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PV-Lab / bayesim

Bayes for anything!
https://pv-lab.github.io/bayesim/_build/html/index.html
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NoSuchNodeError: group ``/`` does not have a child named ``//data`` #1

Closed kdn82 closed 5 years ago

kdn82 commented 5 years ago

I am getting an error in ideal_diode when saving in "dd.io.save('obs_data.h5',data)", see error below. When using the obs_data.h5 file supplied with example, the same error is generated further by "m.run()". So I cannot run an ideal_diode example. I am running Python 3 in Jupiter installed with Anaconda3 on Windows 7 enterprise. Error: NoSuchNodeError Traceback (most recent call last) C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\pytables.py in get_node(self, key) 1159 key = '/' + key -> 1160 return self._handle.get_node(self.root, key) 1161 except _table_mod.exceptions.NoSuchNodeError:

C:\ProgramData\Anaconda3\lib\site-packages\tables\file.py in get_node(self, where, name, classname) 1643 nodepath = join_path(basepath, name or '') or '/' -> 1644 node = where._v_file._get_node(nodepath) 1645 elif isinstance(where, (six.stringtypes, numpy.str)):

C:\ProgramData\Anaconda3\lib\site-packages\tables\file.py in _get_node(self, nodepath) 1598 -> 1599 node = self._node_manager.get_node(nodepath) 1600 assert node is not None, "unable to instantiate node %s" % nodepath

C:\ProgramData\Anaconda3\lib\site-packages\tables\file.py in get_node(self, key) 436 if self.node_factory: --> 437 node = self.node_factory(key) 438 self.cache_node(node, key)

C:\ProgramData\Anaconda3\lib\site-packages\tables\group.py in _g_load_child(self, childname) 1180 # Is the node a group or a leaf? -> 1181 node_type = self._g_check_has_child(childname) 1182

C:\ProgramData\Anaconda3\lib\site-packages\tables\group.py in _g_check_has_child(self, name) 397 "group %s does not have a child named %s" --> 398 % (self._v_pathname, name)) 399 return node_type

NoSuchNodeError: group / does not have a child named //data

During handling of the above exception, another exception occurred:

AttributeError Traceback (most recent call last)

in 33 # save them to HDF5 34 data = pd.DataFrame.from_records(data=data,columns=['V','T','J','uncertainty']) ---> 35 dd.io.save('obs_data.h5',data) 36 37 # these next few lines are for generating the plot C:\ProgramData\Anaconda3\lib\site-packages\deepdish\io\hdf5io.py in save(path, data, compression) 594 else: 595 _save_level(h5file, group, data, name='data', --> 596 filters=filters, idtable=idtable) 597 # Mark this to automatically unpack when loaded 598 group._v_attrs[DEEPDISH_IO_UNPACK] = True C:\ProgramData\Anaconda3\lib\site-packages\deepdish\io\hdf5io.py in _save_level(handler, group, level, name, filters, idtable) 251 elif _pandas and isinstance(level, (pd.DataFrame, pd.Series, pd.Panel)): 252 store = _HDFStoreWithHandle(handler) --> 253 store.put(group._v_pathname + '/' + name, level) 254 255 elif isinstance(level, (sparse.dok_matrix, C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\pytables.py in put(self, key, value, format, append, **kwargs) 887 format = get_option("io.hdf.default_format") or 'fixed' 888 kwargs = self._validate_format(format, kwargs) --> 889 self._write_to_group(key, value, append=append, **kwargs) 890 891 def remove(self, key, where=None, start=None, stop=None): C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\pytables.py in _write_to_group(self, key, value, format, index, append, complib, encoding, **kwargs) 1365 def _write_to_group(self, key, value, format, index=True, append=False, 1366 complib=None, encoding=None, **kwargs): -> 1367 group = self.get_node(key) 1368 1369 # remove the node if we are not appending C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\pytables.py in get_node(self, key) 1159 key = '/' + key 1160 return self._handle.get_node(self.root, key) -> 1161 except _table_mod.exceptions.NoSuchNodeError: 1162 return None 1163 AttributeError: 'NoneType' object has no attribute 'exceptions'
kdn82 commented 5 years ago

Update: the same error appears when runing ideal_diode in cloud binder from page https://pv-lab.github.io/bayesim/_build/html/examples.html

rkurchin commented 5 years ago

All fixed! The Binder works now too.

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 4:25 PM Rachel Kurchin rkurchin@mit.edu wrote:

Okay, the version that you get with pip install should work properly now but in the process I've broken the Binder. Still working on fixing that again...but in the meantime you should certainly be able to clone the repository and run it locally in Jupyter.

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:58 AM Rachel Kurchin rkurchin@mit.edu wrote:

Okay, it's actually a Pandas thing. I have a fix, I just need to figure out the cleanest way to release it into the code. Hopefully will be resolved by the end of today!

Thanks again for pointing this out!

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:44 AM Rachel Kurchin rkurchin@mit.edu wrote:

Hi Dmitry,

I'm starting to look at this – my best guess is it has to do with the latest update to the pytables package. Will update you as I figure out more.

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Wed, May 15, 2019 at 12:37 PM Dmitry Krasikov < notifications@github.com> wrote:

Update: the same error appears when runing ideal_diode in cloud binder from page https://pv-lab.github.io/bayesim/_build/html/examples.html

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PV-Lab/bayesim/issues/1?email_source=notifications&email_token=ACVWT4JNNQWEVZ7MAEZIES3PVQ35BA5CNFSM4HNE34EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVPHNHY#issuecomment-492730015, or mute the thread https://github.com/notifications/unsubscribe-auth/ACVWT4PHJAAWN3ZVQXTRVTTPVQ35BANCNFSM4HNE34EA .

rkurchin commented 5 years ago

Okay, it's actually a Pandas thing. I have a fix, I just need to figure out the cleanest way to release it into the code. Hopefully will be resolved by the end of today!

Thanks again for pointing this out!

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:44 AM Rachel Kurchin rkurchin@mit.edu wrote:

Hi Dmitry,

I'm starting to look at this – my best guess is it has to do with the latest update to the pytables package. Will update you as I figure out more.

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Wed, May 15, 2019 at 12:37 PM Dmitry Krasikov notifications@github.com wrote:

Update: the same error appears when runing ideal_diode in cloud binder from page https://pv-lab.github.io/bayesim/_build/html/examples.html

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PV-Lab/bayesim/issues/1?email_source=notifications&email_token=ACVWT4JNNQWEVZ7MAEZIES3PVQ35BA5CNFSM4HNE34EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVPHNHY#issuecomment-492730015, or mute the thread https://github.com/notifications/unsubscribe-auth/ACVWT4PHJAAWN3ZVQXTRVTTPVQ35BANCNFSM4HNE34EA .

rkurchin commented 5 years ago

Hi Dmitry,

I'm starting to look at this – my best guess is it has to do with the latest update to the pytables package. Will update you as I figure out more.

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Wed, May 15, 2019 at 12:37 PM Dmitry Krasikov notifications@github.com wrote:

Update: the same error appears when runing ideal_diode in cloud binder from page https://pv-lab.github.io/bayesim/_build/html/examples.html

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PV-Lab/bayesim/issues/1?email_source=notifications&email_token=ACVWT4JNNQWEVZ7MAEZIES3PVQ35BA5CNFSM4HNE34EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVPHNHY#issuecomment-492730015, or mute the thread https://github.com/notifications/unsubscribe-auth/ACVWT4PHJAAWN3ZVQXTRVTTPVQ35BANCNFSM4HNE34EA .

rkurchin commented 5 years ago

Okay, the version that you get with pip install should work properly now but in the process I've broken the Binder. Still working on fixing that again...but in the meantime you should certainly be able to clone the repository and run it locally in Jupyter.

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:58 AM Rachel Kurchin rkurchin@mit.edu wrote:

Okay, it's actually a Pandas thing. I have a fix, I just need to figure out the cleanest way to release it into the code. Hopefully will be resolved by the end of today!

Thanks again for pointing this out!

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:44 AM Rachel Kurchin rkurchin@mit.edu wrote:

Hi Dmitry,

I'm starting to look at this – my best guess is it has to do with the latest update to the pytables package. Will update you as I figure out more.

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Wed, May 15, 2019 at 12:37 PM Dmitry Krasikov < notifications@github.com> wrote:

Update: the same error appears when runing ideal_diode in cloud binder from page https://pv-lab.github.io/bayesim/_build/html/examples.html

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PV-Lab/bayesim/issues/1?email_source=notifications&email_token=ACVWT4JNNQWEVZ7MAEZIES3PVQ35BA5CNFSM4HNE34EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVPHNHY#issuecomment-492730015, or mute the thread https://github.com/notifications/unsubscribe-auth/ACVWT4PHJAAWN3ZVQXTRVTTPVQ35BANCNFSM4HNE34EA .

kdn82 commented 5 years ago

Rachel, thanks, I'll try it out and let you know if there will be any further issues.

Thanks again, Dmitry

On Fri, May 31, 2019 at 3:41 AM Rachel Kurchin notifications@github.com wrote:

All fixed! The Binder works now too.

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 4:25 PM Rachel Kurchin rkurchin@mit.edu wrote:

Okay, the version that you get with pip install should work properly now but in the process I've broken the Binder. Still working on fixing that again...but in the meantime you should certainly be able to clone the repository and run it locally in Jupyter.

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:58 AM Rachel Kurchin rkurchin@mit.edu wrote:

Okay, it's actually a Pandas thing. I have a fix, I just need to figure out the cleanest way to release it into the code. Hopefully will be resolved by the end of today!

Thanks again for pointing this out!

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Thu, May 30, 2019 at 10:44 AM Rachel Kurchin rkurchin@mit.edu wrote:

Hi Dmitry,

I'm starting to look at this – my best guess is it has to do with the latest update to the pytables package. Will update you as I figure out more.

Rachel

Rachel C. Kurchin PhD Candidate, Materials Science & Engineering MIT Photovoltaics Research Laboratory http://pv.mit.edu/ rkurchin.github.io

On Wed, May 15, 2019 at 12:37 PM Dmitry Krasikov < notifications@github.com> wrote:

Update: the same error appears when runing ideal_diode in cloud binder from page https://pv-lab.github.io/bayesim/_build/html/examples.html

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/PV-Lab/bayesim/issues/1?email_source=notifications&email_token=ACVWT4JNNQWEVZ7MAEZIES3PVQ35BA5CNFSM4HNE34EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVPHNHY#issuecomment-492730015 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ACVWT4PHJAAWN3ZVQXTRVTTPVQ35BANCNFSM4HNE34EA

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PV-Lab/bayesim/issues/1?email_source=notifications&email_token=AF2JIMCSVSUGXDKV72SHAY3PYDJBVA5CNFSM4HNE34EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWUOZ7I#issuecomment-497609981, or mute the thread https://github.com/notifications/unsubscribe-auth/AF2JIMEUXY74XKRHTDG2QMLPYDJBVANCNFSM4HNE34EA .