Initial commit - docs copied from uw3 repo

.binder/apt.txt

@@ -0,0 +1,8 @@
+libgl1-mesa-glx
+libxcursor-dev
+libglu1 
+libxft2 
+libxinerama1 
+libfltk1.3-dev  
+libfreetype6-dev  
+libgl1-mesa-dev 

.binder/environment.yml

@@ -0,0 +1,32 @@
+name: uw3
+channels:
+  - jgiordani
+  - conda-forge
+dependencies:
+  - python=3.11
+  - jgiordani::uw3_env
+  - mpmath<=1.3
+  - mesalib
+  - numpy
+  - scipy
+  # - mpich-mpicc
+  # - mpich-mpicxx
+  # - cython=3.*
+  # - petsc>=3.20.5
+  # - petsc4py>=3.20.5
+  # - mpi4py
+  # - h5py
+  - sympy
+  - pytest
+  - ipython 
+  - pyvista[all]
+  - quarto
+  - pip
+  - pip:  
+    - gmsh
+    - jupyterlab>=4.1
+    - jupytext>=1.16.1
+    - pygments>=2.17.0
+    - trame-vtk
+    - trame-vuetify
+

.binder/postBuild

@@ -0,0 +1,45 @@
+#!/bin/bash -v
+
+
+# echo
+# echo Install uw3_env during postBuild phase
+# echo
+
+# conda env list
+
+# # conda init
+# # conda activate notebook
+# # mamba install --yes -c jgiordani uw3_env
+
+echo
+echo Install jupyter extensions
+echo
+
+# install required python packages
+python3 -m pip install "jupyter-server-proxy"
+python3 -m pip install "jupyterlab-quarto>=0.3.3"
+python3 -m pip install "jupytext>=1.16.1"
+python3 -m pip install "trame_jupyter_extension"
+
+# We install the local code "properly" - no point in a dev build here
+
+echo
+echo Install local UW3 
+echo
+
+# Note: we would be better to find a way to access this directly
+# CONDA_PREFIX=`conda run -n notebook bash -c "echo \${CONDA_PREFIX}"`
+
+export CONDA_PREFIX=/srv/conda/envs/notebook/
+export PYTHONPATH=$CONDA_PREFIX/lib
+
+# debugging if required
+# python -c "import petsc4py; print(petsc4py.get_config())"
+# python -c "from petsc4py import PETSc; print('Imported PETSc')"
+
+pip install .
+
+
+echo
+echo Completed
+echo

.binder/start

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+## This is not required for the conda-forge version of petsc but
+## it is needed if we install the uw3_env dependencies
+
+export PYTHONPATH=$CONDA_PREFIX/lib/ 
+
+exec "$@"

.github/.devcontainer/DOCKERFILE_GHCS

@@ -0,0 +1,28 @@
+FROM mcr.microsoft.com/devcontainers/miniconda:0-3
+
+RUN conda install -n base -c conda-forge mamba
+
+# Here we can install all the dependencies using mamba (as we do in the test scripts)
+
+COPY .devcontainer/uw_environment.yml  /tmp/conda-tmp/
+RUN  mamba env update -n base --file /tmp/conda-tmp/uw_environment.yml 
+
+RUN export PETSC_DIR=/opt/conda \
+    && pip install petsc4py 
+
+RUN pip install gmsh
+
+# Add other dependencies that can't be installed correctly.
+
+##
+## gmsh seems to be broken in this installation
+## 
+
+# [Optional] Uncomment to install a different version of Python than the default
+# RUN conda install -y python=3.6 \
+#     && pip install --no-cache-dir pipx \
+#     && pipx reinstall-all
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get install ffmpeg libsm6 libxext6 

.github/.devcontainer/devcontainer.json

@@ -0,0 +1,23 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
+{
+    "name": "Underworld3",
+    "build": {
+        "context": "..",
+        "dockerfile": "DOCKERFILE_GHCS"
+    },
+    // Features to add to the dev container. More info: https://containers.dev/features.
+    // "features": {},
+    // The following are needed by gmsh even though we don't want to use X
+    "features": {
+        "ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
+            "packages": "libgl1,libcairo2-dev,libxcursor-dev, libxinerama-dev"
+        }
+    },
+    // 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": "conda init && cd /workspaces/underworld3 && export PETSC_DIR=/opt/conda && python3 setup.py build_ext && sudo -E /opt/conda/bin/pip install ."
+    // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+    // "remoteUser": "root"
+}

.github/.devcontainer/uw_environment.yml

@@ -0,0 +1,20 @@
+name: uw3_runtime
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - numpy
+  - sympy
+  - mpich-mpicc
+  - mpich-mpicxx
+  - cython
+  - petsc=3.18.0
+  - mpi4py
+  - h5py
+  - mesalib
+  - pytest
+  - ipython # needed for "display" functionality (should be optional !)
+  - pyvista # flagged in some tests (should not be needed for tests !)
+  - pip
+
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,12 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+What version of underworld3 are you running and how to reproduce the bug.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've 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.

.github/ISSUE_TEMPLATE/runtime-error.md

@@ -0,0 +1,25 @@
+---
+name: Runtime Error
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the runtime issue**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+E.g. Model snippet, or command line used.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 0.5]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/🐛-bug-report.md

@@ -0,0 +1,16 @@
+---
+name: "\U0001F41B Bug report"
+about: Create an report to help us improve
+title: "[BUG] - add title"
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+- What is the bug?
+- What version code?
+- What system are you running the code on?
+- Steps to reproduce?
+
+**Screenshots**

.github/workflows/CI.yml

@@ -0,0 +1,38 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+
+  build_docker_image:
+    name: Build Underworld 3 Docker image
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PWORD }}
+
+      - name: Build Base Docker Image
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          file: ./Dockerfile
+          platforms: linux/amd64, linux/arm64
+          tags: underworldcode/carbonite

.github/workflows/build_deploy_jbdoc.yml

@@ -0,0 +1,52 @@
+name: API docs / jupyterbook
+
+# We should trigger this from an upload event 
+
+on:
+  push:   # We publish the beta docs as well - but on a different url (by branch name)
+    branches: 
+      - main 
+      - development
+
+
+  workflow_dispatch:
+
+jobs:
+  deploy:
+    runs-on: macos-latest
+    steps:
+
+      - uses: actions/checkout@v3
+
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: ./.github/workflows/envs/build_jb.yml
+          cache-downloads: true
+
+      # - name: install jupyterbook dependencies
+      #   run: |
+      #     pip install jupyter-book
+      #     pip install jupytext
+
+      - name: Build docs with jupyterbook
+        shell: bash -l {0}
+        run: |
+          cd Jupyterbook
+          ./build_book.sh 
+
+
+      ## Always deploy to version directory
+      - name: Deploy JB
+        uses: peaceiris/actions-gh-pages@v3
+
+        with:
+          # deploy_key: ${{ secrets.GH_PAGES_DEPLOY_PR_KEY }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          destination_dir: ${{ github.ref_name }}    # The dest dir is identified by branch 
+          publish_dir: jupyterbook/_build/html
+
+
+
+