Trying to run gpseudotime with Julia v0.5.2

[finmod]

gpseudotime is the only instance of running GPLVM in Julia: bgplvm.jl.
Trying to run the gpseudotime.ipynb in the current version of Julia (0.5.2), I find that {} should be replaced by [] in bgplvm.jl.
The creation and update of data files in h5 gives me the following errors:

Write synthetic to HDF5

h5write(trace_file, "synthetic/X", X)
h5write(trace_file, "synthetic/n", n)
h5write(trace_file, "synthetic/lambda", lambda)
h5write(trace_file, "synthetic/sigma", sigma)
h5write(trace_file, "synthetic/t_gt", t_gt)

Error creating dataset //synthetic/X

in h5d_create(::Int32, ::String, ::Int32, ::Int32, ::Int32, ::Int32, ::Int32) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:2089
in d_create(::HDF5.HDF5File, ::String, ::HDF5.HDF5Datatype, ::HDF5.HDF5Dataspace, ::HDF5.HDF5Properties, ::HDF5.HDF5Properties, ::HDF5.HDF5Properties) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:809
in _d_create(::HDF5.HDF5File, ::String, ::Array{Float64,2}) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:1539
in _d_write(::HDF5.HDF5File, ::String, ::Array{Float64,2}) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:1560
in h5write(::String, ::String, ::Array{Float64,2}) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:613

Also synth_analysis.jl does not appear to be in the repository.

A re-run of this demo with updated packages would be appreciated.

[kieranrcampbell]

gpseudotime is the only instance of running GPLVM in Julia: bgplvm.jl.
Trying to run the gpseudotime.ipynb in the current version of Julia (0.5.2), I find that {} should be replaced by [] in bgplvm.jl.

The Julia version on my machine is 0.3.11 so it should work with this, I'm not sure what changes have been made to the core language since then

Error creating dataset //synthetic/X

That is a little odd - can you write hdf5 files successfully otherwise?

Also synth_analysis.jl does not appear to be in the repository.

I think this was an old example. The files such as "gpseudotime_all.ipynb" will create the MCMC traces if the hdf5 file write works correctly

Note that this repository just implements Metropolis-Hastings sampling for GPLVM in Julia, rather than a particular GPLVM package for Julia.

Kieran