Merge pull request #33 from landlab/barnhark/update_testing_proceedures

Update testing procedures
landlab · Sep 21, 2018 · 1e5cf0a · 1e5cf0a
2 parents 9b0aef5 + 9af929f
commit 1e5cf0a
Show file tree

Hide file tree

Showing 21 changed files with 3,049 additions and 2,718 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,9 @@
 
 *.out
 *.pyc
+
+\.pytest_cache/README\.md
+
+\.pytest_cache/v/cache/lastfailed
+
+\.pytest_cache/v/cache/nodeids
diff --git a/.travis.yml b/.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
diff --git a/ecohydrology/cellular_automaton_vegetation_DEM/Ecohyd_functions_DEM.py b/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')

diff --git a/ecohydrology/cellular_automaton_vegetation_flat_surface/Ecohyd_functions_flat.py b/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')

diff --git a/...ellular_automaton_vegetation_flat_surface/cellular_automaton_vegetation_flat_domain.ipynb b/...ellular_automaton_vegetation_flat_surface/cellular_automaton_vegetation_flat_domain.ipynb
diff --git a/flexure/lots_of_loads.ipynb b/flexure/lots_of_loads.ipynb
diff --git a/...plication of flow__distance utility.ipynb → ...plication_of_flow__distance_utility.ipynb b/...plication of flow__distance utility.ipynb → ...plication_of_flow__distance_utility.ipynb
diff --git a/flow_direction_and_accumulation/Comparison of FlowDirectors.ipynb b/flow_direction_and_accumulation/Comparison of FlowDirectors.ipynb
diff --git a/flow_direction_and_accumulation/Introduction to FlowDirectors.ipynb b/flow_direction_and_accumulation/Introduction to FlowDirectors.ipynb
diff --git a/flow_direction_and_accumulation/Introduction to the FlowAccumulator.ipynb b/flow_direction_and_accumulation/Introduction to the FlowAccumulator.ipynb
diff --git a/flow_direction_and_accumulation/compare_FlowDirectors.ipynb b/flow_direction_and_accumulation/compare_FlowDirectors.ipynb
diff --git a/flow_direction_and_accumulation/the_FlowAccumulator.ipynb b/flow_direction_and_accumulation/the_FlowAccumulator.ipynb
diff --git a/flow_direction_and_accumulation/the_FlowDirectors.ipynb b/flow_direction_and_accumulation/the_FlowDirectors.ipynb
diff --git a/making_components/making_components.ipynb b/making_components/making_components.ipynb
diff --git a/normal_fault/normal_fault_component_tutorial.ipynb b/normal_fault/normal_fault_component_tutorial.ipynb
diff --git a/plotting/landlab-plotting.ipynb b/plotting/landlab-plotting.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,4 @@
+jupyter
+dask
+holoviews
+pytest
diff --git a/run-all-tests.sh b/run-all-tests.sh
diff --git a/run_notebook.py b/run_notebook.py
diff --git a/test_notebooks.py b/test_notebooks.py
@@ -0,0 +1,66 @@
+import os
+import subprocess
+import tempfile
+
+import nbformat
+
+_TEST_DIR = os.path.abspath(os.path.dirname(__file__))
+_EXCLUDE = ["Python_intro.ipynb", "animate-landlab-output.ipynb"]
+
+
+def all_notebooks(path="."):
+    notebooks = []
+    for root, dirs, files in os.walk(path):
+        if ".ipynb_checkpoints" in root:
+            continue
+        for file in files:
+            if file.endswith(".ipynb") and (file not in _EXCLUDE):
+                notebooks.append(os.path.join(root, file))
+    return notebooks
+
+
+def pytest_generate_tests(metafunc):
+    if "notebook" in metafunc.fixturenames:
+        metafunc.parametrize("notebook", all_notebooks(_TEST_DIR))
+
+
+def _notebook_run(path):
+    """Execute a notebook via nbconvert and collect output.
+       :returns (parsed nb object, execution errors)
+    """
+    _, notebook = os.path.split(path)
+    base, ext = os.path.splitext(notebook)
+
+    with tempfile.NamedTemporaryFile("w", suffix=".ipynb") as fp:
+        args = [
+            "jupyter",
+            "nbconvert",
+            "--to",
+            "notebook",
+            "--execute",
+            "--ExecutePreprocessor.kernel_name=python",
+            "--ExecutePreprocessor.timeout=None",
+            "--output",
+            fp.name,
+            "--output-dir=.",
+            path,
+        ]
+        subprocess.check_call(args)
+
+        nb = nbformat.read(fp.name, nbformat.current_nbformat, encoding="UTF-8")
+
+    errors = [
+        output
+        for cell in nb.cells
+        if "outputs" in cell
+        for output in cell["outputs"]
+        if output.output_type == "error"
+    ]
+
+    return nb, errors
+
+
+def test_notebook(tmpdir, notebook):
+    with tmpdir.as_cwd():
+        nb, errors = _notebook_run(notebook)
+        assert not errors