CHANGELOG

Changes in 0.3.0 and later are documented in the release notes.

Changes in Version 0.2.3 (2021-10-30)
=====================================
- Installs numpy before build on newer versions of pip (thanks Michael Hirsch)
- Fixes install with new versions of setuptools
- Better handling of unusual status of .spacepy directory
- More robust handling of Windows library loading on Python 3.8+
coordinates
 - Added Coords methods to convert to/from Astropy SkyCoord instances
irbempy
 - Update IRBEMlib to git commit a4759c0 (2021-06-30)
 - This update fixes an uninitialized GSM to SM transform that would return NaN
 - Fix bug in multiprocessed get_lstar when explicitly passing omni values
plot
 - Deprecate colourmaps; they were in matplotlib 1.5.
tests
 - Add spacepy_testing module to provide helper functions for testing.
 - Add assertWarns and assertDoesntWarn context managers.
time
 - Fix warning for out-of-date leapseconds.
 - Apply post-1972 leapsecond rules to pre-1972.
toolbox
 - Fix bootHisto passing of kwargs to histogram and bar.
pybats
 - Fix bug in reading RAM pressure files (affected electrons and total)
pycdf
 - Add support for Sparse Records variables.
 - Fix changing compression when creating variable from existing var/data.

Changes in Version 0.2.2 (2020-12-29)
=====================================
- Document end of support for Python 2
- Quaternion math functions moved to coordinates module
- Remove message on first import.
- Fixed setup.py not finding f2py on some OSX installs
coordinates
 - Include upstream fix for SPH->RLL coordinate transform
datamodel
 - Fix in SpaceData.toXXX() methods which would fail in some cases, now work as intended
 - Documentation update and default units change in createISTPattrs
datamanager
 - New function "rebin", rebin an axis of an array by contents of another
irbempy
 - Update IRBEMlib to rev620
 - Rev620 adds IGRF13 coefficients
 - Add conversion so all systems supported by coordinates can be passed
   to IRBEMlib routines
 - Fix compilation on Raspberry Pi
plot
 - utils.EventClicker support for non-line plots (e.g. pcolor)
 - New method for adding arrows to lines in utils
 - spectrogram.spectrogram class renamed to Spectrogram to avoid collision
   with its module.
pycdf
 - VarCopy objects now carry information to help reproduce original
 - Newly-public method nelems to get number of elements in zVar
 - New function concatCDF to read data from multiple CDFs
 - Fix assignment of "raw" values to EPOCH16 Attribute
 - Fix "minimum value" calculation for TT2000 types
 - Fix carryover of compression parameter when making a variable from
   another variable
 - istp.VariableChecks adds check for VALID/SCALE MIN/MAX Entry types
 - istp.VariableChecks adds check for DELTA attributes
 - istp.VariableChecks adds check for FILLVAL
 - istp.VariableChecks and FileChecks add check for empty attribute Entries
 - istp.VarBundle class to copy variables, slices, and depends between CDFs
 - istp.nanfill function to replace fill values with NaN
 - Warn if make CDF without explicitly setting backward compatible mode
   (either true or false); default will change to NOT backward compatible.
 - Warn if assign datetime to a variable without specifying a type;
   default will change to CDF_TIME_TT2000.
 - Fix epoch_to_num with newer versions of matplotlib.
pybats
 - Added support for multi-frame IDL files (*.outs files).
 - Updated parse_filename_time to handle ranges of times and updated file name formats.
 - Updated gitm.GitmBin reader to fix failures in Python 3.x.
 - Fix for incorrect Kyoto Kp plots.
 - Fixed open/closed tolerance kwarg not working in add_b_magsphere.
 - Added new stream trace visualization method for Bats2d objects: add_stream_scatter
 - Bats2d.add_b_magsphere and add_stream_scatter now have kwargs for adding arrows on ray traces
 - Updates to ram.RamSat including omnidirectional flux calculation
 - ram.PressureFile fixed for Python 3.x failures
 - Corrected MLT labels in ram.RamSat plotting
 - rim.Iono objects now load poorly-formatted files; rim.fix_format deprecated
 - Fix reading of files with absolute paths on Windows.
time
 - Fix handling of leapseconds before 1961.
 - For types that cannot represent leapseconds (e.g. UTC datetime), time
   within the leap second is now converted to the end of the day rather
   than the beginning of the next day.
 - Fractional leapsecond counts are now rounded to the integer rather than
   truncated.
 - Fix conversions to ISO before 1900 on Python 2.
 - Include leapseconds in JD/MJD calculation, so the length of a second on a
   day with leapseconds is slightly shorter but leap second times are not lost.
 - Most time systems are now converted to/from TAI. This may cause small
   differences with previous versions of SpacePy, on order of a double
   precision. Time conversions around leapseconds may also be different;
   in many cases they were undefined in previous versions.
 - now and today return UTC times, not local.
 - matplotlib no longer required, including RDT and randomDate.
 - Add support for conversion to/from astropy.time.Time
 - Warn about out-of-date leapseconds files (configurable option).
toolbox
 - New function get_url to retrieve data from a URL
 - Change update to retrieve OMNI2 data from SPDF not ViRBO
 - Change update to supplement ViRBO Qin-Denton files with NMC daily files
 - Change update to get leapseconds from NASA MODIS instead of USNO
 - New functions quaternionFromMatrix/quaternionToMatrix to convert between
   quaternions and 3D rotation matrices.
 - Fix human_sort; this had been broken since 0.1.6.
 - Fix function bootHisto to pass through RNG seed if provided
 - Deprecate function feq in favor of numpy.isclose.

Changes in Version 0.2.1 (2019-10-02)
=====================================
datamodel
 - Allow access to attributes via "meta" property
irbempy
 - Fix compilation issues on certain systems
poppy
 - Fix bootstrapping when aggregating function has multiple outputs
pycdf
 - Allow access to attributes via "meta" property
 - Single element references now return Python types not numpy scalars
 - Fix type-guessing on numpy object arrays with no values
 - New "istp" module supporting CDFs with ISTP-compliant metadata

Changes in Version 0.2.0 (2019-06-22)
=====================================
- Many installer updates, including binary wheels for Windows
- Fix writing of configuration file on Windows
ae9ap9
 - Fix handling of gzipped files under Windows/Python2
datamodel
 - Datatypes are now explicitly preserved by function "toRecArray"
irbempy
 - Update IRBEMlib to rev616
 - Update build for compatibility with numpy>=1.16 and GCC 8
 - Update retrieval of TS07 dynamic coefficient files
pybats
 - Many small changes and bugfixes (thanks John Haiducek)
 - Fix handling of gzipped files under Windows/Python2
pycdf
 - Proper handling of type guessing for negative integers, numpy scalars, and
   object arrays.
 - Allow ... to get all gEntries
 - Allow insert, append on gAttrs
 - Properly handle reading from empty variables
 - Fix some type-guessing ordering in Python 3.6
 - Reading empty NRV variables will now return empty array (not padding)
 - Fix more cases of BAD_ENTRY_NUM when reading attribute entries
 - Fix UTC-to-TT2000 conversions on ARM (thanks Rodrigue Piberne for the bug)
 - Speed up many operations by cacheing variable numbers. This is the biggest
   change to pycdf internals in several years; please report any bugs.
 - Fix TT2000-to-EPOCH16 conversions crashing in very rare cases.
 - Minimize setting/unsetting readonly mode, as this can be very slow.
 - Update for API changes in CDF library 3.7.1 (compatibility maintained
   with earlier versions)

Changes in Version 0.1.6 (2016-09-08)
=====================================
- Improvements to test suite (coverage and design)
coordinates
 - Bugfix to allow correct slicing behavior when Coords class has attached ticks
datamanager
 - New module to help in finding, slicing, and manipulating data
 - Function "apply_index": help sort one multi-dimensional data set by another
 - Function "array_interleave": combine data from two arrays to make a new
 - Function "axis_index": prepare indices along the axis of an array
 - Function "flatten_idx": convert an index to an index into flattened array
 - Function "insert_fill" to make explicit gaps in irregular data
 - Function "rev_index": convert an index into its complement
 - Function "values_to_steps": convert values to index of unique, sorted values
datamodel
 - Fix reading JSON-headed ASCII in numpy 1.4, 1.5
 - New function resample to change the time cadence of a SpaceData with
   windowMean
 - SpaceData gained methods for toCDF, toHDF, and toJSONheadedASCII
 - SpaceData keys can be multiple called, see __getitem__
 - New function toRecArray to create numpy record arrays from SpaceData objects
 - New function fromRecArray to create SpaceData objects from numpy record
   arrays
empiricals
 - Fix normalization of Vampola pitch angle model
 - New function omniFromDirectionalFlux, calculates omnidirection flux from
   directional fluxes
 - New function getSolarRotation, returns Carrington or Bartels number
 - New model in getPlasmaPause,  RT1970 -- Rycroft et al 1970
 - New function getSolarProtonSpectra, returns a fluence spectra for SEP events
irbempy
 - updated to latest revision of IRBEM library (rev541)
 - updated AlphaOfK to use vector inputs
 - minor bugfixes and speedups
plot
 - Packages in plot are imported on import of plot module
 - Addition of dual_half_circle() to overlay a light/dark "Earth"
 - Addition of simpleSpectrogram() in spacepy.plot.spectrogram
 - Addition of Carrington/Bartel plotting for 1D series
   (in spacepy.plot.carrington)
 - Updated smartTimeTicks, applySmartTimeTicks and added set_target
   (from PyBATS)
 - SpacePy style sheets added. Autoimported with plot, but with functionality
   to change style
 - Fix utils.collapse_vertical when called with sequences other than lists
 - Update to utils.timestamp adding more customization
pybats
 - Updated docstrings across all modules.
 - rim.py updated to be consistent with other pybats modules.
 - many bugfixes
 - Unified BATS-R-US calculation of number density and composition.
 - New class for magnetometer grid files: MagGridFile
 - New function for automatic latex label creation.
 - Updated Mag and MagFile objects for forward/backward compatibility.
 - IdlBin class renamed IdlFile; can read binary or ascii SWMF-IDL files.
 - Moved core plotting routines (set_target, smart_timeticks,
   apply_smart_timeticks) to plot.utils
pycdf
 - On OSX, search more paths for the CDF library
 - CDF.clone() now returns the new variable
 - Fix re-import after failure to find the CDF library, can now try the import
   again without restarting the Python interpreter
 - Fix some comparisons that might cause problems with future versions of numpy
 - Log the path to the CDF library for debugging purposes
 - Library.epoch_to_num: convert epoch to matplotlib date number (like date2num)
 - Improve handling of CDF_CHAR element count on py3k
 - Change tests to work with padding/stripping of CDF library 3.6.2 and later
	- It's not clear where the CDF library is stripping and/or padding
	  and pycdf has limited ability to work around this.
 - Improve type-guessing of attribute entries, particularly for zAttrs
 - Fix BAD_ENTRY_NUM when looking up zEntry type (or assigning to zEntry)
time
 - Speed improvement update to TickTock.getleapsecond
 - Overall speed improvements with for loop removal
 - ISO improvements via special cases for string input
 - Added classmethod today()
toolbox
 - Added function unique_columns
 - Added windowMean keyword op to allow arbitrary operations
 - Bugfixes in windowmean
        - double counting of points on window boundaries
        - one window's width of data could dropped from output series
python3 support
 -updates for python3 support, seems to be complete
AE9AP9
 - added ae9ap9 module to parse and work with output files from the
   AE9/AP9/SPM models (beta)

Changes in Version 0.1.5 (2014-12-23)
=====================================
- Python 3 support
- documentation updates across many packages
- installer should work better w/pip
- minor bugfixes throughout
datamodel
 - fromHDF5 now reads most netCDF4 and MatLab (v7.3+; r2011b onward) save files
 - add function dmfilled: create a filled dmarray with any given fill value
 - updates to toCDF to allow/use NRV variables
irbempy
 - add function find_footpoint: traces field line from given location to
   specified altitude
 - add functions find_LCDS and find_LCDS_K to find the last closed drift shell
   at given pitch angle or given second invariant K
 - add function AlphaOfK to find the equatorial pitch angle for a specified
   second invariant K
omni
 - get_omni updated to also read from daily JSON-headed ASCII files in
   custom databases
plot
 - new functions in utils:
   - add_logo: put an image in one corner of a figure
   - annotate_xaxis: add text in line with x tickmarks
   - collapse_vertical: remove space between two subplots
   - shared_ylabel: span a y-axis label across subplots
   - show_used: draw boxes to show the space taken by each plot element
pycdf
 - fix bug with interpreting indexes with ellipses (var[..., 0] gave the
   wrong result).
 - epoch16_to_epoch: round sub-milliseconds rather than truncate.
 - sped up indexing in variable copies
 - improved handling of numpy fancy indexing in variable copies
   (fancy indexing is still not supported for variables themselves.)
 - make assignment to attrs work
 - deprecate from_dict method of attribute lists; it is redundant with clone.
 - fix BAD_DATA_TYPE bug with datetime attributes in backward-compatible CDF
 - fix bug with finding CDF types for negative floats
 - fix matching attribute to variable type when assigning attributes to dict
 - fix handling of existence checks for variables with single quote in name
time
 - dtype in Ticktock can now be a callable (allowing custom time parsing)
toolbox
 - add function timeout_check_call to run another program with a timeout

Changes in Version 0.1.4
========================
- Removed deprecated functions/classes
  - time
    - Tickdelta class (use datetime.timedelta)
    - num2date, date2num functions (use matplotlib.dates)
  - toolbox
    - printfig, smartTimeTicks, applySmartTimeTicks, timestamp functions
      (moved to plot.utils)
    - leapyear, randomDate functions (moved to time)
- Minor bugfixes and speed-ups across package
- Expanded unit-testing
- Changed download prompt on install to information only
datamodel
 - output from datamodel to JSON-headed ASCII added
 - output from datamodel to NASA CDF added
 - new methods on dmarrays (append, concatenate, h/v/dstack)
empiricals
 - fixed bug in getPlasmaPause implementation of Moldwin et al., 2002 model
 - getPlasmaPause accepts optional dict-like of inputs instead of calling omni module
irbempy
 - updated to latest revision of IRBEM library (rev425)
 - consistent with IRBEMlib release version 4.4.0
 - add support for building with Intel Fortran compiler
LANL*
 - added new neural network trained on RAM-SCB model (valid inside 6.6Re)
pybats
 - Nearly all classes inherit from PbData, which is a subclass of SpaceData.
 - All add_* plotting methods have unified "target" and "loc" kwargs for selecting where to place plots.
 - New submodule: dgcpm, for handling the DGCPM model input/output.
 - New class: NgdcIndex, for handling NGDC input data for SWMF runs.
 - Bats2d class: stream tracing navigates native quadtree.
 - Bats2d class: arbitrary interpolation of data to any X,Y point(s).
 - Bats2d class: new variable calculations, including gradients.
 - Bats2d class: better handling of multi-species/fluid variables.
 - Bats2d class: unification of add_pcolor and add_contour syntax.
 - New class: ram.BoundaryGroup for handling groups of boundary files.
 - Expanded documentation for classes and methods.
pycdf
 - fixed bug in time types with pre-3.4.1 CDF library
 - provide new CDF.raw_var method to give access to variables without
   any translation.
 - added functions to translate between EPOCH, EPOCH16, TT2000 without going
   through datetime.
 - add options to CDF.new to allow specification of variable compression
   at creation time.
 - sort lists of variables, attributes by name instead of number.
time
 - fixed bug in addition/subtraction of Ticktocks

Changes in Version 0.1.3
========================
- Substantial updates to documentation
  - including publication list, case studies
- Minor bugfixes throughout
- Expanded unit testing
- Several functions deprecated:
  - toolbox.leap_year (use time.leapyear)
- Several previously deprecated functions removed:
  - toolbox.makePoly (use matplotlib.pyplot.fill_between)
- Several functions moved:
  - leapyear: from toolbox to time
  - randomDate: from toolbox to time
  - applySmartTimeTicks, smartTimeTicks, printfig, timestamp:
    from toolbox to plot.utils
- Number of base level imports limited
- MAJOR BUG in IRBEM library (T01S and TS04 models) fixed.
datamodel
 - new count method on dmarray
 - HDF5 output now supports many more types
 - output from datamodel to HTML table added
irbempy
 - Updated IRBEM library (including major bugfix to T01S and TS04)
 - 'custom' internal B-field model set to Dungey model (dipole + uniform)
 - revised multiprocessing of get_Lstar to use standard library
 - new get_Lm function
LANLstar
 - LANLstar v3 (with improved UI) now packaged with SpacePy
 - Fortran backend replaced (now requires ffnet Python package)
omni
 - additional OMNI parameters added to hourly database
pycdf
 - Convert to numpy-based backend, substantially faster/more flexible
 - Speed up extending variables with additional data (roughly 4x as fast)
 - Better integration with datamodel
 - Deletion bug still present in CDF 3.4; extend workaround to later version
 - Support for new CDF_TIME_TT2000 variable type
time
 - Ticktock is now iterable and adds/subtracts datetime.timedeltas
 - Ticktock time storage is array-based and now has insert and remove methods
 - Timedelta has been deprecated (use datetime.timedelta)
toolbox
 - hypot function speed-up
 - update function:can specify HTTP User Agent in config file

Changes in Version 0.1.2
========================
- Overhaul of all documentation for better organization and clarify
- New C backends speed up several functions in toolbox and time
- Minor bugfixes throughout
- Support for newer compilers on Windows
- Include Fortran runtime with Windows binary installers
Datamodel
 - Support for JSON-headed ASCII data read/write
Empiricals
 - New pitch angle model
pybats
 - PWOM added
plot
 - New EventClicker to manually identify event times on a plot

Changes in Version 0.1.1
========================
- new config file structure
- overhaul of source distribution build
- __contact__ attribute added to each SpacePy module (FR: 3424949)
Datamodel
 - HDF5 file object closure on dump to HDF5
 - file overwriting is now possible in toHDF using overwrite keyword
 - warnings added for incompatible data types on dump to HDF5
Toolbox
 - reformatted example in dist_to_list
 - hypot now takes multiple args or an iterable
 - pmm now handles NaN
 - tOverlap/tOverlapHalf now return iterators for presorted input
 - forcedate keyword added to linspace
 - EventTimer added
 - bin_edges_to_center added to perform inverse of extant bin_center_to_edges
 - listUniq deprecated in favor of numpy.unique
 - feq deprecated in favor of numpy.allclose
SeaPy
 - fixed Sea2d failure caused by incomplete migration to base class for all Sea types
Plot
 - New subpackage plot added to SpacePy (still in heavy development)
 - spectrogram function added
PyBATS
 - pybats is now an extension module
 - major upgrades to internals (qdtree implementation, use of datamodel)
 - new Kyoto index handler

Additional typo fixes in documentation, Py3k compatibility updates and unit test updates

Version 0.1
===========
Original release of SpacePy