simvue 2.5.2__tar.gz → 2.5.4__tar.gz

simvue-2.5.4/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## Description of Bug
+A clear and concise description of what the bug is.
+
+## Steps To Reproduce
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+## Expected behavior
+A clear and concise description of what you expected to happen.
+
+## Actual Behaviour
+A clear and concise description of what you actually see happen.
+
+## Screenshots
+If applicable, add screenshots to help explain your problem.
+
+## Setup
+ - OS: [e.g. Windows 11]
+ - Python version [e.g. v3.13.3]
+
+## Additional context
+Add any other context about the problem here.

simvue-2.5.4/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest a new feature or enhancement to add to the Python API
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Problem Statement
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+## Solution
+A clear and concise description of what you want to happen.
+
+## Alternatives Considered
+A clear and concise description of any alternative solutions or features you've considered.
+
+## Additional Context
+Add any other context or screenshots about the feature request here.

simvue-2.5.4/.github/PULL_REQUEST_TEMPLATE/bug_fix.md

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+# <Title of Bug Fix>
+
+**Issue:** Link to the issue relating to this bug.
+
+**Python Version(s) Tested:** Python versions this fix has been verified against.
+
+**Operating System(s):** Operating systems this fix has been tested in.
+
+## 📝 Summary
+
+Please provide a summary of the original bug, and the fix implemented to address it.
+
+## 🔍 Diagnosis
+
+If applicable, please summarise any information relating to how the bug was identified, and the root causes.
+
+## 🔄 Changes
+
+Provide any additional detail on the changes applied to address the issue.
+
+## ✔️ Checklist
+- [ ] Unit and integration tests passing.
+- [ ] Pre-commit hooks passing.
+- [ ] Quality checks passing.

simvue-2.5.4/.github/PULL_REQUEST_TEMPLATE/feature.md

@@ -0,0 +1,23 @@
+# <Feature Title>
+
+**Issue:** Link to the issue proposing this feature.
+
+**Python Version(s) Tested:** Python versions this feature has been tested on.
+
+**Operating System(s):** Operating systems this feature has been tested on.
+
+**Documentation PR:** Issue on [Docs repo](https://github.com/simvue-io/docs).
+
+## 📝 Summary
+
+Please provide a summary of the feature including why it is beneficial to other users.
+
+## 🔄 Changes
+
+Outline the changes/additions made to implement this feature.
+
+## ✔️ Checklist
+- [ ] Unit and integration tests passing.
+- [ ] Pre-commit hooks passing.
+- [ ] Quality checks passing.
+- [ ] Updated the [documentation](https://github.com/simvue-io/docs).

simvue-2.5.4/.github/dependabot.yml

@@ -0,0 +1,18 @@
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+      time: "00:00"
+    reviewers:
+      - "kzscisoft"
+    commit-message:
+      prefix: "pip"
+      include: "scope"
+    open-pull-requests-limit: 5
+    target-branch: "dev"
+    ignore:
+      - dependency-type: all
+        match:
+          - "tests/**"

simvue-2.5.4/.github/pull_request_template.md

@@ -0,0 +1,5 @@
+Please select from the following templates by clicking 'Preview' and then the relevant link:
+
+🆕 [**Feature**](?expand=1&template=feature.md)
+
+🐛 [**Bug Fix**](?expand=1&template=bug_fix.md)

simvue-2.5.4/.github/workflows/citation.yml

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+name: Citation File Validation
+
+on:
+  push:
+    branches: [ "main", "dev", "hotfix/update-ci" ]
+  pull_request:
+    branches: [ "main", "dev", "hotfix/update-ci" ]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+    - uses: actions/checkout@v5
+    - name: Set up Python
+      uses: actions/setup-python@v6
+    - name: Install Checker
+      run: python3 -m pip install cffconvert
+    - name: Check Citation File
+      run: cffconvert --validate

simvue-2.5.4/.github/workflows/codeql.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "dev", "main" ]
+  pull_request:
+    branches: [ "dev", "main" ]
+  schedule:
+    - cron: '35 15 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+        # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

simvue-2.5.4/.github/workflows/deploy.yaml

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+name: Deploy to PyPi
+on:
+  push:
+    tags:
+      - "v*"
+jobs:
+  build:
+    name: Build Wheels and Package 🛠️
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v5
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.x"
+      - name: Install Poetry
+        run: python -m pip install poetry
+      - name: Build Module
+        run: poetry build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          retention-days: 1
+          if-no-files-found: error
+          name: python-package-distributions
+          path: dist/
+  publish_test:
+    name: Publish to TestPyPi 🧪
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: test_pypi
+      url: https://test.pypi.org/p/simvue
+    permissions:
+      id-token: write
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish to TestPyPi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+  publish:
+    name: Publish to PyPi 🐍📦
+    needs:
+      - publish_test
+    if: "!contains(github.ref, 'rc') && !contains(github.ref, 'beta') && !contains(github.ref, 'alpha')"
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/simvue
+    permissions:
+      id-token: write
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish to PyPi
+        uses: pypa/gh-action-pypi-publish@release/v1
+  github-release:
+    name: Create Signed GitHub Release 🔏
+    needs:
+      - publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          LATESTCHANGES=$(awk '
+            BEGIN { header_found = 0 }
+            /^## / {
+                if (header_found == 0) {
+                    header = $0
+                    header_found = 1
+                    next
+                } else {
+                  exit
+                }
+            }
+            header_found == 1 && /^\- / { print }
+          ' CHANGELOG.md)
+          gh release create
+          '${{ github.ref_name }}'
+          --notes "$LATESTCHANGES"
+          --title 'Simvue ${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

simvue-2.5.4/.github/workflows/examples.yml

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+name: Simvue Examples
+
+on:
+  push:
+    branches: ["main", "dev", "hotfix/update-ci"]
+  pull_request:
+    branches: [ "main", "dev", "hotfix/update-ci" ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  GeometryOptimisation:
+    runs-on: ubuntu-latest
+    if: false # deactivate for now
+    steps:
+        - uses: actions/checkout@v4
+        - name: Download BlueMira
+          uses: actions/checkout@v4
+          with:
+            repository: Fusion-Power-Plant-Framework/bluemira
+            ref: v1.10.0
+            path: blue_mira
+        - uses: conda-incubator/setup-miniconda@v3
+          with:
+            activate-environment: bluemira
+            environment-file: blue_mira/conda/environment.yml
+            miniforge-version: "latest"
+            use-only-tar-bz2: false
+            miniforge-variant: Mambaforge
+            use-mamba: true
+            python-version: "3.11"
+        - name: Install bluemira
+          shell: bash -l {0}
+          run: pip install -e blue_mira
+        - name: Install Simvue
+          shell: bash -l {0}
+          run: pip install -e .
+        - name: Run Example
+          shell: bash -l {0}
+          run: python ./examples/GeometryOptimisation/bluemira_simvue_geometry_optimisation.py
+  Logging:
+    runs-on: ubuntu-latest
+    if: false # deactivate for now
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install Simvue
+        run: python3 -m pip install .
+      - name: Run Example
+        run: |
+          export SIMVUE_URL=${{ secrets.SIMVUE_URL }}
+          export SIMVUE_TOKEN=${{ secrets.SIMVUE_TOKEN }}
+          python3 examples/Logging/logging-to-simvue.py --ci
+  Optuna:
+    runs-on: ubuntu-latest
+    if: false # deactivate for now
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install Simvue
+        run: python3 -m pip install .
+      - name: Install Dependencies
+        run: |
+          python3 -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+          python3 -m pip install -r examples/Optuna/PyTorch/requirements.txt
+      - name: Run Example
+        run: |
+          export SIMVUE_URL=${{ secrets.SIMVUE_URL }}
+          export SIMVUE_TOKEN=${{ secrets.SIMVUE_TOKEN }}
+          python3.11 ./examples/Optuna/PyTorch/simvue_optuna_pytorch.py --ci
+  PyTorch:
+    runs-on: ubuntu-latest
+    if: false # deactivate for now
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install Simvue
+        run: python3 -m pip install .
+      - name: Install Dependencies
+        run: |
+          python3 -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+          python3 -m pip install -r examples/PyTorch/requirements.txt
+      - name: Run Example
+        run: |
+          export SIMVUE_URL=${{ secrets.SIMVUE_URL }}
+          export SIMVUE_TOKEN=${{ secrets.SIMVUE_TOKEN }}
+          python3.11 ./examples/PyTorch/main.py --ci
+  SU2:
+    runs-on: ubuntu-latest
+    if: false # deactivate for now
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Download SU2
+        run: |
+          wget https://github.com/su2code/SU2/releases/download/v8.0.1/SU2-v8.0.1-linux64.zip
+          unzip SU2-v8.0.1-linux64.zip
+      - name: Install dependencies
+        run: |
+          python -m pip install ukaea-multiparser
+          python -m pip install .
+      - name: Run Example
+        run: |
+          export SIMVUE_URL=${{ secrets.SIMVUE_URL }}
+          export SIMVUE_TOKEN=${{ secrets.SIMVUE_TOKEN }}
+          python examples/SU2/SU2.py bin --config tests/example_data/SU2_inv_ONERAM6.cfg --ci
+  TensorFlow:
+    if: false # deactivate for now
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install Simvue
+        run: python3 -m pip install .
+      - name: Install Dependencies
+        run: python3 -m pip install -r examples/Tensorflow/requirements.txt
+      - name: Run Example
+        run: |
+          export SIMVUE_URL=${{ secrets.SIMVUE_URL }}
+          export SIMVUE_TOKEN=${{ secrets.SIMVUE_TOKEN }}
+          python3.11 ./examples/Tensorflow/dynamic_rnn.py --ci
+  GEANT4:
+    if: false # deactivate for now
+    runs-on: ubuntu-latest
+    container:
+      image: artemisbeta/geant4:11.2.1
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install Simvue
+        run: python3 -m pip install .
+      - name: Install Dependencies
+        run: python3 -m pip install -r examples/Geant4/requirements.txt
+      - name: Build Example
+        run: |
+          cmake -DCMAKE_PREFIX_PATH=/usr/local/share/geant4/install/4.11.2/ -Bbuild examples/Geant4/FixedTarget/
+          cmake --build build
+      - name: Run Example
+        run: |
+          export SIMVUE_URL=${{ secrets.SIMVUE_URL }}
+          export SIMVUE_TOKEN=${{ secrets.SIMVUE_TOKEN }}
+          python examples/Geant4/geant4_simvue.py build/MaterialTesting --ci --events 10

simvue-2.5.4/.github/workflows/prek.yml

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+name: Prek Hooks
+
+on:
+  push:
+    branches: ["main", "dev", "hotfix/update-ci", "*prek*"]
+  pull_request:
+    branches: ["main", "dev", "hotfix/update-ci", "*prek*"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  prek:
+    name: Run Prek Hooks
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v6
+      - name: Run Prek
+        uses: j178/prek-action@v2
+        with:
+          extra-args: '--all-files --skip no-commit-to-branch'