UWGeodynamics Merging

.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

@@ -25,10 +25,10 @@ The Underworld development is led by Louis Moresi and is a collaboration between
 Underworld Geodynamics High-level API
 --------------------------------------
 
-[![image](docs/UWGeodynamics/readthedocs/src/img/logos.png)](https://www.earthbyte.org/the-basin-genesis-hub)
+[![image](docs/development/docs_generator/images/UWGeo/logos.png)](https://www.earthbyte.org/the-basin-genesis-hub)
 
 ![image](docs/UWGeodynamics/tutorials/images/Tutorial1.gif)
-![image](docs/UWGeodynamics/readthedocs/src/img/collision_wedge.gif)
+![image](docs/development/docs_generator/images/UWGeo/collision_wedge.gif)
 
 The UWGeodynamics module (`from underworld import UWGoedynamics`) facilitates prototyping of geodynamics models using Underworld. It can be seen as a set of high-level functions within the Underworld ecosystem. It is a means to quickly get the user into Underworld modelling and assumes very little knowledge in coding. The module make some assumptions based on how the user defines the boundary conditions and the properties of the materials (rocks, phases). Its simplicity comes with a relatively more rigid workflow (compared to the classic Underworld functions). However, the user can easily break the high level objects and get back to core Underworld function at any step of model design.
 

docs/UWGeodynamics/benchmarks/1_22_Indentor_Benchmark.ipynb

@@ -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/development/docker/base/Dockerfile

@@ -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/petsc/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/underworld2/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 \

docs/development/docs_generator/UWGeoTutorials.rst

@@ -6,7 +6,7 @@ We provide a series of docs/tutorials as Jupyter notebook:
 
 1. `Tutorial 1 Simple Rift`_
 
-.. image:: img/Tutorial1.gif
+.. image:: images/UWGeo/Tutorial1.gif
    :target: http://nbviewer.jupyter.org/github/underworldcode/underworld2/blob/master/docs/UWGeodynamics/tutorials/Tutorial_1_ThermoMechanical_Model.ipynb
 
 [Output Data](https://www.dropbox.com/s/3gy3boh9mf9s807/Tutorial1_BGH.zip?dl=0)
@@ -17,14 +17,14 @@ We provide a series of docs/tutorials as Jupyter notebook:
 
 3. `Tutorial 3 Sandbox Extension`_
 
-.. image:: img/underworld.png
+.. image:: images/UWGeo/underworld.png
    :target: http://nbviewer.jupyter.org/github/underworldcode/underworld2/blob/master/docs/UWGeodynamics/tutorials/Tutorial_3_SandboxExtension_static_mesh.ipynb
 
 [Output Data](https://www.dropbox.com/s/9j24v5ex1eanro2/Tutorial3_BGH.zip?dl=0)
 
 4. `Tutorial 4 Sandbox Compression`_
 
-.. image:: img/Tutorial4.png
+.. image:: images/UWGeo/Tutorial4.png
    :target: http://nbviewer.jupyter.org/github/underworldcode/underworld2/blob/master/docs/UWGeodynamics/tutorials/Tutorial_4_NumericalSandboxCompression.ipynb
 
 [Output Data](https://www.dropbox.com/s/4wlp3cociwysz3l/Tutorial4_BGH.zip?dl=0)
@@ -43,7 +43,7 @@ We provide a series of docs/tutorials as Jupyter notebook:
 
 9. `Tutorial 9 Passive Margins`_
 
-.. image:: img/Tutorial_9.gif
+.. image:: images/UWGeo/Tutorial_9.gif
    :target: http://nbviewer.jupyter.org/github/underworldcode/underworld2/blob/master/docs/UWGeodynamics/tutorials/Tutorial_9_passive_margins.ipynb
 
 [Output Data](https://www.dropbox.com/s/g1ocpse0mld4tiy/Tutorial9_BGH.zip?dl=0)
@@ -56,7 +56,7 @@ We provide a series of docs/tutorials as Jupyter notebook:
 
 [Output Data](https://www.dropbox.com/s/qpzrxp9fcf35w38/Tutorial11_BGH.zip?dl=0)
 
-.. image:: img/Tutorial11.gif
+.. image:: images/UWGeo/Tutorial11.gif
    :target: http://nbviewer.jupyter.org/github/underworldcode/underworld2/blob/master/docs/UWGeodynamics/tutorials/Tutorial_11_Coupling_with_Badlands.ipynb
 
 .. _Tutorial 1 Simple Rift: http://nbviewer.jupyter.org/github/underworldcode/underworld2/blob/master/docs/UWGeodynamics/tutorials/Tutorial_1_ThermoMechanical_Model.ipynb

docs/development/docs_generator/UWGeoUserGuide.rst

@@ -23,7 +23,7 @@ appending the method, variable or function with ``?``.
 Design principles
 -----------------
 
-.. image:: /img/Design.svg
+.. image:: /images/UWGeo/Design.svg
 
 
 import *UWGeodynamics*
@@ -146,7 +146,7 @@ or simply
 You can have a quick overview of all the units available by hitting tab
 after the ``.`` of the u object.
 
-.. image:: img/tabtab.gif
+.. image:: images/UWGeo/tabtab.gif
 
 Quantities can then be defined as follow:
 
@@ -314,7 +314,7 @@ MaterialRegistry object:
    materials_database = GEO.MaterialRegistry()
 
 
-.. image:: /img/MaterialRegistry.gif
+.. image:: /images/UWGeo/MaterialRegistry.gif
 
 .. note::
 
@@ -340,7 +340,7 @@ Materials are defined using the **Material** object as follow:
 Typing the name of the material in an empty cell will return a table
 which summarizes the property of the material:
 
-.. image:: img/Material1.png
+.. image:: images/UWGeo/Material1.png
 
 As you can see, most of the property are undefined.
 
@@ -492,7 +492,7 @@ There are a range of available/pre-defined shapes
    ...
    >>> Fig.show()
 
-.. image:: /img/layers.png
+.. image:: /images/UWGeo/layers.png
 
 **Polygon**
 
@@ -512,7 +512,7 @@ There are a range of available/pre-defined shapes
    >>> Fig.Points(Model.swarm, Model.materialField)
    >>> Fig.show()
 
-.. image:: /img/polygon.png
+.. image:: /images/UWGeo/polygon.png
 
 **Box**
 
@@ -531,7 +531,7 @@ There are a range of available/pre-defined shapes
    >>> Fig.Points(Model.swarm, Model.materialField)
    >>> Fig.show()
 
-.. image:: /img/box.png
+.. image:: /images/UWGeo/box.png
 
 **Disk**
 
@@ -550,7 +550,7 @@ There are a range of available/pre-defined shapes
    >>> Fig.Points(Model.swarm, Model.materialField)
    >>> Fig.show()
 
-.. image:: /img/disk.png
+.. image:: /images/UWGeo/disk.png
 
 
 **Sphere (3D)**
@@ -585,7 +585,7 @@ There are a range of available/pre-defined shapes
    >>> Fig.Points(Model.swarm, Model.materialField)
    >>> Fig.show()
 
-.. image:: /img/annulus.png
+.. image:: /images/UWGeo/annulus.png
 
 
 **CombinedShape**
@@ -611,7 +611,7 @@ Several shapes can be combined to form a material shape:
    >>> Fig.Points(Model.swarm, Model.materialField)
    >>> Fig.show()
 
-.. image:: /img/multishape.png
+.. image:: /images/UWGeo/multishape.png
 
 You can also take the intersection of some shapes:
 
@@ -634,7 +634,7 @@ You can also take the intersection of some shapes:
   >>> Fig.Points(Model.swarm, Model.materialField)
   >>> Fig.show()
 
-.. image:: /img/multishape-1.png
+.. image:: /images/UWGeo/multishape-1.png
 
 **HalfSpace**
 
@@ -646,7 +646,7 @@ defined by the normal vector.
 
    HalfSpaces can be combined to define 3D shapes / volumes.
 
-.. image:: /img/3D_halfspaces.png
+.. image:: /images/UWGeo/3D_halfspaces.png
 
 .. code:: python
 
@@ -678,7 +678,7 @@ defined by the normal vector.
    >>> viewer.window()
 
 
-.. image:: /img/3D_halfspaces2.png
+.. image:: /images/UWGeo/3D_halfspaces2.png
 
 **Multiple materials**
 
@@ -770,7 +770,7 @@ activation energy, `P` the pressure, `V` the activation volume, `n` the stress e
 *UWGeodynamics* provides a library of commonly used Viscous Creep Flow Laws.
 These can be accessed using the `GEO.ViscousCreepRegistry`:
 
-.. image:: /img/ViscousCreepRegistry.gif
+.. image:: /images/UWGeo/ViscousCreepRegistry.gif
 
 
 .. note::
@@ -909,7 +909,7 @@ As with Viscous Creep, we also provide a registry of commmonly used
 plastic behaviors.
 They can be accessed using the `GEO.PlasticityRegistry` registry.
 
-.. image:: /img/PlasticityRegistry.gif
+.. image:: /images/UWGeo/PlasticityRegistry.gif
 
 .. note::
 
@@ -1128,7 +1128,7 @@ vertically along the side walls.
    ...                       top=[None,0.])
    ...
 
-.. image:: /img/mechanicalBCs1.png
+.. image:: /images/UWGeo/mechanicalBCs1.png
 
 3D
 ^^
@@ -1182,7 +1182,7 @@ the part of the left wall below 32 kilometre. Velocity is set to be
    ...                       top=[None,0.])
    ...
 
-.. image:: /img/mechanicalBCs2.png
+.. image:: /images/UWGeo/mechanicalBCs2.png
 
 
 Stress Conditions

docs/development/docs_generator/UWGeodynamics.rst

@@ -1,9 +1,9 @@
 Welcome to UWGeodynamics's documentation!
 =========================================
 
-.. image:: ./img/Tutorial1.gif
+.. image:: ./images/UWGeo/Tutorial1.gif
 
-.. image:: ./img/collision_wedge.gif
+.. image:: ./images/UWGeo/collision_wedge.gif
 
 .. toctree::
    :hidden:
@@ -78,5 +78,5 @@ software can actually be useful to you.
 The ressource are however limited and you should not try to run model with high resolution.
 3D models can not be run in the binder.
 
-.. image:: ./img/SandboxCompression.gif
+.. image:: ./images/UWGeo/SandboxCompression.gif