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aarondjohnson avatar hazboun6 avatar

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la_forge's Issues

Feature request: concatenate chains from multiple directories into single Core

Pat Meyers requested that we add a feature to the Core objects to easily combine multiple independent chains into a single Core object.

This could work by allowing the user to input a list of chain directories into Core at which point they would have the burn-in segments on each chain removed and the chains concatenated.

This could also be extended to HypermodelCores (I think SlicesCore already does this for its use cases).

Use key word dictionaries for plots

I would like to follow the design concept of corner more and use **kwargs calls in the various plotting functions wherever possible to allow users to tweak plots as they see fit. One example of this is in in diagnostics.plot_chains where there are options for a hist_kwargs and plot_kwargs dictionary.

plot_chains plots acceptance chains and it probably shouldn't

When you call diagnostics.plot_chains for a core, it outputs histograms of the acceptance, which don't really make sense.

Most people probably want the histograms or traces for model parameters and the posterior, and maybe the likelihood too. We should skip the acceptance parameters when making the histograms.

Problem saving HyperModelCores

There is an issue saving HyperModel cores to hdf5. The param_dict needs to special treatment since the entries of the dictionary are lists of strings.

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-23-07c838164516> in <module>
      1 pnm = 'tester'
----> 2 cH.save(f'./sw_noise_cores/{pnm}.h5')

~/software_development/la_forge/la_forge/core.py in save(self, filepath)
    444                 if getattr(self, d) is not None:
    445                     print(d)
--> 446                     self._dict2hdf5(hf, getattr(self, d), d)
    447 
    448     def _dict2hdf5(self, hdf5, d, name):

~/software_development/la_forge/la_forge/core.py in _dict2hdf5(self, hdf5, d, name)
    464         g = hdf5.create_group(name)
    465         for ky, val in d.items():
--> 466             g.create_dataset(ky, data=val)
    467 
    468     def _hdf5_2dict(self, hdf5, name, dtype=float, set_return='set'):

~/anaconda3/envs/enterprise_dev/lib/python3.6/site-packages/h5py/_hl/group.py in create_dataset(self, name, shape, dtype, data, **kwds)
    134 
    135         with phil:
--> 136             dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
    137             dset = dataset.Dataset(dsid)
    138             if name is not None:

~/anaconda3/envs/enterprise_dev/lib/python3.6/site-packages/h5py/_hl/dataset.py in make_new_dset(parent, shape, dtype, data, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue, scaleoffset, track_times, external, track_order, dcpl)
    116         else:
    117             dtype = numpy.dtype(dtype)
--> 118         tid = h5t.py_create(dtype, logical=1)
    119 
    120     # Legacy

h5py/h5t.pyx in h5py.h5t.py_create()

h5py/h5t.pyx in h5py.h5t.py_create()

h5py/h5t.pyx in h5py.h5t.py_create()

TypeError: No conversion path for dtype: dtype('<U35')

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