UWGeodynamics Merging

Author: rbeucher

.github/workflows/CI.yml

@@ -212,12 +212,12 @@ jobs:
       - name: Build dependencies
         run: |
           apt-get update -qq 
-          DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends build-essential pkg-config python3-dev swig libxml2-dev
+          DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends build-essential pkg-config python3-dev swig libxml2-dev cmake ninja-build
 
       - name: Runtime dependencies
         run: |
           apt-get update -qq
-          DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends libxml2 libpython3.9
+          DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends libxml2 libpython3.10
 
       - name: Checkout
         uses: actions/checkout@v2
@@ -229,7 +229,8 @@ jobs:
       - name: Run Tests
         run: |
           pip install pytest
-          python -m pytest -vvv docs/pytests
+          pytest -vvv docs/pytests
+          pytest -vvv docs/test/UWGeodynamics
 
   conda_build:
       name: Conda Build (Python ${{matrix.python-version}} ${{ matrix.os }})
@@ -266,3 +267,24 @@ jobs:
               anaconda login --hostname github-actions-${{ matrix.os  }}-$RANDOM --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
               conda-build --channel conda-forge --user geo-down-under conda
               anaconda logout
+
+  pypi:
+    name: Pypi Source Distribution
+    runs-on: ubuntu-latest
+    env:
+      TWINE_USERNAME: ${{ secrets.TWINE_USERNAME }}
+      TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Package for Pypi
+        run: |
+          python setup.py sdist
+      - name: Push to Pypi
+        if: github.event_name == 'release'
+        run: |
+          pip install twine
+          python -m twine upload dist/* -r

README.md

@@ -76,12 +76,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from underworld.mesh import FeMesh_IndexSet\n",
+    "\n",
     "cond1 = (Model.mesh.data[Model.top_wall.data][:, 0] < 0.0625)\n",
     "cond2 = (Model.mesh.data[Model.top_wall.data][:, 0] > -0.0625)\n",
     "\n",
     "indices = Model.top_wall.data[cond1 * cond2]\n",
     "\n",
-    "IndexSet = GEO.uw.mesh.FeMesh_IndexSet(Model.mesh, topologicalIndex=0, size=Model.mesh.nodesGlobal, fromObject=indices)"
+    "IndexSet = FeMesh_IndexSet(Model.mesh, topologicalIndex=0, size=Model.mesh.nodesGlobal, fromObject=indices)"
    ]
   },
   {
@@ -207,7 +209,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -221,7 +223,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

docs/UWGeodynamics/benchmarks/1_22_Indentor_Benchmark.ipynb

@@ -31,12 +31,9 @@ RUN apt-get update -qq \
         python3-virtualenv \
         python3-pip \
         python3-numpy \
-        python3-numpy-dbg \
         vim \
         less \
         git \
-        cmake \
-        gcc python3-dev \
         valgrind valgrind-dbg valgrind-mpi \
         gdb cgdb \ 
 &&  apt-get clean \

docs/development/docker/base/Dockerfile

@@ -71,7 +71,7 @@ RUN ldconfig
 # create venv now for forthcoming python packages
 USER $NB_USER
 RUN /usr/bin/python3 -m virtualenv --system-site-packages --python=/usr/bin/python3 ${VIRTUAL_ENV}
-RUN pip3 install --no-cache-dir mpi4py
+RUN pip3 install --no-cache-dir Cython git+https://github.com/mpi4py/mpi4py@3.1.0
 
 USER root
 # build petsc

docs/development/docker/petsc/Dockerfile

@@ -11,6 +11,7 @@ RUN apt-get update -qq \
 &&  DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
         libxml2 \
         libpython${PYVER}
+        
 
 FROM base_runtime AS build_base
 # install build requirements
@@ -20,6 +21,7 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
         pkg-config \
         python3-dev \
         cmake \
+        ninja-build \
         make \
         swig \
         libxml2-dev \