merge stable with master

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,57 @@
+<!--To help us understand and resolve your issue, please fill out the form to
+the best of your ability.-->
+<!--You can feel free to delete the sections that do not apply.-->
+
+### Bug report
+
+**Bug summary**
+
+<!--A short 1-2 sentences that succinctly describes the bug-->
+
+**Code for reproduction**
+
+<!--A minimum code snippet required to reproduce the bug, also minimizing the
+number of dependencies required.-->
+
+<!-- If you need to use a data file to trigger the issue you're having, consider
+using one of the datasets from the yt data hub (http://yt-project.org/data). If
+your issue cannot be triggered using a public dataset, you can use the yt
+curldrop (https://docs.hub.yt/services.html#curldrop) to share data
+files. Please include a link to the dataset in the issue if you use the
+curldrop.-->
+
+```python
+# Paste your code here
+#
+#
+```
+
+**Actual outcome**
+
+<!--The output produced by the above code, which may be a screenshot, console
+output, etc.-->
+
+```
+# If applicable, paste the console output here
+#
+#
+```
+
+**Expected outcome**
+
+<!--A description of the expected outcome from the code snippet-->
+<!--If this used to work in an earlier version of yt, please note the
+version it used to work on-->
+
+**Version Information**
+<!--Please specify your platform and versions of the relevant libraries you are
+using:-->
+  * Operating System:
+  * Python Version:
+  * yt version:
+  * Other Libraries (if applicable): 
+
+<!--Please tell us how you installed yt and python e.g., from source,
+pip, conda. If you installed from conda, please specify which channel you used
+if not the default-->
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,31 @@
+<!--Thank you so much for your PR! To help us review, fill out the form
+to the best of your ability.  Please make use of the development guide at
+http://yt-project.org/docs/dev/developing/index.html-->
+
+<!--Provide a general summary of your changes in the title above, for
+example "Raises ValueError on Non-Numeric Input to set_xlim".  Please avoid
+non-descriptive titles such as "Addresses issue #8576".-->
+
+<!--If you are able to do so, please do not create the PR out of master, but out
+of a separate branch. -->
+
+## PR Summary
+
+<!--Please provide at least 1-2 sentences describing the pull request in
+detail.  Why is this change required?  What problem does it solve?-->
+
+<!--If it fixes an open issue, please link to the issue here.-->
+
+## PR Checklist
+
+<!-- Note that some of these check boxes may not apply to all pull requests -->
+
+- [ ] Code passes flake8 checker
+- [ ] New features are documented, with docstrings and narrative docs
+- [ ] Adds a test for any bugs fixed. Adds tests for new features.
+
+<!--We understand that PRs can sometimes be overwhelming, especially as the
+reviews start coming in.  Please let us know if the reviews are unclear or the
+recommended next step seems overly demanding , or if you would like help in
+addressing a reviewer's comments.  And please ping us if you've been waiting
+too long to hear back on your PR.-->

.gitignore

@@ -0,0 +1,87 @@
+build
+yt.egg-info
+__config__.py
+freetype.cfg
+hdf5.cfg
+png.cfg
+rockstar.cfg
+yt_updater.log
+yt/frontends/artio/_artio_caller.c
+yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.c
+yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c
+yt/analysis_modules/ppv_cube/ppv_utils.c
+yt/analysis_modules/photon_simulator/utils.c
+yt/frontends/ramses/_ramses_reader.cpp
+yt/frontends/sph/smoothing_kernel.c
+yt/geometry/fake_octree.c
+yt/geometry/grid_container.c
+yt/geometry/grid_visitors.c
+yt/geometry/oct_container.c
+yt/geometry/oct_visitors.c
+yt/geometry/particle_deposit.c
+yt/geometry/particle_oct_container.c
+yt/geometry/particle_smooth.c
+yt/geometry/selection_routines.c
+yt/utilities/amr_utils.c
+yt/utilities/lib/autogenerated_element_samplers.c
+yt/utilities/kdtree/forthonf2c.h
+yt/utilities/libconfig_wrapper.c
+yt/utilities/spatial/ckdtree.c
+yt/utilities/lib/allocation_container.c
+yt/utilities/lib/alt_ray_tracers.c
+yt/utilities/lib/amr_kdtools.c
+yt/utilities/lib/basic_octree.c
+yt/utilities/lib/bitarray.c
+yt/utilities/lib/bounding_volume_hierarchy.c
+yt/utilities/lib/contour_finding.c
+yt/utilities/lib/depth_first_octree.c
+yt/utilities/lib/distance_queue.c
+yt/utilities/lib/element_mappings.c
+yt/utilities/lib/fnv_hash.c
+yt/utilities/lib/fortran_reader.c
+yt/utilities/lib/freetype_writer.c
+yt/utilities/lib/geometry_utils.c
+yt/utilities/lib/image_samplers.c
+yt/utilities/lib/image_utilities.c
+yt/utilities/lib/interpolators.c
+yt/utilities/lib/kdtree.c
+yt/utilities/lib/lenses.c
+yt/utilities/lib/line_integral_convolution.c
+yt/utilities/lib/mesh_construction.cpp
+yt/utilities/lib/mesh_intersection.cpp
+yt/utilities/lib/mesh_samplers.cpp
+yt/utilities/lib/mesh_traversal.cpp
+yt/utilities/lib/mesh_triangulation.c
+yt/utilities/lib/mesh_utilities.c
+yt/utilities/lib/misc_utilities.c
+yt/utilities/lib/particle_mesh_operations.c
+yt/utilities/lib/partitioned_grid.c
+yt/utilities/lib/primitives.c
+yt/utilities/lib/origami.c
+yt/utilities/lib/particle_mesh_operations.c
+yt/utilities/lib/pixelization_routines.c
+yt/utilities/lib/png_writer.c
+yt/utilities/lib/points_in_volume.c
+yt/utilities/lib/quad_tree.c
+yt/utilities/lib/ragged_arrays.c
+yt/utilities/lib/cosmology_time.c
+yt/utilities/lib/grid_traversal.c
+yt/utilities/lib/marching_cubes.c
+yt/utilities/lib/png_writer.h
+yt/utilities/lib/write_array.c
+yt/utilities/lib/perftools_wrap.c
+yt/utilities/lib/partitioned_grid.c
+yt/utilities/lib/volume_container.c
+yt/utilities/lib/lenses.c
+yt/utilities/lib/image_samplers.c
+*.pyc
+*.pyd
+.*.swp
+*.so
+.idea/*
+tests/results/*
+doc/build/*
+doc/source/reference/api/generated/*
+doc/_temp/*
+doc/source/bootcamp/.ipynb_checkpoints/
+dist

.hgignore

@@ -23,17 +23,21 @@ yt/geometry/particle_oct_container.c
 yt/geometry/particle_smooth.c
 yt/geometry/selection_routines.c
 yt/utilities/amr_utils.c
+yt/utilities/lib/autogenerated_element_samplers.c
 yt/utilities/kdtree/forthonf2c.h
 yt/utilities/libconfig_wrapper.c
 yt/utilities/spatial/ckdtree.c
+yt/utilities/lib/allocation_container.c
 yt/utilities/lib/alt_ray_tracers.c
 yt/utilities/lib/amr_kdtools.c
 yt/utilities/lib/basic_octree.c
 yt/utilities/lib/bitarray.c
 yt/utilities/lib/bounding_volume_hierarchy.c
 yt/utilities/lib/contour_finding.c
 yt/utilities/lib/depth_first_octree.c
+yt/utilities/lib/distance_queue.c
 yt/utilities/lib/element_mappings.c
+yt/utilities/lib/fnv_hash.c
 yt/utilities/lib/fortran_reader.c
 yt/utilities/lib/freetype_writer.c
 yt/utilities/lib/geometry_utils.c

.mailmap

@@ -0,0 +1,89 @@
+Stephen Skory <[email protected]> Stephen Skory <[email protected]>
+Stephen Skory <[email protected]> "Stephen Skory [email protected]" <"Stephen Skory [email protected]">
+Yuan Li <[email protected]> Yuan Li <[email protected]>
+Chris Moody <[email protected]> Chris Moody <[email protected]>
+Chris Moody <[email protected]> Christopher Erick Moody <[email protected]>
+Cameron Hummels <[email protected]> Cameron Hummels <[email protected]>
+Cameron Hummels <[email protected]> chummels <[email protected]>
+John Wise <[email protected]> John Wise <[email protected]>
+Sam Skillman <[email protected]> Sam Skillman <[email protected]>
+Sam Skillman <[email protected]> samskillman <[email protected]>
+Casey Stark <[email protected]> Casey Stark <[email protected]>
+Christian Karch <[email protected]> chiffre <none@none>
+Christian Karch <[email protected]> Christian Karch <none@none>
+Andrew Myers <[email protected]> Andrew Myers <[email protected]>
+Andrew Myers <[email protected]> atmyers <none@none>
+Douglas Rudd <[email protected]> drudd <none@none>
+Andrew Wetzel <[email protected]> awetzel <none@none>
+David Collins <[email protected]> David Collins <[email protected]>
+David Collins <[email protected]> dcollins4096 <none@none>
+David Collins <[email protected]> David Collins ([email protected]) <David Collins ([email protected])>
+Tom Abel <[email protected]> tabel <none@none>
+Kaylea Nelson <[email protected]> sername=kayleanelson <none@none>
+Kaylea Nelson <[email protected]> kayleanelson <none@none
+Kaylea Nelson <[email protected]> kayleanelson <none@none>
+Stephanie Tonnesen <[email protected]> stonnes <[email protected]>
+John Forbes <[email protected]> John Forbes <[email protected]>
+Elliott Biondo <[email protected]> Elliott Biondo <[email protected]>
+Sam Geen <[email protected]> Sam Geen <[email protected]>
+Alex Bogert <[email protected]> fbogert <none@none>
+Brian O'Shea <[email protected]> bwoshea <none@none>
+Ji-hoon Kim <[email protected]> Ji-hoon Kim <[email protected]>
+Kirk Barrow <[email protected]> Kirk Barrow <[email protected]>
+Kirk Barrow <[email protected]> Kirk Barrow <[email protected]>
+Kirk Barrow <[email protected]> kbarrow <none@none>
+Kirk Barrow <[email protected]> kbarrow <[email protected]>
+Antoine Strugarek <[email protected]> Antoine Strugarek <[email protected]>
+Antoine Strugarek <[email protected]> astrugarek <[email protected]>
+Antoine Strugarek <[email protected]> Antoine Strugarek <[email protected]>
+Anna Rosen <[email protected]> Anna Rosen <[email protected]>
+John ZuHone <[email protected]> jzuhone <none@none>
+John ZuHone <[email protected]> jzuhone <[email protected]>
+Kenza Arraki <[email protected]> Kenza Arraki <[email protected]>
+Allyson Julian <[email protected]> Allyson Julian <[email protected]>
+Allyson Julian <[email protected]> Allyson Julian <[email protected]>
+Allyson Julian <[email protected]> Allyson Julian <[email protected]>
+Allyson Julian <[email protected]> AJ <[email protected]>
+Allyson Julian <[email protected]> Al Jul <[email protected]>
+Allyson Julian <[email protected]> AJ <[email protected]>
+Allyson Julian <[email protected]> AJ <[email protected]>
+Brian Crosby <[email protected]> bcrosby <[email protected]>
+Ben Thompson <[email protected]> Ben Thompson <none@none>
+Ben Thompson <[email protected]> cosmosquark <none@none>
+Chris Malone <[email protected]> Chris Malone <[email protected]>
+Chris Malone <[email protected]> ChrisMalone <[email protected]>
+Chris Malone <[email protected]> ChrisMalone <[email protected]>
+Jill Naiman <[email protected]> Jill Naiman <[email protected]>
+Jill Naiman <[email protected]> jnaiman <none@none>
+Jill Naiman <[email protected]> jnaiman <[email protected]>
+Ricarda Beckmann <[email protected]> RicardaBeckmann <[email protected]>
+Miguel de Val-Borro <[email protected]> Miguel de Val-Borro <[email protected]>
+Stuary Levy <[email protected]> Stuart Levy <[email protected]>
+Ben Keller <[email protected]> Ben Keller <[email protected]>
+Daniel Fenn <[email protected]> dfenn <none@none>
+Meagan Lang <[email protected]> langmm <none@none>
+Joseph Tomlinson <[email protected]> jmt354 <none@none>
+Desika Narayanan <[email protected]> desika <none@none>
+Nathan Goldbaum <[email protected]> Nathan Goldbaum <[email protected]>
+Nathan Goldbaum <[email protected]> Nathan Goldbaum <[email protected]>
+Fabian Koller <[email protected]> [email protected] <[email protected]>
+Fabian Koller <[email protected]> [email protected] <[email protected]>
+Fabian Koller <[email protected]> [email protected] <[email protected]>
+Fabian Koller <[email protected]> [email protected] <[email protected]>
+Fabian Koller <[email protected]> Fabian Koller <none@none>
+Rafael Ruggiero <[email protected]> Rafael Ruggiero <none@none>
+John Regan <[email protected]> John Regan <[email protected]>
+Axel Huebl <[email protected]> Axel Huebl <[email protected]>
+Gabriel Altay <[email protected]> galtay <[email protected]>
+Mark Richardson <[email protected]> Mark Richardson <[email protected]>
+Jared Coughlin <[email protected]> Jared <none@none>
+Corentin Cadiou <[email protected]> cphyc <[email protected]>
+Corentin Cadiou <[email protected]> [email protected] <[email protected]>
+Corentin Cadiou <[email protected]> [email protected] <[email protected]>
+Corentin Cadiou <[email protected]> Corentin Cadiou <[email protected]>
+convert-repo <none@none> None <none@none>
+Patrick Shriwise <[email protected]> pshriwise <[email protected]>
+Michael Zingale <[email protected]> Michael  Zingale <[email protected]>
+Sam Leitner <[email protected]> Sam  Leitner <[email protected]>
+Geoffrey So <[email protected]> gsiisg <[email protected]>
+Matthew Turk <[email protected]> Matt Turk <[email protected]>

.travis.yml

@@ -0,0 +1,74 @@
+language: python
+sudo: false
+cache:
+  pip: true
+  directories:
+    - $HOME/.ccache  # https://github.com/travis-ci/travis-ci/issues/5853
+
+addons:
+  apt:
+    packages:
+      - libhdf5-serial-dev
+
+env:
+  global:
+    NUMPY=numpy
+    CYTHON=cython
+    MATPLOTLIB=matplotlib
+    SYMPY=sympy
+    H5PY=h5py
+    SCIPY=scipy
+    IPYTHON=ipython
+    FASTCACHE=fastcache
+
+matrix:
+  include:
+    - python: 2.7
+      env: NUMPY=numpy==1.10.4 CYTHON=cython==0.24 MATPLOTLIB=matplotlib==1.5.3 SYMPY=sympy==1.0 H5PY= SCIPY= FASTCACHE= IPYTHON=ipython==1.0
+    - python: 2.7
+    - python: 3.4
+    - python: 3.5
+    - python: 3.6
+    - os: osx
+      osx_image: xcode7.3
+      language: generic  # https://github.com/travis-ci/travis-ci/issues/2312
+      cache:
+        pip: false
+        directories:
+          - $HOME/Library/Caches/pip
+          # `cache` does not support `env`-like `global` so copy-paste from top
+          - $HOME/.ccache  # https://github.com/travis-ci/travis-ci/issues/5853
+
+before_install:
+  - |
+    if [[ $TRAVIS_OS_NAME != 'osx' ]]; then
+      pip install --upgrade virtualenv
+      python -m virtualenv venv
+      source venv/bin/activate
+      export PATH=/usr/lib/ccache:$PATH
+    else
+      brew update
+      brew install ccache hdf5
+      export PATH=/usr/local/opt/ccache/libexec:$PATH
+    fi
+    mkdir -p $HOME/.config/yt
+    echo "[yt]" > $HOME/.config/yt/ytrc
+    echo "suppressStreamLogging = True" >> $HOME/.config/yt/ytrc
+    cat $HOME/.config/yt/ytrc
+
+install:
+  - |
+    # setup environment
+    ccache -s
+    # Upgrade pip and setuptools and wheel to get clean install
+    pip install --upgrade pip
+    pip install --upgrade wheel
+    pip install --upgrade setuptools
+    # Install dependencies
+    pip install mock $NUMPY $SCIPY $H5PY $CYTHON $MATPLOTLIB $SYMPY $FASTCACHE $IPYTHON nose flake8 nose-timer
+    # install yt
+    pip install -e .
+
+script:
+  - |
+    nosetests --nologcapture --with-timer -sv yt