CI: Run coverage on as many tests as possible

.travis.yml

@@ -30,12 +30,6 @@ matrix:
     - python: 3.4
       dist: trusty
       sudo: false
-    - python: 2.7
-      env:
-        - COVERAGE=1
-    - python: 3.5
-      env:
-        - COVERAGE=1
     # Absolute minimum dependencies
     - python: 2.7
       env:
@@ -99,25 +93,20 @@ matrix:
       env:
         - OPTIONAL_DEPENDS="indexed_gzip"
 before_install:
-    - source tools/travis_tools.sh
-    - python -m pip install --upgrade pip
-    - pip install --upgrade virtualenv
+    - travis_retry python -m pip install --upgrade pip
+    - travis_retry pip install --upgrade virtualenv
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install -U pip setuptools>=27.0 wheel
+    - travis_retry pip install -U pip setuptools>=27.0 wheel
+    - travis_retry pip install coverage
     - if [ "${CHECK_TYPE}" == "test" ]; then
-      retry pip install nose mock;
+      travis_retry pip install nose mock;
       fi
     - if [ "${CHECK_TYPE}" == "style" ]; then
-      retry pip install flake8;
-      fi
-    - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
-    - if [ "${COVERAGE}" == "1" ]; then
-      pip install coverage;
-      pip install coveralls;
-      pip install codecov;
+      travis_retry pip install flake8;
       fi
+    - travis_retry pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
 # command to install dependencies
 install:
     - |
@@ -128,7 +117,6 @@ install:
           python setup_egg.py sdist
           pip install $EXTRA_PIP_FLAGS dist/*.tar.gz
       elif [ "$INSTALL_TYPE" == "wheel" ]; then
-          pip install wheel
           python setup_egg.py bdist_wheel
           pip install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
@@ -146,7 +134,9 @@ script:
       elif [ "${CHECK_TYPE}" == "import" ]; then
           # Import nibabel without attempting to test
           # Allows us to check missing dependencies masked by testing libraries
-          python -c 'import nibabel; print(nibabel.__version__)'
+          printf 'import nibabel\nprint(nibabel.__version__)\n' > import_only.py
+          cat import_only.py
+          coverage run import_only.py
       elif [ "${CHECK_TYPE}" == "doc_doctests" ]; then
           cd doc
           pip install -r ../doc-requirements.txt
@@ -156,16 +146,18 @@ script:
           # Change into an innocuous directory and find tests from installation
           mkdir for_testing
           cd for_testing
-          if [ "${COVERAGE}" == "1" ]; then
-              cp ../.coveragerc .;
-              COVER_ARGS="--with-coverage --cover-package nibabel";
-          fi
-          nosetests --with-doctest $COVER_ARGS nibabel;
+          cp ../.coveragerc .
+          nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
       else
           false
       fi
 after_success:
-    - if [ "${COVERAGE}" == "1" ]; then coveralls; codecov; fi
+    - |
+      if [ "${CHECK_TYPE}" == "test" ]; then
+        travis_retry pip install coveralls codecov
+        coveralls
+        codecov
+      fi
 
 notifications:
     webhooks: http://nipy.bic.berkeley.edu:54856/travis

appveyor.yml

@@ -23,7 +23,8 @@ install:
 
   # Install the dependencies of the project.
   - python -m pip install --upgrade pip setuptools wheel
-  - pip install numpy scipy matplotlib nose h5py mock pydicom
+  - pip install numpy scipy matplotlib h5py pydicom
+  - pip install nose mock coverage codecov
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data
 
@@ -33,4 +34,8 @@ test_script:
   # Change into an innocuous directory and find tests from installation
   - mkdir for_testing
   - cd for_testing
-  - nosetests --with-doctest nibabel
+  - cp ../.coveragerc .
+  - nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
+
+after_test:
+  - codecov

nibabel/streamlines/array_sequence.py

@@ -23,6 +23,16 @@ def is_ndarray_of_int_or_bool(obj):
             np.issubdtype(obj.dtype, np.bool_)))
 
 
+def _safe_resize(a, shape):
+    """ Resize an ndarray safely, using minimal memory """
+    try:
+        a.resize(shape)
+    except ValueError:
+        a = a.copy()
+        a.resize(shape, refcheck=False)
+    return a
+
+
 class _BuildCache(object):
     def __init__(self, arr_seq, common_shape, dtype):
         self.offsets = list(arr_seq._offsets)
@@ -196,7 +206,7 @@ def _resize_data_to(self, n_rows, build_cache):
         if self._data.size == 0:
             self._data = np.empty(new_shape, dtype=build_cache.dtype)
         else:
-            self._data.resize(new_shape)
+            self._data = _safe_resize(self._data, new_shape)
 
     def shrink_data(self):
         self._data.resize((self._get_next_offset(),) + self.common_shape,

nibabel/streamlines/tests/test_array_sequence.py

@@ -219,6 +219,10 @@ def test_arraysequence_extend(self):
         seq = SEQ_DATA['seq'].copy()  # Copy because of in-place modification.
         assert_raises(ValueError, seq.extend, data)
 
+        # Extend after extracting some slice
+        working_slice = seq[:2]
+        seq.extend(ArraySequence(new_data))
+
     def test_arraysequence_getitem(self):
         # Get one item
         for i, e in enumerate(SEQ_DATA['seq']):