From fb1a2861ee30d4b2af396d227d9fe626cba96f32 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 26 Jan 2023 16:42:02 +0000 Subject: [PATCH] [IO-557][internal] Move to use Poetry for packaging and publishing (#512) # Move to use [Poetry](https://python-poetry.org/) for packaging and publishing [Poetry](https://python-poetry.org/) is a dependency manager tool, that creates dev environments and installs requisite dependencies. It's also [PEP-518](https://peps.python.org/pep-0518/) compliant, which is no longer optional after the current default version of `pip`, so moving to [PEP-518](https://peps.python.org/pep-0518/) compliance was not optional if we wish to carry on publishing on [pypi.org]. Further details in #512. # Changelog message Changed our build system from old style `setup.py` to `PEP-518` style, based on `pyproject.toml`. Incorporated use of Poetry as a virtual environment and dependency manager, as this is already meeting these requirements. --- .github/ISSUE_TEMPLATE | 40 + .github/workflows/document.yml | 11 +- .github/workflows/pythonpublish_sdist.yml | 16 +- .github/workflows/tests.yml | 57 +- .python-version | 1 + docs/README.md | 73 + poetry.lock | 1570 +++++++++++++++++++++ pyproject.toml | 90 ++ setup.cfg | 9 - setup.py | 59 - 10 files changed, 1815 insertions(+), 111 deletions(-) create mode 100644 .github/ISSUE_TEMPLATE create mode 100644 .python-version create mode 100644 docs/README.md create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.github/ISSUE_TEMPLATE b/.github/ISSUE_TEMPLATE new file mode 100644 index 000000000..4928b12a5 --- /dev/null +++ b/.github/ISSUE_TEMPLATE @@ -0,0 +1,40 @@ +name: Bug Report +description: File a bug report +title: "[Bug]: " +labels: ["bug", "triage"] +body: + - type: markdown + attributes: + value: | + Thanks for taking the time to fill out this bug report! + - type: input + id: contact + attributes: + label: Contact Details + description: How can we get in touch with you if we need more info? + placeholder: ex. email@example.com + validations: + required: false + - type: textarea + id: what-happened + attributes: + label: What happened? + description: Also tell us, what did you expect to happen? + placeholder: Tell us what you see! + validations: + required: true + - type: textbox + id: version + attributes: + label: What version of darwin-py were you using? + description: Run darwin-py --version at command line and paste the output here + validations: + required: true + - type: checkboxes + id: terms + attributes: + label: Code of Conduct + description: By submitting this issue, you agree to follow our [Code of Conduct](https://example.com) + options: + - label: I agree to follow this project's Code of Conduct + required: true \ No newline at end of file diff --git a/.github/workflows/document.yml b/.github/workflows/document.yml index 27da875a5..4bd1daf08 100644 --- a/.github/workflows/document.yml +++ b/.github/workflows/document.yml @@ -2,7 +2,7 @@ name: Documentation on: push: - branches: ['master'] + branches: ["master"] workflow_dispatch: jobs: @@ -20,8 +20,11 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install setuptools wheel - pip install --editable ".[test,medical]" + pip install poetry + poetry install --all-extras --no-interaction --no-root + pip install wheel + pip install --upgrade setuptools + pip install --editable ".[test,ml,medical,dev]" pip install torch torchvision pip install -U sphinx # Locking mistune version so m2r works. More info on issue: @@ -35,7 +38,7 @@ jobs: m2r README.md mv README.rst source/ - name: Generate new docs - env: + env: PYTHONPATH: "." run: | rm -rf docs/* diff --git a/.github/workflows/pythonpublish_sdist.yml b/.github/workflows/pythonpublish_sdist.yml index 727804101..f0cdbc91f 100644 --- a/.github/workflows/pythonpublish_sdist.yml +++ b/.github/workflows/pythonpublish_sdist.yml @@ -14,14 +14,18 @@ jobs: uses: actions/setup-python@v2 with: python-version: "3.x" + - run: pip install pip --upgrade + - name: Setup Poetry + uses: abatilo/actions-poetry@v2 + with: + poetry-version: "1.3.1" - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install setuptools wheel twine - python setup.py sdist + poetry install --no-interaction --no-root --all-extras -vvv + poetry build - name: Publish env: - TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} - TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + POETRY_HTTP_BASIC_PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }} + POETRY_HTTP_BASIC_PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }} run: | - twine upload dist/* + poetry publish diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 78a1bee91..5c53d47ff 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,49 +1,40 @@ name: Testing -on: [push] +on: + push: + branches: + - master + pull_request: + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true jobs: - ubuntu: - runs-on: ubuntu-latest - timeout-minutes: 30 + ci: strategy: + fail-fast: false matrix: - python-version: [3.7, 3.8, 3.9, "3.10"] - + python-version: ["3.8", "3.9", "3.10"] + poetry-version: ["1.3.1"] + os: [ubuntu-latest, windows-latest] + runs-on: ${{ matrix.os }} steps: - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install wheel - pip install --upgrade setuptools - pip install --editable ".[test,ml,medical]" - - - name: Run tests - run: pytest - windows: - runs-on: windows-latest - timeout-minutes: 30 - strategy: - matrix: - python-version: [3.6, 3.7, 3.8, 3.9, "3.10"] - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - run: pip install pip --upgrade + - name: Setup Poetry + uses: abatilo/actions-poetry@v2 with: - python-version: ${{ matrix.python-version }} + poetry-version: ${{ matrix.poetry-version }} - name: Install dependencies run: | - python -m pip install --upgrade pip + poetry install --no-interaction --no-root --all-extras -vvv pip install wheel pip install --upgrade setuptools - pip install --editable ".[test,ml,medical]" - - - name: Run tests + pip install --editable ".[test,ml,medical,dev]" + pip install pytest pytest-describe + - name: Run Tests run: pytest diff --git a/.python-version b/.python-version new file mode 100644 index 000000000..c8cfe3959 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.10 diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..db911718c --- /dev/null +++ b/docs/README.md @@ -0,0 +1,73 @@ +# Developing for `darwin-py` + +`darwin-py` uses a `pyproject.toml` file, and manages it with `poetry` + +- [Developing for `darwin-py`](#developing-for-darwin-py) + - [Development environment](#development-environment) + - [Basic poetry commands](#basic-poetry-commands) + - [Add a package to general dependencies:](#add-a-package-to-general-dependencies) + - [Add a package to one of the extras groups](#add-a-package-to-one-of-the-extras-groups) + - [Add a package to the poetry dev dependencies](#add-a-package-to-the-poetry-dev-dependencies) + - [The `pyproject.toml` file](#the-pyprojecttoml-file) + + +## Development environment + +You can either: +* Install a `poetry` environment, and work with that, or +* Install `darwin-py` using `pip` from Pypi.org, and make your own arrangements for debugging. + +The recommended setup is to install poetry, and use this to setup a dev environment: + +```sh +$ python --version # must be 3.9 or greater for development tools +$ pip install poetry +$ poetry install --extras "test ml medical dev" -G dev +``` + +This creates a `virtualenv` for the project. If you prefer, you can use `venv` by running this command before `poetry install`: + +```sh +$ python -m venv .venv +``` + +You can give it a different name if you wish, but the name `.venv` is pre-ignored in the `.gitignore` file. + + +## Basic poetry commands + +### Add a package to general dependencies: +```sh +$ poetry add [PACKAGENAME] +``` + + +### Add a package to one of the extras groups + +(these are those that are used in `pip install darwinpy[option]` type commands - ours are `test`, `ml`, `medical`, and `dev` - `dev` is for developers who don't want to use poetry - so they can install using `pip`) + +```sh +$ poetry add [PACKAGENAME] --extras="extra group names" +``` + + +Packages added this way will be installable with `pip` once a release has been made to PyPi. + + +### Add a package to the poetry dev dependencies + +```sh +$ poetry add [PACKAGENAME] -G groupname +``` + +Currently the only group is `dev` and contains dev tools for developers using `poetry`. `poetry` 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