From 30d08bb4127afa33c9443d776b36c746c7c6f2a1 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 11:40:19 +0900
Subject: [PATCH 01/23] add description

---
 ml_interfaces/bayesopt_interfaces/setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ml_interfaces/bayesopt_interfaces/setup.py b/ml_interfaces/bayesopt_interfaces/setup.py
index 290dbe0..d13c984 100644
--- a/ml_interfaces/bayesopt_interfaces/setup.py
+++ b/ml_interfaces/bayesopt_interfaces/setup.py
@@ -9,7 +9,7 @@ def _requires_from_file(filename):
     version='0.1.0',
     author='Yuki Asano',
     author_email='yasano@g.ecc.u-tokyo.ac.jp',
-    description='',
+    description='Interface for Bayesian Optimization',
     packages=find_packages(),
     install_requires = _requires_from_file('requirements.txt')
 )

From 2fea4d7b5d7633848185370f93ad018bdef28d6b Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 11:45:47 +0900
Subject: [PATCH 02/23] add ci

---
 .github/workflows/bayesopt_interfaces.yaml | 28 ++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 .github/workflows/bayesopt_interfaces.yaml

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
new file mode 100644
index 0000000..b0e94bc
--- /dev/null
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -0,0 +1,28 @@
+name: test
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+    name: Run tests with pytest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.8]
+        os: [ubuntu-20.04]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install pytest
+      - name: Run pytest
+        run: pytest -v ml_interfaces/bayesopt_interfaces/tests

From 3f36036e37bee7e8d9739093e313e6b30f7e18d6 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 11:48:40 +0900
Subject: [PATCH 03/23] mod

---
 .github/workflows/bayesopt_interfaces.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index b0e94bc..32196d5 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -24,5 +24,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           pip install pytest
+          pip install -r ml_interfaces/bayesopt_interfaces/requirements.txt
       - name: Run pytest
         run: pytest -v ml_interfaces/bayesopt_interfaces/tests

From ab84d2753884b05a98851bddc277926d037df985 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 11:51:37 +0900
Subject: [PATCH 04/23] mod

---
 .github/workflows/bayesopt_interfaces.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index 32196d5..755d3cc 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -1,5 +1,3 @@
-name: test
-
 on:
   push:
   pull_request:
@@ -24,6 +22,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           pip install pytest
-          pip install -r ml_interfaces/bayesopt_interfaces/requirements.txt
+          #pip install -r ml_interfaces/bayesopt_interfaces/requirements.txt
+      - name: Install bayesopt_interfaces
+        run: |
+          pip install ml_interfaces/bayesopt_interfaces
       - name: Run pytest
         run: pytest -v ml_interfaces/bayesopt_interfaces/tests

From f4d3882c1b2a0cba229b24edc263ae9b5b48dcb7 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 12:00:27 +0900
Subject: [PATCH 05/23] mod

---
 .github/workflows/bayesopt_interfaces.yaml         | 2 +-
 ml_interfaces/bayesopt_interfaces/requirements.txt | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index 755d3cc..3c82758 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -27,4 +27,4 @@ jobs:
         run: |
           pip install ml_interfaces/bayesopt_interfaces
       - name: Run pytest
-        run: pytest -v ml_interfaces/bayesopt_interfaces/tests
+        run: pytest -v ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
diff --git a/ml_interfaces/bayesopt_interfaces/requirements.txt b/ml_interfaces/bayesopt_interfaces/requirements.txt
index 5a7eca9..4000a06 100644
--- a/ml_interfaces/bayesopt_interfaces/requirements.txt
+++ b/ml_interfaces/bayesopt_interfaces/requirements.txt
@@ -1,2 +1,3 @@
 matplotlib
+pandas
 physbo

From ce59a39a6764f3139c26896e22511acc922f46c6 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 12:02:46 +0900
Subject: [PATCH 06/23] mod

---
 ml_interfaces/bayesopt_interfaces/requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ml_interfaces/bayesopt_interfaces/requirements.txt b/ml_interfaces/bayesopt_interfaces/requirements.txt
index 4000a06..a3b25d0 100644
--- a/ml_interfaces/bayesopt_interfaces/requirements.txt
+++ b/ml_interfaces/bayesopt_interfaces/requirements.txt
@@ -1,3 +1,4 @@
 matplotlib
 pandas
 physbo
+pyyaml

From 84305a6d6625f965e60a75dc4c63b7a1653e8893 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 12:32:16 +0900
Subject: [PATCH 07/23] mod test_physbo_interface files

---
 .../examples/data/candidates.csv              | 21 ++++++++
 .../examples/data/results.csv                 | 21 ++++++++
 .../bayesopt_interfaces/examples/run_combo.py | 38 ++++++++++++++
 .../examples/run_physbo.py                    | 50 +++++++++++++++++++
 .../tests/data/candidates-correct.csv         | 21 ++++++++
 .../tests/test_physbo_interface.py            | 13 +++--
 6 files changed, 157 insertions(+), 7 deletions(-)
 create mode 100644 ml_interfaces/bayesopt_interfaces/examples/data/candidates.csv
 create mode 100644 ml_interfaces/bayesopt_interfaces/examples/data/results.csv
 create mode 100755 ml_interfaces/bayesopt_interfaces/examples/run_combo.py
 create mode 100755 ml_interfaces/bayesopt_interfaces/examples/run_physbo.py
 create mode 100644 ml_interfaces/bayesopt_interfaces/tests/data/candidates-correct.csv

diff --git a/ml_interfaces/bayesopt_interfaces/examples/data/candidates.csv b/ml_interfaces/bayesopt_interfaces/examples/data/candidates.csv
new file mode 100644
index 0000000..2a1b71f
--- /dev/null
+++ b/ml_interfaces/bayesopt_interfaces/examples/data/candidates.csv
@@ -0,0 +1,21 @@
+p1,p2,p3,p4,y
+180,0,100,200,
+180,0,200,200,
+180,0,300,200,
+180,0,400,200,
+180,100,100,200,
+180,100,200,200,
+180,100,300,200,
+180,100,400,200,
+180,200,100,200,
+180,200,200,200,
+180,200,300,200,
+180,200,400,200,
+180,300,100,200,
+180,300,200,200,
+180,300,300,200,
+180,300,400,200,
+180,400,100,200,
+180,400,200,200,
+180,400,300,200,
+180,400,400,200,
diff --git a/ml_interfaces/bayesopt_interfaces/examples/data/results.csv b/ml_interfaces/bayesopt_interfaces/examples/data/results.csv
new file mode 100644
index 0000000..be0f592
--- /dev/null
+++ b/ml_interfaces/bayesopt_interfaces/examples/data/results.csv
@@ -0,0 +1,21 @@
+y
+0.001
+0.401
+0.398
+0.305
+0.001
+0.352
+0.350
+0.237
+0.350
+0.374
+0.288
+0.262
+0.290
+0.250
+0.245
+0.204
+0.216
+0.129
+0.151
+0.091
diff --git a/ml_interfaces/bayesopt_interfaces/examples/run_combo.py b/ml_interfaces/bayesopt_interfaces/examples/run_combo.py
new file mode 100755
index 0000000..bca9c10
--- /dev/null
+++ b/ml_interfaces/bayesopt_interfaces/examples/run_combo.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import random
+import sys
+
+import combo
+from bayesopt_if.combo_interface import ComboInterface
+
+
+def main():
+    # dir setting
+    candidates_path  = './data/candidates.csv'
+    policy_load_dir = './data/load'
+    policy_save_dir = './data/result'
+
+    # Generate combo
+    ci = ComboInterface(combo, candidates_path, policy_load_dir, policy_save_dir, use_saved_policy=False)
+    ci.start_bayesopt()
+
+    # Write combo operation below
+    ## Following procedure is important for correct generation of result data.
+    ## search -> write(and update -> visualize)
+    for i in range(1):
+        ci.search_next_param_random()
+        ci.write_result(random.random())  # write result
+    for i in range(1):
+        ci.search_next_param_bayes()
+        ci.write_result(random.random())  # write result
+
+    raw_input('Press enter to save and finish\n')
+
+    ci.save_data(policy_save_dir)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/ml_interfaces/bayesopt_interfaces/examples/run_physbo.py b/ml_interfaces/bayesopt_interfaces/examples/run_physbo.py
new file mode 100755
index 0000000..1b97ff5
--- /dev/null
+++ b/ml_interfaces/bayesopt_interfaces/examples/run_physbo.py
@@ -0,0 +1,50 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import csv
+import os
+import sys
+
+from bayesopt_if.physbo_interface import PhysboInterface
+
+
+def get_data_from_result_list(index):
+    with open('./data/results.csv') as f:
+        reader = csv.reader(f)
+        l = [row for row in reader]
+
+    return float(l[index+1][0])
+
+
+def main():
+    # dir setting
+    candidates_path  = './data/candidates.csv'
+    policy_load_dir = './data/load'
+    policy_save_dir = './data/result'
+
+    # Generate physbo
+    pi = PhysboInterface(candidates_path, policy_load_dir, policy_save_dir, use_saved_policy=False, search_score='EI')
+    pi.start_bayesopt()
+
+    # Procedure of search and register data to PHYSBO
+    # - Following procedure is important for correct generation of result data.
+    # - search -> write (and update -> visualize)
+
+    # Search with Random search for initial step
+    for i in range(3):
+        pi.search_next_param_random()
+        result = get_data_from_result_list(pi.get_next_index())  # get result/evaluation data from experiment. (Result list is used for this test program).
+        pi.write_result(result)  # write result to PHYSBO
+    # Search with Bayesian optimization
+    for i in range(3):
+        pi.search_next_param_bayes()
+        result = get_data_from_result_list(pi.get_next_index())
+        pi.write_result(result)
+
+    input('Press enter to save and finish\n')
+
+    pi.save_data(policy_save_dir)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/ml_interfaces/bayesopt_interfaces/tests/data/candidates-correct.csv b/ml_interfaces/bayesopt_interfaces/tests/data/candidates-correct.csv
new file mode 100644
index 0000000..67d7216
--- /dev/null
+++ b/ml_interfaces/bayesopt_interfaces/tests/data/candidates-correct.csv
@@ -0,0 +1,21 @@
+p1,p2,p3,p4,y
+180,0,100,200,0.001
+180,0,200,200,0.401
+180,0,300,200,0.398
+180,0,400,200,0.305
+180,100,100,200,0.001
+180,100,200,200,0.352
+180,100,300,200,0.35
+180,100,400,200,0.237
+180,200,100,200,0.35
+180,200,200,200,0.374
+180,200,300,200,0.288
+180,200,400,200,0.262
+180,300,100,200,0.29
+180,300,200,200,0.25
+180,300,300,200,0.245
+180,300,400,200,0.204
+180,400,100,200,0.216
+180,400,200,200,0.129
+180,400,300,200,0.151
+180,400,400,200,0.091
diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
index 1b97ff5..b3b9741 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import csv
+import filecmp
 import os
 import sys
 
@@ -16,9 +17,10 @@ def get_data_from_result_list(index):
     return float(l[index+1][0])
 
 
-def main():
+def test_physbo_interface():
     # dir setting
     candidates_path  = './data/candidates.csv'
+    correct_candidates_path = './data/candidates-correct.csv'
     policy_load_dir = './data/load'
     policy_save_dir = './data/result'
 
@@ -36,15 +38,12 @@ def main():
         result = get_data_from_result_list(pi.get_next_index())  # get result/evaluation data from experiment. (Result list is used for this test program).
         pi.write_result(result)  # write result to PHYSBO
     # Search with Bayesian optimization
-    for i in range(3):
+    for i in range(17):
         pi.search_next_param_bayes()
         result = get_data_from_result_list(pi.get_next_index())
         pi.write_result(result)
 
-    input('Press enter to save and finish\n')
-
+    #input('Press enter to save and finish\n')
     pi.save_data(policy_save_dir)
 
-
-if __name__ == '__main__':
-    main()
+    assert filecmp.cmp(candidates_path, correct_candidates_path)

From e610f08fc7b595553e1d9eadd6c7ed06bd4c733f Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 12:49:58 +0900
Subject: [PATCH 08/23] fix path

---
 .../tests/test_physbo_interface.py                    | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
index b3b9741..b1ef838 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
@@ -8,6 +8,9 @@
 
 from bayesopt_if.physbo_interface import PhysboInterface
 
+file_dir = os.path.dirname(__file__)
+data_dir = os.path.join(file_dir, 'data')
+
 
 def get_data_from_result_list(index):
     with open('./data/results.csv') as f:
@@ -19,10 +22,10 @@ def get_data_from_result_list(index):
 
 def test_physbo_interface():
     # dir setting
-    candidates_path  = './data/candidates.csv'
-    correct_candidates_path = './data/candidates-correct.csv'
-    policy_load_dir = './data/load'
-    policy_save_dir = './data/result'
+    candidates_path  = os.path.join(data_dir, 'candidates.csv')
+    correct_candidates_path = os.path.join(data_dir, 'candidates-correct.csv')
+    policy_load_dir = os.path.join(data_dir, 'load')
+    policy_save_dir = os.path.join(data_dir, 'result')
 
     # Generate physbo
     pi = PhysboInterface(candidates_path, policy_load_dir, policy_save_dir, use_saved_policy=False, search_score='EI')

From 67a5a6c2ca69d702701cfa13ad2cf1d4a955f73b Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 12:52:58 +0900
Subject: [PATCH 09/23] fix path

---
 .../bayesopt_interfaces/tests/test_physbo_interface.py         | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
index b1ef838..e2dabb5 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
@@ -13,7 +13,8 @@
 
 
 def get_data_from_result_list(index):
-    with open('./data/results.csv') as f:
+    results_path = os.path.join(data_dir, 'results.csv')
+    with open(results_path) as f:
         reader = csv.reader(f)
         l = [row for row in reader]
 

From 512f5bbc52911e7ef21f27f6c64e350f84514a88 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 13:09:20 +0900
Subject: [PATCH 10/23] add test for combo_interface

---
 .github/workflows/bayesopt_interfaces.yaml | 37 +++++++++++++++++++---
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index 3c82758..2fd18d8 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -3,14 +3,13 @@ on:
   pull_request:
 
 jobs:
-  build:
-    name: Run tests with pytest
+  tests_physbo_interface:
+    name: Run tests for physbo_interface
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: [3.8]
         os: [ubuntu-20.04]
-
     steps:
       - name: Checkout
         uses: actions/checkout@v3
@@ -22,9 +21,39 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           pip install pytest
-          #pip install -r ml_interfaces/bayesopt_interfaces/requirements.txt
       - name: Install bayesopt_interfaces
         run: |
           pip install ml_interfaces/bayesopt_interfaces
       - name: Run pytest
         run: pytest -v ml_interfaces/bayesopt_interfaces/tests/test_physbo_interface.py
+
+  tests_combo_interface:
+    name: Run tests for combo_interface
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [2.7]
+        os: [ubuntu-20.04]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install pytest
+      - name: Install combo
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git clone https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/tsudalab/combo.git
+          cd combo
+          python setup.py install
+      - name: Install bayesopt_interfaces
+        run: |
+          pip install ml_interfaces/bayesopt_interfaces
+      - name: Run pytest
+        run: pytest -v ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py

From 4905b5cfc7d0b6f8a80fabb129c87a0db167e869 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 13:28:56 +0900
Subject: [PATCH 11/23] use python2 image

---
 .github/workflows/bayesopt_interfaces.yaml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index 2fd18d8..2b53e71 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -32,15 +32,18 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [2.7]
+        #python-version: [2.7]
         os: [ubuntu-20.04]
+    container:
+        image: python:2.7.18-buster
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+
+      #- name: Set up Python ${{ matrix.python-version }}
+      #  uses: actions/setup-python@v5
+      #  with:
+      #    python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools

From d52021d51f43a28a61f3306bca7a5ebbe1f461cc Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 13:34:15 +0900
Subject: [PATCH 12/23] add cython

---
 .github/workflows/bayesopt_interfaces.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index 2b53e71..460d20d 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -47,7 +47,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools
-          pip install pytest
+          pip install pytest cython
       - name: Install combo
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From 8261336fe387b0a9f4d02dfe8e0d35edd6f236fb Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 13:35:29 +0900
Subject: [PATCH 13/23] add numpy

---
 .github/workflows/bayesopt_interfaces.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index 460d20d..c1a38f8 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -47,7 +47,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools
-          pip install pytest cython
+          pip install pytest cython numpy
       - name: Install combo
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From b6068cead40cb69de7130167b0316e49bfb528aa Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 13:42:30 +0900
Subject: [PATCH 14/23] mod test for combo_interface

---
 .../tests/test_combo_interface.py             | 40 ++++++++++++++-----
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index bca9c10..9dc06eb 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import csv
+import filecmp
 import os
 import random
 import sys
@@ -8,12 +10,25 @@
 import combo
 from bayesopt_if.combo_interface import ComboInterface
 
+file_dir = os.path.dirname(__file__)
+data_dir = os.path.join(file_dir, 'data')
 
-def main():
+
+def get_data_from_result_list(index):
+    results_path = os.path.join(data_dir, 'results.csv')
+    with open(results_path) as f:
+        reader = csv.reader(f)
+        l = [row for row in reader]
+
+    return float(l[index+1][0])
+
+
+def test_combo_interface():
     # dir setting
-    candidates_path  = './data/candidates.csv'
-    policy_load_dir = './data/load'
-    policy_save_dir = './data/result'
+    candidates_path  = os.path.join(data_dir, 'candidates.csv')
+    correct_candidates_path = os.path.join(data_dir, 'candidates-correct.csv')
+    policy_load_dir = os.path.join(data_dir, 'load')
+    policy_save_dir = os.path.join(data_dir, 'result')
 
     # Generate combo
     ci = ComboInterface(combo, candidates_path, policy_load_dir, policy_save_dir, use_saved_policy=False)
@@ -22,17 +37,20 @@ def main():
     # Write combo operation below
     ## Following procedure is important for correct generation of result data.
     ## search -> write(and update -> visualize)
-    for i in range(1):
+    for i in range(3):
         ci.search_next_param_random()
-        ci.write_result(random.random())  # write result
-    for i in range(1):
+        result = get_data_from_result_list(ci.get_next_index())  # get result/evaluation data from experiment. (Result list is used for this test program).
+        ci.write_result(result)  # write result
+    for i in range(17):
         ci.search_next_param_bayes()
-        ci.write_result(random.random())  # write result
-
-    raw_input('Press enter to save and finish\n')
+        result = get_data_from_result_list(ci.get_next_index())
+        ci.write_result(result)  # write result
 
+    #raw_input('Press enter to save and finish\n')
     ci.save_data(policy_save_dir)
 
+    assert filecmp.cmp(candidates_path, correct_candidates_path)
+
 
 if __name__ == '__main__':
-    main()
+    test_combo_interface()

From 948a9c41c14dbac6adddf7aaea3351bb52a4dd7d Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 14:08:57 +0900
Subject: [PATCH 15/23] display

---
 .github/workflows/bayesopt_interfaces.yaml                | 8 +++++++-
 .../bayesopt_interfaces/tests/test_combo_interface.py     | 4 ----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index c1a38f8..fd91624 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -59,4 +59,10 @@ jobs:
         run: |
           pip install ml_interfaces/bayesopt_interfaces
       - name: Run pytest
-        run: pytest -v ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+        run: |
+          disp=:99
+          screen=0
+          geom=640x480x24
+          exec Xvfb $disp -screen $screen $geom 2>/tmp/Xvfb.log &
+          export DISPLAY=:99
+          pytest -v ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index 9dc06eb..a08c16a 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -50,7 +50,3 @@ def test_combo_interface():
     ci.save_data(policy_save_dir)
 
     assert filecmp.cmp(candidates_path, correct_candidates_path)
-
-
-if __name__ == '__main__':
-    test_combo_interface()

From 2b055b67f5c9d5681e6a9f8d69a7086a2c19459f Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 14:32:46 +0900
Subject: [PATCH 16/23] fix viaulization

---
 .github/workflows/bayesopt_interfaces.yaml          | 10 +++++-----
 .../bayesopt_if/combo_interface.py                  | 13 ++++++++-----
 .../bayesopt_if/physbo_interface.py                 |  3 ++-
 .../tests/test_combo_interface.py                   |  2 +-
 4 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index fd91624..bab8e75 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -60,9 +60,9 @@ jobs:
           pip install ml_interfaces/bayesopt_interfaces
       - name: Run pytest
         run: |
-          disp=:99
-          screen=0
-          geom=640x480x24
-          exec Xvfb $disp -screen $screen $geom 2>/tmp/Xvfb.log &
-          export DISPLAY=:99
+          #disp=:99
+          #screen=0
+          #geom=640x480x24
+          #exec Xvfb $disp -screen $screen $geom 2>/tmp/Xvfb.log &
+          #export DISPLAY=:99
           pytest -v ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
diff --git a/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py b/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py
index 592ae83..bf74711 100755
--- a/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py
@@ -20,7 +20,7 @@
 
 
 class ComboInterface():
-    def __init__(self, bayesopt, candidates_path='candidates.csv', policy_load_dir='.', policy_save_dir='.', use_saved_policy=False, search_score='PI'):
+    def __init__(self, bayesopt, candidates_path='candidates.csv', policy_load_dir='.', policy_save_dir='.', use_saved_policy=False, visualize=True, search_score='PI'):
         self.data = None
         self.X = None
         self.actions = None
@@ -32,6 +32,7 @@ def __init__(self, bayesopt, candidates_path='candidates.csv', policy_load_dir='
         self.policy_load_dir = policy_load_dir
         self.policy_save_dir = policy_save_dir
         self.use_saved_policy = use_saved_policy
+        self.visualize = visualize
         self.search_mode = 0  # 0: random search, 1: bayes
         self.search_score = search_score  # score: PI, EI, TS
         self.is_write_completed = False
@@ -54,10 +55,11 @@ def start_bayesopt(self):
             self.generate_policy()
 
         # for visualization
-        self.fig, self.ax = plt.subplots(2, 1, tight_layout=True)  # avoid overlap of labels
+        if self.visualize:
+            self.fig, self.ax = plt.subplots(2, 1, tight_layout=True)  # avoid overlap of labels
 
-        # visualize
-        self.visualize()
+            # visualize
+            self.visualize()
 
 
     def load_dataset(self):
@@ -214,7 +216,8 @@ def save_candidates_with_scores(self, policy_save_dir='.'):
 
     def save_plt(self, policy_save_dir='.'):
         # update before save
-        self.visualize()
+        if self.visualize:
+            self.visualize()
         # save plot
         plt_save_path_png = os.path.join(policy_save_dir, 'plt.png')
         plt_save_path_pdf = os.path.join(policy_save_dir, 'plt.pdf')
diff --git a/ml_interfaces/bayesopt_interfaces/bayesopt_if/physbo_interface.py b/ml_interfaces/bayesopt_interfaces/bayesopt_if/physbo_interface.py
index d3d347e..c295a54 100755
--- a/ml_interfaces/bayesopt_interfaces/bayesopt_if/physbo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/bayesopt_if/physbo_interface.py
@@ -10,7 +10,7 @@
 
 
 class PhysboInterface(ComboInterface):
-    def __init__(self, candidates_path='candidates.csv', policy_load_dir='.', policy_save_dir='.', use_saved_policy=False, search_score='PI'):
+    def __init__(self, candidates_path='candidates.csv', policy_load_dir='.', policy_save_dir='.', use_saved_policy=False, visualize=True, search_score='PI'):
         self.candidates_path = candidates_path
         self.policy_load_dir = policy_load_dir
         self.policy_save_dir = policy_save_dir
@@ -24,6 +24,7 @@ def __init__(self, candidates_path='candidates.csv', policy_load_dir='.', policy
                          self.policy_load_dir,
                          self.policy_save_dir,
                          self.use_saved_policy,
+                         self.visualize,
                          self.search_score)  # python3 description
 
 
diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index a08c16a..5889622 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -31,7 +31,7 @@ def test_combo_interface():
     policy_save_dir = os.path.join(data_dir, 'result')
 
     # Generate combo
-    ci = ComboInterface(combo, candidates_path, policy_load_dir, policy_save_dir, use_saved_policy=False)
+    ci = ComboInterface(combo, candidates_path, policy_load_dir, policy_save_dir, use_saved_policy=False, visualize=False)
     ci.start_bayesopt()
 
     # Write combo operation below

From 95bf741779998ec4fc8818de066e04213d95ff26 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 14:43:04 +0900
Subject: [PATCH 17/23] fix

---
 ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index 5889622..952754e 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -41,7 +41,7 @@ def test_combo_interface():
         ci.search_next_param_random()
         result = get_data_from_result_list(ci.get_next_index())  # get result/evaluation data from experiment. (Result list is used for this test program).
         ci.write_result(result)  # write result
-    for i in range(17):
+    for i in range(16):
         ci.search_next_param_bayes()
         result = get_data_from_result_list(ci.get_next_index())
         ci.write_result(result)  # write result

From 604cd141eb3c3b36eb3c738fe668c80699eab71d Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 15:01:32 +0900
Subject: [PATCH 18/23] mod

---
 .github/workflows/bayesopt_interfaces.yaml | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/.github/workflows/bayesopt_interfaces.yaml b/.github/workflows/bayesopt_interfaces.yaml
index bab8e75..1aee45d 100644
--- a/.github/workflows/bayesopt_interfaces.yaml
+++ b/.github/workflows/bayesopt_interfaces.yaml
@@ -32,18 +32,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        #python-version: [2.7]
         os: [ubuntu-20.04]
     container:
         image: python:2.7.18-buster
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-
-      #- name: Set up Python ${{ matrix.python-version }}
-      #  uses: actions/setup-python@v5
-      #  with:
-      #    python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools
@@ -60,9 +54,4 @@ jobs:
           pip install ml_interfaces/bayesopt_interfaces
       - name: Run pytest
         run: |
-          #disp=:99
-          #screen=0
-          #geom=640x480x24
-          #exec Xvfb $disp -screen $screen $geom 2>/tmp/Xvfb.log &
-          #export DISPLAY=:99
           pytest -v ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py

From 2341f16fddde03825d081b5a5f0f31f9785ca78e Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 15:02:28 +0900
Subject: [PATCH 19/23] mod

---
 .../bayesopt_interfaces/tests/test_combo_interface.py        | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index 952754e..b0a8932 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -23,6 +23,7 @@ def get_data_from_result_list(index):
     return float(l[index+1][0])
 
 
+@pytest.mark.filterwarnings("ignore:SettingWithCopyWarning")
 def test_combo_interface():
     # dir setting
     candidates_path  = os.path.join(data_dir, 'candidates.csv')
@@ -41,10 +42,10 @@ def test_combo_interface():
         ci.search_next_param_random()
         result = get_data_from_result_list(ci.get_next_index())  # get result/evaluation data from experiment. (Result list is used for this test program).
         ci.write_result(result)  # write result
-    for i in range(16):
+    for i in range(17):
         ci.search_next_param_bayes()
         result = get_data_from_result_list(ci.get_next_index())
-        ci.write_result(result)  # write result
+        ci.write_result(result)
 
     #raw_input('Press enter to save and finish\n')
     ci.save_data(policy_save_dir)

From 78dd9e05cc85ae2032a39d9e3c5a4ac76097f263 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 15:09:18 +0900
Subject: [PATCH 20/23] mod

---
 ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index b0a8932..42c050b 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -4,6 +4,7 @@
 import csv
 import filecmp
 import os
+import pytest
 import random
 import sys
 

From c12540aa7b732da9dfab6bfc172fe8498070252c Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 15:15:36 +0900
Subject: [PATCH 21/23] mod

---
 .../bayesopt_interfaces/bayesopt_if/combo_interface.py      | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py b/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py
index bf74711..a7cb755 100755
--- a/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/bayesopt_if/combo_interface.py
@@ -171,7 +171,8 @@ def save_data(self, policy_save_dir='.'):
         self.save_policy(self.policy_save_dir)
         self.save_candidates_and_actions(self.policy_save_dir)  # csv
         self.save_candidates_with_scores(self.policy_save_dir)  # csv
-        self.save_plt(self.policy_save_dir)
+        if self.visualize:
+            self.save_plt(self.policy_save_dir)
 
 
     def save_policy(self, policy_save_dir='.'):
@@ -216,8 +217,7 @@ def save_candidates_with_scores(self, policy_save_dir='.'):
 
     def save_plt(self, policy_save_dir='.'):
         # update before save
-        if self.visualize:
-            self.visualize()
+        self.visualize()
         # save plot
         plt_save_path_png = os.path.join(policy_save_dir, 'plt.png')
         plt_save_path_pdf = os.path.join(policy_save_dir, 'plt.pdf')

From 42be4ecdb6e06860c6e1319a2599299a9211e3f1 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 15:18:02 +0900
Subject: [PATCH 22/23] mod

---
 ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
index 42c050b..78221b2 100755
--- a/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
+++ b/ml_interfaces/bayesopt_interfaces/tests/test_combo_interface.py
@@ -4,7 +4,6 @@
 import csv
 import filecmp
 import os
-import pytest
 import random
 import sys
 
@@ -24,7 +23,6 @@ def get_data_from_result_list(index):
     return float(l[index+1][0])
 
 
-@pytest.mark.filterwarnings("ignore:SettingWithCopyWarning")
 def test_combo_interface():
     # dir setting
     candidates_path  = os.path.join(data_dir, 'candidates.csv')

From 86110a305bd7ad0c34f849584f6a2a286e45e4c5 Mon Sep 17 00:00:00 2001
From: Yuki Asano <yasano@g.ecc.u-tokyo.ac.jp>
Date: Wed, 12 Feb 2025 15:18:10 +0900
Subject: [PATCH 23/23] mod gitignore

---
 ml_interfaces/bayesopt_interfaces/.gitignore | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/ml_interfaces/bayesopt_interfaces/.gitignore b/ml_interfaces/bayesopt_interfaces/.gitignore
index ff043ed..6dfb7ca 100644
--- a/ml_interfaces/bayesopt_interfaces/.gitignore
+++ b/ml_interfaces/bayesopt_interfaces/.gitignore
@@ -1,2 +1,6 @@
 *.~
-*.pyc
\ No newline at end of file
+*.pyc
+examples/data/chosen_actions.csv
+examples/data/result
+tests/data/chosed_actions.csv
+tests/data/result