Update cruft

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/cthoyt/cookiecutter-snekpack",
-  "commit": "640faa5f1e39285d9f8103a3f5877db999abebc7",
+  "commit": "12edfcfa5f519467b5d834f0d4e706fb7cf4f065",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/codecov.yml

@@ -0,0 +1,4 @@
+# see https://docs.codecov.com/v4.6/docs/codecov-yaml
+ignore:
+  - "src/pyobo/__main__.py"
+  - "src/pyobo/cli.py"

README.md

@@ -23,10 +23,12 @@
         <img src="https://codecov.io/gh/biopragmatics/pyobo/branch/main/graph/badge.svg" alt="Codecov status" /></a>  
     <a href="https://github.com/cthoyt/cookiecutter-python-package">
         <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /></a>
-    <a href='https://github.com/psf/black'>
-        <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /></a>
+    <a href="https://github.com/astral-sh/ruff">
+        <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff" style="max-width:100%;"></a>
     <a href="https://github.com/biopragmatics/pyobo/blob/main/.github/CODE_OF_CONDUCT.md">
         <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
+    <a href="https://doi.org/10.5281/zenodo.3381961">
+        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3381961.svg" alt="DOI"></a>
 </p>
 
 Tools for biological identifiers, names, synonyms, xrefs, hierarchies, relations, and properties through the
@@ -414,14 +416,14 @@ and make update to the `url` entry for that namespace in the Bioregistry.
 The most recent release can be installed from
 [PyPI](https://pypi.org/project/pyobo/) with:
 
-```shell
-pip install pyobo
+```console
+python3 -m pip install pyobo
 ```
 
 The most recent code and data can be installed directly from GitHub with:
 
-```shell
-pip install git+https://github.com/biopragmatics/pyobo.git
+```console
+python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
 ```
 
 ## 👐 Contributing
@@ -478,10 +480,10 @@ 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:
 
-```bash
+```console
 git clone git+https://github.com/biopragmatics/pyobo.git
 cd pyobo
-pip install -e .
+python3 -m pip install -e .
 ```
 
 ### Updating Package Boilerplate
@@ -490,8 +492,8 @@ This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
 configuration)
 up-to-date with the upstream cookiecutter package. Update with the following:
 
-```shell
-pip install cruft
+```console
+python3 -m pip install cruft
 cruft update
 ```
 
@@ -500,10 +502,11 @@ available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-pr
 
 ### 🥼 Testing
 
-After cloning the repository and installing `tox` with `pip install tox tox-uv`, 
+After cloning the repository and installing `tox` with
+`python3 -m pip install tox tox-uv`,
 the unit tests in the `tests/` folder can be run reproducibly with:
 
-```shell
+```console
 tox -e py
 ```
 
@@ -514,12 +517,12 @@ Additionally, these tests are automatically re-run with each commit in a
 
 The documentation can be built locally using the following:
 
-```shell
+```console
 git clone git+https://github.com/biopragmatics/pyobo.git
 cd pyobo
 tox -e docs
 open docs/build/html/index.html
-``` 
+```
 
 The documentation automatically installs the package as well as the `docs`
 extra specified in the [`pyproject.toml`](../../Desktop/pyobo/pyproject.toml). `sphinx` plugins
@@ -575,38 +578,23 @@ 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. Create a file in your home directory called
-`.pypirc` and include the following:
-
-```ini
-[distutils]
-index-servers =
-    pypi
-    testpypi
-
-[pypi]
-username = __token__
-password = <the API token you just got>
+You have to do the following steps once per machine. 
 
-# This block is optional in case you want to be able to make test releases to the Test PyPI server
-[testpypi]
-repository = https://test.pypi.org/legacy/
-username = __token__
-password = <an API token from test PyPI>
+```console
+$ uv tool install keyring
+$ keyring set https://upload.pypi.org/legacy/ __token__
+$ keyring set https://test.pypi.org/legacy/ __token__
 ```
 
-Note that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim.
-If you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers`
-key and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can
-be found [here](https://packaging.python.org/en/latest/specifications/pypirc).
+Note that this deprecates previous workflows using `.pypirc`.
 
 #### Uploading to PyPI
 
 After installing the package in development mode and installing
-`tox` with `pip install tox tox-uv`,
-run the following from the shell:
+`tox` with `python3 -m pip install tox tox-uv`,
+run the following from the console:
 
-```shell
+```console
 tox -e finish
 ```
 
@@ -617,7 +605,7 @@ This script does the following:
    and [`docs/source/conf.py`](../../Desktop/pyobo/docs/source/conf.py) to not have the `-dev` suffix
 2. Packages the code in both a tar archive and a wheel using
    [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)
-3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine).
+3. Uploads to PyPI using [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).
 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
    use `tox -e bumpversion -- minor` after.

docs/source/conf.py

@@ -36,7 +36,7 @@
 version = parsed_version.expand(r"\g<major>.\g<minor>.\g<patch>")
 
 if parsed_version.group("release"):
-    tags.add("prerelease")  # noqa: F821
+    tags.add("prerelease")  # noqa:F821
 
 # See https://about.readthedocs.com/blog/2024/07/addons-by-default/
 # Define the canonical URL if you are using a custom domain on Read the Docs

tox.ini

@@ -212,33 +212,19 @@ commands =
 # 3. Get account recovery codes
 # 4. Set up 2-Factor Authentication
 # 5. Get an API token from https://pypi.org/manage/account/token/
-# 6. Create a file called .pypirc in the home directory if it does not already exist.
-# 7. Add the following content to the .pypirc file
-#
-#    [distutils]
-#    index-servers=
-#      pypi
-#      testpypi
-#
-#    [pypi]
-#    username = __token__
-#    password = <the API token you just got>
-#
-#    If there's already an `index-servers =` list, just make sure you add `pypi` to it.
-#    More information about .pypirc can be found at https://packaging.python.org/en/latest/specifications/pypirc/
+# 6. Install keyring with `uv tool install keyring`
+# 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
 skip_install = true
-passenv =
-    TWINE_USERNAME
-    TWINE_PASSWORD
 deps =
     {[testenv:build]deps}
-    twine >= 1.5.0
+    uv
+    keyring
 commands =
     {[testenv:build]commands}
-    twine upload --skip-existing dist/*
+    uv publish --username __token__ --keyring-provider subprocess --publish-url https://upload.pypi.org/legacy/
 
 [testenv:finish]
 description =
@@ -247,8 +233,6 @@ description =
 skip_install = true
 passenv =
     HOME
-    TWINE_USERNAME
-    TWINE_PASSWORD
 deps =
     {[testenv:release]deps}
     bump-my-version
@@ -273,34 +257,19 @@ allowlist_externals =
 # 3. Get account recovery codes
 # 4. Set up 2-Factor Authentication
 # 5. Get an API token from https://test.pypi.org/manage/account/token/
-# 6. Create a file called .pypirc in the home directory if it does not already exist.
-# 7. Add the following content to the .pypirc file
-#
-#    [distutils]
-#    index-servers=
-#      pypi
-#      testpypi
-#
-#    [testpypi]
-#    repository = https://test.pypi.org/legacy/
-#    username = __token__
-#    password = <the API token you just got>
-#
-#    If there's already an `index-servers =` list, just make sure you add `testpypi` to it.
-#    More information about .pypirc can be found at https://packaging.python.org/en/latest/specifications/pypirc/
+# 6. Install keyring with `uv tool install keyring`
+# 7. Add your token to keyring with `keyring set https://test.pypi.org/legacy/ __token__`
 
 [testenv:testrelease]
 description = Release the code to the test PyPI site
 skip_install = true
-passenv =
-    TWINE_USERNAME
-    TWINE_PASSWORD
 deps =
     {[testenv:build]deps}
-    twine >= 1.5.0
+    uv
+    keyring
 commands =
     {[testenv:build]commands}
-    twine upload --skip-existing --repository testpypi dist/*
+    uv publish --username __token__ --keyring-provider subprocess --publish-url https://test.pypi.org/legacy/
 
 [testenv:testfinish]
 description =
@@ -309,8 +278,6 @@ description =
 skip_install = true
 passenv =
     HOME
-    TWINE_USERNAME
-    TWINE_PASSWORD
 deps =
     {[testenv:testrelease]deps}
     bump-my-version