Barnhark/update after refactor

.travis.yml

@@ -1,8 +1,8 @@
 env:
   matrix:
   - TRAVIS_PYTHON_VERSION="2.7"
-  - TRAVIS_PYTHON_VERSION="3.5"
   - TRAVIS_PYTHON_VERSION="3.6"
+  - TRAVIS_PYTHON_VERSION="3.7"
   global:
     - CONDA_PREFIX=$HOME/miniconda
     - MINICONDA_URL_BASE="https://repo.continuum.io/miniconda/Miniconda3-latest"
@@ -38,8 +38,8 @@ install:
 - conda install scripting -c csdms-stack
 - |
   if [[ "$TRAVIS_BRANCH" == "release" ]]; then
-    conda install landlab -c landlab
-    conda install terrainbento -c terrainbento
+    conda install landlab -c conda-forge
+    conda install terrainbento -c conda-forge
   else
     pushd ../..
     git clone --depth=50 https://github.com/landlab/landlab.git landlab/landlab

Welcome_to_TerrainBento.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "You have just cloned the `examples_test_and_tutorials` repository for the terrainbento multi-model package. Congratulations! \n",
     "\n",
-    "If you are interested in reading about the details of terrainbento, this package is described in the following OpenAccess manuscript [LINK TO MANUSCRIPT].\n",
+    "If you are interested in reading about the details of terrainbento, this package is described in [Barnhart et al. (2019)](https://www.geosci-model-dev-discuss.net/gmd-2018-204/).\n",
     "\n",
     "The documentation for the package is provided [here](http://terrainbento.readthedocs.io/en/latest/).\n",
     "\n",
@@ -22,9 +22,9 @@
     "\n",
     "The simplest model, called Basic, evolves topography using stream power and linear diffusion. It has the following governing equation:\n",
     "\n",
-    "$\\frac{\\partial \\eta}{\\partial t} = - KA^{1/2}S + D\\nabla^2 \\eta$\n",
+    "$\\frac{\\partial \\eta}{\\partial t} = - KQ^{1/2}S + D\\nabla^2 \\eta$\n",
     "\n",
-    "Other models modify Basic by adding or changing a process component. \n",
+    "where $K$ and $D$ are constants, $Q$ is discharge, $S$ is local slope, and $\\eta$ is the topography. Other models modify Basic by adding or changing a process component and changing the governing equation. See the [model Basic documentation](https://terrainbento.readthedocs.io/en/latest/source/terrainbento.derived_models.model_basic.html) for additional information. \n",
     "\n",
     "## Example usage\n",
     "\n",
@@ -34,51 +34,49 @@
     "    \n",
     "2) [Introduction to boundary conditions in terrainbento](http://localhost:8888/notebooks/example_usage/introduction_to_boundary_conditions.ipynb)\n",
     "    \n",
-    "3) [Introduction to OutputWriters in terrainbento](http://localhost:8888/notebooks/example_usage/introduction_to_output_writers.ipynb). \n",
+    "3) [Introduction to output writers in terrainbento](http://localhost:8888/notebooks/example_usage/introduction_to_output_writers.ipynb). \n",
     "    \n",
     "\n",
     "## Example Coupled Models\n",
     "\n",
     "This section provides links to five notebooks that show the usage of five example models provided in terrainbento. In each of these notebooks we provide the governing equation(s) for the model, initialize and run the model, make a slope-area plot, save a NetCDF of the final topography, and plot a image of the final topography. \n",
     "\n",
-    "1) [Basic](http://localhost:8888/notebooks/coupled_process_elements/model_000_COUPLED_steady_solution.ipynb) the simplest landscape evolution model in the terrainbento package.\n",
+    "1) [Basic](http://localhost:8888/notebooks/coupled_process_elements/model_basic_steady_solution.ipynb) the simplest landscape evolution model in the terrainbento package.\n",
     "\n",
-    "2) [BasicVm](http://localhost:8888/notebooks/coupled_process_elements/model_001_COUPLED_steady_solution.ipynb) which permits the drainage area exponent to change\n",
+    "2) [BasicVm](http://localhost:8888/notebooks/coupled_process_elements/model_basic_var_m_steady_solution.ipynb) which permits the drainage area exponent to change\n",
     "\n",
-    "3) [BasicCh](http://localhost:8888/notebooks/coupled_process_elements/model_040_COUPLED_steady_solution.ipynb) which uses a non-linear hillslope erosion and transport law\n",
+    "3) [BasicCh](http://localhost:8888/notebooks/coupled_process_elements/model_basicCh_steady_solution.ipynb) which uses a non-linear hillslope erosion and transport law\n",
     "\n",
-    "4) [BasicVs](http://localhost:8888/notebooks/coupled_process_elements/model_200_COUPLED_steady_solution.ipynb) which uses variable source area hydrology\n",
+    "4) [BasicVs](http://localhost:8888/notebooks/coupled_process_elements/model_basicVs_steady_solution.ipynb) which uses variable source area hydrology\n",
     "\n",
-    "5) [BasisRt](http://localhost:8888/notebooks/coupled_process_elements/model_800_COUPLED_steady_solution.ipynb) which allows for two lithologies with different K values"
+    "5) [BasisRt](http://localhost:8888/notebooks/coupled_process_elements/model_basicCh_steady_solution.ipynb) which allows for two lithologies with different K values"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.14"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

coupled_process_elements/readme_example.ipynb

@@ -0,0 +1,124 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from terrainbento import Basic\n",
+    "\n",
+    "params = {\n",
+    "    # create the Clock.\n",
+    "    \"clock\": {\"start\": 0, \n",
+    "              \"step\": 10,\n",
+    "              \"stop\": 1e5},\n",
+    "    \n",
+    "    # Create the Grid.\n",
+    "    \"grid\": {\"grid\": {\"RasterModelGrid\":[(200, 320), {\"xy_spacing\": 10}]},\n",
+    "             \"fields\": {\"at_node\": {\"topographic__elevation\":{\"random\":[{\"where\":\"CORE_NODE\"}]}}}},\n",
+    "    \n",
+    "    # Set up Boundary Handlers\n",
+    "    \"boundary_handlers\":{\"NotCoreNodeBaselevelHandler\": {\"modify_core_nodes\": True, \n",
+    "                                                         \"lowering_rate\": -0.001}},\n",
+    "    # Parameters that control output.\n",
+    "    \"output_interval\": 1e3, \n",
+    "    \"save_first_timestep\": True,\n",
+    "    \"fields\":[\"topographic__elevation\"],\n",
+    "             \n",
+    "    # Parameters that control process and rates.\n",
+    "    \"water_erodability\" : 0.001,\n",
+    "    \"m_sp\" : 0.5,\n",
+    "    \"n_sp\" : 1.0, \n",
+    "    \"regolith_transport_parameter\" : 0.2,           \n",
+    "         }\n",
+    "\n",
+    "model = Basic.from_dict(params)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Figure size 432x288 with 0 Axes>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "from landlab import imshow_grid\n",
+    "\n",
+    "filenames = []\n",
+    "ds = model.to_xarray_dataset()\n",
+    "for i in range(ds.topographic__elevation.shape[0]):\n",
+    "    filename = \"temp_output.\"+str(i)+\".png\"\n",
+    "    imshow_grid(model.grid, \n",
+    "                ds.topographic__elevation.values[i, :, :], \n",
+    "                cmap=\"viridis\", \n",
+    "                limits=(0, 12), \n",
+    "                output=filename)\n",
+    "    filenames.append(filename)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import imageio\n",
+    "with imageio.get_writer(\"terrainbento_example.gif\", mode=\"I\") as writer:\n",
+    "    for filename in filenames:\n",
+    "        image = imageio.imread(filename)\n",
+    "        writer.append_data(image)\n",
+    "        os.remove(filename)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.remove_output_netcdfs()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}