initial commit

.devcontainer/Dockerfile

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+FROM mcr.microsoft.com/devcontainers/base:bullseye
+# FROM mcr.microsoft.com/devcontainers/base:jammy 
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG USER=vscode
+
+RUN DEBIAN_FRONTEND=noninteractive \
+    && apt-get update \ 
+    && apt-get install -y build-essential --no-install-recommends make \
+        ca-certificates \
+        git \
+        libssl-dev \
+        zlib1g-dev \
+        libbz2-dev \
+        libreadline-dev \
+        libsqlite3-dev \
+        wget \
+        curl \
+        llvm \
+        libncurses5-dev \
+        xz-utils \
+        tk-dev \
+        libxml2-dev \
+        libxmlsec1-dev \
+        libffi-dev \
+        liblzma-dev
+
+# Python and poetry installation
+USER $USER
+ARG HOME="/home/$USER"
+ARG PYTHON_VERSION=3.11
+# ARG PYTHON_VERSION=3.10
+
+ENV PYENV_ROOT="${HOME}/.pyenv"
+ENV PATH="${PYENV_ROOT}/shims:${PYENV_ROOT}/bin:${HOME}/.local/bin:$PATH"
+
+RUN echo "done 0" \
+    && curl https://pyenv.run | bash \
+    && echo "done 1" \
+    && pyenv install ${PYTHON_VERSION} \
+    && echo "done 2" \
+    && pyenv global ${PYTHON_VERSION} \
+    && echo "done 3" \
+    && curl -sSL https://install.python-poetry.org | python3 - \
+    && poetry config virtualenvs.in-project true

.devcontainer/devcontainer.json

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+{
+	"name": "poetry3-poetry-pyenv",
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+
+	// 👇 Features to add to the Dev Container. More info: https://containers.dev/implementors/features.
+	// "features": {},
+
+	// 👇 Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// 👇 Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "poetry install --with dev --no-interaction",
+
+	// 👇 Configure tool-specific properties.
+	"customizations": {
+        "vscode": {
+            "extensions":["ms-python.python", "njpwerner.autodocstring"]
+            }
+        }
+
+	// 👇 Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.github/workflows/docs.yml

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+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: docs
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+
+    - name: Install dependencies
+      run: |
+        curl -sSL https://install.python-poetry.org | python3
+        poetry install --with dev --no-interaction
+        
+    - name: Build
+      run: |
+        cd docs
+        sudo apt-get install pandoc
+        poetry run make html
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/_build/html
+        destination_dir: ./

.github/workflows/python-test.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main, dev ]
+  pull_request:
+    branches: [ main , dev ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10','3.11']
+
+    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 dependencies
+      run: |
+        curl -sSL https://install.python-poetry.org | python3
+        poetry install --with dev --no-interaction
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=examples
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=examples
+
+    - name: Test with pytest
+      run: |
+        poetry run pytest --cov-report=term-missing --cov=temperer tests/ | tee pytest-coverage.txt
+
+    - name: Comment coverage
+      if: ${{ github.event_name == 'pull_request' && github.event.action == 'opened' }}
+      uses: coroo/[email protected]
+      with:
+        pytest-coverage: pytest-coverage.txt

.gitignore

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+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+#others
+*.spyproject
+INPUTS/
+RESULTS/
+.ipynb_checkpoints
+dask-worker-space/
+*.mat
+*.vscode
+*.DS_Store
+venv/
+others/
+__pycache__/
+*.egg-info/
+.eggs/
+
+.testmondata
+.pytest_cache
+.coverage
+
+nodes-mapA/
+out-mapA/
+out-mapA-2
+temp/
+
+exec/
+exec2/
+exec3/
+exec4/
+exec5/
+exec6/
+exec7/
+exec8/
+exec9/
+exec10/
+exec11/
+exec12/
+exec13/
+
+docs/_build

README.md

@@ -1 +1,74 @@
-# pysubsheat
+# SubsHeat
+## Forward modeling of thermal evolution in geological time
+
+![Build Status](https://github.com/equinor/SubsHeat/actions/workflows/python-test.yml/badge.svg?branch=main)
+![Build Status](https://github.com/equinor/SubsHeat/actions/workflows/docs.yml/badge.svg?branch=main)
+
+[Documentation](https://curly-adventure-5mpe5wj.pages.github.io/)
+
+SubsHeat is a python package used for modeling thermal evolution based on McKenzie's type basin extension. It can be use for:
+
+- Finding beta factor
+- Calculating subsidence and thermal history
+- Basement heat flow through time
+
+## Features
+
+- Build model from either: 
+    - Python objects
+    - [XTGeo](https://github.com/equinor/xtgeo/) supported surface formats
+    - [PetroMod](https://www.software.slb.com/products/petromod) models using [petromodder](https://github.com/equinor/petromodder)
+- Multi-rift phase support
+- Numba accelerated
+- Dask support
+
+## SubsHeat3D
+3D simulations in SubsHeat are under active development. Currently, yhey are based on a uniform reactangular grid of 1D nodes (defined in a NodeGrid data structure). The sediment inputs, horizons are present day, are provided as .gri files, which are read into a SedimentStack class. 
+
+### Pre-requisite: grid of 1D node simulation
+The complete 1D SubsHeat simulation is run for some of the 1D nodes. For other 1D nodes the subsidence, beta factor, and crustal thickness are interpolated. The 1D simulations can be run using the script [parallel-1Dsed.py](subsheat3D/parallel-1Dsed.py).  Results for each node are pickled to a separate file (this is to be improved!).
+
+### 3D heat equation simulation using dolfinx
+The 3D simulation performs a series of heat equation solves, regularly updating the mesh positions from the 1D nodes. The equations are solved using the PETSc solver from the dolfinx package (part of the FeNiCs project). The compute mesh is built by defining hexahedra for every rectangle of 1D nodes and for every layer (i.e. each sediment, the crust, the lithosphere, and the aesthenosphere), which are then subdivided into tetrahedra. 
+
+The dolfinx model building and solving is managed by the class [UniformNodeGridFixedSizeMeshModel](subsheat3D/fixed_mesh_model.py).  The use of this class is demonstrated in [subsheat3D_mapA_example.py](tests/subsheat3D_mapA_example.py). Note that the NodeGrid class definition in this script should match the definition used in [parallel-1Dsed.py](subsheat3D/parallel-1Dsed.py) to compute the 1D solutions. This script writes the results (mesh positions and function values) at every 1M years in xdmf format for visualization in ParaView. 
+
+### RESQML output
+The test script [subsheat3D_mapA_example.py](tests/subsheat3D_mapA_example.py) further demonstrates writing the unstructured grid (with properties) in RESQML format, as a pair of .epc and .h5 files.  The RESQML I/O functions are in a separate file, [resqpy_helpers.py](subsheat3D/resqpy_helpers.py), and require a modified version of the resqpy library.  To visualise RESQML data in ParaView, a 3rd-party plug-in can be installed, see [fespp](https://github.com/F2I-Consulting/fespp). 
+
+### SubsHeat3D dependencies
+The dolfinx package is Linux-only(?) and has to be compiled from source or installed using apt-get.  The resqpy dependency can be installed with pip, but, for now, some writing of properties on unstructured grids requires a change in resqpy that is not yet merged.  The other dependencies xtgeo and meshio can be installed using pip (requirements file is to be added).
+
+
+## Installation
+
+SubsHeat support Python >=3.7, <3.10.
+
+Install from source by cloning this repo 
+
+```
+git clone https://github.com/equinor/SubsHeat.git
+pip install -e .
+```
+or install from Azure private feed. Contact us for access
+
+```
+pip install --extra-index-url \
+https://x:<token>@pkgs.dev.azure.com/Equinor/DIPVP/_packaging/ET_PSM/pypi/simple \
+subsheat
+```
+
+## Development
+
+Easiest is to use codespace:
+https://docs.github.com/en/codespaces/getting-started/quickstart
+
+Or use our devcontainer:
+https://code.visualstudio.com/docs/remote/containers
+
+## Run tests
+
+`poetry run pytest --cov-report=term-missing --cov=subsheat tests/ | tee pytest-coverage.txt`
+
+## License
+

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/apireference.rst

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+==================================
+API Reference
+==================================
+
+
+Model
+---------------
+.. automodule:: temperer.model
+    :members:
+
+Model builder
+---------------
+.. automodule:: temperer.build
+    :members:
+.. autoclass:: temperer.build.Builder
+    :members:
+
+Parameters
+---------------
+.. automodule:: temperer.parameters
+    :members:
+
+Forward model
+---------------
+.. automodule:: temperer.forward_modelling
+    :members:
+
+Simulator
+---------------
+.. automodule:: temperer.simulator
+    :members:
+
+Results
+---------------
+.. automodule:: temperer.postprocessing
+    :members: