pre-commit: run mypy in the main virtualenv

`pre-commit` will by default create an isolated virtualenv
to run hooks such as `mypy`. This creates well-known issues
because `mypy` won't have access to packages the code depends
on. See python/mypy#13916 for
recommendations by the `mypy` maintainer.

By running `mypy` as a `system` hook as suggested, it will see the exact
same packages as running `mypy` standalone (or through an IDE) will,
which avoids discrepancies that appear only at commit time.

The compromise is that running `mypy` through `pre-commit` will require
a properly initialized virtualenv. However because we add a `files:`
filter to the `mypy` hook, `pre-commit` will not run if no Python
file has been changed; and if Python files have been changed it seems
reasonable to expect a proper development environment has been set up.

Also following the recommendation we set `pass_filenames: false` so that
`pre-commit` does not pass only the changed files to `mypy`.

.pre-commit-config.yaml

@@ -13,9 +13,10 @@ repos:
       hooks:
       -   id: flake8
           additional_dependencies: [flake8-bugbear,flake8-sfs]
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: 'v1.9.0'
+    - repo: local
       hooks:
       -   id: mypy
-          args: [--config-file=.pre-commit.mypy.ini]
-          additional_dependencies: [numpy]
+          name: check types with mypy
+          language: system
+          pass_filenames: false
+          entry: mypy src