ENH: Add enforcement for whitespace cleanup

geojunky · Jun 11, 2018 · 5397716 · 5397716
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diff --git a/.gitignore b/.gitignore
@@ -22,4 +22,4 @@ MANIFEST
 /*.egg
 .eggs/
 *.so
-*~
+*~
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,6 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
diff --git a/.travis.yml b/.travis.yml
@@ -24,6 +24,7 @@ env:
     - TOXENV=docs
     - TOXENV=check-manifest
     - TOXENV=checkreadme
+    - TOXENV=pre-commit
 
 matrix:
   include:

diff --git a/ANN.rst b/ANN.rst
@@ -6,7 +6,7 @@ The h5py team is happy to announce the availability of h5py 2.5.0.
 This release introduces experimental support for the highly-anticipated
 "Single Writer Multiple Reader" (SWMR) feature in the upcoming HDF5 1.10
 release.  SWMR allows sharing of a single HDF5 file between multiple processes
-without the complexity of MPI or multiprocessing-based solutions.  
+without the complexity of MPI or multiprocessing-based solutions.
 
 This is an experimental feature that should NOT be used in production code.
 We are interested in getting feedback from the broader community with respect
@@ -42,7 +42,7 @@ Changes
 * Fixed an issue with 64-bit float VLENS
 * Cython warning cleanups related to "const"
 * Entire code base ported to "six"; 2to3 removed from setup.py
-  
+
 
 Acknowledgements
 ----------------

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -30,3 +30,4 @@ recursive-exclude other *
 recursive-exclude .github *
 exclude pavement.py
 exclude *.yml
+exclude *.yaml
diff --git a/ci/appveyor/vs2008_patch/setup_x64.bat b/ci/appveyor/vs2008_patch/setup_x64.bat
@@ -10,4 +10,4 @@ regedit /s x64\656d8763-2429-11d7-8bf6-00b0d03daa06.reg
 regedit /s x64\656d8766-2429-11d7-8bf6-00b0d03daa06.reg
 
 copy "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\vcpackages\AMD64.VCPlatform.config" "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\vcpackages\AMD64.VCPlatform.Express.config"
-copy "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.config" "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.Express.config"
+copy "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.config" "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.Express.config"
diff --git a/ci/appveyor/vs2008_patch/setup_x86.bat b/ci/appveyor/vs2008_patch/setup_x86.bat
@@ -10,4 +10,4 @@ regedit /s x86\656d8763-2429-11d7-8bf6-00b0d03daa06.reg
 regedit /s x86\656d8766-2429-11d7-8bf6-00b0d03daa06.reg
 
 copy "C:\Program Files\Microsoft Visual Studio 9.0\VC\vcpackages\AMD64.VCPlatform.config" "C:\Program Files\Microsoft Visual Studio 9.0\VC\vcpackages\AMD64.VCPlatform.Express.config"
-copy "C:\Program Files\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.config" "C:\Program Files\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.Express.config"
+copy "C:\Program Files\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.config" "C:\Program Files\Microsoft Visual Studio 9.0\VC\vcpackages\Itanium.VCPlatform.Express.config"
diff --git a/docs/faq.rst b/docs/faq.rst
@@ -32,7 +32,7 @@ Variable length array               Any supported type
 Unsupported types:
 
 =========================           ============================================
-Type                                Status                                 
+Type                                Status
 =========================           ============================================
 HDF5 "time" type
 NumPy "U" strings                   No HDF5 equivalent
@@ -61,7 +61,7 @@ What file drivers are available?
 --------------------------------
 
 A number of different HDF5 "drivers", which provide different modes of access
-to the filesystem, are accessible in h5py via the high-level interface. The 
+to the filesystem, are accessible in h5py via the high-level interface. The
 currently supported drivers are:
 
 =================================== =========================================== ============================
@@ -95,10 +95,10 @@ This layer is object-oriented with respect to HDF5 identifiers, supports
 reference counting, automatic translation between NumPy and HDF5 type objects,
 translation between the HDF5 error stack and Python exceptions, and more.
 
-This greatly simplifies the design of the complicated high-level interface, by 
+This greatly simplifies the design of the complicated high-level interface, by
 relying on the "Pythonicity" of the C API wrapping.
 
-There's also a PyTables perspective on this question at the 
+There's also a PyTables perspective on this question at the
 `PyTables FAQ <http://www.pytables.org/FAQ.html#how-does-pytables-compare-with-the-h5py-project>`_.
 
 
@@ -138,14 +138,14 @@ Appending data to a dataset
 The short response is that h5py is NumPy-like, not database-like. Unlike the
 HDF5 packet-table interface (and PyTables), there is no concept of appending
 rows. Rather, you can expand the shape of the dataset to fit your needs. For
-example, if I have a series of time traces 1024 points long, I can create an 
+example, if I have a series of time traces 1024 points long, I can create an
 extendable dataset to store them:
 
     >>> dset = myfile.create_dataset("MyDataset", (10, 1024), maxshape=(None, 1024))
     >>> dset.shape
     (10,1024)
 
-The keyword argument "maxshape" tells HDF5 that the first dimension of the 
+The keyword argument "maxshape" tells HDF5 that the first dimension of the
 dataset can be expanded to any size, while the second dimension is limited to a
 maximum size of 1024. We create the dataset with room for an initial ensemble
 of 10 time traces. If we later want to store 10 more time traces, the dataset
@@ -163,7 +163,7 @@ Each axis can be resized up to the maximum values in "maxshape". Things to note:
 
 Unicode
 -------
-As of h5py 2.0.0, Unicode is supported for file names as well as for objects 
+As of h5py 2.0.0, Unicode is supported for file names as well as for objects
 in the file. When object names are read, they are returned as Unicode by default.
 
 However, HDF5 has no predefined datatype to represent fixed-width UTF-16 or
@@ -205,6 +205,3 @@ containing a compiled, shared-library build of HDF5 (containing things like "inc
     $ python setup.py test
 
 Report any failing tests to the mailing list (h5py at googlegroups), or by filing a bug report at GitHub.
-
-
-
diff --git a/docs/high/attr.rst b/docs/high/attr.rst
@@ -117,6 +117,3 @@ Reference
         :type name:     String
 
         :param value:   New value.  Will be put through ``numpy.array(value)``.
-
-
-
diff --git a/docs/high/file.rst b/docs/high/file.rst
@@ -53,7 +53,7 @@ of supported drivers and their options:
     'sec2'
         Unbuffered, optimized I/O using standard POSIX functions.
 
-    'stdio' 
+    'stdio'
         Buffered I/O using functions from stdio.h.
 
     'core'

diff --git a/docs/high/group.rst b/docs/high/group.rst
@@ -86,7 +86,7 @@ is to create an :ref:`HDF5 datasets <dataset>`::
     >>> out = grp["name"]
     >>> out
     <HDF5 dataset "name": shape (), type "<i8">
-    
+
 When the object being stored is an existing Group or Dataset, a new link is
 made to the object::
 
@@ -430,7 +430,7 @@ Link classes
 
     :param filename:    Name of the file to which the link points
     :type filename:     String
-    
+
     :param path:        Path to the object in the external file.
     :type path:         String
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -52,7 +52,7 @@ Advanced topics
 
 .. toctree::
     :maxdepth: 1
-    
+
     config
     special
     strings

diff --git a/docs/licenses.rst b/docs/licenses.rst
@@ -22,8 +22,8 @@ Copyright Notice and Statement for the h5py Project
        documentation and/or other materials provided with the
        distribution.
 
-    c. Neither the name of the author nor the names of contributors may 
-       be used to endorse or promote products derived from this software 
+    c. Neither the name of the author nor the names of contributors may
+       be used to endorse or promote products derived from this software
        without specific prior written permission.
 
     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
@@ -179,7 +179,7 @@ stdint.h (Windows version) License
     EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
     SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
     PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-    OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+    OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
     WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
     OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
     ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
@@ -229,4 +229,3 @@ Python license
 
 #. By copying, installing or otherwise using Python Python 2.7.5, Licensee agrees
    to be bound by the terms and conditions of this License Agreement.
-
diff --git a/docs/mpi.rst b/docs/mpi.rst
@@ -147,4 +147,3 @@ More information
 Parallel HDF5 is a new feature in h5py.  If you have any questions, feel free to
 ask on the mailing list (h5py at google groups).  We welcome bug reports,
 enhancements and general inquiries.
-
diff --git a/docs/quick.rst b/docs/quick.rst
@@ -185,5 +185,3 @@ implements the dictionary interface::
     True
 
 For more, see :ref:`attributes`.
-
-
diff --git a/docs/refs.rst b/docs/refs.rst
@@ -45,7 +45,7 @@ opening any other object:
 Using region references
 -----------------------
 
-Region references always contain a selection.  You create them using the 
+Region references always contain a selection.  You create them using the
 dataset property "regionref" and standard NumPy slicing syntax:
 
     >>> myds = myfile.create_dataset('dset', (200,200))
@@ -119,5 +119,3 @@ indicate whether or not it is null:
     >>> nullref = ref_dataset[50]
     >>> print bool(nullref)
     False
-
-
diff --git a/docs/special.rst b/docs/special.rst
@@ -62,7 +62,7 @@ dtype.  In h5py, variable-length strings are mapped to object arrays.  A
 small amount of metadata attached to an "O" dtype tells h5py that its contents
 should be converted to VL strings when stored in the file.
 
-Existing VL strings can be read and written to with no additional effort; 
+Existing VL strings can be read and written to with no additional effort;
 Python strings and fixed-length NumPy strings can be auto-converted to VL
 data and stored.
 
@@ -100,7 +100,7 @@ arrays::
 
     >>> dset[0:2]
     array([array([1, 2, 3], dtype=int32), array([1, 2, 3, 4, 5], dtype=int32)], dtype=object)
-    
+
 
 Enumerated types
 ----------------

diff --git a/docs/swmr.rst b/docs/swmr.rst
@@ -8,25 +8,25 @@ Starting with version 2.5.0, h5py includes support for the HDF5 SWMR features.
 What is SWMR?
 -------------
 
-The SWMR features allow simple concurrent reading of a HDF5 file while it is 
+The SWMR features allow simple concurrent reading of a HDF5 file while it is
 being written from another process. Prior to this feature addition it was not
 possible to do this as the file data and meta-data would not be synchronised
 and attempts to read a file which was open for writing would fail or result in
 garbage data.
 
 A file which is being written to in SWMR mode is guaranteed to always be in a
-valid (non-corrupt) state for reading. This has the added benefit of leaving a 
-file in a valid state even if the writing application crashes before closing 
+valid (non-corrupt) state for reading. This has the added benefit of leaving a
+file in a valid state even if the writing application crashes before closing
 the file properly.
 
 This feature has been implemented to work with independent writer and reader
 processes. No synchronisation is required between processes and it is up to the
-user to implement either a file polling mechanism, inotify or any other IPC 
+user to implement either a file polling mechanism, inotify or any other IPC
 mechanism to notify when data has been written.
 
 The SWMR functionality requires use of the latest HDF5 file format: v110. In
-practice this implies using at least HDF5 1.10 (this can be checked via 
-`h5py.info`) and setting the libver bounding to "latest" when opening or 
+practice this implies using at least HDF5 1.10 (this can be checked via
+`h5py.info`) and setting the libver bounding to "latest" when opening or
 creating the file.
 
 
@@ -87,30 +87,30 @@ Examples
 --------
 
 In addition to the above example snippets, a few more complete examples can be
-found in the examples folder. These examples are described in the following 
+found in the examples folder. These examples are described in the following
 sections
 
 Dataset monitor with inotify
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The inotify example demonstrate how to use SWMR in a reading application which
 monitors live progress as a dataset is being written by another process. This
-example uses the the linux inotify 
-(`pyinotify <https://pypi.python.org/pypi/pyinotify>`_ python bindings) to 
+example uses the the linux inotify
+(`pyinotify <https://pypi.python.org/pypi/pyinotify>`_ python bindings) to
 receive a signal each time the target file has been updated.
 
 .. literalinclude:: ../examples/swmr_inotify_example.py
 
 Multiprocess concurrent write and read
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The SWMR multiprocess example starts two concurrent child processes: 
+The SWMR multiprocess example starts two concurrent child processes:
 a writer and a reader.
 The writer process first creates the target file and dataset. Then it switches
 the file into SWMR mode and the reader process is notified (with a
 multiprocessing.Event) that it is safe to open the file for reading.
 
-The writer process then continue to append chunks to the dataset. After each 
+The writer process then continue to append chunks to the dataset. After each
 write it notifies the reader that new data has been written. Whether the new
 data is visible in the file at this point is subject to OS and file system
 latencies.
@@ -126,7 +126,7 @@ it will drop out of the loop and exit.
 The example output below (from a virtual Ubuntu machine) illustrate some
 latency between the writer and reader::
 
-    python examples/swmr_multiprocess.py 
+    python examples/swmr_multiprocess.py
       INFO  2015-02-26 18:05:03,195        root  Starting reader
       INFO  2015-02-26 18:05:03,196        root  Starting reader
       INFO  2015-02-26 18:05:03,197      reader  Waiting for initial event
@@ -150,5 +150,3 @@ latency between the writer and reader::
       INFO  2015-02-26 18:05:03,217      reader  Read dset shape: (20,)
       INFO  2015-02-26 18:05:03,218      reader  Read dset shape: (20,)
       INFO  2015-02-26 18:05:03,219        root  Waiting for reader to finish
-
-
diff --git a/docs/whatsnew/2.0.rst b/docs/whatsnew/2.0.rst
@@ -166,12 +166,3 @@ Known issues
 * There are reports of crashes related to storing object and region references.
   If this happens to you, please post on the mailing list or contact the h5py
   author directly.
-
-
-
-
-
-
-
-
-
diff --git a/docs/whatsnew/2.2.rst b/docs/whatsnew/2.2.rst
@@ -6,7 +6,7 @@ Support for Parallel HDF5
 -------------------------
 
 On UNIX platforms, you can now take advantage of MPI and Parallel HDF5.
-Cython, ``mpi4py`` and an MPI-enabled build of HDF5 are required..  
+Cython, ``mpi4py`` and an MPI-enabled build of HDF5 are required..
 See :ref:`parallel` in the documentation for details.
 
 
@@ -98,4 +98,3 @@ The method ``Group.move`` allows this to be performed in one step::
     >>> f.move('a', 'b')
 
 Both the source and destination must be in the same file.
-
diff --git a/docs/whatsnew/2.4.rst b/docs/whatsnew/2.4.rst
@@ -6,17 +6,17 @@ Build system changes
 
 The setup.py-based build system has been reworked to be more maintainable, and
 to fix certain long-standing bugs.  As a consequence, the options to setup.py
-have changed; a new top-level "configure" command handles options like 
+have changed; a new top-level "configure" command handles options like
 ``--hdf5=/path/to/hdf5`` and ``--mpi``.  Setup.py now works correctly under
 Python 3 when these options are used.
 
 Cython (0.17+) is now required when building from source on all platforms;
-the .c files are no longer shipped in the UNIX release.  The minimum NumPy 
+the .c files are no longer shipped in the UNIX release.  The minimum NumPy
 version is now 1.6.1.
 
 Files will now auto-close
 -------------------------
-  
+
 Files are now automatically closed when all objects within them
 are unreachable. Previously, if File.close() was not explicitly called,
 files would remain open and "leaks" were possible if the File object

diff --git a/docs/whatsnew/2.5.rst b/docs/whatsnew/2.5.rst
@@ -64,4 +64,3 @@ Other changes
 
 Acknowledgements
 ----------------
-
diff --git a/docs/whatsnew/2.7.rst b/docs/whatsnew/2.7.rst
@@ -92,4 +92,3 @@ Other changes
 
 Acknowledgements
 ----------------
-
diff --git a/docs_api/h5.rst b/docs_api/h5.rst
@@ -39,6 +39,3 @@ Module constants
 .. data:: ITER_DEC
 
     Traverse index in decreasing order
-
-
-
diff --git a/docs_api/h5a.rst b/docs_api/h5a.rst
@@ -26,5 +26,3 @@ Attribute objects
 
 .. autoclass:: AttrID
     :members:
-
-
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,4 +22,4 @@ MANIFEST @@
     /*.egg
     .eggs/
     *.so
-    *~
+    *~
Original file line number	Diff line number	Diff line change
Expand Up		@@ -117,6 +117,3 @@ Reference
		:type name: String

		:param value: New value. Will be put through ``numpy.array(value)``.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -147,4 +147,3 @@ More information
		Parallel HDF5 is a new feature in h5py. If you have any questions, feel free to
		ask on the mailing list (h5py at google groups). We welcome bug reports,
		enhancements and general inquiries.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -185,5 +185,3 @@ implements the dictionary interface::
		True

		For more, see :ref:`attributes`.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -166,12 +166,3 @@ Known issues
		* There are reports of crashes related to storing object and region references.
		If this happens to you, please post on the mailing list or contact the h5py
		author directly.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -64,4 +64,3 @@ Other changes

		Acknowledgements
		----------------
Original file line number	Diff line number	Diff line change
Expand Up		@@ -92,4 +92,3 @@ Other changes

		Acknowledgements
		----------------
Original file line number	Diff line number	Diff line change
Expand Up		@@ -39,6 +39,3 @@ Module constants
		.. data:: ITER_DEC

		Traverse index in decreasing order
Original file line number	Diff line number	Diff line change
Expand Up		@@ -26,5 +26,3 @@ Attribute objects

		.. autoclass:: AttrID
		:members: