From 19615c073631d6994d0fe957c7630b7a17f8ea06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Xavier=20Go=C3=A1s=20Aguililla?= Date: Wed, 19 Feb 2025 08:15:15 +0000 Subject: [PATCH] chore: rescaffold with Substrate --- .copier-answers.yml | 13 + .cruft.json | 29 - .devcontainer/devcontainer.json | 33 +- .dockerignore | 3 + .github/workflows/publish.yml | 16 +- .github/workflows/test.yml | 15 +- .gitignore | 12 +- .pre-commit-config.yaml | 21 +- Dockerfile | 108 +- README.md | 60 +- docker-compose.yml | 32 +- poetry.lock | 4133 ------------------------------- pyproject.toml | 97 +- uv.lock | 2413 ++++++++++++++++++ 14 files changed, 2561 insertions(+), 4424 deletions(-) create mode 100644 .copier-answers.yml delete mode 100644 .cruft.json delete mode 100644 poetry.lock create mode 100644 uv.lock diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..e2735b6 --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,13 @@ +_commit: v1.1.0 +_src_path: gh:superlinear-ai/substrate +author_email: laurent@superlinear.eu +author_name: Laurent Sorber +project_description: A Python package that adds conformal prediction of coherent quantiles + and intervals to any scikit-learn regressor or Darts forecaster. +project_name: Conformal Tights +project_type: package +project_url: https://github.com/superlinear-ai/conformal-tights +python_version: '3.10' +typing: strict +with_conventional_commits: true +with_typer_cli: false diff --git a/.cruft.json b/.cruft.json deleted file mode 100644 index 5f3a775..0000000 --- a/.cruft.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "template": "https://github.com/superlinear-ai/poetry-cookiecutter", - "commit": "0b4edb2d3ea619bfc3b2ffd440e2e95ca997f0f2", - "checkout": null, - "context": { - "cookiecutter": { - "project_type": "package", - "project_name": "Conformal Tights", - "project_description": "A Python package that adds conformal prediction of coherent quantiles and intervals to any scikit-learn regressor or Darts forecaster.", - "project_url": "https://github.com/superlinear-ai/conformal-tights", - "author_name": "Laurent Sorber", - "author_email": "laurent@superlinear.ai", - "python_version": "3.10", - "development_environment": "strict", - "with_conventional_commits": "1", - "with_fastapi_api": "0", - "with_typer_cli": "0", - "continuous_integration": "GitHub", - "private_package_repository_name": "", - "private_package_repository_url": "", - "__docker_image": "python:$PYTHON_VERSION-slim", - "__docstring_style": "NumPy", - "__project_name_kebab_case": "conformal-tights", - "__project_name_snake_case": "conformal_tights", - "_template": "https://github.com/superlinear-ai/poetry-cookiecutter" - } - }, - "directory": null -} diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ecb509c..3d6330a 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -3,10 +3,20 @@ "dockerComposeFile": "../docker-compose.yml", "service": "devcontainer", "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}/", - "remoteUser": "user", + "features": { + "ghcr.io/devcontainers/features/node:1": {}, + "ghcr.io/devcontainers-extra/features/starship": {} + }, "overrideCommand": true, - "postStartCommand": "cp --update /opt/build/poetry/poetry.lock /workspaces/${localWorkspaceFolderBasename}/ && mkdir -p /workspaces/${localWorkspaceFolderBasename}/.git/hooks/ && cp --update /opt/build/git/* /workspaces/${localWorkspaceFolderBasename}/.git/hooks/", + "postCreateCommand": "echo 'eval \"$(starship init bash)\"' >> ~/.bashrc", + "postStartCommand": "uv sync --python ${PYTHON_VERSION:-3.10} ${RESOLUTION_STRATEGY:+--resolution $RESOLUTION_STRATEGY} --all-extras && pre-commit install --install-hooks", "customizations": { + "jetbrains": { + "backend": "PyCharm", + "plugins": [ + "com.github.copilot" + ] + }, "vscode": { "extensions": [ "charliermarsh.ruff", @@ -41,8 +51,13 @@ 100 ], "files.autoSave": "onFocusChange", + "github.copilot.chat.agent.enabled": true, + "github.copilot.chat.edits.codesearch.enabled": true, "github.copilot.chat.edits.enabled": true, - "jupyter.kernels.excludePythonEnvironments": ["/usr/local/bin/python"], + "github.copilot.nextEditSuggestions.enabled": true, + "jupyter.kernels.excludePythonEnvironments": [ + "/usr/local/bin/python" + ], "mypy-type-checker.importStrategy": "fromEnvironment", "mypy-type-checker.preferDaemon": true, "notebook.codeActionsOnSave": { @@ -50,16 +65,16 @@ "notebook.source.organizeImports": "explicit" }, "notebook.formatOnSave.enabled": true, - "python.defaultInterpreterPath": "/opt/conformal-tights-env/bin/python", + "python.defaultInterpreterPath": "/opt/venv/bin/python", "python.terminal.activateEnvironment": false, "python.testing.pytestEnabled": true, "ruff.importStrategy": "fromEnvironment", "ruff.logLevel": "warning", - "terminal.integrated.defaultProfile.linux": "zsh", - "terminal.integrated.profiles.linux": { - "zsh": { - "path": "/usr/bin/zsh" - } + "terminal.integrated.env.linux": { + "GIT_EDITOR": "code --wait" + }, + "terminal.integrated.env.mac": { + "GIT_EDITOR": "code --wait" } } } diff --git a/.dockerignore b/.dockerignore index c17c79a..aa210ca 100644 --- a/.dockerignore +++ b/.dockerignore @@ -3,3 +3,6 @@ # Git .git/ + +# Python +.venv/ diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index fb01aa5..2f8b7ae 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -7,21 +7,15 @@ on: jobs: publish: - runs-on: ubuntu-latest + runs-on: ghcr.io/astral-sh/uv:3.10-bookworm steps: - name: Checkout uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.10" - - - name: Install Poetry - run: pip install --no-input poetry - - name: Publish package run: | - poetry config pypi-token.pypi "${{ secrets.POETRY_PYPI_TOKEN_PYPI }}" - poetry publish --build + uv build + uv publish + env: + UV_PUBLISH_TOKEN: ${{ secrets.UV_PUBLISH_TOKEN }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9cc343d..8d35212 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,9 +14,10 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.10", "3.12"] + resolution-strategy: ["highest", "lowest-direct"] - name: Python ${{ matrix.python-version }} + name: Python ${{ matrix.python-version }} (resolution=${{ matrix.resolution-strategy }}) steps: - name: Checkout @@ -28,21 +29,15 @@ jobs: node-version: 23 - name: Install @devcontainers/cli - run: npm install --location=global @devcontainers/cli@0.72.0 + run: npm install --location=global @devcontainers/cli@0.73.0 - name: Start Dev Container run: | git config --global init.defaultBranch main - PYTHON_VERSION=${{ matrix.python-version }} devcontainer up --workspace-folder . + PYTHON_VERSION=${{ matrix.python-version }} RESOLUTION_STRATEGY=${{ matrix.resolution-strategy }} devcontainer up --workspace-folder . - name: Lint package run: devcontainer exec --workspace-folder . poe lint - name: Test package run: devcontainer exec --workspace-folder . poe test - - - name: Upload coverage - uses: codecov/codecov-action@v5 - with: - files: reports/coverage.xml - token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore index 3b903be..35409ef 100644 --- a/.gitignore +++ b/.gitignore @@ -2,7 +2,7 @@ htmlcov/ reports/ -# cruft +# Copier *.rej # Data @@ -30,6 +30,9 @@ notebooks/ # macOS .DS_Store +# mise +mise.local.toml + # mypy .dmypy.json .mypy_cache/ @@ -37,10 +40,6 @@ notebooks/ # Node.js node_modules/ -# Poetry -.venv/ -dist/ - # PyCharm .idea/ @@ -52,7 +51,10 @@ dist/ # Python __pycache__/ +*.egg-info/ *.py[cdo] +.venv/ +dist/ # Ruff .ruff_cache/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d87be9a..59934b5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,13 +16,14 @@ repos: - id: rst-inline-touching-normal - id: text-unicode-replacement-char - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v5.0.0 hooks: - id: check-added-large-files - id: check-ast - id: check-builtin-literals - id: check-case-conflict - id: check-docstring-first + - id: check-illegal-windows-names - id: check-json - id: check-merge-conflict - id: check-shebang-scripts-are-executable @@ -51,6 +52,13 @@ repos: require_serial: true language: system stages: [commit-msg] + - id: uv-lock-check + name: uv lock check + entry: uv lock + args: ["--check"] + require_serial: true + language: system + pass_filenames: false - id: ruff-check name: ruff check entry: ruff check @@ -65,17 +73,6 @@ repos: require_serial: true language: system types_or: [python, pyi] - - id: shellcheck - name: shellcheck - entry: shellcheck - args: [--check-sourced] - language: system - types: [shell] - - id: poetry-check - name: poetry check - entry: poetry check - language: system - pass_filenames: false - id: mypy name: mypy entry: mypy diff --git a/Dockerfile b/Dockerfile index 4b7bb80..36a7e96 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,101 +1,17 @@ # syntax=docker/dockerfile:1 -ARG PYTHON_VERSION=3.10 -FROM python:$PYTHON_VERSION-slim AS base +FROM ghcr.io/astral-sh/uv:python3.10-bookworm AS dev -# Remove docker-clean so we can keep the apt cache in Docker build cache. -RUN rm /etc/apt/apt.conf.d/docker-clean +# Create and activate a virtual environment [1]. +# [1] https://docs.astral.sh/uv/concepts/projects/config/#project-environment-path +ENV VIRTUAL_ENV=/opt/venv +ENV PATH=$VIRTUAL_ENV/bin:$PATH +ENV UV_PROJECT_ENVIRONMENT=$VIRTUAL_ENV -# Configure Python to print tracebacks on crash [1], and to not buffer stdout and stderr [2]. -# [1] https://docs.python.org/3/using/cmdline.html#envvar-PYTHONFAULTHANDLER -# [2] https://docs.python.org/3/using/cmdline.html#envvar-PYTHONUNBUFFERED -ENV PYTHONFAULTHANDLER 1 -ENV PYTHONUNBUFFERED 1 - -# Create a non-root user and switch to it [1]. -# [1] https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user -ARG UID=1000 -ARG GID=$UID -RUN groupadd --gid $GID user && \ - useradd --create-home --gid $GID --uid $UID user --no-log-init && \ - chown user /opt/ -USER user - -# Create and activate a virtual environment. -ENV VIRTUAL_ENV /opt/conformal-tights-env -ENV PATH $VIRTUAL_ENV/bin:$PATH -RUN python -m venv $VIRTUAL_ENV - -# Set the working directory. -WORKDIR /workspaces/conformal-tights/ - - - -FROM base AS poetry - -USER root - -# Install Poetry in separate venv so it doesn't pollute the main venv. -ENV POETRY_VERSION 1.8.0 -ENV POETRY_VIRTUAL_ENV /opt/poetry-env -RUN --mount=type=cache,target=/root/.cache/pip/ \ - python -m venv $POETRY_VIRTUAL_ENV && \ - $POETRY_VIRTUAL_ENV/bin/pip install poetry~=$POETRY_VERSION && \ - ln -s $POETRY_VIRTUAL_ENV/bin/poetry /usr/local/bin/poetry - -# Install compilers that may be required for certain packages or platforms. -RUN --mount=type=cache,target=/var/cache/apt/ \ - --mount=type=cache,target=/var/lib/apt/ \ - apt-get update && \ - apt-get install --no-install-recommends --yes build-essential - -USER user - -# Install the run time Python dependencies in the virtual environment. -COPY --chown=user:user poetry.lock* pyproject.toml /workspaces/conformal-tights/ -RUN mkdir -p /home/user/.cache/pypoetry/ && mkdir -p /home/user/.config/pypoetry/ && \ - mkdir -p src/conformal_tights/ && touch src/conformal_tights/__init__.py && touch README.md -RUN --mount=type=cache,uid=$UID,gid=$GID,target=/home/user/.cache/pypoetry/ \ - poetry install --only main --all-extras --no-interaction - - - -FROM poetry AS dev - -# Install development tools: curl, git, gpg, ssh, starship, sudo, vim, and zsh. -USER root -RUN --mount=type=cache,target=/var/cache/apt/ \ - --mount=type=cache,target=/var/lib/apt/ \ - apt-get update && \ - apt-get install --no-install-recommends --yes curl git gnupg ssh sudo vim zsh && \ - sh -c "$(curl -fsSL https://starship.rs/install.sh)" -- "--yes" && \ - usermod --shell /usr/bin/zsh user && \ - echo 'user ALL=(root) NOPASSWD:ALL' > /etc/sudoers.d/user && chmod 0440 /etc/sudoers.d/user +# Tell Git that the workspace is safe to avoid 'detected dubious ownership in repository' warnings. RUN git config --system --add safe.directory '*' -USER user - -# Install the development Python dependencies in the virtual environment. -RUN --mount=type=cache,uid=$UID,gid=$GID,target=/home/user/.cache/pypoetry/ \ - poetry install --all-extras --no-interaction - -# Persist output generated during docker build so that we can restore it in the dev container. -COPY --chown=user:user .pre-commit-config.yaml /workspaces/conformal-tights/ -RUN mkdir -p /opt/build/poetry/ && cp poetry.lock /opt/build/poetry/ && \ - git init && pre-commit install --install-hooks && \ - mkdir -p /opt/build/git/ && cp .git/hooks/commit-msg .git/hooks/pre-commit /opt/build/git/ -# Configure the non-root user's shell. -ENV ANTIDOTE_VERSION 1.8.6 -RUN git clone --branch v$ANTIDOTE_VERSION --depth=1 https://github.com/mattmc3/antidote.git ~/.antidote/ && \ - echo 'zsh-users/zsh-syntax-highlighting' >> ~/.zsh_plugins.txt && \ - echo 'zsh-users/zsh-autosuggestions' >> ~/.zsh_plugins.txt && \ - echo 'source ~/.antidote/antidote.zsh' >> ~/.zshrc && \ - echo 'antidote load' >> ~/.zshrc && \ - echo 'eval "$(starship init zsh)"' >> ~/.zshrc && \ - echo 'HISTFILE=~/.history/.zsh_history' >> ~/.zshrc && \ - echo 'HISTSIZE=1000' >> ~/.zshrc && \ - echo 'SAVEHIST=1000' >> ~/.zshrc && \ - echo 'setopt share_history' >> ~/.zshrc && \ - echo 'bindkey "^[[A" history-beginning-search-backward' >> ~/.zshrc && \ - echo 'bindkey "^[[B" history-beginning-search-forward' >> ~/.zshrc && \ - mkdir ~/.history/ && \ - zsh -c 'source ~/.zshrc' +# Configure the user's shell. +RUN echo 'HISTFILE=~/.history/.bash_history' >> ~/.bashrc && \ + echo 'bind "\"\e[A\": history-search-backward"' >> ~/.bashrc && \ + echo 'bind "\"\e[B\": history-search-forward"' >> ~/.bashrc && \ + mkdir ~/.history/ diff --git a/README.md b/README.md index a65bc7d..cc4869e 100644 --- a/README.md +++ b/README.md @@ -254,15 +254,11 @@ plt.tight_layout()
Prerequisites -
-1. Set up Git to use SSH - 1. [Generate an SSH key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key) and [add the SSH key to your GitHub account](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account). 1. Configure SSH to automatically load your SSH keys: - ```sh cat << EOF >> ~/.ssh/config - + Host * AddKeysToAgent yes IgnoreUnknown UseKeychain @@ -270,46 +266,30 @@ plt.tight_layout() ForwardAgent yes EOF ``` - -
- -
-2. Install Docker - 1. [Install Docker Desktop](https://www.docker.com/get-started). - - *Linux only*: - - Export your user's user id and group id so that [files created in the Dev Container are owned by your user](https://github.com/moby/moby/issues/3206): - - ```sh - cat << EOF >> ~/.bashrc - - export UID=$(id --user) - export GID=$(id --group) - EOF - ``` - -
- -
-3. Install VS Code or PyCharm - 1. [Install VS Code](https://code.visualstudio.com/) and [VS Code's Dev Containers extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers). Alternatively, install [PyCharm](https://www.jetbrains.com/pycharm/download/). -2. *Optional:* install a [Nerd Font](https://www.nerdfonts.com/font-downloads) such as [FiraCode Nerd Font](https://github.com/ryanoasis/nerd-fonts/tree/master/patched-fonts/FiraCode) and [configure VS Code](https://github.com/tonsky/FiraCode/wiki/VS-Code-Instructions) or [configure PyCharm](https://github.com/tonsky/FiraCode/wiki/Intellij-products-instructions) to use it. - -
- -
+1. _Optional:_ install a [Nerd Font](https://www.nerdfonts.com/font-downloads) such as [FiraCode Nerd Font](https://github.com/ryanoasis/nerd-fonts/tree/master/patched-fonts/FiraCode) and [configure VS Code](https://github.com/tonsky/FiraCode/wiki/VS-Code-Instructions) or [PyCharm](https://github.com/tonsky/FiraCode/wiki/Intellij-products-instructions) to use it.
Development environments The following development environments are supported: -1. ⭐️ *GitHub Codespaces*: click on *Code* and select *Create codespace* to start a Dev Container with [GitHub Codespaces](https://github.com/features/codespaces). -1. ⭐️ *Dev Container (with container volume)*: click on [Open in Dev Containers](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/superlinear-ai/conformal-tights) to clone this repository in a container volume and create a Dev Container with VS Code. -1. *Dev Container*: clone this repository, open it with VS Code, and run Ctrl/⌘ + ⇧ + P → *Dev Containers: Reopen in Container*. -1. *PyCharm*: clone this repository, open it with PyCharm, and [configure Docker Compose as a remote interpreter](https://www.jetbrains.com/help/pycharm/using-docker-compose-as-a-remote-interpreter.html#docker-compose-remote) with the `dev` service. -1. *Terminal*: clone this repository, open it with your terminal, and run `docker compose up --detach dev` to start a Dev Container in the background, and then run `docker compose exec dev zsh` to open a shell prompt in the Dev Container. +1. ⭐️ _GitHub Codespaces_: click on [Open in GitHub Codespaces](https://github.com/codespaces/new/superlinear-ai/conformal-tights) to start developing in your browser. +1. ⭐️ _VS Code Dev Container (with container volume)_: click on [Open in Dev Containers](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/superlinear-ai/conformal-tights) to clone this repository in a container volume and create a Dev Container with VS Code. +1. ⭐️ _uv_: clone this repository and run the following from root of the repository: + ```sh + # Create and install a virtual environment + uv sync --python 3.10 --all-extras + + # Activate the virtual environment + source .venv/bin/activate + + # Install the pre-commit hooks + pre-commit install --install-hooks + ``` +1. _VS Code Dev Container_: clone this repository, open it with VS Code, and run Ctrl/⌘ + ⇧ + P → _Dev Containers: Reopen in Container_. +1. _PyCharm Dev Container_: clone this repository, open it with PyCharm, [create a Dev Container with Mount Sources](https://www.jetbrains.com/help/pycharm/start-dev-container-inside-ide.html), and [configure an existing Python interpreter](https://www.jetbrains.com/help/pycharm/configuring-python-interpreter.html#widget) at `/opt/venv/bin/python`.
@@ -318,8 +298,8 @@ The following development environments are supported: - This project follows the [Conventional Commits](https://www.conventionalcommits.org/) standard to automate [Semantic Versioning](https://semver.org/) and [Keep A Changelog](https://keepachangelog.com/) with [Commitizen](https://github.com/commitizen-tools/commitizen). - Run `poe` from within the development environment to print a list of [Poe the Poet](https://github.com/nat-n/poethepoet) tasks available to run on this project. -- Run `poetry add {package}` from within the development environment to install a run time dependency and add it to `pyproject.toml` and `poetry.lock`. Add `--group test` or `--group dev` to install a CI or development dependency, respectively. -- Run `poetry update` from within the development environment to upgrade all dependencies to the latest versions allowed by `pyproject.toml`. -- Run `cz bump` to bump the package's version, update the `CHANGELOG.md`, and create a git tag. +- Run `uv add {package}` from within the development environment to install a run time dependency and add it to `pyproject.toml` and `uv.lock`. Add `--dev` to install a development dependency. +- Run `uv sync --upgrade` from within the development environment to upgrade all dependencies to the latest versions allowed by `pyproject.toml`. Add `--only-dev` to upgrade the development dependencies only. +- Run `cz bump` to bump the package's version, update the `CHANGELOG.md`, and create a git tag. Then push the changes and the git tag with `git push origin main --tags`. diff --git a/docker-compose.yml b/docker-compose.yml index 9465f6c..c1d489e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,41 +1,13 @@ -version: "3.9" - services: devcontainer: build: - context: . target: dev - args: - PYTHON_VERSION: ${PYTHON_VERSION:-3.10} - UID: ${UID:-1000} - GID: ${GID:-1000} environment: - - POETRY_PYPI_TOKEN_PYPI + - UV_PUBLISH_TOKEN volumes: - ..:/workspaces - - command-history-volume:/home/user/.history/ - - dev: - extends: devcontainer - stdin_open: true - tty: true - entrypoint: [] - command: - [ - "sh", - "-c", - "sudo chown user $$SSH_AUTH_SOCK && cp --update /opt/build/poetry/poetry.lock /workspaces/conformal-tights/ && mkdir -p /workspaces/conformal-tights/.git/hooks/ && cp --update /opt/build/git/* /workspaces/conformal-tights/.git/hooks/ && zsh" - ] - environment: - - POETRY_PYPI_TOKEN_PYPI - - SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock - volumes: - - ~/.gitconfig:/etc/gitconfig - 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