hyper-surrogate 0.1.0__tar.gz

hyper_surrogate-0.1.0/.editorconfig

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+max_line_length = 120
+
+[*.json]
+indent_style = space
+indent_size = 4

hyper_surrogate-0.1.0/.github/actions/setup-uv-env/action.yml

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+name: "setup-uv-env"
+description: "Composite action to setup Python and uv environment."
+
+inputs:
+  python-version:
+    required: false
+    description: "The python version to use"
+    default: "3.12"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
+
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install dependencies
+      run: uv sync --all-groups
+      shell: bash

hyper_surrogate-0.1.0/.github/workflows/main.yml

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+name: Main
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-uv-env
+
+      - name: Run checks
+        run: make check
+
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13"]
+      fail-fast: false
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-groups --extra ml
+
+      - name: Run tests (fast on PR, all on main)
+        run: |
+          if [ "${{ github.event_name }}" = "push" ]; then
+            uv run pytest --doctest-modules tests -m "" --cov --cov-config=pyproject.toml --cov-report=xml
+          else
+            uv run pytest --doctest-modules tests --cov --cov-config=pyproject.toml --cov-report=xml
+          fi
+
+      - name: Run mypy
+        run: uv run mypy
+
+      - name: Upload coverage reports to Codecov on Python 3.13
+        uses: codecov/codecov-action@v4
+        if: ${{ matrix.python-version == '3.13' }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  check-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-uv-env
+
+      - name: Check if documentation can be built
+        run: uv run mkdocs build -s

hyper_surrogate-0.1.0/.github/workflows/on-release-main.yml

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+name: release-main
+
+on:
+  release:
+    types: [published]
+    branches: [main]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-uv-env
+
+      - name: Export tag
+        id: vars
+        run: echo tag=${GITHUB_REF#refs/*/} >> $GITHUB_OUTPUT
+
+      - name: Build and publish
+        run: |
+          sed -i "s/^version = .*/version = \"$RELEASE_VERSION\"/" pyproject.toml
+          make build-and-publish
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
+          RELEASE_VERSION: ${{ steps.vars.outputs.tag }}
+
+  build-and-upload-docs:
+    needs: publish
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-uv-env
+
+      - name: Build documentation
+        run: uv run mkdocs build --clean
+
+      - name: Upload Pages artifact for deployment
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy-docs:
+    needs: build-and-upload-docs
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

hyper_surrogate-0.1.0/.github/workflows/validate-codecov-config.yml

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+name: validate-codecov-config
+
+on:
+  pull_request:
+    paths: [codecov.yaml]
+  push:
+    branches: [main]
+
+jobs:
+  validate-codecov-config:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Validate codecov configuration
+        run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate

hyper_surrogate-0.1.0/.gitignore

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+docs/source
+.worktrees/
+.DS_Store
+
+# Demo artifacts (not part of the library)
+demo.py
+create_demo_animation.py
+create_preview.py
+record_demo.sh
+DEMO_README.md
+hyper_surrogate_demo.*
+
+# Fortran build artifacts
+scripts/
+examples/outputs/
+
+# From https://raw.githubusercontent.com/github/gitignore/main/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Vscode config files
+.vscode/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.qodo

hyper_surrogate-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.6.5"
+    hooks:
+      - id: ruff
+        args: [--exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5 # SEE: https://github.com/pre-commit/pre-commit/issues/3133

hyper_surrogate-0.1.0/CONTRIBUTING.md

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+# Contributing to `hyper-surrogate`
+
+Contributions are welcome, and they are greatly appreciated!
+Every little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+# Types of Contributions
+
+## Report Bugs
+
+Report bugs at https://github.com/jpsferreira/hyper-surrogate/issues
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+## Fix Bugs
+
+Look through the GitHub issues for bugs.
+Anything tagged with "bug" and "help wanted" is open to whoever wants to implement a fix for it.
+
+## Implement Features
+
+Look through the GitHub issues for features.
+Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
+
+## Write Documentation
+
+Cookiecutter PyPackage could always use more documentation, whether as part of the official docs, in docstrings, or even on the web in blog posts, articles, and such.
+
+## Submit Feedback
+
+The best way to send feedback is to file an issue at https://github.com/jpsferreira/hyper-surrogate/issues.
+
+If you are proposing a new feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+# Get Started!
+
+Ready to contribute? Here's how to set up `hyper-surrogate` for local development.
+Please note this documentation assumes you already have `poetry` and `Git` installed and ready to go.
+
+1. Fork the `hyper-surrogate` repo on GitHub.
+
+2. Clone your fork locally:
+
+```bash
+cd <directory_in_which_repo_should_be_created>
+git clone git@github.com:YOUR_NAME/hyper-surrogate.git
+```
+
+3. Now we need to install the environment. Navigate into the directory
+
+```bash
+cd hyper-surrogate
+```
+
+If you are using `pyenv`, select a version to use locally. (See installed versions with `pyenv versions`)
+
+```bash
+pyenv local <x.y.z>
+```
+
+Then, install and activate the environment with:
+
+```bash
+poetry install
+poetry shell
+```
+
+4. Install pre-commit to run linters/formatters at commit time:
+
+```bash
+poetry run pre-commit install
+```
+
+5. Create a branch for local development:
+
+```bash
+git checkout -b name-of-your-bugfix-or-feature
+```
+
+Now you can make your changes locally.
+
+6. Don't forget to add test cases for your added functionality to the `tests` directory.
+
+7. When you're done making changes, check that your changes pass the formatting tests.
+
+```bash
+make check
+```
+
+Now, validate that all unit tests are passing:
+
+```bash
+make test
+```
+
+9. Before raising a pull request you should also run tox.
+   This will run the tests across different versions of Python:
+
+```bash
+tox
+```
+
+This requires you to have multiple versions of python installed.
+This step is also triggered in the CI/CD pipeline, so you could also choose to skip this step locally.
+
+10. Commit your changes and push your branch to GitHub:
+
+```bash
+git add .
+git commit -m "Your detailed description of your changes."
+git push origin name-of-your-bugfix-or-feature
+```
+
+11. Submit a pull request through the GitHub website.
+
+# Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+
+2. If the pull request adds functionality, the docs should be updated.
+   Put your new functionality into a function with a docstring, and add the feature to the list in `README.md`.

hyper_surrogate-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024, Joao Ferreira
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hyper_surrogate-0.1.0/Makefile

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+.PHONY: install
+install: ## Install the environment and pre-commit hooks
+	@echo "🚀 Creating virtual environment using uv"
+	@uv sync --all-groups
+	@uv run pre-commit install
+
+.PHONY: check
+check: ## Run code quality tools.
+	@echo "🚀 Checking lockfile consistency with 'pyproject.toml': Running uv lock --check"
+	@uv lock --check
+	@echo "🚀 Linting code: Running pre-commit"
+	@uv run pre-commit run -a
+	@echo "🚀 Static type checking: Running mypy"
+	@uv run mypy
+	@echo "🚀 Checking for obsolete dependencies: Running deptry"
+	@uv run deptry .
+
+.PHONY: test
+test: ## Test the code with pytest
+	@echo "🚀 Testing code: Running pytest"
+	@uv run pytest --cov --cov-config=pyproject.toml --cov-report=xml
+
+.PHONY: build
+build: clean-build ## Build wheel file
+	@echo "🚀 Creating wheel file"
+	@uv build
+
+.PHONY: clean-build
+clean-build: ## clean build artifacts
+	@rm -rf dist
+
+.PHONY: publish
+publish: ## publish a release to pypi.
+	@echo "🚀 Publishing: Dry run."
+	@uv publish --dry-run
+	@echo "🚀 Publishing."
+	@uv publish
+
+.PHONY: build-and-publish
+build-and-publish: build publish ## Build and publish.
+
+.PHONY: docs-test
+docs-test: ## Test if documentation can be built without warnings or errors
+	@uv run mkdocs build -s
+
+.PHONY: docs
+docs: ## Build and serve the documentation
+	@uv run mkdocs serve
+
+.PHONY: help
+help:
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+.DEFAULT_GOAL := help

hyper_surrogate-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hyper-surrogate
+Version: 0.1.0
+Summary: Hyperelastic Surrogates
+Project-URL: repository, https://github.com/jpsferreira/hyper-surrogate
+Project-URL: documentation, https://jpsferreira.github.io/hyper-surrogate/
+Author-email: Joao Ferreira <fj.ferreira@fe.up.pt>
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: matplotlib>=3.8.3
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: sympy>=1.12
+Requires-Dist: tqdm>=4.66.5
+Provides-Extra: ml
+Requires-Dist: torch>=2.0; extra == 'ml'
+Description-Content-Type: text/markdown
+
+# hyper-surrogate
+
+[![Release](https://img.shields.io/github/v/release/jpsferreira/hyper-surrogate)](https://img.shields.io/github/v/release/jpsferreira/hyper-surrogate)
+[![Build status](https://img.shields.io/github/actions/workflow/status/jpsferreira/hyper-surrogate/main.yml?branch=main)](https://github.com/jpsferreira/hyper-surrogate/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/jpsferreira/hyper-surrogate/branch/main/graph/badge.svg)](https://codecov.io/gh/jpsferreira/hyper-surrogate)
+[![License](https://img.shields.io/github/license/jpsferreira/hyper-surrogate)](https://img.shields.io/github/license/jpsferreira/hyper-surrogate)
+
+Data-driven surrogates for hyperelastic constitutive models in finite element analysis.
+
+- **Github repository**: <https://github.com/jpsferreira/hyper-surrogate/>
+- **Documentation**: <https://jpsferreira.github.io/hyper-surrogate/>
+
+## Features
+
+- **Symbolic mechanics** -- Automatic PK2 stress and stiffness tensor derivation via SymPy
+- **ML surrogates** -- MLP and Input-Convex Neural Network (ICNN) models for constitutive response approximation
+- **Fortran export** -- Transpile trained models to standalone Fortran 90 subroutines with baked-in weights
+- **Analytical UMAT** -- Generate optimized Fortran UMAT subroutines from symbolic expressions
+
+## Quick start
+
+```python
+import hyper_surrogate as hs
+
+# Define material and generate training data
+material = hs.NeoHooke({"C10": 0.5, "KBULK": 1000.0})
+train_ds, val_ds, in_norm, out_norm = hs.create_datasets(
+    material, n_samples=5000, input_type="invariants", target_type="pk2_voigt",
+)
+
+# Train an MLP surrogate
+model = hs.MLP(input_dim=3, output_dim=6, hidden_dims=[32, 32], activation="tanh")
+result = hs.Trainer(model, train_ds, val_ds, loss_fn=hs.StressLoss(), max_epochs=500).fit()
+
+# Export to Fortran 90
+exported = hs.extract_weights(result.model, in_norm, out_norm)
+hs.FortranEmitter(exported).write("nn_surrogate.f90")
+```
+
+See the [examples](https://jpsferreira.github.io/hyper-surrogate/examples/) for more usage patterns.
+
+## Installation
+
+```bash
+pip install hyper-surrogate        # core (NumPy, SymPy)
+pip install hyper-surrogate[ml]    # with PyTorch for ML surrogates
+```
+
+From source with [uv](https://docs.astral.sh/uv/):
+
+```bash
+git clone https://github.com/jpsferreira/hyper-surrogate.git
+cd hyper-surrogate
+uv sync --all-groups --extra ml
+```