Predsim

-------------------

Added
~~~~~

* Ability to write used trees to a file with the ``--trees-file`` option.
* Simple test data for various substitution models.


Changed
~~~~~~~

* Command-line option ``-o`` and ``--output-format`` replaced with ``-f`` and
``--format``, respectively.
* The file with seed numbers may now contain more numbers than being used.
* Content is written to output after completing each simulation (instead
of writing everything to output at the end).
* NEXUS output is written with separate taxa blocks.
* Missing state frequences result in equal frequences instead of raising an error.


Removed
~~~~~~~

* Support for Python versions prior to 3.3.
* Two test files.

`View commits <https://github.com/jmenglund/predsim/compare/v0.5.0...v0.6.0>`_

-------------------

Added
~~~~~

* Several tests in ``test_predsim.py``.
* A directory, ``test_files/``, for files used by the test suite.


Changed
~~~~~~~

* By default, simulated data is written to standard output (stdout)
and it is no longer possible to name an output file (but output
can still be redirected to a file!).
* Records are processed iteratively, and output written after the
processing of an individual record has been finished.
* Opening and closing input files when using the command-line interface.
* Documentation in ``README.rst``.

`View commits <https://github.com/jmenglund/predsim/compare/v0.4.0...v0.5.0>`_

-------------------

Added
~~~~~

* The command-line options ``-o`` and ``--output-format`` now allow
writing output to either the PHYLIP or the NEXUS format.


Changed
~~~~~~~

* The path to the t-file is now correct when using the command-line interface.
* If using number of gamma rate categories, gamma shape is now also required.

`View commits <https://github.com/jmenglund/predsim/compare/v0.3.1...v0.4.0>`_

-------------------

Changed
~~~~~~~

* Small refactoring of the function for reading the p-file.
* Fixed codecov installation in Travis-CI configuration file.

`View commits <https://github.com/jmenglund/predsim/compare/v0.3.0...v0.3.1>`_

-------------------

Changed
~~~~~~~

* Output data is now written in simple Nexus format, i.e. without a separate
taxa block.
* Some refactoring in order to make predsim easier to use as a library (i.e.
without its command-line interface).

`View commits <https://github.com/jmenglund/predsim/compare/v0.2.1...v0.3.0>`_

-------------------

Changed
~~~~~~~

* Minor updates to the documentation in ``README.rst``.

`View commits <https://github.com/jmenglund/predsim/compare/v0.2.0...v0.2.1>`_