1.7.4:
* required python is now >=3.10 for PyTables compatibility
* replace deprecated pkg_resources

1.7.3:
* replace deprecated .isdir and .isfile path API uses with is_dir and is_file
  from version 16.12
* add numpy 2.0 compatibilty

1.7.2:
* required Python is now >=3.9
* fixed consistency in array shape output when track indexing on bigWig files

1.7.1:
* fix array dimensionality consistency for summary statistics on bigWig files
* add debug representation for chromosomes for bigWig files

1.7.0:
* adapted existing python interface to open bigWig files

1.6.0:
* required Python is now >=3.7
* genomedata-load-data: changed to a python script with a c-extension

1.5.0:
* genomedata-load-data: fix bad error message when loading process fails
* genomedata-load-seq: add chromosome name mapping based on assembly reports

1.4.4:
* fixed pkg-config output encoding when finding HDF5 directories

1.4.3:
* fixed genomedata script entry points for Python 3

1.4.2:
* added compatibilty for Python 3
* genomedata-load-seq: adjacent AGP entries are merged into a single supercontig
* Use pkg-config during setup to determine paths to HDF5 directories
* Removed forked-path dependency, added Path.py

1.4.1:
* genomedata-hard-mask: fix verbosity line not outputting to stderr
* genomedata-load-data: fix hdf5 group leak

1.4.0:
* genomedata-close-data: chunk metadata now truncates telomeres and trims large
  gaps between supercontigs
* genomedata-load-data: new option for masking data with --maskfile
* genomedata-hardmask: new command added to filter out track regions
* hardmask_data: new python interface to filter out track regions
* Genome: add ability to open archives for writing
* genomedata-load-seq: AGP are now correctly loaded regardless of filename and
  may be concatenated together
* genomedata-load-seq: fix assertion failure on argument parsing when loading
  fasta sequence (thanks to Kate Cook)
* genomedata-load: fix agp files not being recognized from this entry point
* docs: clarified that agp files cannot be combined
* docs: warned users that globs must be quoted to be parsed by genomedata-load

1.3.6:
* genomedata-load-data now support bigWig files if the bigWigToBedGraph
  utility is installed
* `sizes` command added to `genomedata-info` (Jay Hesselberth)
* Updated installation instructions for installing with PyTables 3.1.1
* toward python3 compatibility (Jay Hesselberth)
  - genomedata now requires python 2.7+
  - moved from `optparse` to `argparse` throughout
  - package-wide `__version__` lets modules report true version number
  - __future__ imports added to all modules and python3 `print()`
    functions

1.3.5:
* Removed platform specific builds from distribution

1.3.4:

* fixed bug related to updated PyTables
* compile works with HDF5 setups even when they were built
  --with-default-api-version=v16
* doc fixes
* fixed DeprecationWarnings associated with PyTables 3.0
* updated dependency to PyTables >= 3.0

1.3.3:

* genomedata-query: new command that prints data from a Genomedata archive for your
  non-Python scripting needs (thanks to Max Libbrecht)
* genomedata-histogram: new command that prints histograms from a Genomedata archive
  (combination of a new module by Max Libbrecht and an old module by Michael Hoffman)
* genomedata-info: add "contigs" subcommand (thanks to Max Libbrecht)
* genomedata-info: friendlier error when unsupported command name used
* genomedata-load-data: friendlier errors when invalid BED3+1/bedGraph data supplied
* genomedata-load-seq: always makes chromosome and supercontig
  coordinates with unsigned 32-bit integers instead of system int
* genomedata-load-data: more detailed error message when initial file open fails
* genomedata-load-data: bugfix
* now compile with -Wextra
* doc fixes

1.3.2:

* API: now allow array of tracks. For example: chromosome[245:270, array([7, 5])]

1.3.1:

* API: now allow lists of tracks when directly accessing chromosome data, for example:
  chromosome[245:270, ["data1", "data3"]] or chromosome[245:270, [7, 5]]
* genomedata-load-seq: add --assembly option which supports AGP files,
  to allow avoid loading seq while still dealing with assembly gaps
  properly
* genomedata-load: now supports --assembly and --sizes options
* genomedata-load-assembly: alias for genomedata-load-seq.
  genomedata-load-seq will be deprecated in the future
* genomedata-load-data: now support DOS-style line endings ("\r\n")
* genomedata-load: print genomedata-load-data error code on failure
* genomedata-load-data: print more informative messages when ignoring data
* genomedata-load: all diagnostics messages to stderr
* genomedata-load: some diagnostics now include timestamp so we can
  see where performance bottlenecks are
* genomedata-load: more descriptive error messages
* genomedata-load-seq: print more descriptive error message when
  attempting to load sequence from a non-FASTA file
* genomedata-load: fixed issue 10: now compiles on gcc 4.6.2
* docs: add links to source code
* docs: genomedata-load: sequence "option" is mandatory. In a future
  version, we should change this to an argument to reflect this.
* test: add tests for DOS-style line-endings

1.3.0:

* genomedata supercontigs are no longer guaranteed to have seq data
* add --sizes option to genomedata-load-seq, to allow avoid loading seq
* Genome.add_track_continuous() has a significant performance
  improvement. This also means that genomedata-open-data will run much
  faster, as well as genomedata-load-data on fresh tracks
* fix bug where genomedata-load-seq didn't work
* fix bug where directory genomedata archive didn't work with only one chromosome

1.2.3:

* DO NOT USE: genomedata-load-seq doesn't work
* allow use with PyTables >=2.2
* new command: genomedata-info: "genomedata-info tracknames ARCHIVE"
  prints the tracknames for ARCHIVE
* Genome.format_version will now return 0 when files are missing a
  genomedata_format_version attribute
* Genome.__init__: future-proof to future versions of file format by throwing an error
* tests: add regression tests, lots of changes
* docs: add man pages

1.2.2:

* genomedata-load: will now support track filenames with "=" in the names
* genomedata-load: now supports UNIX glob wildcards as arguments to -s
* genomedata-load-data: allow other delimiters besides space for
  variableStep and fixedStep, allow wiggle_0 track specification
* genomedata-load-data, genomedata-load: remove unused --chunk-size option
* genomedata-close-data: fix bug where chunk_starts, chunk_ends not
  written for supercontigs with zero present data
* installation: move from path.py to forked-path
* docs: fixed small errors
* various: removed exclamation marks from error messages. It's not *that* exciting.
* some portability improvements
* tests: improve unit test interface

1.2.1:

* Fixed an installation bug where HDF5 installations later in
  LIBRARY_PATH might override those specified first, leading to
  linking errors during build.

1.2.0:
* Added support for adding additional tracks using genomedata-open-data and
  Genome.add_track_continuous().
* Added support for creating Genomedata archives without any tracks.
* Made chromosome.start and chromosome.end be based upon sequence instead
  of supercontigs.
* Made iter(chromosome) and chromosome.itercontinuous() yield supercontigs
  sorted by start index (instead of dictionary order).
* Fixed pointer dereference bug that could cause segfault in
  genomedata-load-data.
* Improved installation script robustness and clarity.

1.1.1:
* Fixed format string warnings on Mac OS X
* Included Gnulib for Mac OS X support
* Updated docs to reflect OS X support

1.1.0:
* Fixed format warning on 32-bit systems
* Fixed Ubuntu format string warnings (switched fprintf to fputs)
* Fixed bug that caused segmentation fault when accessing
  tracknames_continuous before data when Genome was not used as a
  context manager.
* Created a uniform interface for loading Genomedata archives, whether they
  are a directory or a single file (untested). This includes calling improving
  the handling of non-context-manager Genome objects by requiring a call
  to Genome.close() when finished.
* Added an option to genomedata-load-seq and genomedata-load
  to specify the Genomedata archive implementation (directory/file).
  Default is directory if number of sequences is at least 100.
* Added support for replacing data in Genomedata tracks.
* General documentation improvements

1.0.1:
* Fixed OSX bug that caused installer to crash on sys.stdin.flush
* Clarified write-once behavior in documentation
* Added textinput to installation requirements

1.0.0:
* added test module with basic unit tests
* improved documentation, examples
* added verbose flags
* compiled default types in __init__.py
* added _load_data.py wrapper for genomedata_load_data.c

0.1.6:

* extend documentation, including examples
* extended API with: chromosome[start:end], chromosome.seq[start:end],
  and chromosome.supercontigs[start:end]
* added reasonable repr and str return values for Genome, Chromosome,
  and Supercontig

0.1.5:

* add documentation
* change ".h5" suffix to ".genomedata"

0.1.4:

* strip out seq_counts, seq_total_counts, etc. from metadata (big
  speed increase for save-metadata)

0.1.3:

* add genomedata-report
* export genomedata-load-seq script
* _load_data now supports BED, bedGraph input
* added slice support to genomedata.Chromosome
* added genomedata.Supercontig.project()
* Genome.__iter__() now iterates only through files ending in .h5
* add Genome.sums, Genomes.sums_squares, Genome.num_datapoints
* fix bug where use of context manager doesn't actually result in closing all open files
* fix bug in save metadata that causes some regions with data to be ignored
