From ce81d1cab6709d2a21a2a8c4e7edce2a26f7214a Mon Sep 17 00:00:00 2001 From: Chris Pyles Date: Sat, 31 Aug 2024 22:05:05 -0700 Subject: [PATCH] use poetry and pyproject.toml for packaging --- .github/workflows/release.yml | 13 +- .github/workflows/run-tests.yml | 10 + .readthedocs.yml | 13 +- CONTRIBUTING.md | 15 +- MANIFEST.in | 17 - docs/requirements.txt | 6 - environment.yml | 7 +- poetry.lock | 3753 +++++++++++++++++++++++++++++++ pyproject.toml | 87 + release.py | 14 + requirements-export.txt | 3 - requirements-test.txt | 17 - requirements.txt | 17 - rtd_environment.yml | 12 - setup.py | 44 - 15 files changed, 3896 insertions(+), 132 deletions(-) delete mode 100644 MANIFEST.in delete mode 100644 docs/requirements.txt create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 requirements-export.txt delete mode 100644 requirements-test.txt delete mode 100644 requirements.txt delete mode 100644 rtd_environment.yml delete mode 100644 setup.py diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 8a757e112..94201fc66 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -17,20 +17,25 @@ jobs: TAR: /bin/tar steps: - - name: Set up Python 3.8 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.10 - name: Only allow releases off of master (or temp for patches) run: | python3 -c 'import os, sys; sys.exit(os.environ["GITHUB_REF"] != "refs/heads/master" and os.environ["GITHUB_REF"] != "refs/heads/temp")' + - uses: liskin/gh-pipx@v1 + with: + packages: >- + poetry + - uses: actions/checkout@v2 - name: Install dependencies run: | - python3 -m pip install -r requirements.txt twine wheel setuptools + poetry install - name: Update versions run: | @@ -53,7 +58,7 @@ jobs: TWINE_USERNAME: __token__ TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} run: | - python3 setup.py sdist bdist_wheel + poetry build python3 -m twine upload dist/* - name: Create a release on GitHub diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 685382a21..e9c38f760 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -41,6 +41,11 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 + - uses: liskin/gh-pipx@v1 + with: + packages: >- + poetry + - uses: mamba-org/setup-micromamba@v1 with: environment-file: environment.yml @@ -49,6 +54,11 @@ jobs: cache-environment: true cache-environment-key: requirements-${{ hashFiles('requirements*.txt') }} + - name: Install dependencies + run: | + micromamba activate otter-grader + poetry install --with test + - name: Install ottr run: | micromamba run -n otter-grader Rscript -e 'install.packages("ottr", dependencies=TRUE, repos="https://cran.r-project.org/")' diff --git a/.readthedocs.yml b/.readthedocs.yml index 319d53ed9..1362ece36 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -18,4 +18,15 @@ conda: build: os: ubuntu-22.04 tools: - python: "mambaforge-22.9" + python: "3.10" + jobs: + post_create_environment: + # Install poetry + # https://python-poetry.org/docs/#installing-manually + - pip install poetry + post_install: + # Install dependencies with 'docs' dependency group + # https://python-poetry.org/docs/managing-dependencies/#dependency-groups + # VIRTUAL_ENV needs to be set manually for now. + # See https://github.com/readthedocs/readthedocs.org/pull/11152/ + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ff5774b87..a44bd7c19 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,19 +6,24 @@ any updates. Make sure to update the changelog with any information about the co ## Environment Setup -To set up an environment for working on Otter, we recommend using -[Conda](https://docs.conda.io/en/latest/miniconda.html). This repo contains an +To set up an environment for working on Otter, we recommend using [Mamba](https://mamba.readthedocs.io/en/latest/) (or Conda). This repo contains an [`environment.yml`](environment.yml) file which defines all of the requirements for an environment used to work on Otter. Running ``` -conda env create -f environment.yml +mamba env create -f environment.yml ``` -will create a conda environment called `otter-grader` with the necessary packages installed for both -Python and R. +will create a conda environment called `otter-grader` with the necessary Python and R versions. + +To install development dependencies, use [`poetry`](https://python-poetry.org/) to update the environment: + +``` +mamba activate otter-grader +poetry install +``` ## Running Tests diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 5454ba5fb..000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,17 +0,0 @@ -include requirements.txt -exclude .coveragerc -exclude .dockerignore -exclude .gitattributes -exclude .github -exclude .gitignore -exclude .readthedocs.yml -exclude Dockerfile -exclude docs -exclude environment.yml -exclude examples -exclude logo -exclude Makefile -exclude release.py -exclude rtd_environment.yml -exclude slack-shields.json -exclude test diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index a3d0827ec..000000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -sphinx>=5.0.0 -sphinx_markdown_tables -sphinx-book-theme==1.1.0 -sphinxcontrib-apidoc -sphinx-click -jinja2 diff --git a/environment.yml b/environment.yml index af340025d..e06078688 100644 --- a/environment.yml +++ b/environment.yml @@ -3,13 +3,8 @@ channels: - conda-forge - defaults dependencies: - - python>=3.6,<3.11 + - python>=3.8 - r-base>=4.0.0 - r-essentials - r-devtools - pip - - pip: - - -r requirements.txt - - -r requirements-export.txt - - -r requirements-test.txt - - -r docs/requirements.txt diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 000000000..ba729940f --- /dev/null +++ b/poetry.lock @@ -0,0 +1,3753 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "accessible-pygments" +version = "0.0.5" +description = "A collection of 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"more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[extras] +plugins = ["google-api-python-client", "google-auth-oauthlib", "gspread", "six"] +r = ["rpy2"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.9" +content-hash = "7e4437bf807079afd2ad9a79b428027af0344383ffc47679908a84f31c6cd943" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..63db3d5c8 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,87 @@ +[tool.poetry] +name = "otter-grader" +version = "5.6.0" +description = "A Python and R autograding solution" +authors = ["Christopher Pyles "] +license = "BSD-3-Clause" +readme = "README.md" +homepage = "https://otter-grader.readthedocs.io/" +repository = "https://github.com/ucbds-infra/otter-grader" +documentation = "https://otter-grader.readthedocs.io/" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", +] +packages = [ + { include = "otter" }, +] +include = [ + { path = "otter/export/exporters/templates/**/*" }, + { path = "otter/generate/templates/**/*" }, + { path = "otter/grade/Dockerfile" }, +] + +[tool.poetry.scripts] +otter = "otter.cli:cli" +gmail_oauth2 = "otter.plugins.builtin.gmail_notifications.bin.gmail_oauth2:main" + +[tool.poetry.dependencies] +python = "^3.9" +astunparse = "^1.6.3" +click = "^8.1.7" +dill = "^0.3.8" +fica = ">=0.3.1" +google-api-python-client = { version = "*", optional = true } +google-auth-oauthlib = { version = "*", optional = true } +six = { version = "*", optional = true } +gspread = { version = "*", optional = true } +ipylab = "^1.0.0" +ipython = "*" +ipywidgets = "^8.1.5" +jinja2 = "^3.1.4" +jupytext = "^1.16.4" +nbconvert = { version = ">=6.0.0", extras = ["webpdf"], markers = "sys_platform != 'emscripten' and sys_platform != 'wasi'" } +nbformat = ">=5.0.0" +pandas = ">=2.0.0" +python-on-whales = "^0.72.0" +pyyaml = "^6.0.2" +requests = "^2.32.3" +rpy2 = { version = "^3.5.16", optional = true } +setuptools = "^74.0.0" +wrapt = "^1.16.0" + +[tool.poetry.extras] +plugins = ["google-api-python-client", "google-auth-oauthlib", "gspread", "six"] +r = ["rpy2"] + +[tool.poetry.group.dev.dependencies] +ipykernel = "*" +jupyter_client = "*" +matplotlib = "*" +pypdf = "*" +scikit-learn = "*" +tqdm = "*" + +[tool.poetry.group.test] +optional = true + +[tool.poetry.group.test.dependencies] +coverage = "^7.2.0" +pytest = "^8.2.2" +pytest-html = "*" +responses = "^0.25.3" + +[tool.poetry.group.docs] +optional = true + +[tool.poetry.group.docs.dependencies] +sphinx = ">=5.0.0" +sphinx-book-theme = "1.1.0" +sphinx-click = "*" +sphinx_markdown_tables = "*" +sphinxcontrib-apidoc = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/release.py b/release.py index fe944e1fd..930fba13e 100644 --- a/release.py +++ b/release.py @@ -90,6 +90,20 @@ with open("otter/version.py", "w") as f: f.write(contents) + # fix pyproject.toml + with open("pyproject.toml") as f: + contents = f.read() + + if args.new_version is not None: + contents = re.sub( + r"version = \"\d+\.\d+\.\d+(?:\.\w+)?\"", + f"version = \"{new_version_number}\"", + contents + ) + + with open("pyproject.toml", "w") as f: + f.write(contents) + # fix CITATION.cff with open("CITATION.cff") as f: contents = f.read() diff --git a/requirements-export.txt b/requirements-export.txt deleted file mode 100644 index bc5988b35..000000000 --- a/requirements-export.txt +++ /dev/null @@ -1,3 +0,0 @@ -nbconvert>=6.0.0 -nbconvert[webpdf] -pypdf diff --git a/requirements-test.txt b/requirements-test.txt deleted file mode 100644 index 4938d7175..000000000 --- a/requirements-test.txt +++ /dev/null @@ -1,17 +0,0 @@ -responses -scikit-learn -nbformat<5.1.0 -tqdm -coverage>=7.2.0 -rpy2 -pytest -jupyter_client -ipykernel -matplotlib -gspread -pytest-html - -# plugins -google-api-python-client -google-auth-oauthlib -six diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 12855b6b1..000000000 --- a/requirements.txt +++ /dev/null @@ -1,17 +0,0 @@ -dill -jinja2 -nbformat -pandas -PyYAML -python-on-whales -requests -wrapt -jupytext -click -fica>=0.3.1 -ipython -astunparse -nbconvert; sys_platform!='emscripten' and sys_platform!='wasi' -ipywidgets -ipylab -setuptools diff --git a/rtd_environment.yml b/rtd_environment.yml deleted file mode 100644 index 448d3ccf1..000000000 --- a/rtd_environment.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: otter-grader -channels: - - conda-forge - - defaults -dependencies: - - python - - pip - - pip: - - -r requirements.txt - - -r docs/requirements.txt - - nbconvert - - ipython diff --git a/setup.py b/setup.py deleted file mode 100644 index 5a94aaf10..000000000 --- a/setup.py +++ /dev/null @@ -1,44 +0,0 @@ -import setuptools - -with open("README.md", "r") as fh: - long_description = fh.read() - -# get version -env = {} -with open("otter/version.py") as f: - exec(f.read(), env) -version = env["__version__"] - -# get requirements -with open("requirements.txt") as f: - install_requires = f.readlines() - -setuptools.setup( - name = "otter-grader", - version = version, - author = "Christopher Pyles", - author_email = "otter-grader@berkeley.edu", - description = "Python and Jupyter Notebook autograder", - long_description = long_description, - long_description_content_type = "text/markdown", - url = "https://github.com/ucbds-infra/otter-grader", - license = "BSD-3-Clause", - packages = setuptools.find_packages(exclude=["test"]), - classifiers = [ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", - ], - install_requires=install_requires, - entry_points = { - "console_scripts": [ - "otter=otter.cli:cli", - "gmail_oauth2=otter.plugins.builtin.gmail_notifications.bin.gmail_oauth2:main", - ], - }, - package_data={ - "otter.export.exporters": ["templates/*", "templates/*/*"], - "otter.generate": ["templates/*", "templates/*/*"], - "otter.grade": ["Dockerfile"], - }, -)