Starfish-develop / Starfish-develop/Starfish
Issues running the example WASP14: pca problem
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 78
- Forks
- 23
- PR merge metrics
- No merged PRs in 30d
Description
Hi! I installed Starfish in my laptop computer (Ubuntu 16.04). I followed the instructions and had no issues until trying to follow the example for WASP14.
The error appear when trying to run:
$ pca.py --create
$ File "pca.py", line 33, in
$ myHDF5 = HDF5Interface()
$ File "/home/angelica/Documentos/Starfish-master/Starfish/grid_tools.py", line 835, in init
$ self.grid_points = hdf5["pars"][:]
$ File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2840)
$ File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2798)
$ File "/home/angelica/.local/lib/python3.5/site-packages/h5py/_hl/group.py", line 169, in getitem
$ oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
$ File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2840)
$ File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2798)
$ File "h5py/h5o.pyx", line 190, in h5py.h5o.open (/tmp/pip-huypgcah-build/h5py/h5o.c:3734)
$ KeyError: "Unable to open object (Object 'pars' doesn't exist)"
Apparently the parameter 'pars' is not defined. I looked in the code 'grid_tools.py' and everything seems to be in order. I have not modified anything in the 'grid_tools.py' code.
I do not know what's wrong, I'd appreciate checking my problem.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running pca.py --create for the WASP14 example and trace the HDF5Interface initialization in Starfish/grid_tools.py, especially the access to hdf5["pars"]. Inspect the generated HDF5 contents and determine why the pars object is absent; done means the example runs without the reported KeyError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100