## Summary
When running Ruff from stdin, we were always falling back to the default
source type, even if the user specified a path (as is the case when
running from the LSP). This PR wires up the source type inference, which
means we now get the expected result when checking `.pyi` and `.ipynb`
files.
Closes#6627.
## Test Plan
Verified that `cat
crates/ruff/resources/test/fixtures/jupyter/valid.ipynb | cargo run -p
ruff_cli -- --force-exclude --no-cache --no-fix --isolated --select ALL
--stdin-filename foo.ipynb -` yielded the expected results (and differs
from the errors you get if you omit the filename).
Verified that `cat foo.pyi | cargo run -p ruff_cli -- --force-exclude
--no-cache --no-fix --format json --isolated --select TCH
--stdin-filename path/to/foo.pyi -` yielded no errors.
## Summary
It can happen that we can't read a file (a python file, a jupyter
notebook or pyproject.toml), which needs to be handled and handled
consistently for all file types. Instead of using `Err` or `error!`, we
emit E602 with the io error as message and continue. This PR makes sure
we handle all three cases consistently, emit E602.
I'm not convinced that it should be possible to disable io errors, but
we now handle the regular case consistently and at least print warning
consistently.
I went with `warn!` but i can change them all to `error!`, too.
It also checks the error case when a pyproject.toml is not readable. The
error message is not very helpful, but it's now a bit clearer that
actually ruff itself failed instead vs this being a diagnostic.
## Examples
This is how an Err of `run` looks now:

With an unreadable file and `IOError` disabled:

(we lint zero files but count files before linting not during so we exit
0)
I'm not sure if it should (or if we should take a different path with
manual ExitStatus), but this currently also triggers when `files` is
empty:

## Test Plan
Unix only: Create a temporary directory with files with permissions
`000` (not readable by the owner) and run on that directory. Since this
breaks the assumptions of most of the test code (single file, `ruff`
instead of `ruff_cli`), the test code is rather cumbersome and looks a
bit misplaced; i'm happy about suggestions to fit it in closer with the
other tests or streamline it in other ways. I added another test for
when the entire directory is not readable.
## Summary
I want to include URLs to the rule documentation in the LSP (the LSP has
a native `code_description` field for this, which, if specified, causes
the source to be rendered as a link to the docs). This PR exposes the
URL to the documentation in the Ruff JSON output.
## Summary
Maintain consistency while deserializing Jupyter notebook to JSON. The
following changes were made:
1. Use string array to store the source value as that's the default
(5781720423/nbformat/v4/nbjson.py (L56-L57))
2. Remove unused structs and enums
3. Reorder the keys in alphabetical order as that's the default.
(5781720423/nbformat/v4/nbjson.py (L51))
### Side effect
Removing the `preserve_order` feature means that the order of keys in
JSON output (`--format json`) will be in alphabetical order. This is
because the value is represented using `serde_json::Value` which
internally is a `BTreeMap`, thus sorting it as per the string key. For
posterity if this turns out to be not ideal, then we could define a
struct representing the JSON object and the order of struct fields will
determine the order in the JSON string.
## Test Plan
Add a test case to assert the raw JSON string.
I noticed in the byte-offsets refactor that the `JsonEmitter` uses one indexed column numbers for the diagnostic start and end locations but not for `edits`.
This PR changes the `JsonEmitter` to emit one-indexed column numbers for edits, as we already do for `Message::location` and `Message::end_location`.
## Open questions
~We'll need to change the LSP to subtract 1 from the columns in `_parse_fix`~
6e44fadf8a/ruff_lsp/server.py (L129-L150)
~@charliermarsh is there a way to get the ruff version in that method? If not, then I recommend adding a `version` that we increment whenever we make incompatible changes to the serialized message. We can then use it in the LSP to correctly compute the column offset.~
I'll use the presence of the `Fix::applicability` field to detect if the Ruff version uses one or zero-based column indices.
See https://github.com/charliermarsh/ruff-lsp/pull/103
In ruff-lsp (https://github.com/charliermarsh/ruff-lsp/pull/76) we want to add a "Disable \<rule\> for this line" quickfix. However, finding the correct line into which the `noqa` comment should be inserted is non-trivial (multi-line strings for example).
Ruff already has this info, so expose it in the JSON output for use by ruff-lsp.