Update cruft

.cruft.json

@@ -1,13 +1,14 @@
 {
   "template": "https://github.com/cthoyt/cookiecutter-snekpack",
-  "commit": "1884310d930f56787c96d4eba45bcb4a5225f7cb",
+  "commit": "0491ce7066df95aec19ca2ff5740207804ac1840",
   "checkout": null,
   "context": {
     "cookiecutter": {
       "package_name": "curies",
       "package_name_stylized": "CURIEs",
       "short_description": "Idiomatic conversion between URIs and compact URIs (CURIEs)",
       "author_name": "Charles Tapley Hoyt",
+      "author_github": "cthoyt",
       "author_email": "[email protected]",
       "github_organization_name": "biopragmatics",
       "github_repository_name": "curies",

.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 `curies`.
+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

@@ -26,7 +26,7 @@ jobs:
     strategy:
       matrix:
         python-version: [ "3.12", "3.9" ]
-        tox-command: ["manifest", "lint", "pyroma", "mypy"]
+        tox-command: ["lint", "pyroma", "mypy"]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"

README.md

@@ -134,9 +134,16 @@ 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/curies.git
-cd curies
-python3 -m pip install -e .
+$ git clone git+https://github.com/biopragmatics/curies.git
+$ cd curies
+$ 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
@@ -231,7 +238,7 @@ 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

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>=0.5.10,<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 = "curies"
@@ -47,10 +48,11 @@ keywords = [
     "URIs",
 ]
 
-# 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 = ">=3.9"
 dependencies = [
@@ -63,7 +65,7 @@ dependencies = [
 [project.optional-dependencies]
 tests = [
     "pytest",
-    "coverage",
+    "coverage[toml]",
     "requests",
 ]
 pandas = [
@@ -90,29 +92,17 @@ 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/curies/issues"
 Homepage = "https://github.com/biopragmatics/curies"
 Repository = "https://github.com/biopragmatics/curies.git"
 Documentation = "https://curies.readthedocs.io"
-
-[tool.setuptools]
-package-dir = { "" = "src" }
-license-files = []
-
-[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]
 curies = "curies.cli:main"
 
-
 [tool.cruft]
 skip = [
     "**/__init__.py",

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.
@@ -45,6 +49,10 @@ extras =
     flask
     fastapi
     rdflib
+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.
@@ -89,12 +97,6 @@ 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.
 
@@ -174,11 +176,9 @@ allowlist_externals =
     mkdir
 
 [testenv:coverage-report]
-# TODO this is broken
-deps = coverage
+deps = coverage[toml]
 skip_install = true
 commands =
-    coverage combine
     coverage report
 
 ####################
@@ -205,7 +205,6 @@ deps =
 skip_install = true
 deps =
     uv
-    setuptools
 commands =
     uv build --sdist --wheel --no-build-isolation
 
@@ -225,7 +224,7 @@ 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}
@@ -235,6 +234,19 @@ 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,