Serialization and representation GP + Small fixes #64

stevetorr · 2019-09-22T23:38:12Z

Introduces a serialization method for GPs (to_ and from_dict methods) and a representation (str) method. Introduced a new string-to-kernel method in kernels.py to facilitate the from_dict method. The serialization is unit tested. Fixed a few style errors in other parts of the code. A method in gp.py sets a 'self.like' attribute and others set self.likelihood. This is also now corrected towards self.likelihood.

This reverts commit f4242da.

This reverts commit 1f626ea.

…om Dicts" This reverts commit 956e3a3.

This reverts commit 5116cbc.

This reverts commit d990bcc.

…cts"" This reverts commit 781a074.

stevetorr · 2019-09-22T23:38:33Z

Closes #63 , addresses #16

Merging master onto Serialization branch

codecov-io · 2019-09-23T19:34:50Z

Codecov Report

Merging #64 into master will increase coverage by 0.52%.
The diff coverage is 80.17%.

@@            Coverage Diff             @@
##           master      #64      +/-   ##
==========================================
+ Coverage   46.96%   47.49%   +0.52%     
==========================================
  Files          37       37              
  Lines        5636     5740     +104     
==========================================
+ Hits         2647     2726      +79     
- Misses       2989     3014      +25

Impacted Files	Coverage Δ
flare/otf.py	`74.47% <ø> (ø)`	⬆️
flare/gp_from_aimd.py	`88.49% <0%> (-2.25%)`	⬇️
tests/test_util.py	`100% <100%> (ø)`	⬆️
tests/test_gp.py	`100% <100%> (ø)`	⬆️
flare/util.py	`90% <100%> (ø)`	⬆️
flare/mc_simple.py	`12.11% <15.38%> (+0.09%)`	⬆️
flare/kernels.py	`19.17% <61.53%> (+1.16%)`	⬆️
flare/gp.py	`86.36% <88.88%> (+0.36%)`	⬆️

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dmclark17 · 2019-09-24T13:33:30Z

Regarding the string to kernel logic, you may be able to refactor the function to use getattr and getattr. You might be able to get away with not needing to define a dictionary mapping strings to functions.

Unclear if this would be better though 🤷‍♂

dmclark17 · 2019-09-24T13:53:33Z

numpy.ndarrays are not JSON serializable using the default encoder. Is there a canonical way to store them on disk for the project?

(As this is mostly regarding the serialization of environments, this might not be the best place for the discussion)

stevetorr · 2019-09-24T14:48:23Z

numpy.ndarrays are not JSON serializable using the default encoder. Is there a canonical way to store them on disk for the project?

I've been using an encoder that I found online which is included in util.py to handle converting numpy arrays to JSON.

Regarding the string to kernel logic, you may be able to refactor the function to use getattr and getattr. You might be able to get away with not needing to define a dictionary mapping strings to functions.

Thanks for looking closely at the methods! What would the getattr correspond to- getattr called on the file itself (to refer to individual callables within the flare.kernels file)? Also can you clarify what the second getattr was supposed to be?

dmclark17 · 2019-09-24T15:11:11Z

I see, I didn't see the NumpyEncoder 👍

Whoops that was suppose to be getattr and hasattr. You can call them on the module itself by doing something like:

current_module = sys.modules[__name__]  # Gets the current module
if hasattr(current_module, "two_body"):
    func = getattr(current_module, "two_body")

…com/mir-group/flare into Serialization_and_representation_GP

jonpvandermause

Looks good. Also used this as an opportunity to address some of the linting issues that have been hanging around gp for awhile.

jonpvandermause · 2019-09-26T14:09:25Z

flare/gp.py

-        # self_kern = self.kernel(x_t, x_t, self.bodies, d, d, self.hyps,
-        #                         self.cutoffs)
-        # pred_var = self_kern - np.matmul(v_vec, v_vec)
-


Nice, these lines needed to go.

jonpvandermause · 2019-09-26T14:09:59Z

flare/gp.py

-        self.like = like
-        self.like_grad = like_grad
+        self.likelihood = like
+        self.likelihood_gradient = like_grad


Good catch, not sure why there were multiple versions of the likelihood.

jonpvandermause · 2019-09-26T14:10:57Z

flare/gp.py

+            for hyp, label in zip(self.hyps, self.hyp_labels):
+                thestr += "{}: {}\n".format(label, hyp)
+
+        return thestr


stevetorr · 2019-09-26T14:42:55Z

Thanks for taking the time to look through and provide feedback!

stevetorr added 13 commits September 22, 2019 18:47

Added unit-tested string and dictionary methods for GPs

5116cbc

Addded string-to-kernel helper functions to facilitate GPs from Dicts

956e3a3

Unit Tests for GP serialization / representation

1f626ea

Improved PEP8 compliance

f4242da

Revert "Improved PEP8 compliance"

a102a74

This reverts commit f4242da.

Revert "Unit Tests for GP serialization / representation"

1e6fb32

This reverts commit 1f626ea.

Revert "Addded string-to-kernel helper functions to facilitate GPs fr…

781a074

…om Dicts" This reverts commit 956e3a3.

Revert "Added unit-tested string and dictionary methods for GPs"

d990bcc

This reverts commit 5116cbc.

Re-Added unit-tested string and dictionary methods for GPs""

344c801

This reverts commit d990bcc.

Re-Addded string-to-kernel helper functions to facilitate GPs from Di…

39a0314

…cts"" This reverts commit 781a074.

Re-add Unit Tests for GP serialization / representation

ee98fc3

"Improved PEP8 compliance

253b8a7

Fixed like attribuet being used in different places

3cc2355

stevetorr requested a review from jonpvandermause September 23, 2019 16:23

stevetorr changed the base branch from development to master September 23, 2019 16:25

Merge pull request #65 from mir-group/master

17cadc5

Merging master onto Serialization branch

dmclark17 mentioned this pull request Sep 23, 2019

Kernel Benchmarks #62

Closed

2 tasks

stevetorr and others added 3 commits September 24, 2019 17:02

Added multicomponent kernels

9a4cc93

Merge branch 'Serialization_and_representation_GP' of https://github.…

790deb6

…com/mir-group/flare into Serialization_and_representation_GP

some linting

f324957

jonpvandermause approved these changes Sep 26, 2019

View reviewed changes

jonpvandermause merged commit 2246c60 into master Sep 26, 2019

jonpvandermause deleted the Serialization_and_representation_GP branch September 26, 2019 14:33

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Serialization and representation GP + Small fixes #64

Serialization and representation GP + Small fixes #64

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stevetorr commented Sep 26, 2019

Serialization and representation GP + Small fixes #64

Serialization and representation GP + Small fixes #64

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