chore: cruft update (#71)

Author: lsorber

.cruft.json

@@ -1,27 +1,26 @@
 {
-  "template": "[email protected]:radix-ai/poetry-cookiecutter.git",
-  "commit": "5abbc2191646a2082996a4e59b47b318859cc461",
+  "template": "[email protected]:radix-ai/poetry-cookiecutter",
+  "commit": "d789ff6aa6eebc31018020da4373e674d8c3b464",
   "checkout": null,
   "context": {
     "cookiecutter": {
       "package_name": "Graphchain",
       "package_description": "An efficient cache for the execution of dask graphs.",
       "package_url": "https://github.com/radix-ai/graphchain",
       "author_name": "Laurent Sorber",
-      "author_email": "[email protected]",
+      "author_email": "[email protected]",
+      "python_version": "3.8",
       "with_fastapi_api": "0",
       "with_jupyter_lab": "0",
       "with_pydantic_typing": "0",
+      "with_sentry_logging": "0",
       "with_streamlit_app": "0",
       "with_typer_cli": "0",
       "continuous_integration": "GitHub",
-      "sentry_dsn": "",
-      "sentry_org": "",
-      "sentry_project": "",
       "private_package_repository_name": "",
       "private_package_repository_url": "",
-      "_template": "[email protected]:radix-ai/poetry-cookiecutter.git"
+      "_template": "[email protected]:radix-ai/poetry-cookiecutter"
     }
   },
   "directory": null
-}
+}

.devcontainer/devcontainer.json

@@ -3,8 +3,9 @@
     "dockerComposeFile": "../docker-compose.yml",
     "service": "dev",
     "workspaceFolder": "/app/",
-    "initializeCommand": "mkdir -p ${POETRY_CACHE_DIR:-~/Library/Caches/pypoetry/}",
-    "onCreateCommand": "poe install",
+    "initializeCommand": "ssh-add --apple-load-keychain || true",
+    "overrideCommand": true,
+    "postStartCommand": "cp --update /var/lib/poetry/poetry.lock /app/ && mkdir -p /app/.git/hooks/ && cp --update /var/lib/git/* /app/.git/hooks/",
     "extensions": [
         "bungcip.better-toml",
         "eamodio.gitlens",
@@ -16,35 +17,28 @@
     ],
     "settings": {
         "coverage-gutters.coverageFileNames": [
-            "reports/coverage.xml"
+            "reports/coveragepy.xml"
         ],
         "editor.codeActionsOnSave": {
             "source.organizeImports": true
         },
-        "editor.formatOnPaste": false,
         "editor.formatOnSave": true,
         "editor.rulers": [
             100
         ],
         "files.autoSave": "onFocusChange",
-        "python.analysis.typeCheckingMode": "off",
-        "python.defaultInterpreterPath": "/usr/local/bin/python",
+        "python.defaultInterpreterPath": "/opt/app-env/bin/python",
         "python.formatting.provider": "black",
-        "python.languageServer": "Pylance",
         "python.linting.flake8Enabled": true,
         "python.linting.mypyEnabled": true,
         "python.linting.pydocstyleEnabled": true,
         "python.linting.pylintEnabled": false,
         "python.terminal.activateEnvironment": false,
-        "python.terminal.activateEnvInCurrentTerminal": false,
-        "python.testing.nosetestsEnabled": false,
         "python.testing.pytestEnabled": true,
-        "python.testing.unittestEnabled": false,
-        "terminal.integrated.defaultProfile.linux": "fish",
-        "terminal.integrated.inheritEnv": false,
+        "terminal.integrated.defaultProfile.linux": "zsh",
         "terminal.integrated.profiles.linux": {
-            "fish": {
-                "path": "/usr/bin/fish"
+            "zsh": {
+                "path": "/usr/bin/zsh"
             }
         }
     }

.flake8

@@ -1,11 +1,13 @@
-# TODO: https://github.com/PyCQA/flake8/issues/234
-# TODO: https://github.com/terrencepreilly/darglint/issues/130
+[flake8]
 # http://flake8.pycqa.org/en/latest/user/configuration.html#project-configuration
 # https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#line-length
-[flake8]
+# TODO: https://github.com/PyCQA/flake8/issues/234
+doctests = True
+ignore = B019,DAR103,E203,E501,FS003,S101,W503
 max_line_length = 100
 max_complexity = 10
+
+# https://github.com/terrencepreilly/darglint#flake8
+# TODO: https://github.com/terrencepreilly/darglint/issues/130
 docstring_style = numpy
-doctests = True
-ignore = DAR103,E203,E501,FS003,S101,W503
-strictness = long
+strictness = long

.github/dependabot.yml

@@ -8,4 +8,4 @@ updates:
   - package-ecosystem: pip
     directory: /
     schedule:
-      interval: weekly
+      interval: monthly

.github/workflows/publish.yml

@@ -14,10 +14,10 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: "3.8"
 
@@ -26,5 +26,5 @@ jobs:
 
       - name: Publish package
         run: |
-          poetry config http-basic.pypi "__token__" "${{ secrets.POETRY_PYPI_TOKEN_PYPI }}"
+          poetry config pypi-token.pypi "${{ secrets.POETRY_PYPI_TOKEN_PYPI }}"
           poetry publish --build

.github/workflows/test.yml

@@ -22,17 +22,17 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache Python environment
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
-          path: .venv
+          path: .venv/
           key: venv-${{ runner.os }}-py${{ matrix.python-version }}-${{ hashFiles('poetry.lock') }}
 
       - name: Install Poetry
@@ -50,6 +50,6 @@ jobs:
         run: poetry run poe test
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
           files: reports/coverage.xml

.gitignore

@@ -46,6 +46,9 @@ dist/
 # PyCharm
 .idea/
 
+# pyenv
+.python-version
+
 # pytest
 .pytest_cache/
 

.pre-commit-config.yaml

@@ -1,4 +1,5 @@
 # https://pre-commit.com
+default_install_hook_types: [commit-msg, pre-commit]
 default_stages: [commit, manual]
 fail_fast: true
 repos:
@@ -48,18 +49,18 @@ repos:
         require_serial: true
         language: system
         stages: [commit-msg]
-      - id: isort
-        name: isort
-        entry: isort
-        require_serial: true
-        language: system
-        types: [python]
       - id: pyupgrade
         name: pyupgrade
         entry: pyupgrade --py38-plus
         require_serial: true
         language: system
         types: [python]
+      - id: isort
+        name: isort
+        entry: isort
+        require_serial: true
+        language: system
+        types: [python]
       - id: black
         name: black
         entry: black
@@ -76,11 +77,6 @@ repos:
         entry: flake8
         language: system
         types: [python]
-      - id: mypy
-        name: mypy
-        entry: mypy
-        language: system
-        types: [python]
       - id: pydocstyle
         name: pydocstyle
         entry: pydocstyle
@@ -92,3 +88,8 @@ repos:
         language: system
         files: pyproject.toml
         pass_filenames: false
+      - id: mypy
+        name: mypy
+        entry: mypy
+        language: system
+        types: [python]

Dockerfile

@@ -1,48 +1,54 @@
 # syntax=docker/dockerfile:experimental
-
-FROM python:3.8-slim AS dev
-
-# Install development tools: compilers, curl, fish, git, ssh, and starship.
-RUN apt-get update && \
-    apt-get install --no-install-recommends --yes build-essential curl git fish ssh && \
-    chsh --shell /usr/bin/fish && \
-    sh -c "$(curl -fsSL https://starship.rs/install.sh)" -- "--yes" && \
-    mkdir -p ~/.config/fish/completions/ && \
-    echo "set fish_greeting" >> ~/.config/fish/config.fish && \
-    echo "starship init fish | source" >> ~/.config/fish/config.fish && \
-    rm -rf /var/lib/apt/lists/*
+FROM python:3.8-slim AS base
 
 # 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
 
+# Install Poetry.
+ENV POETRY_VERSION 1.1.13
+RUN --mount=type=cache,id=poetry,target=/root/.cache/ pip install poetry==$POETRY_VERSION
+
+# Create and activate a virtual environment.
+RUN python -m venv /opt/app-env
+ENV PATH /opt/app-env/bin:$PATH
+ENV VIRTUAL_ENV /opt/app-env
+
 # Set the working directory.
 WORKDIR /app/
 
-# Install base development environment with Poetry and Poe the Poet.
-ENV PATH /root/.local/bin/:$PATH
-RUN --mount=type=cache,target=/root/.cache \
-    pip install --no-input --upgrade pip poethepoet && \
-    curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | python - && \
-    poetry config virtualenvs.create false && \
-    poetry completions fish > ~/.config/fish/completions/poetry.fish && \
-    poe _fish_completion > ~/.config/fish/completions/poe.fish
-
-# Let Poe the Poet know it doesn't need to activate the Python environment.
-ENV POETRY_ACTIVE 1
+FROM base as dev
 
-# Enable Poetry to publish to PyPI [1].
-# [1] https://pythonspeed.com/articles/build-secrets-docker-compose/
-ARG POETRY_PYPI_TOKEN_PYPI
-ENV POETRY_PYPI_TOKEN_PYPI $POETRY_PYPI_TOKEN_PYPI
+# Install development tools: compilers, curl, git, gpg, ssh, starship, vim, and zsh.
+RUN rm /etc/apt/apt.conf.d/docker-clean
+RUN --mount=type=cache,id=apt-cache,target=/var/cache/apt/ \
+    --mount=type=cache,id=apt-lib,target=/var/lib/apt/ \
+    apt-get update && \
+    apt-get install --no-install-recommends --yes build-essential curl git gnupg ssh vim zsh zsh-antigen && \
+    chsh --shell /usr/bin/zsh && \
+    sh -c "$(curl -fsSL https://starship.rs/install.sh)" -- "--yes" && \
+    echo 'source /usr/share/zsh-antigen/antigen.zsh' >> ~/.zshrc && \
+    echo 'antigen bundle zsh-users/zsh-autosuggestions' >> ~/.zshrc && \
+    echo 'antigen apply' >> ~/.zshrc && \
+    echo 'eval "$(starship init zsh)"' >> ~/.zshrc && \
+    zsh -c 'source ~/.zshrc'
+
+# Install the development Python environment.
+COPY .pre-commit-config.yaml poetry.lock* pyproject.toml /app/
+RUN --mount=type=cache,id=poetry,target=/root/.cache/ \
+    mkdir -p src/graphchain/ && touch src/graphchain/__init__.py && touch README.md && \
+    poetry install --no-interaction && \
+    mkdir -p /var/lib/poetry/ && cp poetry.lock /var/lib/poetry/ && \
+    git init && pre-commit install --install-hooks && \
+    mkdir -p /var/lib/git/ && cp .git/hooks/commit-msg .git/hooks/pre-commit /var/lib/git/
 
-FROM dev as ci
+FROM base as ci
 
-# Install the Python environment.
+# Install the run time Python environment.
 # TODO: Replace `--no-dev` with `--without test` when Poetry 1.2.0 is released.
 COPY poetry.lock pyproject.toml /app/
-RUN --mount=type=cache,target=/root/.cache \
+RUN --mount=type=cache,id=poetry,target=/root/.cache/ \
     mkdir -p src/graphchain/ && touch src/graphchain/__init__.py && touch README.md && \
     poetry install --no-dev --no-interaction

README.md

@@ -163,6 +163,14 @@ with dask.config.set(scheduler='sync', delayed_optimize=graphchain.optimize):
     result.compute(location='s3://mybucket/__graphchain_cache__')
 ```
 
+## Contributing
+
+1. Clone this repository.
+2. Start a [Dev Container](https://code.visualstudio.com/docs/remote/containers) in your preferred development environment:
+    - _VS Code_: open the cloned repository and run <kbd>⌘</kbd> + <kbd>⇧</kbd> + <kbd>P</kbd> → _Remote-Containers: Reopen in Container_.
+    - _PyCharm_: open the cloned repository 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).
+    - _Terminal_: open the cloned repository and run `docker compose run --rm dev` to start an interactive Dev Container.
+
 ## Developed by Radix
 
 [Radix](https://radix.ai) is a Belgium-based Machine Learning company.

docker-compose.yml

@@ -3,24 +3,26 @@ version: "3.9"
 services:
   dev:
     build:
-      args:
-        POETRY_PYPI_TOKEN_PYPI: $POETRY_PYPI_TOKEN_PYPI
       context: .
       target: dev
-    command: [ "sleep", "infinity" ]
+    stdin_open: true
+    tty: true
+    entrypoint: []
+    command:
+      [
+        "sh",
+        "-c",
+        "cp --update /var/lib/poetry/poetry.lock /app/ && mkdir -p /app/.git/hooks/ && cp --update /var/lib/git/* /app/.git/hooks/ && zsh"
+      ]
     environment:
+      - POETRY_PYPI_TOKEN_PYPI
       - SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock
     volumes:
-      # app
-      - .:/app/:cached
-      # env
-      - ${POETRY_CACHE_DIR:-~/Library/Caches/pypoetry/}:/root/.cache/pypoetry/:cached
-      - graphchain-env:/usr/local/
-      # git
-      - ~/.gitconfig:/etc/gitconfig:cached
-      # ssh
-      - ${SSH_AGENT_AUTH_SOCK:-/run/host-services/ssh-auth.sock}:/run/host-services/ssh-auth.sock:cached
-      - ~/.ssh/known_hosts:/root/.ssh/known_hosts:cached
+      - .:/app/
+      - app-env:/opt/app-env/
+      - ~/.gitconfig:/etc/gitconfig
+      - ~/.ssh/known_hosts:/root/.ssh/known_hosts
+      - ${SSH_AGENT_AUTH_SOCK:-/run/host-services/ssh-auth.sock}:/run/host-services/ssh-auth.sock
 
 volumes:
-  graphchain-env:
+  app-env: