Merge remote-tracking branch 'origin/main' into update.main

.github/workflows/build_docs.yml

@@ -4,20 +4,20 @@ on: [push]
 
 jobs:
   check-build-doc:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Inject slug/short variables
       uses: rlespinasse/[email protected]
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: main
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
 
     - name: Prepare LaTeX env
       run: |

.github/workflows/deploy_docs.yml

@@ -3,35 +3,35 @@ name: upload docs to gh-pages
 on:
   push:
     branches:
-      - master
-      - develop
-      - ghactions
-      - '*-autodoc'
+      - main
+      # - develop
+      # - ghactions
+      # - '*-autodoc'
       - '!gh-pages'
-    tags: ['*']
+    # tags: ['*']
 
 jobs:
   deploy:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Inject slug/short variables
       uses: rlespinasse/[email protected]
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: main
 
     - name: Checkout gh-pages
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: gh-pages
         path: gh-pages
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
 
     - name: Prepare LaTeX env
       run: |
@@ -63,7 +63,7 @@ jobs:
 
     - name: Push
       env:
-        GIT_USER: "2DMAT Developers"
+        GIT_USER: "ODAT-SE Developers"
         GIT_EMAIL: "[email protected]"
         TARGET_NAME: ${{ env.GITHUB_REF_SLUG }}
       run: |
@@ -76,7 +76,7 @@ jobs:
             mkdir -p "gh-pages/manual/${TARGET_NAME}"
             cp -r "main/doc/${lang}/build/html" "gh-pages/manual/${TARGET_NAME}/${lang}"
             if [ $is_tag = "YES" ]; then
-              # cp "main/doc/${lang}/build/latex/userguid_2dmat_${lang}.pdf" "gh-pages/manual/${TARGET_NAME}/${lang}/2DMAT.pdf"
+              # cp "main/doc/${lang}/build/latex/userguid_odatse_${lang}.pdf" "gh-pages/manual/${TARGET_NAME}/${lang}/ODAT-SE.pdf"
               :
             fi
           done

.github/workflows/deploy_pypi.yml

@@ -2,19 +2,20 @@ name: upload package to PyPI
 
 on:
   push:
-    tags: ['*']
+    # tags: ['*']
+    tags: ['disabled-because-odatse-is-not-yet-ready-in-pypi']
 
 jobs:
   deploy:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
 
     - name: Install python packages
       run: |

.github/workflows/main.yml

@@ -1,23 +1,27 @@
 name: Test
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   main:
-    runs-on: ubuntu-20.04
-    timeout-minutes: 10
     strategy:
       matrix:
-        python-version: [3.6, 3.9]
+        # os: ['ubuntu-22.04']
+        python-version: ['3.9', '3.12']
         sample: [mapper, minsearch, exchange, exchange_mesh, pamc, bayes, transform]
       fail-fast: false
 
+    name: ${{ matrix.sample }} with Python ${{ matrix.python-version }}
+    runs-on: 'ubuntu-22.04'
+    # runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -34,7 +38,7 @@ jobs:
           python -m pip install numpy scipy tomli mpi4py
           python -m pip install physbo
 
-      - name: ${{ matrix.algorithm }}
+      - name: ${{ matrix.sample }}
         run: |
           cd ${GITHUB_WORKSPACE}/tests/${{ matrix.sample }}
           sh ./do.sh

README.md

@@ -13,8 +13,8 @@ In the future, we plan to add other direct problem solvers and search algorithms
 
 | Branch |                Build status                 |                                       Documentation                                       |
 | :----: | :-----------------------------------------: | :---------------------------------------------------------------------------------------: |
-| [master][source/master] (latest, stable) | [![master][ci/master/badge]][ci/master/uri] |        [![doc_en][doc/en/badge]][doc/master/en/uri] [![doc_ja][doc/ja/badge]][doc/master/ja/uri]        |
-| [develop][source/develop] (latest, unstable) |                     --                      | [![doc_en][doc/en/badge]][doc/develop/en/uri] [![doc_ja][doc/ja/badge]][doc/develop/ja/uri] |
+| [main][source/main] (latest, stable) | [![main][ci/main/badge]][ci/main/uri] |        [![doc_en][doc/en/badge]][doc/main/en/uri] [![doc_ja][doc/ja/badge]][doc/main/ja/uri]        |
+<!-- | [develop][source/develop] (latest, unstable) |                     --                      | [![doc_en][doc/en/badge]][doc/develop/en/uri] [![doc_ja][doc/ja/badge]][doc/develop/ja/uri] | -->
 
 ## odat-se
 
@@ -24,7 +24,7 @@ It also offers a driver script to solve the problem with predefined optimization
 ### Prerequists
 
 - Required
-  - python >= 3.6.8
+  - python >= 3.9
   - numpy >= 1.14
   - tomli >= 1.2.0
 - Optional
@@ -98,13 +98,13 @@ Bibtex:
 © *2020- The University of Tokyo. All rights reserved.*
 This software was developed with the support of "*Project for advancement of software usability in materials science*" of The Institute for Solid State Physics, The University of Tokyo.
 
-[source/master]: https://github.com/issp-center-dev/ODAT-SE/
+[source/main]: https://github.com/issp-center-dev/ODAT-SE/
 [source/develop]: https://github.com/issp-center-dev/ODAT-SE/tree/develop
-[ci/master/badge]: https://github.com/issp-center-dev/ODAT-SE/workflows/Test/badge.svg?branch=master
-[ci/master/uri]: https://github.com/issp-center-dev/ODAT-SE/actions?query=branch%3Amaster
+[ci/main/badge]: https://github.com/issp-center-dev/ODAT-SE/workflows/Test/badge.svg?branch=main
+[ci/main/uri]: https://github.com/issp-center-dev/ODAT-SE/actions?query=branch%3Amain
 [doc/en/badge]: https://img.shields.io/badge/doc-English-blue.svg
 [doc/ja/badge]: https://img.shields.io/badge/doc-Japanese-blue.svg
-[doc/master/en/uri]: https://issp-center-dev.github.io/ODAT-SE/manual/master/en/index.html
-[doc/master/ja/uri]: https://issp-center-dev.github.io/ODAT-SE/manual/master/ja/index.html
+[doc/main/en/uri]: https://issp-center-dev.github.io/ODAT-SE/manual/main/en/index.html
+[doc/main/ja/uri]: https://issp-center-dev.github.io/ODAT-SE/manual/main/ja/index.html
 [doc/develop/en/uri]: https://issp-center-dev.github.io/ODAT-SE/manual/develop/en/index.html
 [doc/develop/ja/uri]: https://issp-center-dev.github.io/ODAT-SE/manual/develop/ja/index.html

doc/en/source/start.rst

@@ -3,7 +3,7 @@ Installation of ODAT-SE
 
 Prerequisites
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- Python3 (>=3.6.8)
+- Python3 (>=3.9)
 
     - The following Python packages are required.
         - tomli >= 1.2
@@ -13,7 +13,7 @@ Prerequisites
 
         - mpi4py (required for grid search)
         - scipy (required for Nelder-Mead method)
-        - physbo (>=0.3, required for Baysian optimization)
+        - physbo (>=2.0, required for Baysian optimization)
 
 
 How to download and install

doc/ja/source/introduction.rst

@@ -4,7 +4,7 @@
 ODAT-SEとは
 ----------------------
 
-Open Data Analysis Tool for Science and Engineering (ODAT-SE)は、順問題ソルバーに対して探索アルゴリズムを適用して最適解を探すためのフレームワークです。これまで 2DMAT という名称で開発されてきましたが、Version 3 からは順問題ソルバーと探索アルゴリズムをモジュール化して汎用のデータ解析プラットフォームとして整備しています。
+Open Data Analysis Tool for Science and Engineering (ODAT-SE)は、順問題ソルバーに対して探索アルゴリズムを適用して最適解を探すためのフレームワークです。Version 2までは2DMATという名称で開発されてきましたが、Version 3からは順問題ソルバーと探索アルゴリズムをモジュール化した汎用のデータ解析プラットフォームとして整備しています。
 
 順問題ソルバーはユーザー自身で定義することが可能です。
 標準的な順問題ソルバーとしては2次元物質構造解析向け実験データ解析ソフトウェアが用意されています。

doc/ja/source/start.rst

@@ -3,7 +3,7 @@ ODAT-SE のインストール
 
 実行環境・必要なパッケージ
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- python 3.6.8 以上
+- python 3.9 以上
 
     - 必要なpythonパッケージ
 
@@ -14,7 +14,7 @@ ODAT-SE のインストール
 
         - mpi4py (グリッド探索利用時)
         - scipy (Nelder-Mead法利用時)
-        - physbo (ベイズ最適化利用時, ver. 0.3以上)
+        - physbo (ベイズ最適化利用時, ver. 2.0以上)
 
 ダウンロード・インストール
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

pyproject.toml

@@ -13,7 +13,7 @@ packages = [
   ]
 
 [tool.poetry.dependencies]
-python = ">=3.6.8"
+python = ">=3.9"
 numpy = "^1.14"
 tomli = ">=1.2"
 scipy = {version = "^1", optional = true}
@@ -26,10 +26,6 @@ bayes = ["physbo"]
 exchange = ["mpi4py"]
 all = ["scipy", "mpi4py", "physbo"]
 
-[tool.poetry.dev-dependencies]
-black = "^22.3.0"
-pynvim = "^0.4.3"
-
 [tool.poetry.scripts]
 odatse = "odatse:main"
 odatse_neighborlist = "odatse.util.neighborlist:main"

src/odatse/_info.py

@@ -26,18 +26,43 @@
 
 
 class Info:
+    """
+    A class to represent the information structure for the data-analysis software.
+    """
+
     base: dict
     algorithm: dict
     solver: dict
     runner: dict
 
     def __init__(self, d: Optional[MutableMapping] = None):
+        """
+        Initialize the Info object.
+
+        Parameters
+        ----------
+        d : MutableMapping (optional)
+            A dictionary to initialize the Info object.
+        """
         if d is not None:
             self.from_dict(d)
         else:
             self._cleanup()
 
     def from_dict(self, d: MutableMapping) -> None:
+        """
+        Initialize the Info object from a dictionary.
+
+        Parameters
+        ----------
+        d : MutableMapping
+            A dictionary containing the information to initialize the Info object.
+
+        Raises
+        ------
+        exception.InputError
+            If any required section is missing in the input dictionary.
+        """
         for section in ["base", "algorithm", "solver"]:
             if section not in d:
                 raise exception.InputError(
@@ -58,6 +83,9 @@ def from_dict(self, d: MutableMapping) -> None:
         )
 
     def _cleanup(self) -> None:
+        """
+        Reset the Info object to its default state.
+        """
         self.base = {}
         self.base["root_dir"] = Path(".").absolute()
         self.base["output_dir"] = self.base["root_dir"]
@@ -67,6 +95,28 @@ def _cleanup(self) -> None:
 
     @classmethod
     def from_file(cls, file_name, fmt="", **kwargs):
+        """
+        Create an Info object from a file.
+
+        Parameters
+        ----------
+        file_name : str
+            The name of the file to load the information from.
+        fmt : str
+            The format of the file (default is "").
+        **kwargs
+            Additional keyword arguments.
+
+        Returns
+        -------
+        Info
+            An Info object initialized with the data from the file.
+
+        Raises
+        ------
+        ValueError
+            If the file format is unsupported.
+        """
         if fmt == "toml" or fnmatch(file_name.lower(), "*.toml"):
             inp = {}
             if mpi.rank() == 0:

src/odatse/_main.py

@@ -18,7 +18,14 @@
 import odatse
 
 def main():
+    """
+    Main function to run the data-analysis software for quantum beam diffraction experiments
+    on 2D material structures. It parses command-line arguments, loads the input file,
+    selects the appropriate algorithm and solver, and executes the analysis.
+    """
+
     info, run_mode = odatse.initialize()
+
     alg_module = odatse.algorithm.choose_algorithm(info.algorithm["name"])
 
     solvername = info.solver["name"]