906.0,
+    "minor_radius": 292.258,
+    "pedistal_radius": 0.8 * 292.258,
+    "plasma_id": 1,
+    "shafranov_shift": 44.789,
+    "triangularity": 0.270,
+    "ion_temperature_beta": 6,
+}
+
+
+@pytest.fixture(scope="session")
+def plasma_source():
+    """Make a plasma source to use as a test fixture."""
+    return PlasmaSource(**plasma_params)
+
+
+class TestPlasmaSource:
+    """A class to run tests against the plasma source."""
+
+    def test_ion_density_magnetic_origin(self, plasma_source):
+        """Test the ion density at the magnetic origin."""
+        ion_density = plasma_source.ion_density(0.0)
+
+        assert pytest.approx(ion_density, 1.09e20)
+
+    def test_ion_density_inside_pedestal(self, plasma_source):
+        """Test the ion density inside the pedestal."""
+        ion_density = plasma_source.ion_density(0.2)
+
+        assert pytest.approx(ion_density, 1.09e20)
+
+    def test_ion_density_outside_pedestal(self, plasma_source):
+        """Test the ion density outside the pedestal."""
+        ion_density = plasma_source.ion_density(2.4)
+
+        assert pytest.approx(ion_density, 1.00628584e20)
+
+    def test_ion_density_boundary(self, plasma_source):
+        """Test the ion density at the boundary."""
+        boundary = plasma_params["minor_radius"] / 100.0
+        ion_density = plasma_source.ion_density(boundary)
+
+        assert pytest.approx(
+            ion_density, plasma_params["ion_density_seperatrix"]
+        )
+
+    def test_ion_temperature_magnetic_origin(self, plasma_source):
+        """Test the ion temperature at the magnetic origin."""
+        ion_temperature = plasma_source.ion_temperature(0.0)
+
+        assert pytest.approx(
+            ion_temperature, plasma_params["ion_temperature_origin"]
+        )
+
+    def test_ion_temperature_inside_pedestal(self, plasma_source):
+        """Test the ion temperature inside the pedestal."""
+        ion_temperature = plasma_source.ion_temperature(0.2)
+
+        assert pytest.approx(ion_temperature, 45.89987429)
+
+    def test_ion_temperature_outside_pedestal(self, plasma_source):
+        """Test the ion temperature outside the pedestal."""
+        ion_temperature = plasma_source.ion_temperature(2.4)
+
+        assert pytest.approx(ion_temperature, 5.45525594)
+
+    def test_ion_temperature_boundary(self, plasma_source):
+        """Test the ion temperature at the boundary."""
+        boundary = plasma_params["minor_radius"] / 100.0
+        ion_temperature = plasma_source.ion_temperature(boundary)
+
+        assert pytest.approx(
+            ion_temperature, plasma_params["ion_temperature_seperatrix"]
+        )
+
+    def test_dt_cross_section(self, plasma_source):
+        """Test the dt cross section at a specific temperature."""
+        dt_cross_section = plasma_source.dt_xs(4.25e7)
+
+        assert pytest.approx(dt_cross_section, 0.0)