=================
 Release changes
=================

Sunflower 1.1.0
===============
* added tabdelim driver contributed by Alison Meynert
* docs updates
* more descriptive error messages in some places rather than assertions

Sunflower 1.0.1
===============
* prereq: setuptools 0.6c9 is now required
* pwm2sfl: add default of --output to --help text
* sunflower: fix seqrecords2_dict bug
* docs updates

Sunflower 1.0.0
===============
* first release

Sunflower 0.2.0a5
=================
* docs
  * new FAQ in doc/FAQ.rst: please check this first

* pwm2sfl
  * new option ``--coop``, ``--coop-distance``, ``coop-strength`` for
    cooperativity state (thanks to Alison Meynert)
  * new option ``--gc`` for G+C content (thanks to Alison Meynert)

* sunflower
  * accumulator change: sum_sqdiff_unbound to sum_sqrtabsdiff_unbound
    all ``--mutate`` results will be totally different now
  * fix ``--driver-help`` when ``--driver=hdf5``
  * add --range support --mutate (significant speedup)
  * strip out leading whitespace on defline identifiers

* sunsplit
  * new program to support now-defunct multi-accumulator branch

Sunflower 0.2.0a4
=================
* hmm
  * asserts that appropriate probabilities add to 0 or 1 before saving

* pwm2sfl
  * fixed bug in cooperativity states

* sunflower
  * now things like TBP.f0 and TBP.r0 are added into one column called "TBP"
    * new option ``--separate-directions`` turns this off
  * attribute ``reference`` now called ``seq``
  * new option ``--range`` to not avoid calculating and saving flanking
    nucleotides
  * new option ``--no-sequence`` won't include reference sequence in output
    array
  * new driver architecture for storing to different output formats
    * new options ``--driver``, ``--driver-help``
  * new driver ``sql`` with run-length encoding
  * new attribute ``run_info`` in individual tables
  * automatically get starts from Ensembl-style genomic sequence file

* sunreport
  * ``--average`` now called ``--aggregate``
  * new options ``--hist-bins``, ``--hist-max``

* data
  * remove jaspar/core/human (use ``--resource human`` now instead, which
    contains all vertebrate TFs and human base composition)

Sunflower 0.2.0a3
=================
* setup
  * Quick Start is that much quicker now!

* pwm2sfl
  * add cooperativity states based on code by Alison Meynert
  * add selection based on sysgroup

* sunflower
  * ``--resource`` now supports a species lookup table
    * jaspar/core/human is now deprecated
  * ``--position`` now called ``--start``
  * add ``--total``, ``--no-total``
  * takes directive on start from defline. You can add something like
    ``[sunflower start=-1000]`` to the end of a defline instead of using
    ``--start=-1000``
  * skips sequences with illegal (non-ACGT) characters instead of exiting
  * short option for ``--states`` is now ``-S``, not ``-s`` which is
    for ``--start``
  * no longer warns on sequences with non-[A-Za-z0-9_] characters in
    defline
  * significant startup time speedup for large arrays

* sunreport
  * new ``--range`` option averages over a range of positions
  * produce d_T output

* data
  * add vertebrate, insect, plant models
  * info for aedes, anopheles, chicken, chimp, dog, fruitfly, human,
    fugu, medaka, mouse, rat, rhesus, zebrafish (please ask for your
    favorite species)

* h5attr
  * new program

* h5cat
  * new program

* test data
  * add directives to BRCA deflines

Sunflower 0.2.0a2
=================
* sunflower
  * improve output so can be read by non-Python HDF5 programs
  * add an attribute to contain a default position for a sequence

* sunreport
  * 5x speed improvement
  * can produce sequential reports over a range of sequences instead
    of just average reports
  * now eliminates extraneous columns from output
  * default offset of -1000 has been removed

* test data
  * move ``brca2_tss.fna`` -> ``brca_tss.fna``
  * add BRCA1 to ``brca_tss.fna``

* setup improvements

* README updates

Sunflower 0.2.0a1
=================
* sunflower
  * produces HDF5 output even against reference sequence

* pwm2sfl
  * previously called jaspar2sfl

* data
  * include JASPAR CORE human 2006

* setup
  * now requires fewer prerequisites installed in advance

* many other changes

Sunflower 0.1.0
===============
first release
