Merge branch 'barnhark/update_testing_proceedures' into barnhark/rockblock

Author: kbarnhart

.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 $TRAVIS_PYTHON_VERSION"
 - |
@@ -33,26 +35,24 @@ install:
 - conda config --set always_yes yes --set changeps1 no
 - conda create -n _testing python=$TRAVIS_PYTHON_VERSION
 - source activate _testing
-- conda install scripting -c csdms-stack
 - |
   if [[ "$TRAVIS_BRANCH" == "release" ]]; then
-    conda install landlab -c landlab
+    conda install landlab -c conda-forge
   else
-    pwd
-    cd ../..
+    pushd ../..
     git clone --depth=50 https://github.com/landlab/landlab.git landlab/landlab
-    cd 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
-    cd ../../landlab/tutorials
+    popd
+    popd
   fi
-- conda install jupyter dask holoviews pytest
+- conda install --file=requirements.txt
 - conda info -a && conda list
 script:
-- pwd
-- travis_wait 50 pytest # the cellular atomata test takes over 10 minutes, and the entire process takes about 30 minutes, so we'll give it 50 min
+- 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')

requirements.txt

@@ -0,0 +1,4 @@
+jupyter
+dask
+holoviews
+pytest

test_notebooks.py

@@ -1,10 +1,31 @@
 import os
 import subprocess
+
 import nbformat
+import pytest
+
+
+_TEST_DIR = os.path.abspath(os.path.dirname(__file__))
+_EXCLUDE = ["Python_intro.ipynb", "animate-landlab-output.ipynb"]
+
 
-_TEST_DIR = os.path.dirname(__file__)
+def all_notebooks():
+    notebooks = []
+    for root, dirs, files in os.walk(_TEST_DIR):
+        for file in files:
+            if (
+                file.endswith(".ipynb")
+                and (file not in _EXCLUDE)
+                and ("checkpoint" not in file)
+            ):
+                notebooks.append(os.path.join(root, file))
+    return notebooks
+
+
+def pytest_generate_tests(metafunc):
+    if "notebook" in metafunc.fixturenames:
+        metafunc.parametrize("notebook", all_notebooks())
 
-_EXCLUDE = ['Python_intro.ipynb']
 
 def _notebook_run(path):
     """Execute a notebook via nbconvert and collect output.
@@ -13,189 +34,39 @@ def _notebook_run(path):
     dirname, __ = os.path.split(path)
     os.chdir(dirname)
 
-    in_fn = os.path.split(path)[-1].split('.')[0]
-    temp_file_prefix = 'output_' + in_fn
-    temp_file_out = temp_file_prefix + '.ipynb'
-
-    args = ["jupyter", "nbconvert", "--to", "notebook", "--execute",
-      "--ExecutePreprocessor.kernel_name=python",
-      "--ExecutePreprocessor.timeout=None",
-      "--output", temp_file_prefix, path]
+    in_fn = os.path.split(path)[-1].split(".")[0]
+    temp_file_prefix = "output_" + in_fn
+    temp_file_out = temp_file_prefix + ".ipynb"
+
+    args = [
+        "jupyter",
+        "nbconvert",
+        "--to",
+        "notebook",
+        "--execute",
+        "--ExecutePreprocessor.kernel_name=python",
+        "--ExecutePreprocessor.timeout=None",
+        "--output",
+        temp_file_prefix,
+        path,
+    ]
     subprocess.check_call(args)
 
-    nb = nbformat.read(temp_file_out, nbformat.current_nbformat, encoding='UTF-8')
+    nb = nbformat.read(temp_file_out, 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"]
+    errors = [
+        output
+        for cell in nb.cells
+        if "outputs" in cell
+        for output in cell["outputs"]
+        if output.output_type == "error"
+    ]
     os.remove(temp_file_out)
 
     return nb, errors
 
 
-def test_tutorial_template():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "tutorial_template.ipynb"))
-    assert errors == []
-
-
-def test_gradient_and_divergence():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "gradient_and_divergence/gradient_and_divergence.ipynb"))
-    assert errors == []
-
-
-def test_component_tutorial():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "component_tutorial/component_tutorial.ipynb"))
-    assert errors == []
-
-
-def test_landlab_fault_scarp():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "fault_scarp/landlab-fault-scarp.ipynb"))
-    assert errors == []
-
-
-def test_TLHDiff_tutorial():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "transport-length_hillslope_diffuser/TLHDiff_tutorial.ipynb"))
-    assert errors == []
-
-
-def test_the_FlowDirectors():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "flow_direction_and_accumulation/the_FlowDirectors.ipynb"))
-    assert errors == []
-
-
-def test_compare_FlowDirectors():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "flow_direction_and_accumulation/compare_FlowDirectors.ipynb"))
-    assert errors == []
-
-
-def test_the_FlowAccumulator():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "flow_direction_and_accumulation/the_FlowAccumulator.ipynb"))
-    assert errors == []
-
-
-def test_overland_flow_driver():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "overland_flow/overland_flow_driver.ipynb"))
-    assert errors == []
-
-
-def test_making_components():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "making_components/making_components.ipynb"))
-    assert errors == []
-
-
-def test_landlab_plotting():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "plotting/landlab-plotting.ipynb"))
-    assert errors == []
-
-
-# this notebook not tested because it requires FFMPEG
-# def test_animate_landlab_output():
-#     nb, errors = _notebook_run(os.path.join(_TEST_DIR, "plotting/animate-landlab-output.ipynb"))
-#     assert errors == []
-
-
-def test_grid_object_demo():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "grid_object_demo/grid_object_demo.ipynb"))
-    assert errors == []
-
-
-def test_normal_fault_component_tutorial():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "normal_fault/normal_fault_component_tutorial.ipynb"))
-    assert errors == []
-
-
-def test_working_with_fields():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "fields/working_with_fields.ipynb"))
-    assert errors == []
-
-
-def test_mappers():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "mappers/mappers.ipynb"))
-    assert errors == []
-
-
-def test_flexure_1d():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "flexure/flexure_1d.ipynb"))
-    assert errors == []
-
-
-def test_lots_of_loads():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "flexure/lots_of_loads.ipynb"))
-    assert errors == []
-
-
-def test_set_BCs_on_raster_perimeter():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "boundary_conds/set_BCs_on_raster_perimeter.ipynb"))
-    assert errors == []
-
-
-def test_set_BCs_from_xy():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "boundary_conds/set_BCs_from_xy.ipynb"))
-    assert errors == []
-
-
-def test_set_watershed_BCs_raster():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "boundary_conds/set_watershed_BCs_raster.ipynb"))
-    assert errors == []
-
-
-def test_set_BCs_on_voronoi():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "boundary_conds/set_BCs_on_voronoi.ipynb"))
-    assert errors == []
-
-
-def test_lithology_and_litholayers(): # this doesn't exist on this branch yet
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "lithology/lithology_and_litholayers.ipynb"))
-    assert errors == []
-
-
-def test_reading_dem_into_landlab():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "reading_dem_into_landlab/reading_dem_into_landlab.ipynb"))
-    assert errors == []
-
-
-def test_application_of_flow__distance_utility():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "flow__distance_utility/application_of_flow__distance_utility.ipynb"))
-    assert errors == []
-
-
-def test_cellular_automaton_vegetation_flat_domain():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "ecohydrology/cellular_automaton_vegetation_flat_surface/cellular_automaton_vegetation_flat_domain.ipynb"))
-    assert errors == []
-
-
-def test_cellular_automaton_vegetation_DEM():
-    nb, errors = _notebook_run(os.path.join(_TEST_DIR, "ecohydrology/cellular_automaton_vegetation_DEM/cellular_automaton_vegetation_DEM.ipynb"))
-    assert errors == []
-
-
-# def test_Python_intro():
-#     nb, errors = _notebook_run(os.path.join(_TEST_DIR, "python_intro/Python_intro.ipynb"))
-#     assert errors == []
-
-
-# def test_all_ipynbs():
-#     failed = []
-#     to_run = []
-#
-#     for root, dirs, files in os.walk(_TEST_DIR):
-#         for file in files:
-#             if (file.endswith('.ipynb') and (file not in _EXCLUDE) and ('checkpoint' not in file)):
-#                 to_run.append(os.path.join(root, file))
-#     for fp in to_run:
-#         print('STARTING: '+os.path.split(fp)[-1])
-#         nb, errors = _notebook_run(os.path.join(fp))
-#         try:
-#             assert errors == []
-#             print('PASSED : '+file)
-#         except AssertionError:
-#             print('FAILED : '+file)
-#             print(errors)
-#             failed.append(file)
-#         except:
-#             failed.append(file)
-#
-#     print(str(len(failed)) + ' notebooks failed')
-#     for fnb in failed:
-#         print(fnb)
-#     assert failed == []
+def test_notebook(tmpdir, notebook):
+    with tmpdir.as_cwd():
+        nb, errors = _notebook_run(notebook)
+        assert not errors