CHANGELOG

1.4.0a1 - 2020/06/22
  - Cartopy (version > 0.17.0) is now supported in addition to Basemap for map
    projections. 
  - Error reporting for openmulti() has been improved.
  - Non-ASCII character support in NetCDF attributes are now better handled.
  - Improvements and bugfixes in stats module
  - Fixed crash in eof module.
  - Changed default netcdf opener to use standard netcdf4 python package.

1.3.1 - 2020/06/14
  - Fix bug where pygeode.formats.netcdf4 fails if the libnetcdf shared library
    is not installed on the system.  It should not be required, since the
    interface uses the Python netCDF4 package to handle I/O.
  - Updated the INSTALL file with more up-to-date information.
  - Removed warning message when libnetcdf unavailable.  This was always
    displayed, even when libnetcdf was not actually needed.  This could cause
    confusion if using the newer pygeode.formats.netcdf4 interface, since it
    doesn't require the shared library at all.

1.3.0 - 2019/10/02
  - Support for Python 3.
  - Fix ext_xarray.from_xarray() method, which was failing on xarray versions
    > 0.10.0.
  - Handle Var objects passed into netcdf.save and netcdf4.save.
  - Properly detect attributes that are 1-element list of strings when writing
    to netcdf.
  - Force attributes from netcdf4 module to be string instead of unicode.
  - Support for netcdf4 groups.
  - Fix lazy variable loading for netcdf4 module.
  - Added new bar() and errorbar() plot wrappers.
  - Fix colorbar=False option for showvar.
  - Fix nl=0 option for clfdict.
  - Updated progress bar to be compatible with progressbar2 package.
  - New rotatelon() and clip() functions.

1.2.2 - 2018/07/06
  - Handle netCDF time units that are separated by a "T" instead of a space.
    E.g., "hours since 2010-02-01T03:00:00".

1.2.1 - 2018/05/18
  - Fix bug in plot_v1, where the 'projection' entry was removed from the
    projection dictionary supplied by the user.  This was causing problems
    when creating sequential plots, where only the first one had the right
    projection.
  - Fix bug in hdf4 interface.  Files that had dimensions with no associated
    coordinate variable were crashing with a KeyError.

1.2.0 - 2018/03/21
  - Added nan-aware versions of climatological mean operations.
  - Added standard deviation and nan-aware standard deviation classes for all
    time subdivisions of climatological operations.
  - Added count operations in climat module that return number of non-NaN
    elements.
  - Climatology operators can now be invoked as methods of Var objects.
  - Add a "netcdf4" format for interfacing with the netCDF4 python module.
  - Add support for entry points for pygeode.plugins and pygeode.formats.
  - Add entry points for custom axes.
  - Added pcolor operation to AxesWrapper.
  - Better support for dimensionless Var objects (issue #108).
  - Fix stack overflow when dealing with large 1D arrays (issue #107).
  - New module pygeode.ext_xarray for converting to/from xarray objects.
  - New hasaxis() and getaxis() methods for Dataset objects.
  - Var.get() now returns a writeable copy the array.

1.1.1 - 2018/01/19
  - Fixed some padding logic in showgrid.
  - Corrected bug that was happening when the inx coordinate variable was
    provided with more than one axis but not as many axes as the data.
  - Disable prefix checks when there's an exact match to an axis name.
    Fixes bug triggered by axis names that contain underscores.

1.1.0 - 2017/06/17
  - Allow some settings to be read from a configuration file (pygrc).
  - Added an option to disable lazy array evaluation, for cases where this
    feature gets in the way.
  - Option to back variables into "shorts" when saving netCDF files,
    triggered by passing pack=True to netcdf.save().
  - Allow specifying an "unlimited" dimension when saving netCDF files.
  - Added load() method to Dataset objects, to load all the associated
    variables in memory.
  - New plot routines: vstreamplot, vhist, and fill_between.
  - New plot.cm module to help with colormaps.
  - New plot.cnt_helpers module for setting up contour intervals.
  - New "yearlymean" and "climstdev" operators in climat module.
  - Allow weights to be used in variance operator.
  - Added second-derivative operator (triggered by passing df=2 to "deriv").
  - New forward difference operator ("diff").
  - Added conjugation operator ("conj").
  - Added option to compute covariance matrix of regression coefficients in
    multiple_regress.
  - New "s_" prefix for axis subsetting, to "squeeze" the axis out after
    selecting a particular value.
  - New "n_" prefix for axis subsetting, to "negate" the selection criteria.
  - New "station" axis, for data that's sample at predetermined surface stations.
  - Also, added more general "non-coordinate" axes where the values are not
    part of a continuum, and need not even be numeric.
  - New time axis constructor helpers (standardtimerange, standardtimen,
    modeltime365range, modeltime365n, modeltime360range, modeltime360n,
    yearlessn).
  - New "check_multi" routine in formats.multifile, to pre-scan all files and
    report any problems with the files.
  - New "formats.data_scanner" module for loading more general (heterogeneous)
    files together into a dataset.
  - Added some new and interesting bugs to the code.

1.0.6 - 2017/03/31
 - Fixed missing parentheses in interp.c, which could cause a compilation failure.
 - Fixed RPM installation configuration.
 - Switched from distutils to setuptools, in order to make wheel files.

1.0.5 - 2016/07/07
 - Fixed segmentation fault when initializing a time axis with an invalid month.
   (issue #76).
 - Allow tools.loopover to handle Axis arguments.  Certain operations such as
   smooth() were crashing when operating on an Axis object (issue #86).
 - Preserve variable metadata when doing climatologies (issue #89).
 - In multifile.openall(), don't require a format if an opener is provided.
   (issue #90).
 - Fixed a pointer issue in interpcore, in the case where there aren't enough
   valid points to do an interpolation.

1.0.4 - 2015/11/04
 - Set attribute Conventions="CF-1.0" in netcdf output files, so other netcdf
   utilities know how to parse our data.
 - Added system include paths for non-standard prefix installs (conda), as well
   as to the libhelper routines for finding libraries

1.0.3 - 2015/06/16
 - Allow other PyGeode formats to be installed in parallel Python paths.
 - Add LD_LIBRARY_PATH to search path in libhelper.find_library().
 - Force double-precision in val_as_date, to prevent precision loss when
   computing dates.

1.0.2 - 2015/03/24
 - Fixed bugs in regress and correlate in axis matching logic.
 - Allow timeaxes to support unordered values (issue 69).
 - Fixed issue in removeleapyears.

1.0.1 - 2014/07/09
 - Fixed small colourbar bug.
 - In multifile, allow for case where files are passed in as a tuple.
 - Allow showvar() to work without basemap installed.

1.0.0 - 2014/04/14

  General updates to the code:
  - Converted C shared libraries to Python extension modules, to improve
    portability of the package.
  - New top-level "open" and "save" commands, which guess the appropriate file
    format to use.

  Updates to Var class:
  - Change the behaviour of Var.__getitem__, so that degenerate axes are
    removed.  This brings our array slicing behaviour closer to numpy.

  Updates to axis module:
  - For axes, added in a tolerance autodetection for closeness of matches,
    based on spacing in axis.
  - New functions "regularlat" & "regularlon" to create regularly spaced
    latitude and longitude axes.

  New modules:
  - New 'spectral' module, which defines a Spectral axis.

  Updates to the plot module:
  - Can output to PDF.
  - Improved support for Basemap.
  - Support for scatter plots, quiver plots, and significance masks.
  - Various usability improvements

  Updates to the old (v1) plot module:
  - Added hatching option for old significance mask.

  Updates to the stats module:
  - Added option to scale effective degrees of freedom in regress().
  - Regress now takes a comma-separated string to specify outputs, like EOF.
  - New function "multiple_regress" - code to do multiple linear regression.

  Updates to the reduce module:
  - Added argmin() operator.

  Updates to the ufunc module:
  - We now keep the original variable name if we're doing an arithmetic scalar
    operation on the variable.

  Updates to the formats.cfmeta module:
  - Better detection and handling of (malformed) time axes.

  Bug fixes:
  - Correct portability issue with timeaxiscore module; also improved its error 
    reporting.
  - Fixed issue with concatenating along dummy axis.
  - Fixed issue with "smooth" module (issue 44), and changed the smooth
    interface a bit to make it easier to use your own kernels.


0.7.3 - 2014/01/13
  - Add support for more netcdf data types (issue 54).
  - Minor bugfix for ufunc (var name was not being set properly).

0.7.2 - 2013/09/16
  - Fix ufunc operators dropping metadata (issue 39).

0.7.1 - 2013/06/05
  - Fix missing header message in progress bars (issue 33).
  - Fix axis values being overwritten in plotvar (issue 36).

0.7.0 - 2012/08/17

  Updates to Var and Axis classes:
  - Vars now have a 'units' attribute
  - Vars and Axes now have a 'plotatts' dictionary, which contains all plotting 
    parameters.  Some possible keys are:
      plottitle   - The title to use for plots of this variable (or the axis
                    label, if this is an Axis)
      plotname    - A shorter title, used for axis labels.
      plotunits   - The units of the variable (overrides the 'units' attribute
                    of the variable).
      plotscale   - The type of scaling to apply to the values, either 'linear'
                    or 'log'.
      plotorder   - The direction to plot the axis coordinates.  1 = away from
                    origin, -1 = towards origin.
      formatstr   - A special string for formatting the values on axis ticks
                    and plot titles.
      scalefactor - unit conversion, to get values in the plotunits
      offset      - unit conversion, to get values in the plotunits
  - Auto-completion of axis & variable members of Var and Dataset objects
    (works in ipython).  These members are also listed in dir() calls now.

  Updates to the plot module:
  - Added 'every' keyword to plotquiver() to thin the vector field, implemented 
    lblx, lbly kwargs.
  - In plotsigmask(), added "alpha" kwarg to control alpha value of mask
  - Keyword arguments "scaleAx", "scaleX", "scaleY" control scaling the values
    by one of the axis coordinates.  This preserves integrals under a
    logarithmic axis.
  - added log10-scaling of 2D field values with new kwarg 'logVal'
  - apply scalefactor and offset from plotatts, if they're defined.  Only
    triggers if var.plotatts['plotunits'] is different from var.units.
  - disable anti-aliasing in 2D plots.  In some versions of matplotlib (e.g.
    the one shipped with Ubuntu 11.10), antialiasing causes annoying gaps
    between polygons in various plots (contourf, pcolor, etc.).
  - Created a more modularized set of plotting routines.  This gives greater
    control over the construction of the plots, e.g. for publication.  The old
    'plotvar' routine is still available for cases where the automatic
    formatting is good enough.

  Updates to the stats module:
  - Added some t test code:
      difference(X, Y) - Calculates difference between the mean values of X
                         and Y averaged over the dimensions specified by axes.
                         Returns X - Y, p values, confidence intervals, and
                         degrees of freedom.
      isnonzero(X)     - Determines if X is non-zero, assuming X is normally
                         distributed.  Returns mean of X along axes, p value,
                         and confidence interval.
  - Updated regress() to work on arbitrary axes
  - can now specify which axes to correlate()
  - correlate() now works with NaN values.

  Updates to the timeutils module:
  - Lag variable for lagged correlations
  - Moved _uniquify, modify, reltime, delta, wrapdate, and date_diff from
    timeaxis module to timeutils module.
  - New operator removeleapyears() to convert a standard time axis to a 365-day
    or 360-day axis.
  - New operator splittimeaxis() to split a time axis into 2 dimensions (e.g.
    year, day-of-year).
  - New function conform_values() to make 2 time axes have the same units and
    start date.
  - New operator jointimeaxes() to convert a 2D time representation (e.g. year,
    day-of-year) to a single time axis.

  Other updates:
  - Interpolation now is nan-aware and can extrapolate linearly.  By default,
    no extrapolation is done (gives NaNs outside the data range).
  - Improved compatibility with newer versions of the progressbar package.
  - In concat module, allow the concatenation axis to be specified by the user,
    so it doesn't have to be guessed.
  - Added argmax() operator (works on one dimension)
  - In composite operator, events that extend past the edge of the data now are
    filled with NaNs
  - Improved handling of endpoints in the 'smooth' operator.


0.6.3 - 2012/08/16
  - Fix bug with NaN-friendly reductions (nansum,nanmean,nanmin,nanmax).  They
    were crashing when doing a full reduction to a scalar.
    See issue 32 - https://github.com/pygeode/pygeode/issues/32

0.6.2 - 2012/06/15
  - Backported fix for year=0 infinite loop in timeaxis.
  - Fix issue 28 (https://github.com/pygeode/pygeode/issues/28)
  - Backported more robust handling of time axis in cfmeta module.

0.6.1 - 2011/11/23
  - Fix issue 23 (https://github.com/pygeode/pygeode/issues/23)
  - Fix issue 25 (https://github.com/pygeode/pygeode/issues/25)
  - Don't abort on missing 'A' and 'B' coefficients when loading netcdf files
    with hybrid vertical coordinates.

0.6.0 - 2011/08/11
  - Initial stable release