Initial commit

Signed-off-by: bvandekerkhof <bas.vandekerkhof@shell.com>

.github/bump_version.py

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import re
+
+with open("pyproject.toml", "r") as file:
+    version_content = file.read()
+# Match regex for <version="0.0.0a",> pattern
+old_semantic_version = re.findall(r'version = "(\d+\.\d+\.[a-zA-Z0-9]+)"', version_content)
+major_version, minor_version, patch_version = old_semantic_version[0].split(".")
+patch_version = int(re.findall(r"\d+", patch_version)[0])
+new_semantic_version = f"{major_version}.{minor_version}.{patch_version + 1}"
+regex_bumped_patch_version = f"\g<1>{new_semantic_version}"
+# Match regex for <version = "0.0.0a"> pattern
+bumped_version_content = re.sub(r'(version = ")\d+\.\d+\.[a-zA-Z0-9]+', regex_bumped_patch_version, version_content)
+with open("pyproject.toml", "w") as file:
+    file.write(bumped_version_content)
+print(new_semantic_version)  # Print is required for release in GitHub action

.github/pull_request_template.md

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+<!--
+SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+
+SPDX-License-Identifier: Apache-2.0
+-->
+
+# Description
+
+Please include a summary of the changes and the related issue. Please also include relevant motivation and context. 
+List any dependencies that are required for this change.
+
+Fixes # (issue)
+
+## Type of change
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+# Jupyter Notebooks
+
+If your changes involve Jupyter notebooks please explicitly state here what the change consists of, e.g. only output 
+cells have changes or specific input changes. This to make sure we capture these changes correctly in the review process.
+
+# How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. 
+Please also list any relevant details for your test configuration
+
+- [ ] Test A
+- [ ] Test B
+
+
+# Checklist:
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my code
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published in downstream modules
+

.github/workflows/build_package.yml

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: Building the package
+on:
+  push:
+    branches:
+      - 'main'
+jobs:
+  Build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.11" ]
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install --upgrade build
+      - name: Build the package
+        run: |
+          python -m build
+      - name: Upload build files
+        uses: actions/upload-artifact@v3
+        with:
+          name: openmcmc_whl
+          path: ./dist/*.whl

.github/workflows/code_formatting.yml

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: Code formatting
+on:
+  - push
+jobs:
+  Black:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Specify all python versions you might want to perform the actions on
+        python-version: [ "3.11" ]
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black 
+          pip install isort
+      - name: Run isort, black checks
+        run: |
+          isort . --check
+          black . --check
+      - name: Run isort and black when required and commit back
+        if: failure()
+        env:
+          GITHUB_ACCESS_TOKEN: ${{ secrets.OPENMCMC_TOKEN }}
+        run: |
+          isort .
+          black .
+          git config --global user.name 'code_reformat'
+          git config --global user.email ''
+          git remote set-url origin "https://$GITHUB_ACCESS_TOKEN@github.com/$GITHUB_REPOSITORY"
+          git commit --signoff -am "Automatic reformat of code"
+          git push

.github/workflows/publish_docs.yml

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: publish documentation
+on:
+  push:
+    branches:
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+      - run: pip install mkdocs-material
+      - run: pip install mkdocstrings-python
+      - run: mkdocs gh-deploy --force

.github/workflows/pydocstyle_check.yml

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: pydocstyle
+on:
+  - push
+jobs:
+  pydocstyle:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Specify all python versions you might want to perform the actions on
+        python-version: [ "3.11" ]
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pydocstyle
+      - name: Run PydocStyle check
+        run: |
+          pydocstyle .

.github/workflows/pylint_check.yml

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+on:
+  - push
+
+name: Pylint Check
+jobs:
+  Pylint:
+    # Specify the operating system GitHub has to use to perform the checks (ubuntu seems to be default)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Specify all python versions you might want to perform the actions on
+        python-version: ["3.11"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+        pip install .
+    - name: Analysing the code with pylint
+      if: ${{ always() }}
+    # Run through the src/openmcmc/ directory and check all .py files with pylint
+      run: |
+        python -m pylint `find -regextype egrep -regex '(.*src/openmcmc/.*.py)$'` --output-format=parseable:pylint_report.out
+    - name: Upload pylint results
+      if: ${{ always() }}
+      uses: actions/upload-artifact@v3
+      with:
+        name: pylint_report
+        path: pylint_report.out

.github/workflows/release_tagging.yml

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+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: ReleaseTag
+
+# Trigger when a python file is changed on main branch either from pull request or push
+# but not when only pyproject.toml is changed due to version bump
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '**.py'
+      - '!pyproject.toml'
+      - 'requirements.txt'
+
+jobs:
+  # Releases new Python version when Pull Requests are merged into "main"
+  Release:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Specify all python versions you might want to perform the actions on
+        python-version: [ "3.11" ]
+    steps:
+      # Checkout
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Bump version and commit bumped version back to branch
+        env:
+          GITHUB_ACCESS_TOKEN: ${{ secrets.OPENMCMC_TOKEN }}
+        id: version
+        run: |
+          version=$(python .github/bump_version.py)
+          git config --global user.name 'bump_version'
+          git config --global user.email 'action@github.com'
+          git remote set-url origin "https://$GITHUB_ACCESS_TOKEN@github.com/$GITHUB_REPOSITORY"
+          git commit --signoff -am "Bumped minor version"
+          git push
+          echo "BUMPED_VERSION=$(echo v$version)" >> $GITHUB_ENV
+          echo "New version: $version"
+      - name: Create Release
+        run: gh release create ${{ env.BUMPED_VERSION }} --generate-notes
+        env:
+          GITHUB_TOKEN: ${{ secrets.OPENMCMC_TOKEN }}

.github/workflows/reuse_compliance.yml

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+name: REUSE Compliance Check
+
+on:
+  - push
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+    - name: REUSE Compliance Check
+      uses: fsfe/reuse-action@v2