Merge pull request #19 from landlab/barnhark/rockblock

Create Lithology and LithoLayers Tutorial

Author: kbarnhart

.gitignore

@@ -3,3 +3,9 @@
 
 *.out
 *.pyc
+
+\.pytest_cache/README\.md
+
+\.pytest_cache/v/cache/lastfailed
+
+\.pytest_cache/v/cache/nodeids

.travis.yml

@@ -18,6 +18,8 @@ before_install:
     brew cleanup -s
     rm -rf $(brew --cache)
   fi
+- mkdir $MPLCONFIGDIR
+- touch $MPLCONFIGDIR/matplotlibrc
 install:
 - echo "Build on $TRAVIS_OS_NAME for Python $TRAVIS_PYTHON_VERSION"
 - |
@@ -33,12 +35,25 @@ install:
 - conda config --set always_yes yes --set changeps1 no
 - conda create -n _testing python=$TRAVIS_PYTHON_VERSION
 - source activate _testing
-- conda install scripting -c csdms-stack
-- conda install landlab jupyter -c landlab
+- |
+  if [[ "$TRAVIS_BRANCH" == "release" ]]; then
+    conda install landlab -c conda-forge
+  else
+    pushd ../..
+    git clone --depth=50 https://github.com/landlab/landlab.git landlab/landlab
+    pushd landlab/landlab
+    git fetch origin master
+    git checkout -qf master
+    git submodule update --init --recursive
+    conda install --file=requirements.txt
+    python setup.py develop
+    popd
+    popd
+  fi
+- conda install --file=requirements.txt
 - conda info -a && conda list
 script:
-- mkdir -p $MPLCONFIGDIR
-- "echo backend: Agg > $MPLCONFIGDIR/matplotlibrc"
-- ./run-all-tests.sh
+- mkdir -p $HOME/.config/matplotlib # For Python 3.5
+- travis_wait 50 pytest -vvv # the cellular atomata test takes over 10 minutes, and the entire process takes about 30 minutes, so we'll give it 50 min
 virtualenv:
   system_site_packages: false

ecohydrology/cellular_automaton_vegetation_DEM/Ecohyd_functions_DEM.py

@@ -187,9 +187,7 @@ def Plot_(grid, VegType, yrs, yr_step=10):
     pic += 1
     plt.figure(pic)
     plt.plot(years, grass_cov, '-g', label='Grass')
-    plt.hold(True)
     plt.plot(years, shrub_cov, '-r', label='Shrub')
-    plt.hold(True)
     plt.plot(years, tree_cov, '-k', label='Tree')
     plt.ylabel(' % Coverage ')
     plt.xlabel('Time in years')

ecohydrology/cellular_automaton_vegetation_flat_surface/Ecohyd_functions_flat.py

@@ -111,7 +111,7 @@ def Empty_arrays(n, grid, grid1):
     Time = np.empty(n)  # To record time elapsed from the start of simulation
 #    CumWaterStress = np.empty([n/55, grid1.number_of_cells])
     # Cum Water Stress
-    VegType = np.empty([n/55, grid1.number_of_cells], dtype=int)
+    VegType = np.empty([int(n/55), grid1.number_of_cells], dtype=int)
     PET_ = np.zeros([365, grid.number_of_cells])
     Rad_Factor = np.empty([365, grid.number_of_cells])
     EP30 = np.empty([365, grid.number_of_cells])
@@ -187,9 +187,7 @@ def Plot_(grid, VegType, yrs, yr_step=10):
     pic += 1
     plt.figure(pic)
     plt.plot(years, grass_cov, '-g', label='Grass')
-    plt.hold(True)
     plt.plot(years, shrub_cov, '-r', label='Shrub')
-    plt.hold(True)
     plt.plot(years, tree_cov, '-k', label='Tree')
     plt.ylabel(' % Coverage ')
     plt.xlabel('Time in years')