Merge pull request #22 from jungtaekkim/0.5.0

0.5.0

.coveragerc

@@ -6,5 +6,5 @@ source =
 [report]
 exclude_lines =
     pragma: no cover
-    raise NotImplementedError
     print
+    raise NotImplementedError

.gitignore

@@ -102,9 +102,9 @@ ENV/
 
 # Jungtaek
 *.swp
+*.dat
 .DS_Store
+.pytest_cache/
 __MACOSX/
 results/
 figures/
-.pytest_cache/
-*.dat

.pylintrc

@@ -1,9 +1,12 @@
 [MASTER]
 
+# command
+# pylint --rcfile=.pylintrc bayeso
+
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code.
-extension-pkg-whitelist=
+extension-pkg-whitelist=numpy
 
 # Specify a score threshold to be exceeded before program exits with error.
 fail-under=10.0
@@ -552,7 +555,7 @@ max-attributes=15
 max-bool-expr=5
 
 # Maximum number of branch for function / method body.
-max-branches=15
+max-branches=16
 
 # Maximum number of locals for function / method body.
 max-locals=35

.readthedocs.yml

@@ -5,8 +5,8 @@ sphinx:
   configuration: docs/conf.py
 
 formats:
-  - pdf
   - htmlzip
+  - pdf
 
 python:
   version: 3.7

.travis.yml

@@ -4,12 +4,9 @@ python:
   - '3.6'
   - '3.7'
   - '3.8'
+  - '3.9'
 install:
   - pip install .
-  - pip install tensorflow
-  - pip install tensorflow-probability
-  - pip install torch
-  - pip install gpytorch
 script:
   - pip install coveralls
   - pip install pytest-timeout

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017-2020 Jungtaek Kim
+Copyright (c) 2017-2021 Jungtaek Kim
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,4 +1,4 @@
-include LICENSE
 include CODE_OF_CONDUCT.md
+include LICENSE
 include requirements.txt
 include requirements-optional.txt

README.md

@@ -15,7 +15,7 @@ Simple, but essential Bayesian optimization package.
 * [Online documentation](http://bayeso.readthedocs.io)
 
 ## Installation
-We recommend it should be installed in `virtualenv`.
+We recommend installing it with `virtualenv`.
 You can choose one of three installation options.
 
 * Using PyPI repository (for user installation)
@@ -67,6 +67,7 @@ We test our package in the following versions.
 * Python 3.6
 * Python 3.7
 * Python 3.8
+* Python 3.9
 
 ## Contributor
 * [Jungtaek Kim](http://jungtaek.github.io) (POSTECH)

bayeso/__init__.py

@@ -1,7 +1,8 @@
 #
 # author: Jungtaek Kim (jtkim@postech.ac.kr)
-# last updated: September 24, 2020
+# last updated: March 14, 2021
 #
-"""BayesO is a simple, but essential Bayesian optimization package, implemented in Python."""
+"""BayesO is a simple, but essential Bayesian optimization
+package, implemented in Python."""
 
-__version__ = '0.4.3'
+__version__ = '0.5.0'

bayeso/acquisition.py

@@ -2,7 +2,8 @@
 # author: Jungtaek Kim (jtkim@postech.ac.kr)
 # last updated: September 24, 2020
 #
-"""It defines acquisition functions."""
+"""It defines acquisition functions, each of which
+is employed to determine where next to evaluate."""
 
 import numpy as np
 import scipy.stats
@@ -16,7 +17,7 @@ def pi(pred_mean: np.ndarray, pred_std: np.ndarray, Y_train: np.ndarray,
     jitter: float=constants.JITTER_ACQ
 ) -> np.ndarray:
     """
-    It is a probability improvement criterion.
+    It is a probability of improvement criterion.
 
     :param pred_mean: posterior predictive mean function over `X_test`.
         Shape: (l, ).