diff --git a/.github/workflows/macos-python.yml b/.github/workflows/macos-python.yml index 3e54502..48cb6fb 100644 --- a/.github/workflows/macos-python.yml +++ b/.github/workflows/macos-python.yml @@ -25,7 +25,6 @@ jobs: - name: install-test-dependencies run: | pip install matplotlib pillow seaborn scipy - brew tap homebrew/cask-fonts && brew install font-linux-biolinum - name: test run: | python ./python-examples/bayesian-optimization.py diff --git a/.github/workflows/ubuntu-python.yml b/.github/workflows/ubuntu-python.yml index 55b0b6d..d1d1220 100644 --- a/.github/workflows/ubuntu-python.yml +++ b/.github/workflows/ubuntu-python.yml @@ -26,7 +26,6 @@ jobs: - name: install-test-dependencies run: | pip install matplotlib pillow seaborn scipy - sudo apt-get install fonts-linuxlibertine - name: test run: | python ./python-examples/bayesian-optimization.py diff --git a/examples/gaussian-process-regression/main.cpp b/examples/gaussian-process-regression/main.cpp index fc8aab4..bb9df95 100644 --- a/examples/gaussian-process-regression/main.cpp +++ b/examples/gaussian-process-regression/main.cpp @@ -1,12 +1,13 @@ #include #include +#include #include #include -#include #include #include -#include #include +#include +#include using Eigen::MatrixXd; using Eigen::VectorXd; diff --git a/examples/log-determinant/main.cpp b/examples/log-determinant/main.cpp index 33f0836..08d1b8a 100644 --- a/examples/log-determinant/main.cpp +++ b/examples/log-determinant/main.cpp @@ -2,6 +2,7 @@ #include #include #include +#include #include #include diff --git a/external/optimization-test-functions b/external/optimization-test-functions index a9a78f5..815b0c1 160000 --- a/external/optimization-test-functions +++ b/external/optimization-test-functions @@ -1 +1 @@ -Subproject commit a9a78f5d0929b81e7179f9589357700a9f1104f2 +Subproject commit 815b0c131c400b04f9b2469d432dab6942c8e88e diff --git a/external/pybind11 b/external/pybind11 index 80d4524..a2e59f0 160000 --- a/external/pybind11 +++ b/external/pybind11 @@ -1 +1 @@ -Subproject commit 80d452484c5409444b0ec19383faa84bb7a4d351 +Subproject commit a2e59f0e7065404b44dfe92a28aca47ba1378dc4 diff --git a/external/timer b/external/timer index dc301bc..559def8 160000 --- a/external/timer +++ b/external/timer @@ -1 +1 @@ -Subproject commit dc301bc7991304770e9b6fd0466c86bfb1864300 +Subproject commit 559def88266105ba149c11501e7a99327696ae07 diff --git a/include/mathtoolbox/backtracking-line-search.hpp b/include/mathtoolbox/backtracking-line-search.hpp index 687042c..8de5940 100644 --- a/include/mathtoolbox/backtracking-line-search.hpp +++ b/include/mathtoolbox/backtracking-line-search.hpp @@ -1,9 +1,10 @@ #ifndef MATHTOOLBOX_BACKTRACKING_LINE_SEARCH_HPP #define MATHTOOLBOX_BACKTRACKING_LINE_SEARCH_HPP -#include +#include #include #include +#include namespace mathtoolbox { diff --git a/include/mathtoolbox/rbf-interpolation.hpp b/include/mathtoolbox/rbf-interpolation.hpp index 56f21b2..6ec26df 100644 --- a/include/mathtoolbox/rbf-interpolation.hpp +++ b/include/mathtoolbox/rbf-interpolation.hpp @@ -1,11 +1,12 @@ #ifndef MATHTOOLBOX_RBF_INTERPOLATION_HPP #define MATHTOOLBOX_RBF_INTERPOLATION_HPP -#include +#include #include #include #include #include +#include namespace mathtoolbox { diff --git a/include/mathtoolbox/strong-wolfe-conditions-line-search.hpp b/include/mathtoolbox/strong-wolfe-conditions-line-search.hpp index be3ae4d..9d78246 100644 --- a/include/mathtoolbox/strong-wolfe-conditions-line-search.hpp +++ b/include/mathtoolbox/strong-wolfe-conditions-line-search.hpp @@ -1,10 +1,10 @@ #ifndef MATHTOOLBOX_STRONG_WOLFE_CONDITIONS_LINE_SEARCH_HPP #define MATHTOOLBOX_STRONG_WOLFE_CONDITIONS_LINE_SEARCH_HPP -#include #include #include #include +#include #define MATHTOOLBOX_VERBOSE_LINE_SEARCH_WARNINGS diff --git a/python-examples/bayesian-optimization.py b/python-examples/bayesian-optimization.py index c9dd0f9..7d3cfeb 100644 --- a/python-examples/bayesian-optimization.py +++ b/python-examples/bayesian-optimization.py @@ -34,7 +34,6 @@ def objective_func(x: np.ndarray) -> float: # Set up the plot design sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] for i in range(NUM_ITERS): # Proceed the optimization step @@ -61,7 +60,7 @@ def objective_func(x: np.ndarray) -> float: # Prepare a figure object fig = plt.figure(figsize=FIG_SIZE, dpi=DPI, constrained_layout=True) grid_spec = fig.add_gridspec(3, 1) - fig.suptitle("Bayesian Optimization [#iterations = {:02}]".format(i + 1)) + fig.suptitle("Bayesian Optimization [#iter = {:02}]".format(i + 1)) # Begin to draw the top plot ax = fig.add_subplot(grid_spec[0:2, 0]) diff --git a/python-examples/classical-mds-image.py b/python-examples/classical-mds-image.py index 1f4d004..0c9b591 100644 --- a/python-examples/classical-mds-image.py +++ b/python-examples/classical-mds-image.py @@ -29,7 +29,6 @@ # Set style sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Draw plot fig = plt.figure(figsize=FIG_SIZE, dpi=DPI) diff --git a/python-examples/rbf-interpolation-comparison.py b/python-examples/rbf-interpolation-comparison.py index 6ca84b4..1e861b4 100644 --- a/python-examples/rbf-interpolation-comparison.py +++ b/python-examples/rbf-interpolation-comparison.py @@ -31,7 +31,6 @@ def objective_func(x: np.ndarray) -> float: # Set up the plot design sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Prepare a figure object fig = plt.figure(figsize=FIG_SIZE, dpi=DPI) diff --git a/python-examples/rbf-interpolation-exact.py b/python-examples/rbf-interpolation-exact.py index c557329..6c53c99 100644 --- a/python-examples/rbf-interpolation-exact.py +++ b/python-examples/rbf-interpolation-exact.py @@ -1,6 +1,5 @@ import pymathtoolbox import numpy as np -import random import math import matplotlib.pyplot as plt import seaborn as sns @@ -40,7 +39,6 @@ def objective_func(x: np.ndarray) -> float: # Set up the plot design sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Calculate sequences of interpolated values x_samples = np.arange(0.0, 1.0, 0.001) diff --git a/python-examples/rbf-interpolation-polynomial.py b/python-examples/rbf-interpolation-polynomial.py index 6170a39..29c6017 100644 --- a/python-examples/rbf-interpolation-polynomial.py +++ b/python-examples/rbf-interpolation-polynomial.py @@ -1,7 +1,5 @@ import pymathtoolbox import numpy as np -import random -import math import matplotlib.pyplot as plt import seaborn as sns @@ -18,7 +16,6 @@ # Set up the plot design sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Prepare a figure object fig = plt.figure(figsize=FIG_SIZE, dpi=DPI) diff --git a/python-examples/rbf-interpolation.py b/python-examples/rbf-interpolation.py index c7525c7..d1b6364 100644 --- a/python-examples/rbf-interpolation.py +++ b/python-examples/rbf-interpolation.py @@ -43,7 +43,6 @@ def objective_func(x: np.ndarray) -> float: # Set up the plot design sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Calculate sequences of interpolated values x_samples = np.arange(0.0, 1.0, 0.001) diff --git a/python-examples/som-image-1d.py b/python-examples/som-image-1d.py index 049c39b..fb39f56 100644 --- a/python-examples/som-image-1d.py +++ b/python-examples/som-image-1d.py @@ -18,7 +18,6 @@ # Set plot style sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Load an image asset_dir_path = os.path.dirname(os.path.abspath(__file__)) + "/assets" diff --git a/python-examples/som-image.py b/python-examples/som-image.py index cee0831..a1d9571 100644 --- a/python-examples/som-image.py +++ b/python-examples/som-image.py @@ -17,7 +17,6 @@ # Set plot style sns.set() sns.set_context() -plt.rcParams['font.sans-serif'] = ["Linux Biolinum O", "Linux Biolinum"] # Load an image asset_dir_path = os.path.dirname(os.path.abspath(__file__)) + "/assets" diff --git a/src/acquisition-functions.cpp b/src/acquisition-functions.cpp index c51dd53..dc7bf4e 100644 --- a/src/acquisition-functions.cpp +++ b/src/acquisition-functions.cpp @@ -1,4 +1,5 @@ #include +#include #include #include diff --git a/src/bayesian-optimization.cpp b/src/bayesian-optimization.cpp index ff84f01..7d2bed2 100644 --- a/src/bayesian-optimization.cpp +++ b/src/bayesian-optimization.cpp @@ -1,11 +1,12 @@ +#include #include #include #include +#include #include #include #include #include -#include using Eigen::MatrixXd; using Eigen::VectorXd; diff --git a/src/gaussian-process-regression.cpp b/src/gaussian-process-regression.cpp index eb7a6b1..3eed18a 100644 --- a/src/gaussian-process-regression.cpp +++ b/src/gaussian-process-regression.cpp @@ -1,10 +1,11 @@ +#include #include +#include #include #include #include #include #include -#include using Eigen::MatrixXd; using Eigen::VectorXd; diff --git a/src/kernel-functions.cpp b/src/kernel-functions.cpp index 5aa9d8c..7071776 100644 --- a/src/kernel-functions.cpp +++ b/src/kernel-functions.cpp @@ -1,4 +1,5 @@ #include +#include #include using Eigen::VectorXd; diff --git a/src/matrix-inversion.cpp b/src/matrix-inversion.cpp index 6496c9d..2e5ee2a 100644 --- a/src/matrix-inversion.cpp +++ b/src/matrix-inversion.cpp @@ -1,3 +1,4 @@ +#include #include #include diff --git a/src/probability-distributions.cpp b/src/probability-distributions.cpp index ca4c79d..a7bee50 100644 --- a/src/probability-distributions.cpp +++ b/src/probability-distributions.cpp @@ -1,3 +1,4 @@ +#include #include #include #include diff --git a/src/rbf-interpolation.cpp b/src/rbf-interpolation.cpp index f424bfd..99f75d4 100644 --- a/src/rbf-interpolation.cpp +++ b/src/rbf-interpolation.cpp @@ -1,4 +1,5 @@ #include +#include #include #include diff --git a/src/som.cpp b/src/som.cpp index 1478308..af89600 100644 --- a/src/som.cpp +++ b/src/som.cpp @@ -1,3 +1,4 @@ +#include #include #include #include