Update cruft (#272)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/cthoyt/cookiecutter-snekpack",
-  "commit": "12edfcfa5f519467b5d834f0d4e706fb7cf4f065",
+  "commit": "b3664aa2dd1d01910b33ca36d9bc3493a61fa71c",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/FUNDING.yml

@@ -0,0 +1,3 @@
+# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/displaying-a-sponsor-button-in-your-repository
+github:
+  - cthoyt

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,17 @@
+<!--
+Thanks for contributing to `pyobo`.
+To help us out with reviewing, please consider the following:
+
+- Does this pull request include a summary of the change? (See below.)
+- Does this pull request include a descriptive title?
+- Does this pull request include references to any relevant issues?
+
+Caution: the maintainers often take an active role in pull requests,
+and may push to your branch. Therefore, you should always sync your
+local copy of the repository with the remote before continuing your
+work.
+-->
+
+## Summary
+
+<!-- What's the purpose of the change? What does it do, and why? -->

.github/workflows/tests.yml

@@ -4,6 +4,10 @@
 
 name: Tests
 
+# by default, give the GITHUB_TOKEN no permissions
+# See https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/controlling-permissions-for-github_token
+permissions: { }
+
 on:
   push:
     branches: [ main ]
@@ -13,11 +17,16 @@ on:
 jobs:
   lint:
     name: Code Quality
+    permissions:
+      # give only read-only access to the contents of the repository
+      # this is the only permission this job requires, so keep it to the least privilege
+      # i.e., not to issues, discussions, actions, etc.
+      contents: read
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.12", "3.10" ]
-        tox-command: ["manifest", "lint", "pyroma", "mypy"]
+        python-version: [ "3.13", "3.10" ]
+        tox-command: [ "lint", "pyroma", "mypy" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"
@@ -31,13 +40,15 @@ jobs:
 
   docs:
     name: Documentation
+    permissions:
+      contents: read
     runs-on: ubuntu-latest
     strategy:
       matrix:
         # We only test documentation on the latest version
         # sphinx 8.0 / sphinx-rtd-theme 3.0 discontinued Python 3.9 support
         # a year early, which prompted re-thinking about this.
-        python-version: [ "3.12" ]
+        python-version: [ "3.13" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"
@@ -56,11 +67,13 @@ jobs:
         run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docs-test
   tests:
     name: Tests
+    permissions:
+      contents: read
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.12", "3.10" ]
+        python-version: [ "3.13", "3.10" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"

.readthedocs.yml

@@ -12,9 +12,12 @@ build:
   tools:
     python: "3.12"
 
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+  # adapted from uv recipe at https://docs.readthedocs.io/en/stable/build-customization.html#install-dependencies-with-uv
+  # and comment at https://github.com/readthedocs/readthedocs.org/issues/11289#issuecomment-2103832834
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv venv $READTHEDOCS_VIRTUALENV_PATH
+    - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH UV_PREVIEW=1 uv pip install .[docs]
+    - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs/source $READTHEDOCS_OUTPUT/html

README.md

@@ -481,9 +481,16 @@ The final section of the README is for if you want to get involved by making a c
 To install in development mode, use the following:
 
 ```console
-git clone git+https://github.com/biopragmatics/pyobo.git
-cd pyobo
-python3 -m pip install -e .
+$ git clone git+https://github.com/biopragmatics/pyobo.git
+$ cd pyobo
+$ uv --preview pip install -e .
+```
+
+Alternatively, install using legacy pip with `UV_PREVIEW` mode enabled
+until the uv build backend becomes a stable feature:
+
+```console
+$ UV_PREVIEW=1 python3 -m pip install -e .
 ```
 
 ### Updating Package Boilerplate
@@ -578,7 +585,7 @@ You only have to do the following steps once.
 
 #### Configuring your machine's connection to PyPI
 
-You have to do the following steps once per machine. 
+You have to do the following steps once per machine.
 
 ```console
 $ uv tool install keyring

docs/source/conf.py

@@ -256,3 +256,6 @@
 
 todo_include_todos = True
 todo_emit_warnings = True
+
+# Output SVG inheritance diagrams
+graphviz_output_format = "svg"

docs/source/installation.rst

@@ -5,18 +5,21 @@ The most recent release can be installed from
 
 .. code-block:: shell
 
-    pip install pyobo
+    python3 -m pip install pyobo
 
 The most recent code and data can be installed directly from GitHub with:
 
 .. code-block:: shell
 
-    pip install git+https://github.com/biopragmatics/pyobo.git
+    python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
 
 To install in development mode, use the following:
 
 .. code-block:: shell
 
     git clone git+https://github.com/biopragmatics/pyobo.git
     cd pyobo
-    pip install -e .
+    UV_PREVIEW=1 python3 -m pip install -e .
+
+Note that the ``UV_PREVIEW`` environment variable is required to be
+set until the uv build backend becomes a stable feature.

pyproject.toml

@@ -1,7 +1,8 @@
-# See https://setuptools.readthedocs.io/en/latest/build_meta.html
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["uv>=0.5.13,<0.6.0"]
+# The uv backend entered preview mode in https://github.com/astral-sh/uv/pull/8886/files
+# with the 0.5.0 release. See also https://github.com/astral-sh/uv/issues/3957 for tracking.
+build-backend = "uv"
 
 [project]
 name = "pyobo"
@@ -26,11 +27,14 @@ classifiers = [
     "Framework :: Pytest",
     "Framework :: tox",
     "Framework :: Sphinx",
+    "Natural Language :: English",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3 :: Only",
+    "Typing :: Typed",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Chemistry",
 ]
@@ -47,10 +51,11 @@ keywords = [
     "OBO",
 ]
 
-# License Information. This can be any valid SPDX identifiers that can be resolved
-# with URLs like https://spdx.org/licenses/MIT
-# See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
-license = { file = "LICENSE" }
+# License Information.
+# See PEP-639 at https://peps.python.org/pep-0639/#add-license-files-key
+license-files = [
+    "LICENSE",
+]
 
 requires-python = ">=3.10"
 dependencies = [
@@ -86,7 +91,7 @@ dependencies = [
 [project.optional-dependencies]
 tests = [
     "pytest",
-    "coverage",
+    "coverage[toml]",
 ]
 docs = [
     "sphinx>=8",
@@ -96,22 +101,13 @@ docs = [
 ]
 
 # See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls
+# and also https://packaging.python.org/en/latest/specifications/well-known-project-urls/
 [project.urls]
 "Bug Tracker" = "https://github.com/biopragmatics/pyobo/issues"
 Homepage = "https://github.com/biopragmatics/pyobo"
 Repository = "https://github.com/biopragmatics/pyobo.git"
 Documentation = "https://pyobo.readthedocs.io"
-
-[tool.setuptools]
-package-dir = { "" = "src" }
-
-[tool.setuptools.packages.find]
-# this implicitly sets `packages = ":find"`
-where = ["src"]  # list of folders that contain the packages (["."] by default)
-
-# See https://setuptools.pypa.io/en/latest/userguide/datafiles.html
-[tool.setuptools.package-data]
-"*" = ["*.*"]
+Funding = "https://github.com/sponsors/cthoyt"
 
 [project.scripts]
 pyobo = "pyobo.cli:main"

tox.ini

@@ -16,7 +16,6 @@ envlist =
     format
     # format-docs
     # Code quality assessment
-    manifest
     pyroma
     lint
     mypy
@@ -28,7 +27,12 @@ envlist =
     py
     doctests
     # always keep coverage-report last
-    # coverage-report
+    coverage-report
+
+[testenv:.pkg]
+# this special environment configures the build that tox does itself
+set_env =
+    UV_PREVIEW=1
 
 [testenv]
 description = Run unit and integration tests.
@@ -41,6 +45,10 @@ commands =
 extras =
     # See the [project.optional-dependencies] entry in pyproject.toml for "tests"
     tests
+set_env =
+    # this setting gets inherited into all environments, meaning
+    # that things that call uv commands don't require a --preview
+    UV_PREVIEW=1
 
 [testenv:coverage-clean]
 description = Remove testing coverage artifacts.
@@ -85,12 +93,6 @@ skip_install = true
 commands =
     rstfmt docs/source/
 
-[testenv:manifest]
-deps = check-manifest
-skip_install = true
-commands = check-manifest
-description = Check that the MANIFEST.in is written properly and give feedback on how to fix it.
-
 [testenv:lint]
 description = Check code quality using ruff and other tools.
 
@@ -168,11 +170,9 @@ allowlist_externals =
     mkdir
 
 [testenv:coverage-report]
-# TODO this is broken
-deps = coverage
+deps = coverage[toml]
 skip_install = true
 commands =
-    coverage combine
     coverage report
 
 ####################
@@ -199,7 +199,6 @@ deps =
 skip_install = true
 deps =
     uv
-    setuptools
 commands =
     uv build --sdist --wheel --no-build-isolation
 
@@ -219,7 +218,7 @@ commands =
 # 7. Add your token to keyring with `keyring set https://upload.pypi.org/legacy/ __token__`
 
 [testenv:release]
-description = Release the code to PyPI so users can pip install it
+description = Release the code to PyPI so users can pip install it, using credentials from keyring
 skip_install = true
 deps =
     {[testenv:build]deps}
@@ -229,6 +228,19 @@ commands =
     {[testenv:build]commands}
     uv publish --username __token__ --keyring-provider subprocess --publish-url https://upload.pypi.org/legacy/
 
+[testenv:release-via-env]
+description = Release the code to PyPI so users can pip install it, using credentials from the environment.
+skip_install = true
+deps =
+    {[testenv:build]deps}
+    uv
+commands =
+    {[testenv:build]commands}
+    uv publish --publish-url https://upload.pypi.org/legacy/
+passenv =
+    UV_PUBLISH_USERNAME
+    UV_PUBLISH_PASSWORD
+
 [testenv:finish]
 description =
     Run a workflow that removes -dev from the version, creates a tagged release on GitHub,