All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.
- Added flags
-fand--freqsto manually set base frequences. As a consequence, the flags-oand--out-formathave to be used when specifying the output format.
- Ability to write used trees to a file with the
--trees-fileflag. - Simple test data for various substitution models.
- Command-line flags
-oand--output-formatreplaced with-fand--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.
- Support for Python versions prior to 3.3.
- Two test files.
- Several tests in
test_predsim.py. - A directory,
test_files/, for files used by the test suite.
- 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.
- The command-line flags
-oand--output-formatnow allow writing output to either Phylip or Nexus format.
- 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.
- Small refactoring of the function for reading the p-file.
- Fixed codecov installation in Travis-CI configuration file.
- 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).
- Minor updates to the documentation in
README.rst.
- The command-line option
--seeds-filefor passing seed numbers to Seq-Gen. This option allows the user to exactly repeat simulations. - The command-line option
--commands-filefor outputting Seq-Gen commands to a file (replaces the-coption).
- The pandas library is no longer required.
- The principles of Semantic Versioning will be followed for new releases.
- The command-line
-coption for writing Seq-Gen commands to a file (replaced by the--commands-fileoption).
- Updates to the documentation in
README.rst.
Initial release.