Move xenonpy to poetry and devcontainer

.devcontainer/Dockerfile

@@ -0,0 +1,52 @@
+ARG VARIANT=jammy
+FROM mcr.microsoft.com/devcontainers/base:${VARIANT}
+# FROM mcr.microsoft.com/devcontainers/base:jammy 
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG USER=vscode
+
+RUN DEBIAN_FRONTEND=noninteractive \
+    && apt-get update \ 
+    && apt-get install -y build-essential --no-install-recommends make \
+    ca-certificates \
+    git \
+    libssl-dev \
+    zlib1g-dev \
+    libbz2-dev \
+    libreadline-dev \
+    libsqlite3-dev \
+    wget \
+    curl \
+    zsh \
+    llvm \
+    libncurses5-dev \
+    xz-utils \
+    tk-dev \
+    libxml2-dev \
+    libxmlsec1-dev \
+    libffi-dev \
+    liblzma-dev
+
+# Python and poetry installation
+USER $USER
+ARG HOME="/home/$USER"
+ARG PYTHON_VERSION=3.11
+# ARG PYTHON_VERSION=3.10
+
+ENV PYENV_ROOT="${HOME}/.pyenv"
+ENV PATH="${PYENV_ROOT}/shims:${PYENV_ROOT}/bin:${HOME}/.local/bin:$PATH"
+
+COPY ../pyproject.toml ./
+RUN echo "done 0" \
+    && curl https://pyenv.run | bash \
+    && echo "done 1" \
+    && pyenv install ${PYTHON_VERSION} \
+    && echo "done 2" \
+    && pyenv global ${PYTHON_VERSION} \
+    && echo "done 3" \
+    && curl -sSL https://install.python-poetry.org | python3 - \
+    && poetry config virtualenvs.in-project true \
+    && poetry install --no-root
+
+# expose port
+EXPOSE 8888

.devcontainer/devcontainer.json

@@ -0,0 +1,53 @@
+{
+    "name": "Python 3",
+    // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+    "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bookworm",
+
+    // 👇 Features to add to the Dev Container. More info: https://containers.dev/implementors/features.
+    "features": {
+        "ghcr.io/devcontainers-contrib/features/poetry:2": {
+            "version": "latest"
+        },
+        "ghcr.io/nils-geistmann/devcontainers-features/zsh:0": {
+            "setLocale": true,
+            "theme": "robbyrussell",
+            "plugins": "git poetry",
+            "desiredLocale": "en_US.UTF-8 UTF-8"
+        },
+        "ghcr.io/akhildevelops/devcontainer-features/apt:0": {
+            "PACKAGES": "wget,curl,git,make,ca-certificates,libreadline-dev,libsqlite3-dev,libncurses5-dev,xz-utils,libffi-dev,liblzma-dev,llvm,build-essential"
+        },
+        // "ghcr.io/nikobockerman/devcontainer-features/poetry-persistent-cache:1": {}
+    },
+
+    // 👇 Use 'forwardPorts' to make a list of ports inside the container available locally.
+    "forwardPorts": [8888],
+
+    // 👇 Use 'postCreateCommand' to run commands after the container is created.
+    "postCreateCommand": "poetry config virtualenvs.in-project true && poetry install --no-root",
+
+    // 👇 Configure tool-specific properties.
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "njpwerner.autodocstring",
+                "ms-python.vscode-pylance",
+                "streetsidesoftware.code-spell-checker",
+                "tamasfe.even-better-toml",
+                "charliermarsh.ruff",
+                "ms-vscode.makefile-tools",
+                "ms-azuretools.vscode-docker"
+            ],
+            "settings": {
+                "terminal.integrated.defaultProfile.linux": "zsh",
+                "terminal.integrated.profiles.linux": {
+                    "zsh": {
+                        "path": "/bin/zsh",
+                        "args": ["-l"]
+                    }
+                }
+            }
+        }
+    }
+}

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+  - package-ecosystem: "devcontainers"
+    directory: "/"
+    schedule:
+      interval: weekly

.gitignore

@@ -106,7 +106,6 @@ venv.bak/
 # *.csv
 tags
 .idea/
-.vscode/
 pyinstrument
 
 .pytest_cache/

.vscode/launch.json

@@ -0,0 +1,15 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python Debugger",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "console": "internalConsole"
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,27 @@
+{
+    //Python
+    "[python]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "always"
+        }
+    },
+
+    //toml
+    "[toml]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "tamasfe.even-better-toml"
+    },
+
+    //jupyter
+    "notebook.formatOnSave.enabled": true,
+    "notebook.codeActionsOnSave": {
+        "notebook.source.fixAll": "explicit",
+        "notebook.source.organizeImports": "explicit"
+    },
+
+    //autoDocstring
+    "autoDocstring.docstringFormat": "google"
+}

README.md

@@ -13,6 +13,8 @@
 
 # XenonPy project
 
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/yoshida-lab/XenonPy/tree/full-refactor-with-poetry?quickstart=1)
+
 [![MacOS](https://github.com/yoshida-lab/XenonPy/workflows/MacOS/badge.svg)](https://github.com/yoshida-lab/XenonPy/actions?query=workflow%3AMacOS)
 [![Windows](https://github.com/yoshida-lab/XenonPy/workflows/Windows/badge.svg)](https://github.com/yoshida-lab/XenonPy/actions?query=workflow%3AWindows)
 [![Ubuntu](https://github.com/yoshida-lab/XenonPy/workflows/Ubuntu/badge.svg)](https://github.com/yoshida-lab/XenonPy/actions?query=workflow%3AUbuntu)

conda_env/devtools/extra_env.yml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
 dependencies:
-  - yapf
+  - black
   - pytest
   - pytest-cov
   - pylint