Remove check_pickle argument in delayed. - #903
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Hi @jjerphan, why was this closed? We should probably merge this before releasing |
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Hi @pierreglaser ; I just made some housekeeping on my stalled PRs, I reopen it now. |
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@jjerphan If you find some time, feel free to finish this up :) we should release |
`check_pickle` should have been removed in 0.13.0 as indicated in the `DeprecationWarning`. This commit removes this argument, behavior, and the associated test.
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Codecov Report
@@ Coverage Diff @@
## master #903 +/- ##
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+ Coverage 93.93% 94.56% +0.62%
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Files 47 47
Lines 6956 6933 -23
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+ Hits 6534 6556 +22
+ Misses 422 377 -45
Continue to review full report at Codecov.
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Hi @pierreglaser. I haven't managed to find a reason for the "failure" of the codecov pipeline. |
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Don't worry about the |
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@ogrisel if you want to take a look :) that would be nice to have this merged for 0.16. |
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OK, thank you @pierreglaser for this piece of feedback. |
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Small up. |
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@tomMoral: thanks for the follow up! 🙂 CI checks on Azure are still failing but it is unrelated to those changes. |
It looks all green to me. |
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Thanks! |
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Thanks! |
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Hi there, I am currently trying to run pomgranate to fit a hidden markov model to some data. This library uses joblib to parallelize the model training. However, when I try to train it I get the following error: Empty Traceback (most recent call last)
~/.conda/envs/mypython/lib/python3.6/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
819 try:
--> 820 tasks = self._ready_batches.get(block=False)
821 except queue.Empty:
~/.conda/envs/mypython/lib/python3.6/queue.py in get(self, block, timeout)
160 if not self._qsize():
--> 161 raise Empty
162 elif timeout is None:
Empty:
During handling of the above exception, another exception occurred:
TypeError Traceback (most recent call last)
<ipython-input-7-dcc6125ae320> in <module>
----> 1 df = hmm(df, 3)
~/.conda/envs/mypython/lib/python3.6/site-packages/hmm_bigwigs/bigwig_hmm.py in hmm(df, num_states)
40 vals = df["value"].values
41 model = HiddenMarkovModel.from_samples(
---> 42 NormalDistribution, X=[vals], n_components=num_states
43 )
44 states = model.predict(vals)
~/.conda/envs/mypython/lib/python3.6/site-packages/pomegranate/hmm.pyx in pomegranate.hmm.HiddenMarkovModel.from_samples()
~/.conda/envs/mypython/lib/python3.6/site-packages/pomegranate/kmeans.pyx in pomegranate.kmeans.Kmeans.fit()
~/.conda/envs/mypython/lib/python3.6/site-packages/pomegranate/kmeans.pyx in genexpr()
~/.conda/envs/mypython/lib/python3.6/site-packages/joblib/parallel.py in __call__(self, iterable)
1039 # remaining jobs.
1040 self._iterating = False
-> 1041 if self.dispatch_one_batch(iterator):
1042 self._iterating = self._original_iterator is not None
1043
~/.conda/envs/mypython/lib/python3.6/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
829 big_batch_size = batch_size * n_jobs
830
--> 831 islice = list(itertools.islice(iterator, big_batch_size))
832 if len(islice) == 0:
833 return False
~/.conda/envs/mypython/lib/python3.6/site-packages/pomegranate/kmeans.pyx in genexpr()
TypeError: delayed() got an unexpected keyword argument 'check_pickle'I checked the input file and every variable I feed the model and all is fine there. I tried to find out where the Thanks |
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@dmalzl: the pip install - U pomegranate |
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Ah okay. Since I just installed it today, I thought I already had the newest version. Seems the conda recipe is outdated then. That's what you get from blind trust. Anyway, works now after updating. |
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You're welcome. |
Context:
check_pickleshould have been removed in 0.13.0 as indicated in theDeprecationWarning.Changes: This PR removes this argument, behavior, and the associated test.
Associated Issue: #900