Update cruft and mypy (#73)

Author: cthoyt

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/cthoyt/cookiecutter-snekpack",
-  "commit": "a6f6b5681f77004e7714efb00895d7b5983eb4c3",
+  "commit": "3257f18b9b5dc6922830dea64f9e0ab8b42a40e4",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -18,10 +18,12 @@
       "__runner": "tox -e",
       "__runner_uv": "--with tox-uv tox -e",
       "__runner_pip": "tox tox-uv",
+      "__runner_install_uv": "uv tool install tox --with tox-uv",
+      "__runner_install_pip": "python3 -m pip install tox tox-uv",
       "__runner_tests": "py",
       "__gh_slug": "biopragmatics/bioversions",
       "_template": "https://github.com/cthoyt/cookiecutter-snekpack",
-      "_commit": "a6f6b5681f77004e7714efb00895d7b5983eb4c3"
+      "_commit": "3257f18b9b5dc6922830dea64f9e0ab8b42a40e4"
     }
   },
   "directory": null

README.md

@@ -60,7 +60,7 @@ While https://biopragmatics.github.io/bioversions provides a daily updated
 static listing of the database, you can run a dynamic version with an API from
 your shell with:
 
-```bash
+```console
 $ bioversions web
 ```
 
@@ -84,25 +84,40 @@ assert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!'
 You can use `bioversions get` to incorporate the latest versions in your shell
 scripts or REPL usage like in:
 
-```bash
+```console
 $ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"
 ```
 
 ## 🚀 Installation
 
 The most recent release can be installed from
-[PyPI](https://pypi.org/project/bioversions/) with:
+[PyPI](https://pypi.org/project/bioversions/) with uv:
+
+```console
+$ uv pip install bioversions
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install bioversions
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
 
 ```console
-python3 -m pip install bioversions
+$ uv --preview pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
-The most recent code and data can be installed directly from GitHub with:
+or with pip:
 
 ```console
-python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
+$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
+Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
+backend becomes a stable feature.
+
 ## 👐 Contributing
 
 Contributions, whether filing an issue, making a pull request, or forking, are
@@ -168,22 +183,24 @@ $ cd bioversions
 $ uv --preview pip install -e .
 ```
 
-Alternatively, install using legacy pip with `UV_PREVIEW` mode enabled until the
-uv build backend becomes a stable feature:
+Alternatively, install using pip:
 
 ```console
 $ UV_PREVIEW=1 python3 -m pip install -e .
 ```
 
+Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
+backend becomes a stable feature.
+
 ### Updating Package Boilerplate
 
 This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
 guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Update with the following:
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
 
 ```console
-python3 -m pip install cruft
-cruft update
+$ cruft update
 ```
 
 More info on Cruft's update command is available
@@ -192,11 +209,11 @@ More info on Cruft's update command is available
 ### 🥼 Testing
 
 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:
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the
+unit tests in the `tests/` folder can be run reproducibly with:
 
 ```console
-tox -e py
+$ tox -e py
 ```
 
 Additionally, these tests are automatically re-run with each commit in a
@@ -207,10 +224,10 @@ Additionally, these tests are automatically re-run with each commit in a
 The documentation can be built locally using the following:
 
 ```console
-git clone git+https://github.com/biopragmatics/bioversions.git
-cd bioversions
-tox -e docs
-open docs/build/html/index.html
+$ git clone git+https://github.com/biopragmatics/bioversions.git
+$ cd bioversions
+$ tox -e docs
+$ open docs/build/html/index.html
 ```
 
 The documentation automatically installs the package as well as the `docs` extra
@@ -290,10 +307,11 @@ Note that this deprecates previous workflows using `.pypirc`.
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
-`python3 -m pip install tox tox-uv`, run the following from the console:
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run
+the following from the console:
 
 ```console
-tox -e finish
+$ tox -e finish
 ```
 
 This script does the following:

docs/source/installation.rst

@@ -1,25 +1,49 @@
 Installation
 ============
 The most recent release can be installed from
-`PyPI <https://pypi.org/project/bioversions>`_ with:
+`PyPI <https://pypi.org/project/bioversions>`_ with uv:
 
-.. code-block:: shell
+.. code-block:: console
 
-    python3 -m pip install bioversions
+    $ uv pip install bioversions
 
-The most recent code and data can be installed directly from GitHub with:
+or with pip:
 
-.. code-block:: shell
+.. code-block:: console
 
-    python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
+    $ python3 -m pip install bioversions
 
-To install in development mode, use the following:
+Installing from git
+-------------------
+The most recent code and data can be installed directly from GitHub with uv:
 
-.. code-block:: shell
+.. code-block:: console
 
-    git clone git+https://github.com/biopragmatics/bioversions.git
-    cd bioversions
-    UV_PREVIEW=1 python3 -m pip install -e .
+    $ uv --preview pip install git+https://github.com/biopragmatics/bioversions.git
 
-Note that the ``UV_PREVIEW`` environment variable is required to be
-set until the uv build backend becomes a stable feature.
+or with pip:
+
+.. code-block:: console
+
+    $ UV_PREVIEW=1 python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
+
+.. note::
+
+    The ``UV_PREVIEW`` environment variable is required to be
+    set until the uv build backend becomes a stable feature.
+
+Installing for development
+--------------------------
+To install in development mode with uv:
+
+.. code-block:: console
+
+    $ git clone git+https://github.com/biopragmatics/bioversions.git
+    $cd bioversions
+    $ uv --preview pip install -e .
+
+or with pip:
+
+.. code-block:: console
+
+    $ UV_PREVIEW=1 python3 -m pip install -e .

src/bioversions/sources/kegg.py

@@ -20,7 +20,7 @@ class KEGGGetter(Getter):
     name = "KEGG"
     date_fmt = "%B %d, %Y"
     version_type = VersionType.semver_minor
-    collection: ClassVar[list[str]] = ["kegg", *bioregistry.get_has_parts("kegg")]
+    collection: ClassVar[list[str]] = ["kegg", *(bioregistry.get_has_parts("kegg") or [])]
 
     def get(self) -> Mapping[str, str]:
         """Get the latest KEGG version number."""

src/bioversions/sources/ols.py

@@ -1,7 +1,8 @@
 """Get versions from the OLS."""
 
 import logging
-from collections.abc import Iterable, Mapping
+from collections.abc import Iterable
+from typing import cast
 
 import bioregistry
 from bioregistry.external.ols import get_ols_processing
@@ -16,9 +17,13 @@
 
 def _get_version_type(bioregistry_id: str) -> VersionType | None:
     ols_id = bioregistry.get_ols_prefix(bioregistry_id)
+    if ols_id is None:
+        raise ValueError(f"Missing OLS prefix for bioregistry:{bioregistry_id}")
     ols_config = ols_processing.get(ols_id)
     if ols_config is None:
-        raise
+        raise ValueError(
+            f"Missing OLS configuration for bioregistry:{bioregistry_id} / ols:{ols_id}"
+        )
 
     ols_version_type = ols_config.version_type
     ols_version_date_format = ols_config.version_date_format
@@ -61,12 +66,12 @@ class OlsGetter(Getter):
         """A getter for OLS data from the Bioregistry."""
 
         bioregistry_id = _brid
-        name = _name
+        name = cast(str, _name)
         version_type = _version_type  # type:ignore
 
-        def get(self) -> str | Mapping[str, str]:
+        def get(self) -> str:
             """Get the version from the Bioregistry."""
-            return version
+            return cast(str, version)
 
     return OlsGetter
 

src/bioversions/utils.py

@@ -271,6 +271,8 @@ class OBOFoundryGetter(Getter):
     @property
     def key(self) -> str:
         """Get the OBO Foundry key."""
+        if self.bioregistry_id is None:
+            raise ValueError("missing bioregistry ID")
         rv = bioregistry.get_obofoundry_prefix(self.bioregistry_id)
         if rv is None:
             raise ValueError

tox.ini

@@ -132,16 +132,15 @@ commands = pyroma --min=10 .
 description = Run the pyroma tool to check the package friendliness of the project.
 
 [testenv:mypy]
-description = Run the mypy tool to check static typing on the project.
+description = Run the mypy tool to check static typing on the project. Installs the package to make sure all type stubs get recognized.
 deps =
     mypy
     pydantic
     types-PyYAML
     types-python-dateutil
     types-requests
     types-tabulate
-skip_install = true
-commands = mypy --install-types --non-interactive --ignore-missing-imports src/
+commands = mypy --ignore-missing-imports src/
 
 [testenv:doc8]
 skip_install = true