From fd1a59a1480963311716087284c4c429931eda6b Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 29 Jul 2020 16:43:14 +0000
Subject: [PATCH 01/24] First pass at python CI config

---
 .github/workflows/python.yml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 .github/workflows/python.yml

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
new file mode 100644
index 0000000..34b1f87
--- /dev/null
+++ b/.github/workflows/python.yml
@@ -0,0 +1,26 @@
+name: Python package
+
+on: 
+  push:
+    branches: [ implement_ci ]
+  pull_request:
+    branches: [ implement_ci ]
+
+jobs:
+  build:
+
+    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: |
+        python setup.py sdist
+        python -m pip install --verbose dist/*.tar.gz

From 167e05c02979ace847206a9e202f42bd60b68770 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 29 Jul 2020 16:44:47 +0000
Subject: [PATCH 02/24] Use empty init file

This prevents an error on a fresh build
---
 parametric_plasma_source/__init__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/parametric_plasma_source/__init__.py b/parametric_plasma_source/__init__.py
index 351009c..e69de29 100644
--- a/parametric_plasma_source/__init__.py
+++ b/parametric_plasma_source/__init__.py
@@ -1,2 +0,0 @@
-from .plasma import Plasma
-from .plasma_source import PlasmaSource

From 92e9838a4e937783c8806af85dcacf3a6260001b Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 29 Jul 2020 17:09:00 +0000
Subject: [PATCH 03/24] Build using bdist_wheel rather than sdist

---
 .github/workflows/python.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 34b1f87..dad3c34 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -22,5 +22,5 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install plasma source
       run: |
-        python setup.py sdist
-        python -m pip install --verbose dist/*.tar.gz
+        python setup.py bdist_wheel
+        python -m pip install --verbose dist/*.whl

From 60ab628a5bcc9e7dc1654c80b72fb18657ff77d1 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 29 Jul 2020 17:13:30 +0000
Subject: [PATCH 04/24] Make sure wheel is installed

---
 .github/workflows/python.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index dad3c34..6bc853f 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -22,5 +22,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install plasma source
       run: |
+        pip install wheel
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl

From 07b2e22bb0e4cd8f637fdf9ad25e4801766e7c3c Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 29 Jul 2020 17:15:12 +0000
Subject: [PATCH 05/24] Get submodules in CI

---
 .github/workflows/python.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 6bc853f..1319588 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -22,6 +22,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install plasma source
       run: |
+        git submodule update --init --recursive
         pip install wheel
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl

From 09deb7dd51f701c15845dfa0d9510355014b1813 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 08:34:17 +0100
Subject: [PATCH 06/24] Only build plasma_source for Python

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index af274c5..dab5d91 100644
--- a/setup.py
+++ b/setup.py
@@ -40,7 +40,7 @@ def build_extension(self, ext):
 
         cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
         build_args += ["--", "-j2"]
-        build_args += ["plasma_source"]
+        build_args += ["--target", "plasma_source"]
 
         env = os.environ.copy()
         env["CXXFLAGS"] = "{} -DVERSION_INFO=\\\"{}\\\"".format(

From 4080d7f654a35e7e5be1474eafba40b1217ff5e8 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:17:24 +0100
Subject: [PATCH 07/24] Fix order of build args

Target must come before the make arguements.
---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index dab5d91..65fb269 100644
--- a/setup.py
+++ b/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 += ["--target", "plasma_source"]
 
         env = os.environ.copy()
         env["CXXFLAGS"] = "{} -DVERSION_INFO=\\\"{}\\\"".format(

From a7de90fcd8da7f7e08b3c945a210688022cce424 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:20:16 +0100
Subject: [PATCH 08/24] Do not fail if openmc not found

Makes OpenMC optional but does not build the source_sampling library if
OPENMC_LIB is not found.
---
 CMakeLists.txt | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 578d4ce..0eb1beb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,13 +26,15 @@ list(APPEND source_sampling_SOURCES
 
 add_library(source_sampling SHARED ${source_sampling_SOURCES})
 
-find_library(OPENMC_LIB openmc HINTS ${OPENMC_LIB_DIR})
-
-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)
+find_library(OPENMC_LIB openmc HINTS ${OPENMC_LIB_DIR} OPTIONAL)
+
+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

From 677607dad4024ff01803fda0b10aee4c142233fe Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:35:57 +0100
Subject: [PATCH 09/24] Remove unused RANDOM definition

Random numbers are only generated in the source sample_source method, so
we shouldn't need to link against OpenMC where we don't use OpenMC
functions.
---
 parametric_plasma_source/plasma_source.cpp | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/parametric_plasma_source/plasma_source.cpp b/parametric_plasma_source/plasma_source.cpp
index 3a2fc64..b0b61b0 100644
--- a/parametric_plasma_source/plasma_source.cpp
+++ b/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 {
 

From 53d7e070f268143e3e3c51f5bb0a6b378fa1c1f4 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:40:45 +0100
Subject: [PATCH 10/24] Upload wheel as artefact

---
 .github/workflows/python.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 1319588..731539a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -26,3 +26,8 @@ jobs:
         pip install wheel
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl
+    - name: upload wheel
+      uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist

From cafd6e58949a5710b88a95e2c7af1e355532d0c6 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:46:38 +0100
Subject: [PATCH 11/24] Create new publish step to upload wheels

---
 .github/workflows/python.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 731539a..db52783 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -26,6 +26,9 @@ jobs:
         pip install wheel
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl
+
+  publish:
+
     - name: upload wheel
       uses: actions/upload-artifact@v2
       with:

From 976be58b89c08a32fb15c4990ab14045b49c11d1 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:55:50 +0100
Subject: [PATCH 12/24] Tidy up actions

---
 .github/workflows/python.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index db52783..87d8bfb 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -7,13 +7,15 @@ on:
     branches: [ implement_ci ]
 
 jobs:
-  build:
 
+  setup:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
 
+  build:
+    needs: setup
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
@@ -28,7 +30,9 @@ jobs:
         python -m pip install --verbose dist/*.whl
 
   publish:
-
+    on: push
+    needs: build
+    steps:
     - name: upload wheel
       uses: actions/upload-artifact@v2
       with:

From 5bc783668aa887ed7a3861727bf8b9fca1ca8498 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 09:57:22 +0100
Subject: [PATCH 13/24] Fix syntax error

---
 .github/workflows/python.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 87d8bfb..1157e5f 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -13,15 +13,16 @@ jobs:
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
-
-  build:
-    needs: setup
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+
+  build:
+    needs: setup
+    steps:
     - name: Install plasma source
       run: |
         git submodule update --init --recursive

From 2a1d2e00fd3b25f72044da44d335f7a9775e9b83 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 10:04:53 +0100
Subject: [PATCH 14/24] Another syntax fix

---
 .github/workflows/python.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 1157e5f..d0be5f2 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -31,7 +31,6 @@ jobs:
         python -m pip install --verbose dist/*.whl
 
   publish:
-    on: push
     needs: build
     steps:
     - name: upload wheel

From b4bbe0493b0fc06678388d0f50f5e3cf77e1bd30 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 10:14:50 +0100
Subject: [PATCH 15/24] Revert workflow to single job

---
 .github/workflows/python.yml | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index d0be5f2..731539a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -7,32 +7,25 @@ on:
     branches: [ implement_ci ]
 
 jobs:
+  build:
 
-  setup:
     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 }}
-
-  build:
-    needs: setup
-    steps:
     - name: Install plasma source
       run: |
         git submodule update --init --recursive
         pip install wheel
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl
-
-  publish:
-    needs: build
-    steps:
     - name: upload wheel
       uses: actions/upload-artifact@v2
       with:

From c340abfccf817ffbe22974bb73e9358cdaf5ff8b Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 10:58:47 +0100
Subject: [PATCH 16/24] Implement a simple test

---
 .github/workflows/python.yml |  5 ++++-
 requirements-develop.txt     |  2 ++
 tests/test_plasma_source.py  | 40 ++++++++++++++++++++++++++++++++++++
 3 files changed, 46 insertions(+), 1 deletion(-)
 create mode 100644 requirements-develop.txt
 create mode 100644 tests/test_plasma_source.py

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 731539a..dec0687 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -23,9 +23,12 @@ jobs:
     - name: Install plasma source
       run: |
         git submodule update --init --recursive
-        pip install wheel
+        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
       uses: actions/upload-artifact@v2
       with:
diff --git a/requirements-develop.txt b/requirements-develop.txt
new file mode 100644
index 0000000..0d73fcd
--- /dev/null
+++ b/requirements-develop.txt
@@ -0,0 +1,2 @@
+pytest
+wheel
diff --git a/tests/test_plasma_source.py b/tests/test_plasma_source.py
new file mode 100644
index 0000000..6c42ba0
--- /dev/null
+++ b/tests/test_plasma_source.py
@@ -0,0 +1,40 @@
+"""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)

From aafe8765e2cd312d0c4516f5fe594321081513bf Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 11:05:55 +0100
Subject: [PATCH 17/24] Don't run compile test if OpenMC not installed

---
 tests/test_Compile.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/test_Compile.py b/tests/test_Compile.py
index b4eaf9f..405a275 100644
--- a/tests/test_Compile.py
+++ b/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):

From aa4a9da1075548b4e980ed0c7a957637639d126a Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 11:17:13 +0100
Subject: [PATCH 18/24] Add some more tests

---
 tests/test_plasma_source.py | 56 +++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/tests/test_plasma_source.py b/tests/test_plasma_source.py
index 6c42ba0..56a5437 100644
--- a/tests/test_plasma_source.py
+++ b/tests/test_plasma_source.py
@@ -38,3 +38,59 @@ def test_ion_density_magnetic_origin(self, plasma_source):
         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)

From a869142a0ad8c3381676a4853fc4df7e85b81a8e Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 11:29:58 +0100
Subject: [PATCH 19/24] Add status badge

Also a few format update to README.
---
 README.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index a8192d2..84d791e 100644
--- a/README.md
+++ b/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

From 79a2aefff0efa8e40c6bce46942fe0cbae3cca13 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 13:12:07 +0100
Subject: [PATCH 20/24] Use a clearer job name

---
 .github/workflows/python.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index dec0687..9119e97 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -7,7 +7,7 @@ on:
     branches: [ implement_ci ]
 
 jobs:
-  build:
+  build_and_test:
 
     runs-on: ubuntu-latest
     strategy:

From 69f88a6ef2e83d1340f58c99ffb374e10e070776 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 13:14:16 +0100
Subject: [PATCH 21/24] Only run actions when affecting master

---
 .github/workflows/python.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 9119e97..b09a078 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -2,9 +2,9 @@ name: Python package
 
 on: 
   push:
-    branches: [ implement_ci ]
+    branches: [ master ]
   pull_request:
-    branches: [ implement_ci ]
+    branches: [ master ]
 
 jobs:
   build_and_test:

From b13a1c7b4077432b5d673858083fd32b1d53ef8f Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 14:04:39 +0100
Subject: [PATCH 22/24] Submodules are now retrieved from CMake config

---
 .github/workflows/python.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index b09a078..6cf6598 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -22,7 +22,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install plasma source
       run: |
-        git submodule update --init --recursive
         pip install -r requirements-develop.txt
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl

From 1de521641ad5ca4f9b3738c1d8788568b185a505 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 14:06:54 +0100
Subject: [PATCH 23/24] Pick up submodules from CMake config

---
 CMakeLists.txt | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0eb1beb..412d405 100644
--- a/CMakeLists.txt
+++ b/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

From 3353357af413e20fa2e04365f4dbaaf972030e56 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 30 Jul 2020 14:12:50 +0100
Subject: [PATCH 24/24] Tidy up step names

---
 .github/workflows/python.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 6cf6598..c46ced0 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -25,10 +25,10 @@ jobs:
         pip install -r requirements-develop.txt
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl
-    - name: run tests
+    - name: Run tests
       run: |
         pytest tests
-    - name: upload wheel
+    - name: Upload wheel artifact
       uses: actions/upload-artifact@v2
       with:
         name: dist