diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 00000000..f95e75a2 --- /dev/null +++ b/.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 \ No newline at end of file diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..667e2a2f --- /dev/null +++ b/.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", + + // ๐Ÿ‘‡ 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": {} + }, + + // ๐Ÿ‘‡ Use 'forwardPorts' to make a list of ports inside the container available locally. + "forwardPorts": [8888], + + // ๐Ÿ‘‡ Use 'postCreateCommand' to run commands after the container is created. + "postCreateCommand": "poetry config virtualenvs.in-project true && poetry install --no-root", + + // ๐Ÿ‘‡ 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"] + } + } + } + } + } +} diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..9d8f2d04 --- /dev/null +++ b/.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 diff --git a/.gitignore b/.gitignore index 2fcaa491..4b8622a6 100644 --- a/.gitignore +++ b/.gitignore @@ -106,7 +106,6 @@ venv.bak/ # *.csv tags .idea/ -.vscode/ pyinstrument .pytest_cache/ diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index 60c5e3e0..00000000 --- a/.pylintrc +++ /dev/null @@ -1,15 +0,0 @@ -# Enable the message, report, category or checker with the given id(s). You can -# either give multiple identifier separated by comma (,) or put this option -# multiple time. -#enable= - -# Disable the message, report, category or checker with the given id(s). You -# can either give multiple identifier separated by comma (,) or put this option -# multiple time (only on the command line, not in the configuration file where -# it should appear only once). -#disable= - -[DESIGN] -# custom -max-attributes=15 -max-line-length=120 \ No newline at end of file diff --git a/.style.yapf b/.style.yapf deleted file mode 100644 index 3ab3ed33..00000000 --- a/.style.yapf +++ /dev/null @@ -1,5 +0,0 @@ -[style] -based_on_style = google - -# The column limit. -column_limit=120 diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 00000000..d9a262b9 --- /dev/null +++ b/.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" + } + ] +} diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..0a1c139e --- /dev/null +++ b/.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" +} diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 32ab7e72..00000000 --- a/Dockerfile +++ /dev/null @@ -1,15 +0,0 @@ -FROM yoshidalab/base:cuda11 - -ARG key -ENV api_key=$key - -# install xenonpy locally -WORKDIR /opt/xenonpy -COPY . . -RUN sudo chown -R user:user /opt && find . | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf && \ - pip install --user -v . && pytest tests -v && export api_key="" - -EXPOSE 8888 - -WORKDIR /workspace -CMD [ "jupyter" , "lab", "--ip=0.0.0.0", "--no-browser", "--port=8888", "--allow-root"] diff --git a/README.md b/README.md index 7e263b70..67492dbf 100644 --- a/README.md +++ b/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) diff --git a/conda_env/devtools/extra_env.yml b/conda_env/devtools/extra_env.yml index 57dc56d5..43bb210c 100644 --- a/conda_env/devtools/extra_env.yml +++ b/conda_env/devtools/extra_env.yml @@ -1,7 +1,7 @@ channels: - conda-forge dependencies: - - yapf + - black - pytest - pytest-cov - pylint diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..005940f5 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,4162 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "alabaster" +version = "0.7.16" +description = "A light, configurable Sphinx theme" +optional = false +python-versions = ">=3.9" +files = [ + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = 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