diff --git a/.azuredevops/ado-ci-pipeline-ms-hosted.yml b/.azuredevops/ado-ci-pipeline-ms-hosted.yml index 3ca1a69..c90a433 100644 --- a/.azuredevops/ado-ci-pipeline-ms-hosted.yml +++ b/.azuredevops/ado-ci-pipeline-ms-hosted.yml @@ -27,8 +27,7 @@ steps: python -m venv venv source venv/bin/activate python -m pip install --upgrade pip - pip install -r requirements-dev.txt - pip install pytest-azurepipelines + pip install ruff pytest-azurepipelines displayName: "Install requirements" # files under venv will be automatically excluded from ruff check by default https://docs.astral.sh/ruff/settings/#exclude diff --git a/.azuredevops/ado-ci-pipeline-self-hosted.yml b/.azuredevops/ado-ci-pipeline-self-hosted.yml index 06b58bd..8a59cc3 100644 --- a/.azuredevops/ado-ci-pipeline-self-hosted.yml +++ b/.azuredevops/ado-ci-pipeline-self-hosted.yml @@ -39,8 +39,7 @@ steps: python -m venv venv source venv/bin/activate python -m pip install --upgrade pip - pip install -r requirements-dev.txt - pip install pytest-azurepipelines + pip install ruff pytest-azurepipelines displayName: "Install requirements" - task: UseDotNet@2 diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 24c2486..f8398aa 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -16,6 +16,17 @@ updates: update-types: - "minor" - "patch" + - package-ecosystem: "uv" + directories: + - "**/*" + schedule: + interval: "monthly" + groups: + uv-minor-patch-updates: + applies-to: version-updates + update-types: + - "minor" + - "patch" - package-ecosystem: "github-actions" # Workflow files stored in the default location of `.github/workflows`. (You don't need to specify `/.github/workflows` for `directory`. You can use `directory: "/"`.) directory: "/" diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index dfff799..cdbe8a1 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -12,7 +12,7 @@ * [ ] No PII in logs or output * [ ] Made corresponding changes to the documentation -* [ ] All new packages used are included in requirements.txt +* [ ] All new packages used are included in pyproject.toml * [ ] Functions use type hints, and there are no type hint errors ## Pull Request Type diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 49338e0..e5db0be 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -21,23 +21,12 @@ jobs: - name: Checkout code uses: actions/checkout@v4 - - name: Setup Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: 3.11 - - - name: Install requirements - run: | - python -m venv venv - source venv/bin/activate - python -m pip install --upgrade pip - pip install -r requirements-dev.txt + - name: Install uv + uses: astral-sh/setup-uv@v5 - name: Run ruff linter - # files under venv will be automatically excluded from ruff check by default https://docs.astral.sh/ruff/settings/#exclude run: | - source venv/bin/activate - ruff check --output-format github + uvx ruff check --output-format github - name: Run pytest in docker containers run: ./ci-tests.sh diff --git a/.gitignore b/.gitignore index ad80d94..7fb15d1 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,7 @@ data logs .vscode +.DS_Store # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/README.md b/README.md index 6eeb6a1..baddc14 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ # Dev Containers for ML feasibility study with VS Code -A machine learning and data science project template that makes it easy to work with multiple Docker based [VSCode Dev Containers](https://code.visualstudio.com/docs/devcontainers/containers) in the same repository. The template also makes it easy to transition projects to the cloud and production by including automated code quality checks, pytest configuration, CI pipeline templates and a sample for running on Azure Machine Learning. +[![CI](https://github.com/microsoft/dstoolkit-devcontainers/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/microsoft/dstoolkit-devcontainers/actions/workflows/ci.yaml) + +A machine learning and data science project template that makes it easy to work with multiple Docker based [VSCode Dev Containers](https://code.visualstudio.com/docs/devcontainers/containers) in the same repository. The template leverages [uv](https://github.com/astral-sh/uv), an extremely fast Python package and project manager as a base for better productivity. The template also makes it easy to transition projects to the cloud and production by including automated code quality checks, pytest configuration, CI pipeline templates and a sample for running on Azure Machine Learning. ## Contents @@ -10,7 +12,7 @@ A machine learning and data science project template that makes it easy to work - [Features](#features) - [Getting Started](#getting-started) - [How to setup dev environment?](#how-to-setup-dev-environment) - - [How to create a new directory under src with a new environment](#how-to-create-a-new-directory-under-src-with-a-new-environment) + - [How to update python packages in the dev container](#how-to-update-python-packages-in-the-dev-container) - [Directory Structure](#directory-structure) - [`notebooks` directory vs `src` directory](#notebooks-directory-vs-src-directory) - [AML Example](#aml-example) @@ -57,15 +59,32 @@ This section provides a comprehensive guide on how to set up a development envir 1. Run `Dev Containers: Open Folder in Container...` from the Command Palette (F1) and select the `notebooks` directory. 1. VS Code will then build and start up a container, connect this window to Dev Container: `notebooks`, and install VS Code extensions specified in `notebooks/.devcontainer/devcontainer.json`. `pre-commit install --overwrite` runs as part of `postCreateCommand` in `devcontainer.json` and this will setup your git precommit hook automatically. 1. Now set up is done. If you want to develop in another directory for example under `src`, run `Dev Containers: Open Folder in Container...` and go to that directory that has `.devcontainer` and that will setup an dev environment for that directory. -1. When you or others update either `requirements.txt` or `Dockerfile` in your working directory, make sure to rebuild your container to apply those changes to container. Run `Dev Containers: Rebuild and Reopen in Container...` for that. +1. When you or others update either `pyproject.toml` or `Dockerfile` in your working directory, make sure to rebuild your container to apply those changes to container. Run `Dev Containers: Rebuild and Reopen in Container...` for that. ## How to create a new directory under src with a new environment 1. Copy `src/sample_cpu_project/` under `src` and rename it. If you need gpu environment, base off of `src/sample_pytorch_gpu_project` instead -1. Update `COPY sample_cpu_project/.devcontainer/requirements.txt` in `Dockerfile` with a new path +1. Update `COPY src/sample_cpu_project/.devcontainer/pyproject.toml src/sample_cpu_project/.devcontainer/uv.lock` in `Dockerfile` with a new path 1. Update other parts of `Dockerfile` if you need -1. Update `requirements.txt` if you need 1. Run `Dev Containers: Open Folder in Container...` from the Command Palette (F1) and select the new directory and make sure you can successfully open the new directory on VS Code running in a container +1. If you need to update python packages, stay inside DevContainer you just built and follow the steps below + 1. Update `.devcontainer/pyproject.toml` and add/remove new python packages you need in `project.dependencies` section + 1. Run `uv lock --project $UV_PROJECT_FILE` to update the project's lockfile `.devcontainer/uv.lock` with the updated python packages. `$UV_PROJECT_FILE` is already set automatically during docker build so you don't need to manually set it +1. Rerun `Dev Containers: Open Folder in Container...` from the Command Palette (F1) and select the new directory and make sure you can successfully open the new directory on VS Code running in a container + +## How to update python packages in the dev container + +This solution uses [uv](https://docs.astral.sh/uv) to manage python packages in the dev container. `uv` is a fast and efficient Python package and project manager that simplifies dependency management and ensures consistency across environments. It is installed in the dev container and is used to manage python packages in the dev container. `uv` is also used to create a lock file (`uv.lock`) that contains the list of all python packages and their versions that are installed in the dev container. This lock file is used to ensure that the same versions of the packages and dependencies are installed in every devcontainer build. + +To manage Python packages within your active dev container, execute the following commands according to your needs: + +- To add a package: `uv add requests --project $UV_PROJECT_FILE` +- To add a specific version of a package: `uv add 'requests==2.31.0' --project $UV_PROJECT_FILE` +- To remove a package: `uv remove requests --project $UV_PROJECT_FILE` +- To upgrade a package: `uv lock --upgrade-package requests --project $UV_PROJECT_FILE` + +These commands update both `pyproject.toml` and `uv.lock` files automatically. +Check for more details at [The official documentation for how to manage dependencies in uv](https://docs.astral.sh/uv/guides/projects/#managing-dependencies) ## Directory Structure @@ -83,7 +102,7 @@ This section gives you overview of the directory structure of this template. Onl │ ├── .devcontainer # dev container related configuration files goes to here following VSCode convention │ │ ├── devcontainer.json # dev container configuration and VS Code settings, extensions etc. │ │ ├── Dockerfile # referred in devcontainer.json -│ │ └── requirements.txt # includes python package list for notebooks. used in Dockerfile +│ │ └── pyproject.toml # includes python package list for notebooks. used in Dockerfile │ └── sample_notebook.py # example of interactive python script ├── pyproject.toml # Setting file for ruff, pytest and pytest-cov └── src @@ -93,7 +112,7 @@ This section gives you overview of the directory structure of this template. Onl │ ├── .devcontainer # dev container related configuration files goes to here following VSCode convention │ │ ├── devcontainer.json # dev container configuration and VS Code settings, extensions etc. │ │ ├── Dockerfile # referred in devcontainer.json. Supports only CPU - │ │ └── requirements.txt # includes python package list for sample_cpu_project. used in Dockerfile + │ │ └── pyproject.toml # includes python package list for sample_cpu_project. used in Dockerfile │ ├── sample_main.py │ └── tests # pytest scripts for sample_cpu_project goes here │ └── test_dummy.py # pytest script example @@ -102,7 +121,7 @@ This section gives you overview of the directory structure of this template. Onl ├── .devcontainer # dev container related configuration files goes to here following VSCode convention │ ├── devcontainer.json # dev container configuration and VS Code settings, extensions etc. │ ├── Dockerfile # referred in devcontainer.json. Supports GPU - │ └── requirements.txt # includes python package list for sample_pytorch_gpu_project. used in Dockerfile + │ └── pyproject.toml # includes python package list for sample_pytorch_gpu_project. used in Dockerfile ├── aml_example/ # Sample AML CLI v2 Components-based pipeline, including setup YAML. See sample_pytorch_gpu_project/README for full details of files in this directory. ├── sample_main.py ├── inference.py # Example pytorch inference/eval script that also works with aml_example diff --git a/notebooks/.devcontainer/Dockerfile b/notebooks/.devcontainer/Dockerfile index ebf2302..4b3a313 100644 --- a/notebooks/.devcontainer/Dockerfile +++ b/notebooks/.devcontainer/Dockerfile @@ -1,4 +1,6 @@ FROM python:3.11.11 +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ + # create non-root user and set the default user ARG USERNAME=devuser ARG USER_UID=1000 @@ -11,14 +13,23 @@ RUN groupadd --gid $USER_GID $USERNAME \ && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \ && chmod 0440 /etc/sudoers.d/$USERNAME \ && rm -rf /var/lib/apt/lists/* +# some packages try to create new directories in /usr/local/lib/python3.11/site-packages etc during uv sync so permission needs to be granted +RUN chown -R $USERNAME:$USERNAME /usr/local USER $USERNAME -# make all python tools installed by pip accesible +# make all python tools installed by uv accessible ENV PATH=$PATH:/home/$USERNAME/.local/bin -RUN pip install --no-cache-dir pip --upgrade -COPY requirements-dev.txt . -RUN pip install --no-cache-dir -r requirements-dev.txt +# it tends to improve startup time (at the cost of increased installation time) +ENV UV_COMPILE_BYTECODE=1 +# This prevents uv from creating venv but instead makes it use the system python in container +ENV UV_PROJECT_ENVIRONMENT=/usr/local +ENV UV_PROJECT_FILE=.devcontainer/pyproject.toml +RUN sudo chown -R $USERNAME:$USERNAME /usr/local -# install notebooks related depencencies -COPY notebooks/.devcontainer/requirements.txt . -RUN pip install --no-cache-dir -r requirements.txt +# Changing the default UV_LINK_MODE silences warnings about not being able to use hard links since the cache and sync target are on separate file systems +ENV UV_LINK_MODE=copy +# Install dependencies +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=notebooks/.devcontainer/uv.lock,target=uv.lock \ + --mount=type=bind,source=notebooks/.devcontainer/pyproject.toml,target=pyproject.toml \ + uv sync --locked --project $UV_PROJECT_FILE diff --git a/notebooks/.devcontainer/pyproject.toml b/notebooks/.devcontainer/pyproject.toml new file mode 100644 index 0000000..cd29447 --- /dev/null +++ b/notebooks/.devcontainer/pyproject.toml @@ -0,0 +1,21 @@ +[project] +name = "" +version = "0.1.0" +requires-python = ">=3.11" +dependencies = [ + "ipykernel==6.29.5", + "nbconvert==7.16.6", + "nbformat==5.10.4", +] + +[dependency-groups] +dev = [ + "mypy==1.15.0", + "pytest==8.3.5", + "pre-commit==4.2.0", + "pytest-cov==6.1.0", + "ruff==0.11.2", +] + +[tool.uv] +package = false diff --git a/notebooks/.devcontainer/requirements.txt b/notebooks/.devcontainer/requirements.txt deleted file mode 100644 index 933e2f1..0000000 --- a/notebooks/.devcontainer/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -# notebooks specific 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$USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \ && chmod 0440 /etc/sudoers.d/$USERNAME \ && rm -rf /var/lib/apt/lists/* +# some packages try to create new directories in /usr/local/lib/python3.11/site-packages etc during uv sync so permission needs to be granted +RUN chown -R $USERNAME:$USERNAME /usr/local USER $USERNAME -# make all python tools installed by pip accesible +# make all python tools installed by uv accessible ENV PATH=$PATH:/home/devuser/.local/bin +# it tends to improve startup time (at the cost of increased installation time) +ENV UV_COMPILE_BYTECODE=1 +# This prevents uv from creating venv but instead makes it use the system python in container +ENV UV_PROJECT_ENVIRONMENT=/usr/local +ENV UV_PROJECT_FILE=.devcontainer/pyproject.toml +RUN sudo chown -R $USERNAME:$USERNAME /usr/local -RUN pip install --no-cache-dir pip --upgrade - -COPY src/sample_cpu_project/.devcontainer/requirements.txt . -RUN pip install --no-cache-dir -r requirements.txt +# Changing the default UV_LINK_MODE silences warnings about not being able to use hard links since the cache and sync target are on separate file systems +ENV UV_LINK_MODE=copy +# Install dependencies +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=src/sample_cpu_project/.devcontainer/uv.lock,target=uv.lock \ + --mount=type=bind,source=src/sample_cpu_project/.devcontainer/pyproject.toml,target=pyproject.toml \ + uv sync --locked --project $UV_PROJECT_FILE -# install common module related pacakages +# install common module related packages +# This part can be potentially improved by https://docs.astral.sh/uv/concepts/projects/workspaces/#when-not-to-use-workspaces to move away from requirements.txt and gets its own lock file COPY src/common/requirements.txt . -RUN pip install --no-cache-dir -r requirements.txt - -# install python tools -COPY requirements-dev.txt . -RUN pip install --no-cache-dir -r requirements-dev.txt +RUN uv pip install --no-cache-dir -r 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user @@ -13,23 +14,30 @@ RUN groupadd --gid $USER_GID $USERNAME \ && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \ && chmod 0440 /etc/sudoers.d/$USERNAME \ && rm -rf /var/lib/apt/lists/* +# some packages try to create new directories in /usr/local/lib/python3.11/site-packages etc during uv sync so permission needs to be granted +RUN chown -R $USERNAME:$USERNAME /usr/local USER $USERNAME -# make all python tools installed by pip accesible +# make all python tools installed by uv accessible ENV PATH=$PATH:/home/$USERNAME/.local/bin +# it tends to improve startup time (at the cost of increased installation time) +ENV UV_COMPILE_BYTECODE=1 +# This prevents uv from creating venv but instead makes it use the system python in container +ENV UV_PROJECT_ENVIRONMENT=/usr/local +ENV UV_PROJECT_FILE=.devcontainer/pyproject.toml -RUN pip install pip --upgrade +# Changing the default UV_LINK_MODE silences warnings about not being able to use hard links since the cache and sync target are on separate file systems +ENV UV_LINK_MODE=copy +# Install dependencies +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=src/sample_pytorch_gpu_project/.devcontainer/uv.lock,target=uv.lock \ + --mount=type=bind,source=src/sample_pytorch_gpu_project/.devcontainer/pyproject.toml,target=pyproject.toml \ + uv sync --locked --project $UV_PROJECT_FILE -COPY src/sample_pytorch_gpu_project/.devcontainer/requirements.txt . -RUN pip install --no-cache-dir -r requirements.txt - -# install common module related pacakages +# install common module related packages +# This part can be potentially improved by https://docs.astral.sh/uv/concepts/projects/workspaces/#when-not-to-use-workspaces to move away from requirements.txt and gets its own lock file COPY src/common/requirements.txt . -RUN pip install --no-cache-dir -r requirements.txt - -# install python tools -COPY requirements-dev.txt . -RUN pip install --no-cache-dir -r requirements-dev.txt +RUN uv pip 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b/src/sample_pytorch_gpu_project/README.md index c750b1f..7bf2df2 100644 --- a/src/sample_pytorch_gpu_project/README.md +++ b/src/sample_pytorch_gpu_project/README.md @@ -81,7 +81,7 @@ az ml environment create --file aml_example/aml_setup/create-env.yaml -g