Merge branch 'release' into barnhark/rockblock

Author: kbarnhart

.travis.yml

@@ -53,6 +53,7 @@ install:
 - conda install --file=requirements.txt
 - conda info -a && conda list
 script:
+- 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

test_notebooks.py

@@ -1,58 +1,53 @@
 import os
 import subprocess
+import tempfile
 
 import nbformat
-import pytest
-
 
 _TEST_DIR = os.path.abspath(os.path.dirname(__file__))
 _EXCLUDE = ["Python_intro.ipynb", "animate-landlab-output.ipynb"]
 
 
-def all_notebooks():
+def all_notebooks(path="."):
     notebooks = []
-    for root, dirs, files in os.walk(_TEST_DIR):
+    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)
-                and ("checkpoint" not in file)
-            ):
+            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())
+        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)
     """
-    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,
-    ]
-    subprocess.check_call(args)
-
-    nb = nbformat.read(temp_file_out, nbformat.current_nbformat, encoding="UTF-8")
+    _, 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
@@ -61,7 +56,6 @@ def _notebook_run(path):
         for output in cell["outputs"]
         if output.output_type == "error"
     ]
-    os.remove(temp_file_out)
 
     return nb, errors