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v4 refactor for GP module #5055

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merged 36 commits into from
Nov 21, 2021
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984a1d0
np.int -> int, fix np DepricationWarning
bwengals Oct 5, 2021
bd916ae
remove shape arg from non-kron implementations, TODO for is_observed …
bwengals Oct 6, 2021
490311f
np.int -> int in gp/util.py
bwengals Oct 6, 2021
a64975d
force all mean_func, cov_func args to GP constructors to be required …
bwengals Oct 7, 2021
77c4392
fix predictt functions, rename to _predict_at. because theano -> aesara
bwengals Oct 20, 2021
d1e09fe
fix TP tests, force mean_func, cov_func to be req kwarg
bwengals Oct 27, 2021
31150c3
fix TP reparameterization to sample studentt instead of chi2/norm
bwengals Oct 27, 2021
03c2a13
change naming shape->size where appropriate
bwengals Oct 27, 2021
4bcb448
add deprecation warning for is_observed
bwengals Oct 28, 2021
167cb4e
add jitter arg for covs headed for cholesky decomps, previously fixed…
bwengals Oct 28, 2021
e18b8c4
clean up trivial aesara.function usage to .eval() instead
bwengals Oct 28, 2021
212fb1e
fix gp.util.replace_with_values to handle case with no symbolic value…
bwengals Oct 28, 2021
ad4a1ca
jitter=0 for conditonals/predicts, fix replace_with_values calls
bwengals Oct 28, 2021
a4a4f99
fix more tests
bwengals Oct 28, 2021
9b26ca1
black stuff
bwengals Oct 28, 2021
6072565
Merge branch 'main' into gpv4update
bwengals Oct 28, 2021
76b6c16
small fixes to get kronlatent and kronmarginal to pass
bwengals Oct 28, 2021
90ae450
remove leftover prints
bwengals Oct 28, 2021
df1fe57
dep warning -> future warning
bwengals Oct 30, 2021
dceabf8
roll back mkl and mkl-service version
bwengals Nov 3, 2021
4692407
fix precommit
bwengals Nov 3, 2021
cc16bd5
remove old DeprecationWarning
bwengals Nov 3, 2021
062a9ca
merge from main
bwengals Nov 3, 2021
9763b98
improve tests
bwengals Nov 3, 2021
23fc5c7
fix pre-commit issue
bwengals Nov 4, 2021
158529f
fix precommit on cov.py
bwengals Nov 4, 2021
08a7652
fix comment
bwengals Nov 8, 2021
196e702
dont force blas version in windows dev enviornment (roll back changes)
bwengals Nov 8, 2021
63e5d16
Merge branch 'main' into gpv4update
bwengals Nov 8, 2021
d02e320
update release notes
bwengals Nov 9, 2021
8fee214
add removed ... line from release notes
bwengals Nov 9, 2021
d5474a7
add link to PR
bwengals Nov 13, 2021
5d6e94c
Merge branch 'pymc-devs:main' into gpv4update
bwengals Nov 20, 2021
5348575
remove is_observed usage from TestMarginalVsLatent
bwengals Nov 20, 2021
c2b850d
remove is_observed usage from TestMarginalVsMarginalSparse
bwengals Nov 20, 2021
461d26b
Update RELEASE-NOTES.md
twiecki Nov 21, 2021
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3 changes: 2 additions & 1 deletion conda-envs/windows-environment-test-py38.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@ dependencies:
- fastprogress>=0.2.0
- h5py>=2.7
- libpython
- mkl-service
- mkl==2020.4
- mkl-service==2.3.0
- m2w64-toolchain
- numpy>=1.15.0
- pandas
Expand Down
6 changes: 4 additions & 2 deletions pymc/gp/cov.py
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ def __init__(self, input_dim, active_dims=None):
if active_dims is None:
self.active_dims = np.arange(input_dim)
else:
self.active_dims = np.asarray(active_dims, np.int)
self.active_dims = np.asarray(active_dims, int)

def __call__(self, X, Xs=None, diag=False):
r"""
Expand Down Expand Up @@ -152,7 +152,9 @@ def __array_wrap__(self, result):
elif isinstance(result[0][0], Prod):
return result[0][0].factor_list[0] * A
else:
raise RuntimeError
raise TypeError(
f"Unknown Covariance combination type {result[0][0]}. Known types are `Add` or `Prod`."
)


class Combination(Covariance):
Expand Down
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