ci: requirements for numpy due to np.isnat and pyarrow in requirement…

…s.txt

ci: skip numba for py35

.travis.yml

@@ -42,10 +42,7 @@ before_install:
   - source deactivate
   - source activate test-environment
   - which pip
-  - pip install pybind11
-  # - conda install -c conda-forge pandas kapteyn # these extra installs should disappear
-  # - conda create --name dev --clone test
-#  - pip install -r requirements.txt
+  - pip install -r requirements.txt
 install:
   - source activate test-environment
   - (cd packages/vaex-core; pip install -v .)
@@ -66,7 +63,7 @@ script:
   - source activate test-environment
   - python -m vaex.test.dataset TestDataset
   # - py.test packages/vaex-core/vaex/test/dataset.py::TestDataset 
-  - py.test tests/ -s
+  - py.test tests/
   # - runipy examples/tutorial_ipython_notebook.ipynb
   # - runipy examples/advanced_plotting.ipynb
   # - source activate dev

appveyor.yml

@@ -20,9 +20,9 @@ install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - "conda create -q -n test-environment -c conda-forge python=%PYTHON_VERSION% numpy scipy pyqt matplotlib pyopengl h5py numexpr astropy tornado cython pandas runipy cython pytest numba pyarrow>=0.12 graphviz python-graphviz pcre"
+  - "conda create -q -n test-environment -c conda-forge python=%PYTHON_VERSION% numpy scipy pyqt matplotlib pyopengl h5py numexpr astropy tornado cython pandas runipy cython pytest numba pyarrow graphviz python-graphviz pcre"
   - activate test-environment
-  - pip install pybind11
+  - pip install "numpy>=1.13" "pyarrow>=0.12"
   - pip install -r requirements.txt
   - pushd packages\vaex-core   && pip install . && popd
   - pushd packages\vaex-hdf5   && pip install . && popd

packages/vaex-core/vaex/dataframe.py

@@ -422,6 +422,7 @@ def mutual_information(self, x, y=None, mi_limits=None, mi_shape=256, binby=[],
         @delayed
         def calculate(counts):
             # TODO: mutual information doesn't take axis arguments, so ugly solution for now
+            counts = counts.astype(np.float64)
             fullshape = _expand_shape(shape, len(binby))
             out = np.zeros((fullshape), dtype=float)
             if len(fullshape) == 0:

requirements.txt

@@ -1,9 +1,8 @@
-numpy>=1.7.2
+numpy>=1.13
 scipy>=0.1
 astropy>=0.3
 matplotlib>=1.3.1
 h5py>=2.2.1
-PyOpenGL>=3.1.0
 aplus
 tornado>4.1
 futures>=2.2.0
@@ -15,3 +14,4 @@ psutil>=1.2.1
 pandas
 pillow
 requests
+pyarrow>=0.12

tests/jit_test.py

@@ -13,6 +13,8 @@ def arc_distance(theta_1, phi_1, theta_2, phi_2):
     distance_matrix = 2 * np.arctan2(np.sqrt(temp), np.sqrt(1-temp))
     return distance_matrix
 
+@pytest.mark.skipif(sys.version_info < (3,6) and sys.version_info[0] != 2,
+                    reason="no support for python3.5 (numba segfaults)")
 def test_numba(ds):
     ds_original = ds.copy()
     #ds.columns['x'] = (ds.columns['x']*1).copy()  # convert non non-big endian for now