Refactor scripts to tested package

.github/workflows/python-publish.yml

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+# This yml file will trigger a Github Actions event that builds and upload the
+# Python package to PiPy. This makes use of Twine and is triggered when a push
+# to the main branch occures. For more information see:
+# https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# and for details on the Autobump version section see:
+# https://github.com/grst/python-ci-versioneer
+
+name: Upload Python Package
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel build twine
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python -m build
+        twine check dist/*
+        twine upload dist/*

.github/workflows/test_package.yml

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+
+name: test_existence
+on:  
+  workflow_dispatch:
+  pull_request:    
+    branches:
+    - main  
+  push:
+    branches:
+    - main
+
+
+jobs:
+    run_scripts:
+      runs-on: ubuntu-latest
+      steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install testing dependencies
+        run: |
+          sudo apt-get install libhdf5-serial-dev
+          git clone --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git
+          cd openmc
+          mkdir build
+          cd build
+          cmake ..
+          make -j2
+          sudo make -j2 install
+          cd ..
+          pip install .
+          cd ..
+          pip install .
+
+        # this just check the scripts are accessible after the install
+        # the scripts are not run or checked for correct behaviour
+      - name: Test convert scripts exist
+        run: |
+          convert_fendl --help
+          convert_jeff32 --help
+          convert_jeff33 --help
+          convert_lib80x --help
+          convert_mcnp70 --help
+          convert_mcnp71 --help
+          convert_nndc71 --help
+          convert_tendl --help
+
+      - name: Test generate scripts exist
+        run: |
+          generate_cendl --help
+          generate_endf --help
+          generate_jeff33 --help
+          generate_jendl --help
+
+      - name: Test download h5 scripts exist
+        run: |
+          download_nndc --help
+
+      - name: Test download chain files scripts exist
+        run: |
+          download_nndc_chain --help
+
+      - name: Test other scripts exist
+        run: |
+          combine_libraries --help
+          convert_tendl_rand --help
+          # make_compton --help commented out as the script needs adapting
+          # make_stopping_powers --help commented out as the script needs adapting
+          sample_sandy --help
+
+      - name: Test depletion scripts exist
+        run: |
+          add_branching_ratios --help
+          generate_endf71_chain_casl --help
+          generate_endf_chain --help
+          generate_serpent_fissq --help
+          generate_tendl_chain --help
+          reduce_chain --help

.github/workflows/test_processing.yml

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+
+name: test_convert_scripts
+on:  
+  workflow_dispatch:
+  pull_request:    
+    branches:
+    - main  
+  push:
+    branches:
+    - main
+
+
+jobs:
+    run_scripts:
+      runs-on: ubuntu-latest
+      steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # OR "2" -> To retrieve the preceding commit.
+
+      - name: Get specific changed files
+        id: changed-files-specific
+        uses: tj-actions/changed-files@v19
+        with:
+          files: |
+            openmc_data/convert/convert_*.py
+            openmc_data/download/download_*.py
+
+      - name: Set up Python
+        if: steps.changed-files-specific.outputs.any_changed == 'true'
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install testing dependencies
+        if: steps.changed-files-specific.outputs.any_changed == 'true'
+        run: |
+          sudo apt-get install libhdf5-serial-dev
+          git clone --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git
+          cd openmc
+          mkdir build
+          cd build
+          cmake ..
+          make -j2
+          sudo make -j2 install
+          cd ..
+          pip install .
+          cd ..
+          pip install .
+
+      # convert scripts that require mcnp nuclear data are not tested when the
+      # contents change as the CI doesn't contain that nuclear data.
+      # convert_lib80x.py convert_mcnp70.py convert_mcnp71.py files are not tested here
+
+      - name: test default convert_fendl
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/convert_fendl.py')
+        run: |
+          echo "convert_fendl.py file has been modified."
+          convert_fendl --cleanup
+
+      # this running convert_jeff32 in with default arguments produces 49GB of
+      # data. Hence the use of arguments to process just one temperature
+      - name: test default convert_jeff32
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/convert/convert_jeff32.py')
+        run: |
+          echo "convert_jeff32.py file has been modified."
+          convert_jeff32 -r 3.2 -t 293 --cleanup
+
+      - name: test default convert_jeff33
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/convert/convert_jeff33.py')
+        run: |
+          echo "convert_jeff33.py file has been modified."
+          convert_jeff33 -r 3.3 -t 293 --cleanup
+
+      - name: test default convert_nndc71
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/convert/convert_nndc71.py')
+        run: |
+          echo "convert_nndc71.py file has been modified."
+          convert_nndc71 --cleanup
+
+      - name: test default convert_tendl
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/convert/convert_tendl.py')
+        run: |
+          echo "convert_tendl.py file has been modified."
+          convert_tendl --cleanup
+
+      - name: test default convert_tendl_rand
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/convert/convert_tendl_rand.py')
+        run: |
+          echo "convert_tendl_rand.py file has been modified."
+          convert_tendl_rand --nuclides O16 --cleanup
+
+      # download scripts
+      - name: test default download_nndc
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/download/download_nndc.py')
+        run: |
+          echo "download_nndc.py file has been modified."
+          download_nndc
+
+      - name: test default download_nndc_chain
+        if: contains(steps.changed-files-specific.outputs.modified_files, 'openmc_data/download/download_nndc_chain.py')
+        run: |
+          echo "download_nndc_chain.py file has been modified."
+          download_nndc_chain

.github/workflows/test_urls.yml

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+
+name: test_urls
+on:  
+  workflow_dispatch:
+  pull_request:    
+    branches:
+    - main  
+  push:
+    branches:
+    - main
+  schedule:
+    - cron: "0 0 * * *"
+# cron job runs every day
+
+jobs:
+    ping_urls:
+      runs-on: ubuntu-latest
+      steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install testing dependencies
+        run: |
+          sudo apt-get install libhdf5-serial-dev
+          git clone --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git
+          cd openmc
+          mkdir build
+          cd build
+          cmake ..
+          make -j2
+          sudo make -j2 install
+          cd ..
+          pip install .
+          cd ..
+          pip install .[tests]
+
+      # the -s allows normal print statements in the url testing to be seen in
+      # the pytest output 
+      - name: test urls
+        run: |
+          pytest -v -s tests/test_urls.py