From f5ea847d3c65603b17347f6f9dde9a1723eafb2a Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Thu, 7 Dec 2023 13:04:26 +0000 Subject: [PATCH 01/37] feat: working version of a devcontainer --- .devcontainer/Dockerfile | 23 ++++++ .devcontainer/devcontainer.json | 73 +++++++++++++++++ .devcontainer/postCreateCommand.sh | 7 ++ .pre-commit-config.yaml | 5 -- .vscode/settings.json | 18 +---- poetry.lock | 124 +---------------------------- pyproject.toml | 2 +- 7 files changed, 111 insertions(+), 141 deletions(-) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/postCreateCommand.sh diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 000000000..45df983e8 --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,23 @@ +# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.231.6/containers/python-3/.devcontainer/base.Dockerfile + +# [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster +ARG VARIANT="3.10-bullseye" +FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT} + +ENV POETRY_HOME="/home/vscode/.poetry" +ENV PATH="$POETRY_HOME/bin:$VENV_PATH/bin:$PATH" +ENV POETRY_VERSION=1.7.1 + +# [Optional] Uncomment this section to install additional OS packages. +RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ + && apt-get -y install --no-install-recommends \ + htop \ + fzf \ + && apt-get clean -y && rm -rf /var/lib/apt/lists/* + +COPY pyproject.toml poetry.lock ./ +RUN pipx install poetry==${POETRY_VERSION} + +# Add fzf to .zshrc +RUN echo "source /usr/share/doc/fzf/examples/key-bindings.zsh" >> /home/vscode/.zshrc +RUN echo "source /usr/share/doc/fzf/examples/completion.zsh" >> /home/vscode/.zshrc diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 000000000..0420b614e --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,73 @@ +{ + "name": "OTGdev", + "build": { + "dockerfile": "Dockerfile", + "context": "..", + "args": { + "VARIANT": "3.10-bullseye", + "POETRY_VERSION": "1.7.1" + } + }, + "features": { + "ghcr.io/devcontainers/features/github-cli:1": {}, + "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, + "ghcr.io/devcontainers/features/python:1": { + "version": "3.10" + }, + "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + }, + "mounts": [ + "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", + "source=devcontainer-bashhistory,target=/commandhistory,type=volume", + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" + ], + "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", + "customizations": { + "vscode": { + "extensions": [ + "charliermarsh.ruff", + "ms-python.isort", + "ms-python.mypy-type-checker", + "ms-python.python", + "ms-python.black-formatter", + "esbenp.prettier-vscode", + "mhutchie.git-graph", + "eamodio.gitlens", + "ms-azuretools.vscode-docker", + "github.vscode-github-actions", + "timonwong.shellcheck", + "GitHub.copilot", + "vivaxy.vscode-conventional-commits", + "ms-vscode-remote.remote-ssh", + "ms-toolsai.jupyter", + "ms-vscode.makefile-tools" + ], + "settings": { + "editor.defaultFormatter": "esbenp.prettier-vscode", + "workbench.startupEditor": "readme", + "terminal.integrated.fontFamily": "Fira Code", + "terminal.integrated.defaultProfile.linux": "zsh", + "[python]": { + "editor.defaultFormatter": "ms-python.black-formatter", + "editor.formatOnPaste": false, + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.fixAll": false, + "source.organizeImports": true + } + }, + "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], + "isort.args": ["--profile", "black"], + "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true, + "mypy-type-checker.severity": { + "error": "Information" + }, + "ruff.fixAll": false, + "ruff.organizeImports": false + } + } + } +} diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh new file mode 100644 index 000000000..55f88c394 --- /dev/null +++ b/.devcontainer/postCreateCommand.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +# Install Poetry environment +poetry install --no-interaction --no-root --no-cache + +# Install Pre-commit hooks +poetry run pre-commit install --install-hooks diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 32b480b54..8316252c6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,11 +10,6 @@ repos: - id: check-json - id: check-toml - id: check-yaml - - id: pretty-format-json - args: - - --autofix - - --no-ensure-ascii - - --no-sort-keys - id: check-ast - id: debug-statements - id: check-docstring-first diff --git a/.vscode/settings.json b/.vscode/settings.json index 727b1d959..03c9b0304 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,4 +1,5 @@ { + "editor.defaultFormatter": "esbenp.prettier-vscode", "[python]": { "editor.defaultFormatter": "ms-python.black-formatter", "editor.formatOnPaste": false, @@ -8,11 +9,7 @@ "source.organizeImports": true } }, - "python.terminal.launchArgs": [ - "-m", - "IPython", - "--no-autoindent" - ], + "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "[jsonc]": { "editor.tabSize": 2, "editor.insertSpaces": true, @@ -23,16 +20,9 @@ } }, "json.format.keepLines": true, - "isort.args": [ - "--profile", - "black" - ], + "isort.args": ["--profile", "black"], "autoDocstring.docstringFormat": "google", - "python.testing.pytestArgs": [ - ".", - "--doctest-modules", - "--cov=src/" - ], + "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], "python.testing.unittestEnabled": false, "python.testing.pytestEnabled": true, "mypy-type-checker.severity": { diff --git a/poetry.lock b/poetry.lock index d6cbcccec..5737dc6cb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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"ms-vscode.makefile-tools" + "ms-vscode.makefile-tools", + "GitHub.vscode-pull-request-github" ], "settings": { "editor.defaultFormatter": "esbenp.prettier-vscode", From 8d8cdbda1a10594981acf6e4ac40f8e5ac116cf4 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Thu, 7 Dec 2023 17:25:39 +0000 Subject: [PATCH 03/37] feat: welcome message --- .devcontainer/Dockerfile | 2 ++ .devcontainer/welcome.txt | 3 +++ 2 files changed, 5 insertions(+) create mode 100644 .devcontainer/welcome.txt diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 45df983e8..cd0c4228f 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -21,3 +21,5 @@ RUN pipx install poetry==${POETRY_VERSION} # Add fzf to .zshrc RUN echo "source /usr/share/doc/fzf/examples/key-bindings.zsh" >> /home/vscode/.zshrc RUN echo "source /usr/share/doc/fzf/examples/completion.zsh" >> /home/vscode/.zshrc + +COPY .devcontainer/welcome.txt /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.devcontainer/welcome.txt b/.devcontainer/welcome.txt new file mode 100644 index 000000000..dec3f2092 --- /dev/null +++ b/.devcontainer/welcome.txt @@ -0,0 +1,3 @@ +👋 Welcome to Open Targets Genetics DEV"! + +🛠️ Your environment is fully setup with all the required software. From 01fc5d8680619812a4dc56f18e823239b4af69b4 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Fri, 8 Dec 2023 11:58:24 +0000 Subject: [PATCH 04/37] feat: multiple features --- .devcontainer/devcontainer.json | 30 +++++++----------- .vscode/extensions.json | 7 ++-- .vscode/settings.json | 37 ++++++---------------- .devcontainer/Dockerfile => Dockerfile.dev | 7 ---- 4 files changed, 22 insertions(+), 59 deletions(-) rename .devcontainer/Dockerfile => Dockerfile.dev (84%) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b44372b95..957ef6ad0 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,7 +1,7 @@ { "name": "OTGdev", "build": { - "dockerfile": "Dockerfile", + "dockerfile": "../Dockerfile.dev", "context": "..", "args": { "VARIANT": "3.10-bullseye", @@ -15,7 +15,8 @@ "version": "3.10" }, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers-contrib/features/poetry:2": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", @@ -30,7 +31,7 @@ "ms-python.isort", "ms-python.mypy-type-checker", "ms-python.python", - "ms-python.black-formatter", + "charliermarsh.ruff", "esbenp.prettier-vscode", "mhutchie.git-graph", "eamodio.gitlens", @@ -49,25 +50,16 @@ "workbench.startupEditor": "readme", "terminal.integrated.fontFamily": "Fira Code", "terminal.integrated.defaultProfile.linux": "zsh", + "editor.formatOnPaste": false, + "editor.formatOnSave": true, + "editor.formatOnType": true, + "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], "[python]": { - "editor.defaultFormatter": "ms-python.black-formatter", - "editor.formatOnPaste": false, - "editor.formatOnSave": true, - "editor.codeActionsOnSave": { - "source.fixAll": false, - "source.organizeImports": true - } + "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], - "isort.args": ["--profile", "black"], - "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], - "python.testing.unittestEnabled": false, - "python.testing.pytestEnabled": true, - "mypy-type-checker.severity": { - "error": "Information" - }, - "ruff.fixAll": false, - "ruff.organizeImports": false + "python.defaultInterpreterPath": "/workspaces/genetics_etl_python/.venv/bin/python", + "python.testing.pytestPath": "/workspaces/genetics_etl_python/.venv/bin/pytest" } } } diff --git a/.vscode/extensions.json b/.vscode/extensions.json index e434673de..dd29cfde1 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -3,10 +3,7 @@ "charliermarsh.ruff", "ms-python.isort", "ms-python.mypy-type-checker", - "ms-python.python", - "ms-python.black-formatter" + "ms-python.python" ], - "unwantedRecommendations": [ - "ms-python.flake8" - ] + "unwantedRecommendations": ["ms-python.flake8"] } diff --git a/.vscode/settings.json b/.vscode/settings.json index 03c9b0304..bd035b094 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,33 +1,14 @@ { "editor.defaultFormatter": "esbenp.prettier-vscode", - "[python]": { - "editor.defaultFormatter": "ms-python.black-formatter", - "editor.formatOnPaste": false, - "editor.formatOnSave": true, - "editor.codeActionsOnSave": { - "source.fixAll": false, - "source.organizeImports": true - } - }, - "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], - "[jsonc]": { - "editor.tabSize": 2, - "editor.insertSpaces": true, - "editor.detectIndentation": false, - "editor.formatOnSave": true, - "editor.codeActionsOnSave": { - "source.organizeImports": true - } - }, - "json.format.keepLines": true, - "isort.args": ["--profile", "black"], - "autoDocstring.docstringFormat": "google", + "workbench.startupEditor": "readme", + "terminal.integrated.fontFamily": "Fira Code", + "terminal.integrated.defaultProfile.linux": "zsh", + "editor.formatOnPaste": false, + "editor.formatOnSave": true, + "editor.formatOnType": true, "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], - "python.testing.unittestEnabled": false, - "python.testing.pytestEnabled": true, - "mypy-type-checker.severity": { - "error": "Information" + "[python]": { + "editor.defaultFormatter": "charliermarsh.ruff" }, - "ruff.fixAll": false, - "ruff.organizeImports": false + "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"] } diff --git a/.devcontainer/Dockerfile b/Dockerfile.dev similarity index 84% rename from .devcontainer/Dockerfile rename to Dockerfile.dev index cd0c4228f..a947fb7e5 100644 --- a/.devcontainer/Dockerfile +++ b/Dockerfile.dev @@ -4,10 +4,6 @@ ARG VARIANT="3.10-bullseye" FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT} -ENV POETRY_HOME="/home/vscode/.poetry" -ENV PATH="$POETRY_HOME/bin:$VENV_PATH/bin:$PATH" -ENV POETRY_VERSION=1.7.1 - # [Optional] Uncomment this section to install additional OS packages. RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ && apt-get -y install --no-install-recommends \ @@ -15,9 +11,6 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ fzf \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* -COPY pyproject.toml poetry.lock ./ -RUN pipx install poetry==${POETRY_VERSION} - # Add fzf to .zshrc RUN echo "source /usr/share/doc/fzf/examples/key-bindings.zsh" >> /home/vscode/.zshrc RUN echo "source /usr/share/doc/fzf/examples/completion.zsh" >> /home/vscode/.zshrc From 57a549f79fbb6413ced9d5eaefb5ac57061e59ca Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Fri, 8 Dec 2023 11:59:48 +0000 Subject: [PATCH 05/37] revert: check json --- .devcontainer/devcontainer.json | 2 ++ .pre-commit-config.yaml | 1 - 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 957ef6ad0..6531622b2 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -26,6 +26,7 @@ "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", "customizations": { "vscode": { + // Please keep this file in sync with settings in /.vscode/extensions.json "extensions": [ "charliermarsh.ruff", "ms-python.isort", @@ -45,6 +46,7 @@ "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github" ], + // Please keep this file in sync with settings in /.vscode/settings.json "settings": { "editor.defaultFormatter": "esbenp.prettier-vscode", "workbench.startupEditor": "readme", diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8316252c6..fbff1e451 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,6 @@ repos: - id: debug-statements - id: check-merge-conflict - id: check-case-conflict - - id: check-json - id: check-toml - id: check-yaml - id: check-ast From 4ae2d590319342d3ff6d52ba0c9bef2109ee3e02 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 11 Dec 2023 15:43:01 +0000 Subject: [PATCH 06/37] feat: working version --- .devcontainer/devcontainer.json | 18 +++++++++--------- .devcontainer/postCreateCommand.sh | 7 ++----- .pre-commit-config.yaml | 8 +------- .vscode/settings.json | 11 ++++++++--- pyproject.toml | 12 ++++++------ 5 files changed, 26 insertions(+), 30 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 6531622b2..50a83ffbe 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -11,12 +11,8 @@ "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, - "ghcr.io/devcontainers/features/python:1": { - "version": "3.10" - }, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, - "ghcr.io/devcontainers-contrib/features/poetry:2": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", @@ -49,19 +45,23 @@ // Please keep this file in sync with settings in /.vscode/settings.json "settings": { "editor.defaultFormatter": "esbenp.prettier-vscode", - "workbench.startupEditor": "readme", "terminal.integrated.fontFamily": "Fira Code", "terminal.integrated.defaultProfile.linux": "zsh", "editor.formatOnPaste": false, "editor.formatOnSave": true, "editor.formatOnType": true, - "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], "[python]": { "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], - "python.defaultInterpreterPath": "/workspaces/genetics_etl_python/.venv/bin/python", - "python.testing.pytestPath": "/workspaces/genetics_etl_python/.venv/bin/pytest" + "python.defaultInterpreterPath": "/usr/local/bin/python", + "python.testing.pytestEnabled": true, + "python.testing.pytestArgs": [ + "src/", + "tests/", + "--doctest-modules", + "--cov=src/" + ] } } } diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh index 55f88c394..6a953b5f2 100644 --- a/.devcontainer/postCreateCommand.sh +++ b/.devcontainer/postCreateCommand.sh @@ -1,7 +1,4 @@ #!/bin/bash -# Install Poetry environment -poetry install --no-interaction --no-root --no-cache - -# Install Pre-commit hooks -poetry run pre-commit install --install-hooks +# # Install Pre-commit +pre-commit install --install-hooks diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fbff1e451..24b220f91 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -35,13 +35,7 @@ repos: rev: 5.12.0 hooks: - id: isort - args: - [--add-import, from __future__ import annotations, --profile, black] - - - repo: https://github.com/psf/black - rev: 23.11.0 - hooks: - - id: black + args: [--add-import, from __future__ import annotations] - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook rev: v9.10.0 diff --git a/.vscode/settings.json b/.vscode/settings.json index bd035b094..57451e7d3 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,14 +1,19 @@ { "editor.defaultFormatter": "esbenp.prettier-vscode", - "workbench.startupEditor": "readme", "terminal.integrated.fontFamily": "Fira Code", "terminal.integrated.defaultProfile.linux": "zsh", "editor.formatOnPaste": false, "editor.formatOnSave": true, "editor.formatOnType": true, - "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"], "[python]": { "editor.defaultFormatter": "charliermarsh.ruff" }, - "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"] + "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], + "python.testing.pytestEnabled": true, + "python.testing.pytestArgs": [ + "src/", + "tests/", + "--doctest-modules", + "--cov=src/" + ] } diff --git a/pyproject.toml b/pyproject.toml index a5465cb2f..ead640c88 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,6 @@ wandb = "^0.16.0" [tool.poetry.dev-dependencies] pre-commit = "^3.5.0" -black = {version = "^22.12.0", allow-prereleases = true} mypy = "^1.7" pep8-naming = "^0.13.2" interrogate = "^1.5.0" @@ -80,18 +79,19 @@ upload_to_release = false requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" -[tool.isort] -profile = "black" - [tool.interrogate] fail-under = 95 color = true exclude = ["dist"] [tool.pytest.ini_options] -addopts = "-n auto --doctest-modules --cov=src/ --cov-report=xml" +addopts = [ + "-n=4", + "--doctest-modules", + "--import-mode=importlib" +] pythonpath = [ - ".", + "./src/", "./src/airflow/dags" ] From 4034fba6d3b264c994ceef791455995103510c80 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 11 Dec 2023 16:18:13 +0000 Subject: [PATCH 07/37] feat: development environment dockerfile --- Dockerfile.dev | 75 ++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 69 insertions(+), 6 deletions(-) diff --git a/Dockerfile.dev b/Dockerfile.dev index a947fb7e5..e2434aa71 100644 --- a/Dockerfile.dev +++ b/Dockerfile.dev @@ -2,17 +2,80 @@ # [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster ARG VARIANT="3.10-bullseye" -FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT} +FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT} as development_build -# [Optional] Uncomment this section to install additional OS packages. -RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ - && apt-get -y install --no-install-recommends \ +ARG YOUR_ENV + +ENV PYTHONUNBUFFERED=1 \ + PYTHONFAULTHANDLER=1 \ + PYTHONHASHSEED=random \ + PYTHONDONTWRITEBYTECODE=1 \ + # pip + # PIP_DISABLE_PIP_VERSION_CHECK=1 \ + # PIP_DEFAULT_TIMEOUT=100 \ + PIP_ROOT_USER_ACTION=ignore \ + # Poetry + # https://python-poetry.org/docs/configuration/#using-environment-variables + POETRY_VERSION=1.7.1 \ + # make poetry install to this location + POETRY_HOME="/usr/local" \ + # do not ask any interactive question + POETRY_NO_INTERACTION=1 \ + # cahce dir for poetry + POETRY_CACHE_DIR='/var/cache/pypoetry' \ + # never create virtual environment automatically, only use env prepared by us + POETRY_VIRTUALENVS_CREATE=false + + +# System deps (we don't use exact versions because it is hard to update them, +# pin when needed): +# hadolint ignore=DL3008 +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + default-jdk \ htop \ fzf \ + jq \ + bat \ + # Installing `poetry` package manager: + # https://github.com/python-poetry/poetry + && curl -sSL 'https://install.python-poetry.org' | python - \ + # Enable tab completion for bash + && poetry completions bash >> /home/vscode/.bash_completion \ + # Enable tab completion for Zsh + && mkdir -p /home/vscode/.zfunc/ \ + && poetry completions zsh > /home/vscode/.zfunc/_poetry \ + && echo "fpath+=~/.zfunc\nautoload -Uz compinit && compinit" >> /home/vscode/.zshrc \ + && poetry --version \ + && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* # Add fzf to .zshrc -RUN echo "source /usr/share/doc/fzf/examples/key-bindings.zsh" >> /home/vscode/.zshrc -RUN echo "source /usr/share/doc/fzf/examples/completion.zsh" >> /home/vscode/.zshrc +RUN echo "source /usr/share/doc/fzf/examples/key-bindings.zsh" >> /home/vscode/.zshrc && \ + echo "source /usr/share/doc/fzf/examples/completion.zsh" >> /home/vscode/.zshrc + +ARG USERNAME=vscode +# Used to persist bash history as per https://code.visualstudio.com/remote/advancedcontainers/persist-bash-history +# hadolint ignore=SC2086 +RUN SNIPPET="export PROMPT_COMMAND='history -a' && export HISTFILE=/commandhistory/.zsh_history" \ + && mkdir /commandhistory \ + && touch /commandhistory/.zsh_history \ + && chown -R $USERNAME /commandhistory \ + && echo "$SNIPPET" >> "/home/$USERNAME/.zshrc" COPY .devcontainer/welcome.txt /usr/local/etc/vscode-dev-containers/first-run-notice.txt + +# working directory +WORKDIR /workspaces + +# Copy only requirements, to cache them in docker layer +COPY ./poetry.lock ./pyproject.toml ./README.md ./ +COPY src/otg src/otg +COPY src/utils src/utils + +# Install runtime deps: +# hadolint ignore=SC2046 +RUN --mount=type=cache,target="$POETRY_CACHE_DIR" \ + poetry install --no-interaction --no-ansi + +EXPOSE 8080 From 11a8f0366c23b76db65db022d9c085ab404b8d9c Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 11 Dec 2023 16:18:56 +0000 Subject: [PATCH 08/37] revert: removing black as formatter --- Makefile | 1 - README.md | 2 +- docs/index.md | 1 - 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/Makefile b/Makefile index a098264e1..53a4bc389 100644 --- a/Makefile +++ b/Makefile @@ -27,7 +27,6 @@ check: ## Lint and format code @poetry run pydoclint --config=pyproject.toml src @poetry run pydoclint --config=pyproject.toml --skip-checking-short-docstrings=true tests @echo "Formatting..." - @poetry run black src/otg . @poetry run isort src/otg . test: ## Run tests diff --git a/README.md b/README.md index b1ec5ba19..5be708d82 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,8 @@ [![docs](https://github.com/opentargets/genetics_etl_python/actions/workflows/docs.yaml/badge.svg)](https://opentargets.github.io/genetics_etl_python/) [![codecov](https://codecov.io/gh/opentargets/genetics_etl_python/branch/main/graph/badge.svg?token=5ixzgu8KFP)](https://codecov.io/gh/opentargets/genetics_etl_python) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) -[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python/main.svg)](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python) # Genetics Portal Data Pipeline (experimental) + - [Documentation](https://opentargets.github.io/genetics_etl_python/) diff --git a/docs/index.md b/docs/index.md index 8de285d2f..006477ec3 100644 --- a/docs/index.md +++ b/docs/index.md @@ -21,7 +21,6 @@ hide: ![docs](https://github.com/opentargets/genetics_etl_python/actions/workflows/docs.yaml/badge.svg) [![codecov](https://codecov.io/gh/opentargets/genetics_etl_python/branch/main/graph/badge.svg?token=5ixzgu8KFP)](https://codecov.io/gh/opentargets/genetics_etl_python) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) -[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python/main.svg)](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python) --- From 88d681e205a2adabc38886dd4694d02c113fc9bb Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 11 Dec 2023 17:04:48 +0000 Subject: [PATCH 09/37] chore: poetry lock updated --- poetry.lock | 156 ++++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 120 insertions(+), 36 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5737dc6cb..08d0cbf77 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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Dec 2023 09:23:14 +0000 Subject: [PATCH 10/37] revert: remove dependencies --- .devcontainer/devcontainer.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 50a83ffbe..bac4a6175 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -19,16 +19,15 @@ "source=devcontainer-bashhistory,target=/commandhistory,type=volume", "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" ], + "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", "customizations": { "vscode": { // Please keep this file in sync with settings in /.vscode/extensions.json "extensions": [ "charliermarsh.ruff", - "ms-python.isort", "ms-python.mypy-type-checker", "ms-python.python", - "charliermarsh.ruff", "esbenp.prettier-vscode", "mhutchie.git-graph", "eamodio.gitlens", From 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a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 224891157..2b5c2aa16 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -39,7 +39,8 @@ "ms-vscode-remote.remote-ssh", "ms-toolsai.jupyter", "ms-vscode.makefile-tools", - "GitHub.vscode-pull-request-github" + "GitHub.vscode-pull-request-github", + "redhat.vscode-yaml" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { From 14be555d7cbd4002539975ccac16aea03e784eb3 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Fri, 9 Feb 2024 10:13:04 +0000 Subject: [PATCH 18/37] revert: welcome message not working --- .devcontainer/devcontainer.json | 2 +- .devcontainer/welcome.txt | 3 --- .vscode/extensions.json | 1 - Dockerfile.dev | 2 -- 4 files changed, 1 insertion(+), 7 deletions(-) delete mode 100644 .devcontainer/welcome.txt diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 2b5c2aa16..daf959b2d 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -40,7 +40,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "redhat.vscode-yaml" + "fnando.linter" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { diff --git a/.devcontainer/welcome.txt b/.devcontainer/welcome.txt deleted file mode 100644 index dec3f2092..000000000 --- a/.devcontainer/welcome.txt +++ /dev/null @@ -1,3 +0,0 @@ -👋 Welcome to Open Targets Genetics DEV"! - -🛠️ Your environment is fully setup with all the required software. diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 1be2f117e..99cf238f7 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -4,7 +4,6 @@ "ms-python.mypy-type-checker", "ms-python.python", "esbenp.prettier-vscode", - "redhat.vscode-yaml", "fnando.linter" ], "unwantedRecommendations": ["ms-python.flake8"] diff --git a/Dockerfile.dev b/Dockerfile.dev index 3bc87c75a..aacf7fa1b 100644 --- a/Dockerfile.dev +++ b/Dockerfile.dev @@ -63,8 +63,6 @@ RUN SNIPPET="export PROMPT_COMMAND='history -a' && export HISTFILE=/commandhisto && chown -R $USERNAME /commandhistory \ && echo "$SNIPPET" >> "/home/$USERNAME/.zshrc" -COPY .devcontainer/welcome.txt /usr/local/etc/vscode-dev-containers/first-run-notice.txt - # working directory WORKDIR /workspaces From a01741870fec87448194a49cdb0712a29bb5b581 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Fri, 9 Feb 2024 10:54:22 +0000 Subject: [PATCH 19/37] feat: badge in readme --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index faf21f79e..d5bf2aef9 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,7 @@ image codecov License +Dev Containers DOI

From d2efd86bf96d6fa2a7e2b0885a2637966fcddb25 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Fri, 9 Feb 2024 10:57:56 +0000 Subject: [PATCH 20/37] fix: typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d5bf2aef9..51ceddd99 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ image codecov License -Dev Containers +Dev Containers DOI

From 2ff41084ccd9d08c122893c48fdcbf3f72ce341d Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Fri, 9 Feb 2024 11:02:34 +0000 Subject: [PATCH 21/37] feat: add badge to index --- docs/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/index.md b/docs/index.md index 2147ceb14..80176569b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -28,6 +28,7 @@ hide: image codecov License +Dev Containers DOI

--- From 4af5330d5ddce1b88ea9d2897728a67c088ed4fc Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 12 Feb 2024 10:20:47 +0000 Subject: [PATCH 22/37] docs: devcontainer documentation and cleanup --- docs/development/a_environment.md | 39 +++++++++ docs/development/b_contributing.md | 34 ++++++++ docs/development/{airflow.md => c_airflow.md} | 25 ++++++ docs/development/contributing.md | 86 ------------------- ...roubleshooting.md => d_troubleshooting.md} | 0 docs/development/workflows.md | 27 ------ 6 files changed, 98 insertions(+), 113 deletions(-) create mode 100644 docs/development/a_environment.md create mode 100644 docs/development/b_contributing.md rename docs/development/{airflow.md => c_airflow.md} (71%) delete mode 100644 docs/development/contributing.md rename docs/development/{troubleshooting.md => d_troubleshooting.md} (100%) delete mode 100644 docs/development/workflows.md diff --git a/docs/development/a_environment.md b/docs/development/a_environment.md new file mode 100644 index 000000000..d67e55720 --- /dev/null +++ b/docs/development/a_environment.md @@ -0,0 +1,39 @@ +# Development environment + +## Devcontainer (recommended) + +Developing in a devcontainer ensures a reproducible development environment with minimal setup. To use the devcontainer, you need to have Docker installed on your system and use Visual Studio Code as your IDE. + +For a quick start you can either: + +1. [Open existing folder in container](https://code.visualstudio.com/docs/devcontainers/containers#_quick-start-open-an-existing-folder-in-a-container). + +1. [Clone repository in container volume](https://code.visualstudio.com/docs/devcontainers/containers#_quick-start-open-a-git-repository-or-github-pr-in-an-isolated-container-volume). + +[![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=Open&color=blue&logo=visualstudiocode)](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/opentargets/gentropy) + +If you already have VS Code and Docker installed, you can click the badge above or [here](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/opentargets/gentropy) to get started. Clicking these links will cause VS Code to automatically install the Dev Containers extension if needed, clone the source code into a container volume, and spin up a dev container for use. + +More information on working with devcontainers can be found [here](https://code.visualstudio.com/docs/devcontainers/containers). + +## Codespaces + +A devcontainer can also be triggered within Github using [Codespaces](https://github.com/features/codespaces). This option requires no local setup as the environment is managed by Github. + +## One-time configuration + +To setup a full local environment of the package please follow the next steps. + +Requirements: + +- java +- make +- [Google Cloud SDK](https://cloud.google.com/sdk/docs/install). + +Google Cloud configuration: + +1. Log in to your work Google Account: run `gcloud auth login` and follow instructions. + +1. Obtain Google application credentials: run `gcloud auth application-default login` and follow instructions. + +Finally, run `make setup-dev` to install/update the necessary packages and activate the development environment. diff --git a/docs/development/b_contributing.md b/docs/development/b_contributing.md new file mode 100644 index 000000000..97f526de6 --- /dev/null +++ b/docs/development/b_contributing.md @@ -0,0 +1,34 @@ +--- +title: Contributing guidelines +--- + +# Contributing guidelines + +## Contributing checklist + +When making changes, and especially when implementing a new module or feature, it's essential to ensure that all relevant sections of the code base are modified. + +- [ ] Run `make check`. This will run the linter and formatter to ensure that the code is compliant with the project conventions. +- [ ] Develop unit tests for your code and run `make test`. This will run all unit tests in the repository, including the examples appended in the docstrings of some methods. +- [ ] Update the configuration if necessary. +- [ ] Update the documentation and check it with `make build-documentation`. This will start a local server to browse it (URL will be printed, usually `http://127.0.0.1:8000/`) + +For more details on each of these steps, see the sections below. + +## Documentation + +- If during development you had a question which wasn't covered in the documentation, and someone explained it to you, add it to the documentation. The same applies if you encountered any instructions in the documentation which were obsolete or incorrect. +- Documentation autogeneration expressions start with `:::`. They will automatically generate sections of the documentation based on class and method docstrings. Be sure to update them for: + - Dataset definitions in `docs/python_api/datasource/STEP` (example: `docs/python_api/datasource/finngen/study_index.md`) + - Step definition in `docs/python_api/step/STEP.md` (example: `docs/python_api/step/finngen.md`) + +## Classes + +- Dataset class in `src/gentropy/datasource/STEP` (example: `src/gentropy/datasource/finngen/study_index.py` → `FinnGenStudyIndex`) +- Step main running class in `src/gentropy/STEP.py` (example: `src/gentropy/finngen.py`) + +## Tests + +- Test study fixture in `tests/conftest.py` (example: `mock_study_index_finngen` in that module) +- Test sample data in `tests/data_samples` (example: `tests/data_samples/finngen_studies_sample.json`) +- Test definition in `tests/` (example: `tests/dataset/test_study_index.py` → `test_study_index_finngen_creation`) diff --git a/docs/development/airflow.md b/docs/development/c_airflow.md similarity index 71% rename from docs/development/airflow.md rename to docs/development/c_airflow.md index ff5f7906c..59b49a5e4 100644 --- a/docs/development/airflow.md +++ b/docs/development/c_airflow.md @@ -117,6 +117,31 @@ More information on running Airflow with Docker Compose can be found in the [off 1. **Additional pip packages**. They can be added to the `requirements.txt` file. +## Example: A gentropy running DAG using GCP + +All pipelines in this repository are intended to be run in Google Dataproc. Running them locally is not currently supported. + +In order to run the code: + +1. Manually edit your local `src/airflow/dags/*` file and comment out the steps you do not want to run. + +2. Manually edit your local `pyproject.toml` file and modify the version of the code. + + - This must be different from the version used by any other people working on the repository to avoid any deployment conflicts, so it's a good idea to use your name, for example: `1.2.3+jdoe`. + - You can also add a brief branch description, for example: `1.2.3+jdoe.myfeature`. + - Note that the version must comply with [PEP440 conventions](https://peps.python.org/pep-0440/#normalization), otherwise Poetry will not allow it to be deployed. + - Do not use underscores or hyphens in your version name. When building the WHL file, they will be automatically converted to dots, which means the file name will no longer match the version and the build will fail. Use dots instead. + +3. Manually edit your local `src/airflow/dags/common_airflow.py` and set `OTG_VERSION` to the same version as you did in the previous step. + +4. Run `make build`. + + - This will create a bundle containing the neccessary code, configuration and dependencies to run the ETL pipeline, and then upload this bundle to Google Cloud. + - A version specific subpath is used, so uploading the code will not affect any branches but your own. + - If there was already a code bundle uploaded with the same version number, it will be replaced. + +5. Open Airflow UI and run the DAG. + ## Troubleshooting Note that when you a a new workflow under `dags/`, Airflow will not pick that up immediately. By default the filesystem is only scanned for new DAGs every 300s. However, once the DAG is added, updates are applied nearly instantaneously. diff --git a/docs/development/contributing.md b/docs/development/contributing.md deleted file mode 100644 index a12ac4951..000000000 --- a/docs/development/contributing.md +++ /dev/null @@ -1,86 +0,0 @@ ---- -title: Contributing guidelines ---- - -# Contributing guidelines - -## One-time configuration - -The steps in this section only ever need to be done once on any particular system. - -For Google Cloud configuration: - -1. Install Google Cloud SDK: https://cloud.google.com/sdk/docs/install. - -1. Log in to your work Google Account: run `gcloud auth login` and follow instructions. - -1. Obtain Google application credentials: run `gcloud auth application-default login` and follow instructions. - -Check that you have the `make` utility installed, and if not (which is unlikely), install it using your system package manager. - -Check that you have `java` installed. - -## Environment configuration - -Run `make setup-dev` to install/update the necessary packages and activate the development environment. You need to do this every time you open a new shell. - -It is recommended to use VS Code as an IDE for development. - -## How to run the code - -All pipelines in this repository are intended to be run in Google Dataproc. Running them locally is not currently supported. - -In order to run the code: - -1. Manually edit your local `src/airflow/dags/*` file and comment out the steps you do not want to run. - -2. Manually edit your local `pyproject.toml` file and modify the version of the code. - - - This must be different from the version used by any other people working on the repository to avoid any deployment conflicts, so it's a good idea to use your name, for example: `1.2.3+jdoe`. - - You can also add a brief branch description, for example: `1.2.3+jdoe.myfeature`. - - Note that the version must comply with [PEP440 conventions](https://peps.python.org/pep-0440/#normalization), otherwise Poetry will not allow it to be deployed. - - Do not use underscores or hyphens in your version name. When building the WHL file, they will be automatically converted to dots, which means the file name will no longer match the version and the build will fail. Use dots instead. - -3. Manually edit your local `src/airflow/dags/common_airflow.py` and set `OTG_VERSION` to the same version as you did in the previous step. - -4. Run `make build`. - - - This will create a bundle containing the neccessary code, configuration and dependencies to run the ETL pipeline, and then upload this bundle to Google Cloud. - - A version specific subpath is used, so uploading the code will not affect any branches but your own. - - If there was already a code bundle uploaded with the same version number, it will be replaced. - -5. Open Airflow UI and run the DAG. - -## Contributing checklist - -When making changes, and especially when implementing a new module or feature, it's essential to ensure that all relevant sections of the code base are modified. - -- [ ] Run `make check`. This will run the linter and formatter to ensure that the code is compliant with the project conventions. -- [ ] Develop unit tests for your code and run `make test`. This will run all unit tests in the repository, including the examples appended in the docstrings of some methods. -- [ ] Update the configuration if necessary. -- [ ] Update the documentation and check it with `make build-documentation`. This will start a local server to browse it (URL will be printed, usually `http://127.0.0.1:8000/`) - -For more details on each of these steps, see the sections below. - -### Documentation - -- If during development you had a question which wasn't covered in the documentation, and someone explained it to you, add it to the documentation. The same applies if you encountered any instructions in the documentation which were obsolete or incorrect. -- Documentation autogeneration expressions start with `:::`. They will automatically generate sections of the documentation based on class and method docstrings. Be sure to update them for: - - Dataset definitions in `docs/python_api/datasource/STEP` (example: `docs/python_api/datasource/finngen/study_index.md`) - - Step definition in `docs/python_api/step/STEP.md` (example: `docs/python_api/step/finngen.md`) - -### Configuration - -- Input and output paths in `config/datasets/gcp.yaml` -- Step configuration in `config/step/STEP.yaml` (example: `config/step/finngen.yaml`) - -### Classes - -- Dataset class in `src/gentropy/datasource/STEP` (example: `src/gentropy/datasource/finngen/study_index.py` → `FinnGenStudyIndex`) -- Step main running class in `src/gentropy/STEP.py` (example: `src/gentropy/finngen.py`) - -### Tests - -- Test study fixture in `tests/conftest.py` (example: `mock_study_index_finngen` in that module) -- Test sample data in `tests/data_samples` (example: `tests/data_samples/finngen_studies_sample.json`) -- Test definition in `tests/` (example: `tests/dataset/test_study_index.py` → `test_study_index_finngen_creation`) diff --git a/docs/development/troubleshooting.md b/docs/development/d_troubleshooting.md similarity index 100% rename from docs/development/troubleshooting.md rename to docs/development/d_troubleshooting.md diff --git a/docs/development/workflows.md b/docs/development/workflows.md deleted file mode 100644 index 2269041d8..000000000 --- a/docs/development/workflows.md +++ /dev/null @@ -1,27 +0,0 @@ -# Pipeline workflows - -This page describes the high level components of the pipeline, which are organised as Airflow DAGs (directed acyclic graphs). - -## Note on DAGs and Dataproc clusters - -Each DAG consists of the following general stages: - -1. Create cluster (if it already exists, this step is skipped) - -1. Install dependencies on the cluster - -1. Run data processing steps for this DAG - -1. Delete the cluster - -Within a DAG, all data processing steps run on the same Dataproc cluster as separate jobs. - -There is no need to configure DAGs or steps depending on the size of the input data. Clusters have autoscaling enabled, which means they will increase or decrease the number of worker VMs to accommodate the load. - -## DAG 1: Preprocess - -This DAG contains steps which are only supposed to be run once, or very rarely. They ingest external data and apply bespoke transformations specific for each particular data source. The output is normalised according to the data schemas used by the pipeline. - -## DAG 2: ETL - -The ETL DAG takes the inputs of the previous step and performs the main algorithmic processing. This processing is supposed to be data source agnostic. From 5a5329c8362ca3a7253a46260ce5add828a7a364 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 12 Feb 2024 11:57:13 +0000 Subject: [PATCH 23/37] chore: change devcontainer location --- Dockerfile.dev => .devcontainer/Dockerfile.dev | 0 .devcontainer/devcontainer.json | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename Dockerfile.dev => .devcontainer/Dockerfile.dev (100%) diff --git a/Dockerfile.dev b/.devcontainer/Dockerfile.dev similarity index 100% rename from Dockerfile.dev rename to .devcontainer/Dockerfile.dev diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index daf959b2d..79444e9f4 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,7 +1,7 @@ { "name": "OTGdev", "build": { - "dockerfile": "../Dockerfile.dev", + "dockerfile": "Dockerfile.dev", "context": "..", "args": { "VARIANT": "3.10-bullseye", From a3cb47a4916145c529f564665830e2c713330c91 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 12 Feb 2024 12:20:10 +0000 Subject: [PATCH 24/37] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .devcontainer/devcontainer.json | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 79444e9f4..fe21f2087 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,19 +5,19 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1" - } + "POETRY_VERSION": "1.7.1", + }, }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", - "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -40,7 +40,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter" + "fnando.linter", ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -51,7 +51,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff" + "editor.defaultFormatter": "charliermarsh.ruff", }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -60,9 +60,9 @@ "src/", "tests/", "--doctest-modules", - "--no-cov" - ] - } - } - } + "--no-cov", + ], + }, + }, + }, } From a213a2e14169179d25f7633ff51e69d54dc351fe Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 12 Feb 2024 13:38:20 +0000 Subject: [PATCH 25/37] chore: update lock --- poetry.lock | 143 +++++++++++++++++----------------------------------- 1 file changed, 46 insertions(+), 97 deletions(-) diff --git a/poetry.lock b/poetry.lock index 767eaa810..b9a5acfd9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3405,56 +3405,6 @@ files = [ {file = "google_re2-1.1-3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:d140c7b9395b4d1e654127aa1c99bcc603ed01000b7bc7e28c52562f1894ec12"}, {file = "google_re2-1.1-3-cp39-cp39-win32.whl", hash = "sha256:80c5fc200f64b2d903eeb07b8d6cefc620a872a0240c7caaa9aca05b20f5568f"}, {file = "google_re2-1.1-3-cp39-cp39-win_amd64.whl", hash = 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you can either: 1. [Open existing folder in container](https://code.visualstudio.com/docs/devcontainers/containers#_quick-start-open-an-existing-folder-in-a-container). -1. [Clone repository in container volume](https://code.visualstudio.com/docs/devcontainers/containers#_quick-start-open-a-git-repository-or-github-pr-in-an-isolated-container-volume). - -[![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=Open&color=blue&logo=visualstudiocode)](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/opentargets/gentropy) +1. [Clone repository in container volume](https://code.visualstudio.com/docs/devcontainers/containers#_quick-start-open-a-git-repository-or-github-pr-in-an-isolated-container-volume) [![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=Open&color=blue&logo=visualstudiocode)](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/opentargets/gentropy) If you already have VS Code and Docker installed, you can click the badge above or [here](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/opentargets/gentropy) to get started. Clicking these links will cause VS Code to automatically install the Dev Containers extension if needed, clone the source code into a container volume, and spin up a dev container for use. More information on working with devcontainers can be found [here](https://code.visualstudio.com/docs/devcontainers/containers). +!!! note "I/O performance" + + The Dev Containers extension uses "bind mounts" to source code in your local filesystem by default. While this is the simplest option, on macOS and Windows, you may encounter slower disk performance. There are [few things you can do](https://code.visualstudio.com/remote/advancedcontainers/improve-performance) to resolve these type of issues including cloning repository in container volume. + ## Codespaces A devcontainer can also be triggered within Github using [Codespaces](https://github.com/features/codespaces). This option requires no local setup as the environment is managed by Github. -## One-time configuration +## Local environment To setup a full local environment of the package please follow the next steps. @@ -30,10 +36,11 @@ Requirements: - make - [Google Cloud SDK](https://cloud.google.com/sdk/docs/install). -Google Cloud configuration: +Run `make setup-dev` to install/update the necessary packages and activate the development environment. -1. Log in to your work Google Account: run `gcloud auth login` and follow instructions. +!!! info "Google Cloud configuration" -1. Obtain Google application credentials: run `gcloud auth application-default login` and follow instructions. + To complete the Google Cloud configuration, you need to: -Finally, run `make setup-dev` to install/update the necessary packages and activate the development environment. + - Log in to your work Google Account: run `gcloud auth login` and follow instructions. + - Obtain Google application credentials: run `gcloud auth application-default login` and follow instructions. diff --git a/docs/development/b_contributing.md b/docs/development/b_contributing.md index 97f526de6..fdf7378d5 100644 --- a/docs/development/b_contributing.md +++ b/docs/development/b_contributing.md @@ -1,5 +1,5 @@ --- -title: Contributing guidelines +Title: Contributing --- # Contributing guidelines diff --git a/docs/development/c_airflow.md b/docs/development/c_airflow.md index 59b49a5e4..83402e78a 100644 --- a/docs/development/c_airflow.md +++ b/docs/development/c_airflow.md @@ -1,3 +1,7 @@ +--- +Title: Airflow +--- + # Airflow configuration This section describes how to set up a local Airflow server which will orchestrate running workflows in Google Cloud Platform. This is useful for testing and debugging, but for production use, it is recommended to run Airflow on a dedicated server. diff --git a/docs/development/d_troubleshooting.md b/docs/development/d_troubleshooting.md index b9f7385da..bbe66e7aa 100644 --- a/docs/development/d_troubleshooting.md +++ b/docs/development/d_troubleshooting.md @@ -1,5 +1,5 @@ --- -title: Troubleshooting +Title: Troubleshooting --- # Troubleshooting From ada84c06b1d5e53bc9f4f7011ae28744045bdc35 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Mon, 12 Feb 2024 17:34:24 +0000 Subject: [PATCH 27/37] feat: spark ui port forwarding --- .devcontainer/devcontainer.json | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index fe21f2087..6eb092201 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,19 +5,19 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1", - }, + "POETRY_VERSION": "1.7.1" + } }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", - "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -40,7 +40,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter", + "fnando.linter" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -51,7 +51,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff", + "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -60,9 +60,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov", - ], - }, - }, + "--no-cov" + ] + } + } }, + "portsAttributes": { + "4040": { + "label": "SparkUI", + "onAutoForward": "notify" + } + }, + + "forwardPorts": [4040] } From 85d5ddebbbe3ae21a0f8cafe0fe156e643d007a9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 12 Feb 2024 17:34:44 +0000 Subject: [PATCH 28/37] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .devcontainer/devcontainer.json | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 6eb092201..a8ba32a8d 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,19 +5,19 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1" - } + "POETRY_VERSION": "1.7.1", + }, }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", - "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -40,7 +40,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter" + "fnando.linter", ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -51,7 +51,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff" + "editor.defaultFormatter": "charliermarsh.ruff", }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -60,17 +60,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov" - ] - } - } + "--no-cov", + ], + }, + }, }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify" - } + "onAutoForward": "notify", + }, }, - "forwardPorts": [4040] + "forwardPorts": [4040], } From 7c062764ac2e5715614e6f157869d51f71a99cd9 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Tue, 13 Feb 2024 09:57:25 +0000 Subject: [PATCH 29/37] feat: gcp cli --- .devcontainer/devcontainer.json | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index a8ba32a8d..fc220ae6d 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,19 +5,20 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1", - }, + "POETRY_VERSION": "1.7.1" + } }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, + "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", - "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -40,7 +41,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter", + "fnando.linter" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -51,7 +52,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff", + "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -60,17 +61,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov", - ], - }, - }, + "--no-cov" + ] + } + } }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify", - }, + "onAutoForward": "notify" + } }, - "forwardPorts": [4040], + "forwardPorts": [4040] } From d7327a42238e4d4137180f68a2de9ef30981437a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Feb 2024 09:57:46 +0000 Subject: [PATCH 30/37] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .devcontainer/devcontainer.json | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index fc220ae6d..b6b2b730d 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,20 +5,20 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1" - } + "POETRY_VERSION": "1.7.1", + }, }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", - "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -41,7 +41,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter" + "fnando.linter", ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -52,7 +52,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff" + "editor.defaultFormatter": "charliermarsh.ruff", }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -61,17 +61,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov" - ] - } - } + "--no-cov", + ], + }, + }, }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify" - } + "onAutoForward": "notify", + }, }, - "forwardPorts": [4040] + "forwardPorts": [4040], } From ba432c17d3bf637850a075b1b35183163daa9654 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Tue, 13 Feb 2024 12:26:25 +0000 Subject: [PATCH 31/37] feat: mount gcloud credentials --- .devcontainer/devcontainer.json | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b6b2b730d..8edaa8181 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,20 +5,21 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1", - }, + "POETRY_VERSION": "1.7.1" + } }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", + "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached" ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -41,7 +42,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter", + "fnando.linter" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -52,7 +53,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff", + "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -61,17 +62,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov", - ], - }, - }, + "--no-cov" + ] + } + } }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify", - }, + "onAutoForward": "notify" + } }, - "forwardPorts": [4040], + "forwardPorts": [4040] } From d6967298ea1fab97d862c00441c8fd53fafe3f64 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Feb 2024 12:27:22 +0000 Subject: [PATCH 32/37] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .devcontainer/devcontainer.json | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 8edaa8181..8da67ebf7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,21 +5,21 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1" - } + "POETRY_VERSION": "1.7.1", + }, }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", - "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached" + "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached", ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -42,7 +42,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter" + "fnando.linter", ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -53,7 +53,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff" + "editor.defaultFormatter": "charliermarsh.ruff", }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -62,17 +62,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov" - ] - } - } + "--no-cov", + ], + }, + }, }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify" - } + "onAutoForward": "notify", + }, }, - "forwardPorts": [4040] + "forwardPorts": [4040], } From 55a240f67b0364d9dd945b2c1a87dd455526dfe4 Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Sat, 17 Feb 2024 20:31:17 +0000 Subject: [PATCH 33/37] feat: missing extension --- .devcontainer/devcontainer.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 8da67ebf7..eef18f3a1 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -42,7 +42,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter", + "fnando.linter" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { From c1803b77c6f779670814e5f261cc3f7cc9ed1341 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 17 Feb 2024 20:31:38 +0000 Subject: [PATCH 34/37] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .devcontainer/devcontainer.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index eef18f3a1..8da67ebf7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -42,7 +42,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter" + "fnando.linter", ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { From 05cc6a7468561adfdf1650c00c9caef1c1ee614a Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Sat, 17 Feb 2024 20:31:54 +0000 Subject: [PATCH 35/37] feat: pre-commit edits --- .devcontainer/devcontainer.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index eef18f3a1..8edaa8181 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,21 +5,21 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1", - }, + "POETRY_VERSION": "1.7.1" + } }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", - "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached", + "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached" ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -53,7 +53,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff", + "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -62,17 +62,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov", - ], - }, - }, + "--no-cov" + ] + } + } }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify", - }, + "onAutoForward": "notify" + } }, - "forwardPorts": [4040], + "forwardPorts": [4040] } From 5bdddf0894a02d29a8d85c6a0b4e7603d14a6cd5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 17 Feb 2024 20:33:14 +0000 Subject: [PATCH 36/37] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .devcontainer/devcontainer.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index c75218302..8da67ebf7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,21 +5,21 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1" - } + "POETRY_VERSION": "1.7.1", + }, }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", - "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached" + "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached", ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -53,7 +53,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff" + "editor.defaultFormatter": "charliermarsh.ruff", }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -62,17 +62,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov" - ] - } - } + "--no-cov", + ], + }, + }, }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify" - } + "onAutoForward": "notify", + }, }, - "forwardPorts": [4040] + "forwardPorts": [4040], } From 243b7cc7aa2e252a698ac403bedcf528bc09c2ef Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 21 Feb 2024 11:13:14 +0000 Subject: [PATCH 37/37] chore: pre-commit auto fixes [...] --- .devcontainer/devcontainer.json | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 8da67ebf7..8edaa8181 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,21 +5,21 @@ "context": "..", "args": { "VARIANT": "3.10-bullseye", - "POETRY_VERSION": "1.7.1", - }, + "POETRY_VERSION": "1.7.1" + } }, "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, "ghcr.io/dhoeric/features/google-cloud-cli:1": {}, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}, "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}, - "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} }, "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind", "source=devcontainer-bashhistory,target=/commandhistory,type=volume", "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached", - "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached", + "source=${localEnv:HOME}/.config/gcloud,target=/home/vscode/.config/gcloud,type=bind,consistency=cached" ], "runArgs": ["-e", "GIT_EDITOR=code --wait"], "postCreateCommand": "bash .devcontainer/postCreateCommand.sh", @@ -42,7 +42,7 @@ "ms-toolsai.jupyter", "ms-vscode.makefile-tools", "GitHub.vscode-pull-request-github", - "fnando.linter", + "fnando.linter" ], // Please keep this file in sync with settings in /.vscode/settings.json "settings": { @@ -53,7 +53,7 @@ "editor.formatOnSave": true, "editor.formatOnType": true, "[python]": { - "editor.defaultFormatter": "charliermarsh.ruff", + "editor.defaultFormatter": "charliermarsh.ruff" }, "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"], "python.defaultInterpreterPath": "/usr/local/bin/python", @@ -62,17 +62,17 @@ "src/", "tests/", "--doctest-modules", - "--no-cov", - ], - }, - }, + "--no-cov" + ] + } + } }, "portsAttributes": { "4040": { "label": "SparkUI", - "onAutoForward": "notify", - }, + "onAutoForward": "notify" + } }, - "forwardPorts": [4040], + "forwardPorts": [4040] }