Ruff formatting and fixes that are compatible with current checks (#1817)

Part of #1807 

In #1806 , we fixed a lot of things identified by ruff. This PR
introduces the configuration and finishes the rest of them.

This PR includes formatting changes preferred by `ruff format` for which
unmodified `check/format-incremental` is also happy with. The ruff
formatter is mostly compatible with `black`, please see
https://docs.astral.sh/ruff/formatter/black/

This PR disabled `flynt`. I don't think this is a high-value automation,
we can do it with future ruff checks if we want, and it kept trying to
mangle an fstring in shell_tools that required python 3.12+ (and there's
no simple way to disable it for that line)

cc @fdmalone @mhucka 

-----

this also revealed
https://github.com/quantumlib/Qualtran/pull/1810/changes#r2835413664
which I'll open an issue for if there isn't a simple resolution

Author: mpharrigan

check/format-incremental

@@ -95,13 +95,13 @@ if (( ${#format_files[@]} == 0 )); then
     exit 0
 fi
 
-flynt_args=("--quiet" "-f")
-if (( only_print == 1 )); then
-    flynt_args+=("--dry-run")
-fi
-
-flynt "${format_files[@]}" "${flynt_args[@]}"
-FLYNTSTATUS=$?
+#flynt_args=("--quiet" "-f")
+#if (( only_print == 1 )); then
+#    flynt_args+=("--dry-run")
+#fi
+#
+#flynt "${format_files[@]}" "${flynt_args[@]}"
+FLYNTSTATUS=0
 
 isort_args=()
 if (( only_print == 1 )); then

dev_tools/qualtran_dev_tools/all_call_graph.py

@@ -13,6 +13,7 @@
 #  limitations under the License.
 
 """Generate the library-wide call graph from all bloq examples."""
+
 import logging
 import warnings
 from typing import Iterable

dev_tools/qualtran_dev_tools/make_reference_docs/_components/render_docstring.py

@@ -167,7 +167,7 @@ def _write_yields(f, part: DocstringSectionYields, level: int):
         f.write('\n')
 
     else:
-        subpart: DocstringYield
+        param: DocstringYield
         for param in part.value:
             pname = param.name if param.name else 'yld'
             f.write(f'{pname}\n')

dev_tools/qualtran_dev_tools/make_reference_docs/_make.py

@@ -11,6 +11,8 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
+
+# ruff: noqa: E402
 import ast
 import warnings
 from collections import defaultdict

dev_tools/qualtran_dev_tools/notebook_execution.py

@@ -215,7 +215,7 @@ def __call__(self, nb_rel_path: Path, sourceroot: Path) -> _NotebookRunResult:
         start = time.time()
         err = execute_and_export_notebook(paths)
         end = time.time()
-        print(f"Exported {nb_rel_path} in {end-start:.2f} seconds.")
+        print(f"Exported {nb_rel_path} in {end - start:.2f} seconds.")
         return _NotebookRunResult(paths.nb_in, err, duration_s=end - start)
 
 

dev_tools/qualtran_dev_tools/shell_tools.py

@@ -91,7 +91,9 @@ def run(
         if abbreviate_non_option_arguments:
             cmd_desc = abbreviate_command_arguments_after_switches(cmd_desc)
         print("run:", cmd_desc, file=sys.stderr)
-    return subprocess.run(args, **subprocess_run_kwargs)  # pylint: disable=subprocess-run-check
+    return subprocess.run(  # pylint: disable=subprocess-run-check # noqa: PLW1510
+        args, **subprocess_run_kwargs
+    )
 
 
 def output_of(args: Union[str, List[str]], **kwargs) -> str:

pyproject.toml

@@ -93,7 +93,8 @@ typing = [
 ]
 
 lint = [
-   "pylint~=3.3.1",
+    "pylint~=3.3.1",
+    "ruff~=0.15.0",
 
     # for checking _test.py files
     "pytest",
@@ -111,6 +112,7 @@ format = [
     "flynt~=0.60",
     "black~=24.8.0",
     "isort~=5.10.1",
+    "ruff~=0.15.0",
 ]
 
 doc = [
@@ -131,6 +133,72 @@ skip-string-normalization = true
 skip-magic-trailing-comma = true
 exclude = "qualtran/protos/*"
 
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+exclude = [
+    "qualtran/protos/*",
+    "*_pb2.py",
+    "*.ipynb",
+]
+
+[tool.ruff.lint]
+select = [
+    "E", # pycodestyle
+    "F", # pyflakes
+    # "I", # isort (disabled until we switch formatters)
+    "W", # pycodestyle warnings
+    "PL", # pylint
+]
+ignore = [
+    # From the default ruleset:
+    "E741", # ambiguous variable name 'l', 'O', or 'I'
+    "E743", # ambiguous function definition
+    "E731", # assigning a lambda expression to a variable
+
+    # Handled by the formatter
+    "E501", # line too long (let ruff format handle this)
+    "W291", # trailing whitespace
+    "W293", # blank line contains whitespace
+
+    # We productively use these
+    "PLC0415", # import outside top-level
+    "PLW2901", # loop variable overwritten
+    "PLC0206", # Extracting value from dictionary without calling .items()
+    "PLW0406", # Module import itself
+
+    # Pylint 'refactor' rules
+    "PLR0913", # Too many arguments
+    "PLR0912", # Too many branches
+    "PLR0915", # Too many statements
+    "PLR0914", # Too many local variables
+    "PLR2004", # Magic value used in comparison
+    "PLR0911", # Too many return statements
+    "PLR1704", # Redefining argument with the local name
+    "PLR1714", # Consider merging multiple comparisons
+    "PLR1730", # replace if with min, max. Can be enabled.
+
+    # Might be enabled at some point
+    "PLR0402" # Prevalent in the rotation_synthesis submodule.
+]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = [
+    # Ruff wants us to redundantly re-export symbols in __init__.py files, but the
+    # automated fix isn't in the stable release yet.
+    "F401", # Unused import
+]
+
+
+[tool.ruff.lint.isort]
+order-by-type = false
+force-to-top = []
+split-on-trailing-comma = false
+
+[tool.ruff.format]
+quote-style = "preserve"
+skip-magic-trailing-comma = true
+
 [tool.isort]
 profile = 'black'
 order_by_type = false

qualtran/_infra/bloq.py

@@ -633,7 +633,8 @@ def on(self, *qubits: 'cirq.Qid') -> 'cirq.Operation':
         return cirq.Gate.on(BloqAsCirqGate(bloq=self), *qubits)
 
     def on_registers(
-        self, **qubit_regs: Union['cirq.Qid', Sequence['cirq.Qid'], 'NDArray[cirq.Qid]']  # type: ignore[type-var]
+        self,
+        **qubit_regs: Union['cirq.Qid', Sequence['cirq.Qid'], 'NDArray[cirq.Qid]'],  # type: ignore[type-var]
     ) -> 'cirq.Operation':
         """A `cirq.Operation` of this bloq operating on the given qubit registers.
 

qualtran/_infra/composite_bloq.py

@@ -13,6 +13,7 @@
 #  limitations under the License.
 
 """Classes for building and manipulating `CompositeBloq`."""
+
 from collections.abc import Hashable
 from functools import cached_property
 from typing import (

qualtran/_infra/composite_bloq_test.py

@@ -338,7 +338,10 @@ def signature(self) -> Signature:
         return Signature([Register('control', QBit()), Register('target', QBit(), shape=(2, 3))])
 
     def build_composite_bloq(
-        self, bb: 'BloqBuilder', control: 'Soquet', target: NDArray['Soquet']  # type: ignore[type-var]
+        self,
+        bb: 'BloqBuilder',
+        control: 'Soquet',
+        target: NDArray['Soquet'],  # type: ignore[type-var]
     ) -> Dict[str, SoquetT]:
         for i in range(2):
             for j in range(3):