MAINTAIN: Move to flit for PEP 621 package builds (#1645)

.github/workflows/tests.yml

@@ -194,15 +194,16 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Build package
+      - name: Install flit
         run: |
-          pip install wheel
-          python setup.py sdist bdist_wheel
-      - name: Publish
-        uses: pypa/gh-action-pypi-publish@v1.1.0
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_KEY }}
+          pip install flit~=3.6
+
+      - name: Build and publish
+        run: |
+          flit publish
+        env:
+          FLIT_USERNAME: __token__
+          FLIT_PASSWORD: ${{ secrets.PYPI_KEY }}

.pre-commit-config.yaml

@@ -19,28 +19,16 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
-  # this is not used for now,
-  # since it converts jupyter-book to jupyter_book and removes comments
-  # - repo: https://github.com/asottile/setup-cfg-fmt
-  #   rev: v1.17.0
-  #   hooks:
-  #   - id: setup-cfg-fmt
-
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
-    hooks:
-    - id: check-manifest
-      args: [--no-build-isolation]
-      additional_dependencies: [setuptools>=46.4.0]
-
   - repo: local
     hooks:
     - id: check-doc-req
       name: Check docs/requirements.txt up-to-date
       pass_filenames: false
+      additional_dependencies:
+      - tomli
       files: >-
           (?x)^(
-              setup.cfg|
+              pyproject.toml|
               docs/requirements.txt|
               scripts/check_doc_requirements.py|
           )$

MANIFEST.in

-exclude docs
-recursive-exclude docs *
-exclude tests
-recursive-exclude tests *
-exclude .binder
-recursive-exclude .binder *
-exclude .github
-recursive-exclude .github *
-exclude .circleci
-recursive-exclude .circleci *
-exclude scripts
-recursive-exclude scripts *
-
-exclude .pre-commit-config.yaml
-exclude .pre-commit-hooks.yaml
-exclude .readthedocs.yml
-exclude tox.ini
-exclude codecov.yml
-exclude RELEASES.md
-exclude conftest.py
-
-include LICENSE
-include CHANGELOG.md
-include docs/requirements.txt
-recursive-include examples *
-
-include jupyter_book/default_config.yml
-include jupyter_book/config_schema.json
-recursive-include jupyter_book/book_template *

docs/file-types/jupytext.Rmd

@@ -74,9 +74,16 @@ This mapping allows for "true" error reporting, as described in [](myst-nb:myst/
 between Jupyter Notebook `.ipynb` files and
 [a variety of text-based files](https://jupytext.readthedocs.io/en/latest/formats.html).
 
-Jupyter Book natively supports the Jupytext file format: [notebooks with MyST Markdown](./myst-notebooks.md), but you can add other formats like [RMarkdown](https://rmarkdown.rstudio.com/) or Python files.
+Jupyter Book natively supports the Jupytext file format: [notebooks with MyST Markdown](./myst-notebooks.md).
 
-The configuration looks like:
+You can also add other formats like [RMarkdown](https://rmarkdown.rstudio.com/) or Python files.
+To do so, first ensure Jupytext is installed:
+
+```console
+$ pip install jupytext
+```
+
+Then configure Jupyter book like so:
 
 ```yaml
 sphinx:
@@ -101,9 +108,6 @@ Now you can use RMarkdown blocks:
 print("Hallo I'm an RMarkdown block!")
 ```
 
-:::{important}
-For full compatibility with `myst-parser`, it is necessary to use `jupytext>=1.6.0`.
-:::
 
 (file-types:custom:jupytext)=
 ## Convert a Jupytext file into a MyST notebook

docs/publish/gh-pages.md

@@ -160,10 +160,10 @@ jobs:
     - uses: actions/checkout@v2
 
     # Install dependencies
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
     - name: Install dependencies
       run: |

docs/requirements.txt

-# Copied from 'sphinx' extra of setup.cfg
+# Copied from 'sphinx' extra of pyproject.toml
 altair
 bokeh
 folium
 ipywidgets
+jupytext
 matplotlib
 nbclient
 numpy

pyproject.toml

 [build-system]
-requires = ["setuptools>=46.4.0", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["flit_core >=3.5,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "jupyter-book"
+authors = [{name = "Executable Book Project", email = "executablebooks@gmail.com"}]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Text Processing :: Markup",
+]
+keywords = [
+    "reproducible",
+    "science",
+    "environments",
+    "scholarship",
+    "notebook",
+]
+dynamic = ["description", "version"]
+requires-python = ">=3.7"
+dependencies = [
+    "click>=7.1,<9",
+    "docutils>=0.15,<0.18",
+    "jsonschema<4",
+    "linkify-it-py~=1.0.1",
+    "myst-nb~=0.13.1",
+    "pyyaml",
+    "sphinx>=3,<5",
+    "sphinx-comments",
+    "sphinx-copybutton",
+    "sphinx-external-toc~=0.2.3",
+    "sphinx-jupyterbook-latex~=0.4.6",
+    "sphinx-panels~=0.6.0",
+    "sphinx-thebe~=0.1.1",
+    "sphinx_book_theme~=0.1.4",
+    "sphinx_togglebutton",
+    "sphinxcontrib-bibtex>=2.2.0,<=2.5.0",
+    "sphinx-multitoc-numbering~=0.1.3",
+]
+
+[project.license]
+file = "LICENSE"
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.urls]
+Homepage = "https://executablebooks.org/"
+Documentation = "https://jupyterbook.org"
+Funding = "https://executablebooks.org"
+Source = "https://github.com/executablebooks/jupyter-book/"
+Tracker = "https://github.com/executablebooks/jupyter-book/issues"
+
+[project.optional-dependencies]
+code_style = ["pre-commit~=2.12"]
+pdfhtml = ["pyppeteer"]
+sphinx = [
+    "altair",
+    "bokeh",
+    "folium",
+    "ipywidgets",
+    "jupytext",
+    "matplotlib",
+    "nbclient",
+    "numpy",
+    "pandas",
+    "plotly",
+    "sphinx-click",
+    "sphinx_inline_tabs",
+    "sphinxext-rediraffe~=0.2.3",
+    "sympy",
+    "sphinx-proof",
+]
+testing = [
+    "altair",
+    "beautifulsoup4",
+    "beautifulsoup4",
+    "cookiecutter",
+    "coverage",
+    "jupytext",
+    "matplotlib",
+    "pyppeteer",
+    "pytest>=6.2.4",
+    "pytest-cov",
+    "pytest-regressions",
+    "pytest-timeout",
+    "pytest-xdist",
+    "sphinx_click",
+    "sphinx_tabs",
+    "texsoup",
+]
+
+[project.scripts]
+jb = "jupyter_book.cli.main:main"
+jupyter-book = "jupyter_book.cli.main:main"
+
+[tool.flit.module]
+name = "jupyter_book"
+
+[tool.flit.sdist]
+exclude = [
+  ".*",  # Any hidden folders or files
+  "docs/",
+  "tests/",
+  "scripts/",
+  "tox.ini",
+  "codecov.yml",
+  "conftest.py",
+]
 
 [tool.isort]
 profile = "black"

scripts/check_doc_requirements.py

 #!/usr/bin/env python3
 import sys
-from configparser import ConfigParser
 from pathlib import Path
 
+import tomli
 
-def check_reqs(setup_path="setup.cfg", req_path="docs/requirements.txt"):
-    parser = ConfigParser()
-    parser.read(setup_path)
-    setup_content = parser["options.extras_require"]["sphinx"]
-    setup_content = (
-        "# Copied from 'sphinx' extra of setup.cfg\n" + setup_content.strip()
-    )
+
+def check_reqs(pyproject_path="pyproject.toml", req_path="docs/requirements.txt"):
+    with open(pyproject_path, "rb") as f:
+        toml_dict = tomli.load(f)
+
+    optional_deps = toml_dict["project"]["optional-dependencies"]
+    sphinx_content = "\n".join(optional_deps["sphinx"]).strip()
+    sphinx_content = "# Copied from 'sphinx' extra of pyproject.toml\n" + sphinx_content
     req_content = Path(req_path).read_text()
-    if setup_content != req_content.strip():
-        Path(req_path).write_text(setup_content + "\n")
+    if sphinx_content != req_content.strip():
+        Path(req_path).write_text(sphinx_content + "\n")
         sys.exit(1)
     sys.exit(0)
 

setup.cfg

-[metadata]
-name = jupyter-book
-version = attr: jupyter_book.__version__
-description = Jupyter Book: Create an online book with Jupyter Notebooks
-long_description = file: README.md
-long_description_content_type = text/markdown
-url = https://executablebooks.org/
-author = Executable Book Project
-author_email = jupyter@googlegroups.com
-license = BSD-3-Clause
-license_file = LICENSE
-classifiers =
-    Development Status :: 4 - Beta
-    License :: OSI Approved :: BSD License
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: Implementation :: CPython
-    Topic :: Software Development :: Libraries :: Python Modules
-    Topic :: Text Processing :: Markup
-keywords =
-    reproducible
-    science
-    environments
-    scholarship
-    notebook
-project_urls =
-    Documentation = https://jupyterbook.org
-    Funding = https://executablebooks.org
-    Source = https://github.com/executablebooks/jupyter-book/
-    Tracker = https://github.com/executablebooks/jupyter-book/issues
-
-[options]
-packages = find:
-install_requires =
-    click>=7.1,<9
-    docutils>=0.15,<0.18
-    jsonschema<4
-    # Include Jupytext to ensure users have the right version, even if not strictly necessary
-    jupytext>=1.11.2,<1.12  #markdown-it-py~=1 required and support from 1.11.2
-    linkify-it-py~=1.0.1
-    myst-nb~=0.13.1
-    pyyaml
-    sphinx>=3,<5
-    sphinx-comments
-    sphinx-copybutton
-    sphinx-external-toc~=0.2.3
-    sphinx-jupyterbook-latex~=0.4.6
-    sphinx-panels~=0.6.0
-    sphinx-thebe~=0.1.1
-    sphinx_book_theme~=0.1.4
-    sphinx_togglebutton
-    sphinxcontrib-bibtex>=2.2.0,<=2.5.0
-    sphinx-multitoc-numbering~=0.1.3
-python_requires = >=3.7
-include_package_data = True
-
-[options.entry_points]
-console_scripts =
-    jb = jupyter_book.cli.main:main
-    jupyter-book = jupyter_book.cli.main:main
-
-[options.extras_require]
-code_style =
-    pre-commit~=2.12
-pdfhtml =
-    pyppeteer
-sphinx =
-    altair
-    bokeh
-    folium
-    ipywidgets
-    matplotlib
-    nbclient
-    numpy
-    pandas
-    plotly
-    sphinx-click
-    sphinx_inline_tabs
-    sphinxext-rediraffe~=0.2.3
-    sympy
-    sphinx-proof
-testing =
-    altair
-    beautifulsoup4
-    beautifulsoup4
-    cookiecutter
-    coverage
-    matplotlib
-    pyppeteer
-    pytest>=6.2.4
-    pytest-cov
-    pytest-regressions
-    pytest-timeout
-    pytest-xdist
-    sphinx_click
-    sphinx_tabs
-    texsoup
-
-[flake8]
-max-line-length = 100
-extend-ignore = E203

setup.py

-# This file is needed for editable installs (`pip install -e .`).
-# Can be removed once the following is resolved
-# https://github.com/pypa/packaging-problems/issues/256
-from setuptools import setup
-
-setup()

tox.ini

@@ -67,3 +67,8 @@ markers =
 filterwarnings =
     ignore::DeprecationWarning:pyee.*
     ignore::DeprecationWarning:pybtex.*
+
+# Use tox.ini for flake8 config because it does not yet support pyproject.toml
+[flake8]
+max-line-length = 100
+extend-ignore = E203