From bf7e4b76cd43e4da16cac69b844b0e7cf0477a92 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:13:02 +0100
Subject: [PATCH 01/33] Use cibuildwheel to create wheels

---
 .github/workflows/python.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index e81fb20..c86a5ff 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -30,10 +30,13 @@ jobs:
         cmake ..
         make
         sudo make install
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install cibuildwheel==1.6.1
     - name: Install plasma source
       run: |
         pip install -r requirements-develop.txt
-        python setup.py bdist_wheel
+        python -m cibuildwheel --output-dir dist
         python -m pip install --verbose dist/*.whl
     - name: Run tests
       run: |

From 90288367828f66a7695c3c4dfa40b5e9d7e59f1e Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:27:18 +0100
Subject: [PATCH 02/33] Work in manylinux container

---
 .github/workflows/python.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index c86a5ff..a4410fd 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -10,6 +10,7 @@ jobs:
   build_and_test:
 
     runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux2014_x86_64
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
@@ -30,13 +31,10 @@ jobs:
         cmake ..
         make
         sudo make install
-    - name: Install cibuildwheel
-      run: |
-        python -m pip install cibuildwheel==1.6.1
     - name: Install plasma source
       run: |
         pip install -r requirements-develop.txt
-        python -m cibuildwheel --output-dir dist
+        python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl
     - name: Run tests
       run: |

From 1448b2f1751ddc6fd2223a30aeebd83f9dedc562 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:29:04 +0100
Subject: [PATCH 03/33] No sudo as we're in a container

---
 .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 a4410fd..1c693ab 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -23,14 +23,14 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install OpenMC
       run: |
-        sudo apt-get install -y g++ cmake libhdf5-dev
+        apt-get install -y g++ cmake libhdf5-dev
         git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
         cd openmc
         git checkout
         mkdir build && cd build
         cmake ..
         make
-        sudo make install
+        make install
     - name: Install plasma source
       run: |
         pip install -r requirements-develop.txt

From 828192d9743a76b13859aaccd323efe4c9e516d9 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:31:46 +0100
Subject: [PATCH 04/33] Use yum rather than apt

---
 .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 1c693ab..73d001a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install OpenMC
       run: |
-        apt-get install -y g++ cmake libhdf5-dev
+        yum install -y g++ cmake libhdf5-dev
         git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
         cd openmc
         git checkout

From 35c641bfaee8d8d014d6c8c5f927f5a879579831 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:36:08 +0100
Subject: [PATCH 05/33] Use yum package names

---
 .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 73d001a..64239ca 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install OpenMC
       run: |
-        yum install -y g++ cmake libhdf5-dev
+        yum install -y gcc-c++ cmake hdf5-devel
         git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
         cd openmc
         git checkout

From 3ac1f98fc267305521d91e4ff4671bc7735f07d3 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:40:13 +0100
Subject: [PATCH 06/33] Use cmake3

---
 .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 64239ca..e18b946 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install OpenMC
       run: |
-        yum install -y gcc-c++ cmake hdf5-devel
+        yum install -y gcc-c++ cmake3 hdf5-devel
         git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
         cd openmc
         git checkout

From 7e71022bf4e6e3fa32bc1c58a3f273b7acd8b436 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:45:47 +0100
Subject: [PATCH 07/33] Register cmake3 as alternative for cmake

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index e18b946..7aba6b9 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -24,6 +24,11 @@ jobs:
     - name: Install OpenMC
       run: |
         yum install -y gcc-c++ cmake3 hdf5-devel
+        alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake3 20 \
+        --slave /usr/local/bin/ctest ctest /usr/bin/ctest3 \
+        --slave /usr/local/bin/cpack cpack /usr/bin/cpack3 \
+        --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake3 \
+        --family cmake
         git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
         cd openmc
         git checkout

From 0957ca469240719c2e87e76b61f2fd197ecff289 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 11:57:00 +0100
Subject: [PATCH 08/33] Run pip as a python module

---
 .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 7aba6b9..0c0d59d 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -38,7 +38,7 @@ jobs:
         make install
     - name: Install plasma source
       run: |
-        pip install -r requirements-develop.txt
+        python -m pip install -r requirements-develop.txt
         python setup.py bdist_wheel
         python -m pip install --verbose dist/*.whl
     - name: Run tests

From 15529f2a29d17ffbe3b01d37158bca90c0b914a7 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 18:24:10 +0100
Subject: [PATCH 09/33] Use manylinux installed python

---
 .github/workflows/python.yml | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 0c0d59d..b66b231 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -17,10 +17,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
     - name: Install OpenMC
       run: |
         yum install -y gcc-c++ cmake3 hdf5-devel
@@ -38,14 +34,16 @@ jobs:
         make install
     - name: Install plasma source
       run: |
+        export PYVER=${{ matrix.python-version }}
+        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
         python -m pip install -r requirements-develop.txt
-        python setup.py bdist_wheel
-        python -m pip install --verbose dist/*.whl
+        python -m pip wheel .
+        python -m pip install --verbose wheelhouse/*.whl
     - name: Run tests
       run: |
-        pytest tests
+        python -m pytest tests
     - name: Upload wheel artifact
       uses: actions/upload-artifact@v2
       with:
         name: dist
-        path: dist
+        path: wheelhouse

From fa4a489b6d1df93ac9d3054cea0f2e2f2a56c010 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 18:40:20 +0100
Subject: [PATCH 10/33] Install auditwheel and repair

---
 .github/workflows/python.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index b66b231..e7c0e1f 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -37,7 +37,10 @@ jobs:
         export PYVER=${{ matrix.python-version }}
         alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
         python -m pip install -r requirements-develop.txt
-        python -m pip wheel .
+        python -m pip install auditwheel
+        python setup.py bdist_wheel
+        python -m auditwheel show dist/*.whl
+        python -m auditwheel repair dist/*.whl
         python -m pip install --verbose wheelhouse/*.whl
     - name: Run tests
       run: |

From 0291ab555aea471bf6085aa88480a52e01e6758b Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 24 Sep 2020 18:53:23 +0100
Subject: [PATCH 11/33] Test to determine which python is used for test

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index e7c0e1f..a77a3e2 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -44,6 +44,7 @@ jobs:
         python -m pip install --verbose wheelhouse/*.whl
     - name: Run tests
       run: |
+        which python
         python -m pytest tests
     - name: Upload wheel artifact
       uses: actions/upload-artifact@v2

From b65c7382bb53af1bdb2e35544a7ab0908687724a Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Fri, 25 Sep 2020 08:14:12 +0100
Subject: [PATCH 12/33] Use correct python version for tests

---
 .github/workflows/python.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index a77a3e2..9ff57b0 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -44,7 +44,8 @@ jobs:
         python -m pip install --verbose wheelhouse/*.whl
     - name: Run tests
       run: |
-        which python
+        export PYVER=${{ matrix.python-version }}
+        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
         python -m pytest tests
     - name: Upload wheel artifact
       uses: actions/upload-artifact@v2

From ff643923665d3381a463ba0c1e8a3bba0b67fdeb Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Fri, 25 Sep 2020 08:45:41 +0100
Subject: [PATCH 13/33] Run tests from within tests directory

Ensures we use the installed version of the package
---
 .github/workflows/python.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 9ff57b0..ea83746 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -46,7 +46,8 @@ jobs:
       run: |
         export PYVER=${{ matrix.python-version }}
         alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
-        python -m pytest tests
+        cd tests
+        python -m pytest
     - name: Upload wheel artifact
       uses: actions/upload-artifact@v2
       with:

From 0962c37ab98c1c3084585ca54a19f120496f2740 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Fri, 25 Sep 2020 08:57:08 +0100
Subject: [PATCH 14/33] Support Python 3.9

---
 .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 ea83746..d7d3bba 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -13,7 +13,7 @@ jobs:
     container: quay.io/pypa/manylinux2014_x86_64
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2

From 89798faefc11015a401aeae11c161ffa4ee34070 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Fri, 25 Sep 2020 09:11:34 +0100
Subject: [PATCH 15/33] Publish wheel to test PyPI

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index d7d3bba..2f64db5 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -53,3 +53,12 @@ jobs:
       with:
         name: dist
         path: wheelhouse
+    - name: Publish wheel artifact
+      env:
+        TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
+    run: |
+        export PYVER=${{ matrix.python-version }}
+        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
+        python -m pip install twine
+        python -m twine upload --repository testpypi wheelhouse/*

From 0760dccc4f7c2a5a981d1d8dba4b038fb329316d Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Fri, 25 Sep 2020 09:12:52 +0100
Subject: [PATCH 16/33] Fix indentation

---
 .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 2f64db5..a498a38 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -57,7 +57,7 @@ jobs:
       env:
         TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
-    run: |
+      run: |
         export PYVER=${{ matrix.python-version }}
         alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
         python -m pip install twine

From 9537440137b86d7951dad07a0903e53aa7b12c7d Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Fri, 25 Sep 2020 09:27:30 +0100
Subject: [PATCH 17/33] Don't upload to TestPyPI for now

Avoids having to re-version on each push
---
 .github/workflows/python.yml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index a498a38..d7d3bba 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -53,12 +53,3 @@ jobs:
       with:
         name: dist
         path: wheelhouse
-    - name: Publish wheel artifact
-      env:
-        TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
-      run: |
-        export PYVER=${{ matrix.python-version }}
-        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
-        python -m pip install twine
-        python -m twine upload --repository testpypi wheelhouse/*

From adb71af18eb0013308e88b2df2c391d4413d5e99 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 11:34:55 +0100
Subject: [PATCH 18/33] Generate version from git tags and commits

Formats the version in a way that handles Python versioning standard
(PEP 440) by appending the number of commits since the last tag to a dev
pre-release identifier.
Allows override if release not yet found (we don't have tags yet).
---
 setup.py | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index ede8bd3..7aa85a0 100644
--- a/setup.py
+++ b/setup.py
@@ -58,12 +58,35 @@ def build_extension(self, ext):
         )
 
 
+def get_version(release_override="0.0.1"):
+    cwd = os.path.dirname(os.path.realpath(__file__))
+    version = subprocess.check_output(
+        ["git", "describe", "--always", "--tags"], stderr=None, cwd=cwd
+    ).strip().decode("utf-8")
+    if "." not in version:
+        # Git doesn't know about a tag yet, so manually set a version and get the total
+        # number of commits
+        num_commits = subprocess.check_output(
+            ["git", "rev-list", "--count", "HEAD"], stderr=None, cwd=cwd
+        ).strip().decode("utf-8")
+        version = release_override + ".dev" + num_commits
+    else:
+        if "-" in version:
+            # This commit doesn't correspond to an annotated tag, so mark it as dev and
+            # get the number of commits since the last annotated tag
+            version_split = version.split("-")
+            tag_version = version_split[0]
+            num_commits = version_split[1]
+            version = tag_version + ".dev" + num_commits
+    return version
+
+
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
 setup(
     name="parametric_plasma_source",
-    version="0.0.6",
+    version=get_version("0.0.6"),
     author="Andrew Davis",
     author_email="jonathan.shimwell@ukaea.uk",
     description="Parametric plasma source for fusion simulations in OpenMC",

From e1ffea9b44c6733934f24dd07f1e5cf40bdcda16 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 12:07:24 +0100
Subject: [PATCH 19/33] Refactor actions and include publish to PyPI

---
 .github/workflows/python.yml | 60 ++++++++++++++++++++++++++++++------
 1 file changed, 51 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index d7d3bba..d151a80 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -7,7 +7,7 @@ on:
     branches: [ master ]
 
 jobs:
-  build_and_test:
+  build:
 
     runs-on: ubuntu-latest
     container: quay.io/pypa/manylinux2014_x86_64
@@ -32,7 +32,7 @@ jobs:
         cmake ..
         make
         make install
-    - name: Install plasma source
+    - name: Build plasma source
       run: |
         export PYVER=${{ matrix.python-version }}
         alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
@@ -41,15 +41,57 @@ jobs:
         python setup.py bdist_wheel
         python -m auditwheel show dist/*.whl
         python -m auditwheel repair dist/*.whl
-        python -m pip install --verbose wheelhouse/*.whl
-    - name: Run tests
-      run: |
-        export PYVER=${{ matrix.python-version }}
-        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
-        cd tests
-        python -m pytest
     - name: Upload wheel artifact
       uses: actions/upload-artifact@v2
       with:
         name: dist
         path: wheelhouse
+
+  test:
+    runs-on: ubuntu-latest
+    needs: build
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    -name: Download build
+      uses: actions/download-artifact@v2
+      with:
+        name: dist
+    - name: Install plasma source
+        python -m pip install --no-index --find-links=file:dist parametric-plasma-source
+    - name: Run tests
+      run: |
+        python -m pip install -r requirements-develop.txt
+        cd tests
+        python -m pytest
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: test
+
+    - name: Publish wheel artifact to TestPyPI
+      env:
+        TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
+      run: |
+        export PYVER=${{ matrix.python-version }}
+        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
+        python -m pip install twine
+        python -m twine upload --repository testpypi wheelhouse/*
+    - name: Release wheel artifact to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        export PYVER=${{ matrix.python-version }}
+        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
+        python -m pip install twine
+        python -m twine upload wheelhouse/*

From 1c7db261ce048cd05d7f4fb70762dbdd0ef486bc Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 12:08:51 +0100
Subject: [PATCH 20/33] Fix yaml syntax error

---
 .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 d151a80..0b030e8 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -60,7 +60,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    -name: Download build
+    - name: Download build
       uses: actions/download-artifact@v2
       with:
         name: dist

From 20360325116b4a535415963f5466a7e854adc2ec Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 12:10:45 +0100
Subject: [PATCH 21/33] Add missing steps identifier

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 0b030e8..a0ccc9f 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -76,6 +76,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: test
 
+    steps:
     - name: Publish wheel artifact to TestPyPI
       env:
         TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}

From 3478b537d99f54aa71d90ef8295cc904204ffa1a Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 12:12:08 +0100
Subject: [PATCH 22/33] Add missing run identifier

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index a0ccc9f..c4a0ce7 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -65,6 +65,7 @@ jobs:
       with:
         name: dist
     - name: Install plasma source
+      run: |
         python -m pip install --no-index --find-links=file:dist parametric-plasma-source
     - name: Run tests
       run: |

From 7ded7c2e396467674bc169a9e339c2ad8530e605 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 13:01:13 +0100
Subject: [PATCH 23/33] Action not finding artifact after download

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index c4a0ce7..ff12968 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -64,8 +64,10 @@ jobs:
       uses: actions/download-artifact@v2
       with:
         name: dist
+        path: dist
     - name: Install plasma source
       run: |
+        ls -la
         python -m pip install --no-index --find-links=file:dist parametric-plasma-source
     - name: Run tests
       run: |

From 027557b19f3618992585068385eb0de083f2b4d0 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 13:22:17 +0100
Subject: [PATCH 24/33] GitHub doesn't have 3.9 installed

Also fix publish commands
---
 .github/workflows/python.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index ff12968..6cc4d6a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -13,7 +13,7 @@ jobs:
     container: quay.io/pypa/manylinux2014_x86_64
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -52,7 +52,7 @@ jobs:
     needs: build
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -67,7 +67,6 @@ jobs:
         path: dist
     - name: Install plasma source
       run: |
-        ls -la
         python -m pip install --no-index --find-links=file:dist parametric-plasma-source
     - name: Run tests
       run: |
@@ -80,22 +79,23 @@ jobs:
     needs: test
 
     steps:
+    - name: Download build
+      uses: actions/download-artifact@v2
+      with:
+        name: dist
+        path: dist
     - name: Publish wheel artifact to TestPyPI
       env:
         TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
       run: |
-        export PYVER=${{ matrix.python-version }}
-        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
-        python -m pip install twine
-        python -m twine upload --repository testpypi wheelhouse/*
+        python3 -m pip install twine
+        python3 -m twine upload --repository testpypi dist/*
     - name: Release wheel artifact to PyPI
       if: startsWith(github.ref, 'refs/tags')
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        export PYVER=${{ matrix.python-version }}
-        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
-        python -m pip install twine
-        python -m twine upload wheelhouse/*
+        python3 -m pip install twine
+        python3 -m twine upload dist/*

From 335f23783ec6f6906c141cbe3ab3aa3c799858e1 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 15:07:11 +0100
Subject: [PATCH 25/33] Add some log messages when creating version

---
 setup.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/setup.py b/setup.py
index 7aa85a0..9dc2049 100644
--- a/setup.py
+++ b/setup.py
@@ -69,6 +69,10 @@ def get_version(release_override="0.0.1"):
         num_commits = subprocess.check_output(
             ["git", "rev-list", "--count", "HEAD"], stderr=None, cwd=cwd
         ).strip().decode("utf-8")
+        print(
+            f"Creating version with overridden release tag = {release_override} "
+            f"and num commits = {num_commits}"
+        )
         version = release_override + ".dev" + num_commits
     else:
         if "-" in version:
@@ -77,7 +81,12 @@ def get_version(release_override="0.0.1"):
             version_split = version.split("-")
             tag_version = version_split[0]
             num_commits = version_split[1]
+            print(
+                f"Creating version with overridden tag = {tag_version} "
+                f"and num commits = {num_commits}"
+            )
             version = tag_version + ".dev" + num_commits
+    print(f"Using version = {version}")
     return version
 
 

From 6d9cb9a6a2d5bb768406f837ea35c122630c9023 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 15:25:28 +0100
Subject: [PATCH 26/33] Get full repo history so we know number of commits

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 6cc4d6a..b6c10b4 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -17,6 +17,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0  # Get the repo history so we can version by number of commits
     - name: Install OpenMC
       run: |
         yum install -y gcc-c++ cmake3 hdf5-devel

From 538577138f06483f8c53f42728bb9e1e36ee8421 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 15:44:48 +0100
Subject: [PATCH 27/33] Use post as the version extension

This allows TestPyPI to understand the ordering of versions.
---
 setup.py | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/setup.py b/setup.py
index 9dc2049..556eac1 100644
--- a/setup.py
+++ b/setup.py
@@ -69,24 +69,15 @@ def get_version(release_override="0.0.1"):
         num_commits = subprocess.check_output(
             ["git", "rev-list", "--count", "HEAD"], stderr=None, cwd=cwd
         ).strip().decode("utf-8")
-        print(
-            f"Creating version with overridden release tag = {release_override} "
-            f"and num commits = {num_commits}"
-        )
-        version = release_override + ".dev" + num_commits
+        version = release_override + ".post" + num_commits
     else:
         if "-" in version:
-            # This commit doesn't correspond to an annotated tag, so mark it as dev and
+            # This commit doesn't correspond to an annotated tag, so mark it as post and
             # get the number of commits since the last annotated tag
             version_split = version.split("-")
             tag_version = version_split[0]
             num_commits = version_split[1]
-            print(
-                f"Creating version with overridden tag = {tag_version} "
-                f"and num commits = {num_commits}"
-            )
-            version = tag_version + ".dev" + num_commits
-    print(f"Using version = {version}")
+            version = tag_version + ".post" + num_commits
     return version
 
 

From 13849913e57d3c77736f25d792bd5e87418654b2 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Mon, 28 Sep 2020 16:29:09 +0100
Subject: [PATCH 28/33] Verbose twine output

---
 .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 b6c10b4..c4328ae 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -92,7 +92,7 @@ jobs:
         TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
       run: |
         python3 -m pip install twine
-        python3 -m twine upload --repository testpypi dist/*
+        python3 -m twine upload --repository testpypi dist/* --verbose
     - name: Release wheel artifact to PyPI
       if: startsWith(github.ref, 'refs/tags')
       env:
@@ -100,4 +100,4 @@ jobs:
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python3 -m pip install twine
-        python3 -m twine upload dist/*
+        python3 -m twine upload dist/* --verbose

From d3023d1859118714701a51321e1e61bb1b152998 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 30 Sep 2020 15:08:27 +0100
Subject: [PATCH 29/33] Run workflow when a release is created

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index c4328ae..1aeca7a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -5,6 +5,9 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
+  release:
+    types:
+      - created
 
 jobs:
   build:

From 8d62d309b8e877e6073b25a858615af918ee1c5b Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 30 Sep 2020 15:08:43 +0100
Subject: [PATCH 30/33] Don't reinstall twine

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

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 1aeca7a..7d65f23 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -102,5 +102,4 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python3 -m pip install twine
         python3 -m twine upload dist/* --verbose

From 3d306593d4fdf66409b74f9a10c61b1ead538116 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 30 Sep 2020 15:12:49 +0100
Subject: [PATCH 31/33] Check TestPyPI and PyPI versions

This should be more robust than just using git e.g. if two PRs are worked on
simultaneously.
---
 requirements-develop.txt |  1 +
 setup.py                 | 75 ++++++++++++++++++++++++++++++++--------
 2 files changed, 61 insertions(+), 15 deletions(-)

diff --git a/requirements-develop.txt b/requirements-develop.txt
index 763b67d..50344e4 100644
--- a/requirements-develop.txt
+++ b/requirements-develop.txt
@@ -1,4 +1,5 @@
 black
 flake8
 pytest
+requests
 wheel
diff --git a/setup.py b/setup.py
index 556eac1..cec54a1 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,6 @@
+import json
 import os
+import requests
 import subprocess
 import sys
 
@@ -59,25 +61,68 @@ def build_extension(self, ext):
 
 
 def get_version(release_override="0.0.1"):
+    def get_last_version_root(last_version):
+        if ".post" in last_version or ".dev" in last_version:
+            last_version_root = ".".join(last_version.split(".")[:-1])
+        else:
+            last_version_root = last_version
+        return last_version_root
+
     cwd = os.path.dirname(os.path.realpath(__file__))
-    version = subprocess.check_output(
+    git_version = subprocess.check_output(
         ["git", "describe", "--always", "--tags"], stderr=None, cwd=cwd
     ).strip().decode("utf-8")
-    if "." not in version:
-        # Git doesn't know about a tag yet, so manually set a version and get the total
-        # number of commits
-        num_commits = subprocess.check_output(
-            ["git", "rev-list", "--count", "HEAD"], stderr=None, cwd=cwd
-        ).strip().decode("utf-8")
-        version = release_override + ".post" + num_commits
+
+    if "." not in git_version:
+        # Git doesn't know about a tag yet, so set the version root to release_override
+        version_root = release_override
+    else:
+        version_root = git_version.split("-")[0]
+
+    if "." not in git_version or "-" in git_version:
+        # This commit doesn't correspond to a tag, so mark it as post or dev
+        response = requests.get(
+            "https://test.pypi.org/pypi/parametric-plasma-source/json"
+        )
+        if response.status_code == 200:
+            # Response from TestPyPI was successful - get latest version and increment
+            last_version = json.loads(response.content)["info"]["version"]
+            last_version_root = get_last_version_root(last_version)
+
+            if last_version_root == version_root:
+                # We're still on the same released version, so increment the 'post'
+                post_count = 1
+                if "post" in last_version:
+                    post_index = last_version.rfind("post") + 4
+                    post_count = int(last_version[post_index:])
+                    post_count += 1
+                version = version_root + ".post" + str(post_count)
+            else:
+                response = requests.get(
+                    "https://pypi.org/pypi/parametric-plasma-source/json"
+                )
+                dev_count = 1
+                if response.status_code == 200:
+                    # Response from PyPI was successful - get dev version and increment
+                    last_version = json.loads(response.content)["info"]["version"]
+                    last_version_root = get_last_version_root(last_version)
+
+                    if last_version_root == version_root:
+                        if "dev" in last_version:
+                            dev_index = last_version.rfind("dev") + 3
+                            dev_count = int(last_version[dev_index:])
+                            dev_count += 1
+                version = version_root + ".dev" + str(dev_count)
+        else:
+            # Bad response from TestPyPI, so use git commits (requires git history)
+            # NOTE: May cause version clashes on mutliple branches - use test.pypi
+            # to avoid this.
+            num_commits = subprocess.check_output(
+                ["git", "rev-list", "--count", "HEAD"], stderr=None, cwd=cwd
+            ).strip().decode("utf-8")
+            version = release_override + ".post" + num_commits
     else:
-        if "-" in version:
-            # This commit doesn't correspond to an annotated tag, so mark it as post and
-            # get the number of commits since the last annotated tag
-            version_split = version.split("-")
-            tag_version = version_split[0]
-            num_commits = version_split[1]
-            version = tag_version + ".post" + num_commits
+        version = version_root
     return version
 
 

From 41aa9ec16575c0eb3f6a146492c93494cb519528 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Wed, 30 Sep 2020 15:56:11 +0100
Subject: [PATCH 32/33] Use same account for PyPI and TestPyPI

---
 .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 7d65f23..bc8cbf5 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -91,8 +91,8 @@ jobs:
         path: dist
     - name: Publish wheel artifact to TestPyPI
       env:
-        TWINE_USERNAME: ${{ secrets.TEST_PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python3 -m pip install twine
         python3 -m twine upload --repository testpypi dist/* --verbose

From bb4cdaa049265cfcbe54e2d09a3172fe3baa9190 Mon Sep 17 00:00:00 2001
From: Dan Short <dan.short@ukaea.uk>
Date: Thu, 29 Oct 2020 19:24:53 +0000
Subject: [PATCH 33/33] Use new branch names for CI

---
 .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 e81fb20..3e34105 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -2,9 +2,9 @@ name: python_package
 
 on: 
   push:
-    branches: [ master ]
+    branches: [ main, develop ]
   pull_request:
-    branches: [ master ]
+    branches: [ main, develop ]
 
 jobs:
   build_and_test: