Merge pull request #83 from yuki-koyama/update-versions

yuki-koyama · web-flow · commit 2fd2302e6576 · 2025-11-11T11:10:15.000+09:00
Update cmake and dependency versions, and perform CI maintenance
diff --git 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
@@ -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
@@ -1,12 +1,13 @@
 #include <Eigen/Core>
 #include <cmath>
+#include <cassert>
 #include <fstream>
 #include <iostream>
-#include <mathtoolbox/gaussian-process-regression.hpp>
 #include <random>
 #include <string>
-#include <timer.hpp>
 #include <vector>
+#include <timer.hpp>
+#include <mathtoolbox/gaussian-process-regression.hpp>
 
 using Eigen::MatrixXd;
 using Eigen::VectorXd;
diff --git a/examples/log-determinant/main.cpp b/examples/log-determinant/main.cpp
@@ -2,6 +2,7 @@
 #include <Eigen/Core>
 #include <Eigen/LU>
 #include <cmath>
+#include <cassert>
 #include <iostream>
 #include <mathtoolbox/log-determinant.hpp>
 
diff --git 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
@@ -1 +1 @@
-Subproject commit 80d452484c5409444b0ec19383faa84bb7a4d351
+Subproject commit a2e59f0e7065404b44dfe92a28aca47ba1378dc4
diff --git 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
@@ -1,9 +1,10 @@
 #ifndef MATHTOOLBOX_BACKTRACKING_LINE_SEARCH_HPP
 #define MATHTOOLBOX_BACKTRACKING_LINE_SEARCH_HPP
 
-#include <Eigen/Core>
+#include <cassert>
 #include <functional>
 #include <iostream>
+#include <Eigen/Core>
 
 namespace mathtoolbox
 {
diff --git 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 <Eigen/Core>
+#include <cassert>
 #include <cmath>
 #include <functional>
 #include <memory>
 #include <vector>
+#include <Eigen/Core>
 
 namespace mathtoolbox
 {
diff --git 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 <Eigen/Core>
 #include <cassert>
 #include <functional>
 #include <iostream>
+#include <Eigen/Core>
 
 #define MATHTOOLBOX_VERBOSE_LINE_SEARCH_WARNINGS
 
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,5 @@
 #include <cmath>
+#include <cassert>
 #include <mathtoolbox/acquisition-functions.hpp>
 #include <mathtoolbox/probability-distributions.hpp>
 
diff --git a/src/bayesian-optimization.cpp b/src/bayesian-optimization.cpp
@@ -1,11 +1,12 @@
+#include <cassert>
 #include <algorithm>
 #include <iostream>
 #include <limits>
+#include <vector>
 #include <mathtoolbox/acquisition-functions.hpp>
 #include <mathtoolbox/bayesian-optimization.hpp>
 #include <mathtoolbox/gaussian-process-regression.hpp>
 #include <mathtoolbox/gradient-descent.hpp>
-#include <vector>
 
 using Eigen::MatrixXd;
 using Eigen::VectorXd;
diff --git a/src/gaussian-process-regression.cpp b/src/gaussian-process-regression.cpp
@@ -1,10 +1,11 @@
+#include <cassert>
 #include <iostream>
+#include <tuple>
 #include <mathtoolbox/constants.hpp>
 #include <mathtoolbox/gaussian-process-regression.hpp>
 #include <mathtoolbox/kernel-functions.hpp>
 #include <mathtoolbox/log-determinant.hpp>
 #include <mathtoolbox/numerical-optimization.hpp>
-#include <tuple>
 
 using Eigen::MatrixXd;
 using Eigen::VectorXd;
diff --git a/src/kernel-functions.cpp b/src/kernel-functions.cpp
@@ -1,4 +1,5 @@
 #include <cmath>
+#include <cassert>
 #include <mathtoolbox/kernel-functions.hpp>
 
 using Eigen::VectorXd;
diff --git a/src/matrix-inversion.cpp b/src/matrix-inversion.cpp
@@ -1,3 +1,4 @@
+#include <cassert>
 #include <Eigen/LU>
 #include <mathtoolbox/matrix-inversion.hpp>
 
diff --git a/src/probability-distributions.cpp b/src/probability-distributions.cpp
@@ -1,3 +1,4 @@
+#include <cassert>
 #include <cmath>
 #include <mathtoolbox/constants.hpp>
 #include <mathtoolbox/probability-distributions.hpp>
diff --git a/src/rbf-interpolation.cpp b/src/rbf-interpolation.cpp
@@ -1,4 +1,5 @@
 #include <Eigen/LU>
+#include <cassert>
 #include <cmath>
 #include <mathtoolbox/rbf-interpolation.hpp>
 
diff --git a/src/som.cpp b/src/som.cpp
@@ -1,3 +1,4 @@
+#include <cassert>
 #include <Eigen/SparseCore>
 #include <mathtoolbox/data-normalization.hpp>
 #include <mathtoolbox/som.hpp>
