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dynwrap v1.0.0

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@zouter zouter released this 29 Mar 06:11
· 315 commits to master since this release
v1.0.0
bf9662c

dynwrap 1.0.0 (28-03-2019)

  • MAJOR CHANGE: Add support for Singularity 3.0, drop support for previous
    releases of Singularity and singularity-hub.

  • MAJOR CHANGE: dynwrap now always works with sparse count and expression matrices

  • FEATURE: Add create_ti_method_definition() to create a definition from a local script.

  • DOCUMENTATION: Major update of all documentation for dynbenchmark publication

  • MINOR CHANGE: Rename compute_tented_geodesic_distances() to calculate_geodesic_distances()

  • MINOR CHANGE: Harmonisation of function arguments to either dataset or trajectory

dynwrap 0.3.1.2 (01-02-2019)

  • BUG FIX: simplify_replace_edges() would sometimes swap edges in milestone network around, but forget
    invert percentages.

  • BUG FIX: Close sinks when interupting the R process

  • MINOR CHANGE: Work with new babelwhale, which includes support for singularity 3.0

dynwrap 0.3.1.1 (17-12-2018)

  • CLEAN UP: Removed helper functions that are not required any more:
    get_env_or_null(), read_rds_or_null() and print_processx().

  • MINOR CHANGE: remove requirement that milestone_ids and cell_ids cannot overlap

dynwrap 0.3.1 (19-11-2018)

  • HOTFIX: Use utils::data() to get access to priors.

dynwrap 0.3.0 (19-11-2018)

  • MINOR CHANGE: Added metadata on the different wrapper types implemented in dynwrap.

  • CLEAN UP: Removed plot_fun argument from create_ti_method().

  • MINOR CHANGE: Replaced mc_cores with more flexible map_fun.

  • MINOR CHANGE: Renamed create_ti_method() to create_ti_method_r(),
    and create_ti_method_with_container() to create_ti_method_container().

  • CLEAN UP: Drastically reworked create_ti_method_r() and create_ti_method_container(),
    and the underlying functions for executing a method on a dataset.

  • CLEAN UP: Remove parse_parameter_definition() and thereby dependency on ParamHelpers.

dynwrap 0.2.0 (29-10-2018)

  • BUG FIX: Fixed incorrect calculation of milestone percentage during trajectory simplification.
    Occurs only in a rare edge case, namely when the order of the milestones in the milestone network
    is very different from the order of the milestone ids (0475e94).

  • BUG FIX: Fixed suggested dependencies not being installed in the dynwrap containers (#100).

  • FEATURE REMOVAL: Removed feather data format because it's not being used and creates dependency issues every now and again.

  • BUG FIX: devtools:::shim_system.file() has been moved to pkgload:::shim_system.file().

  • TESTING: Solved issue with the unit tests by not using any helpers.

  • MINOR CHANGE: Have docker images build from dynwrap@devel.

  • BUG FIX: Remove option(echo = FALSE) from .Rprofile in recipes because some packages directly rely
    on standard output from R, so printing the command wreaks havoc.

dynwrap 0.1.0 (07-03-2018)

  • INITIAL RELEASE: dynwrap, functionality for containerised trajectory inference.
  • Wrap the input data of a trajectory inference method, such as expression and prior information
  • Run a trajectory inference method in R, in a docker container or a singularity container
  • Wrap the output of a trajectory inference method, such as the pseudotime, a clustering or a branch network, and convert it into a common trajectory model
  • Further postprocess the trajectory model, such as labelling the milestones and rooting the trajectory
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