update ruff and start applying manual fixes

Author: DocOtak

.pre-commit-config.yaml

@@ -3,12 +3,12 @@
 # https://github.com/python/black#version-control-integration
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.7
+    rev: v0.12.0
     hooks:
       - id: ruff
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         additional_dependencies: [types-requests]

docs/_static/convert_exchange.py

@@ -5,7 +5,7 @@
 from html import escape
 
 from js import Uint8Array, console  # noqa: F401
-from pyscript import display  # type: ignore
+from pyscript import display
 
 from cchdo.hydro import __version__ as hydro_version
 from cchdo.hydro import accessors, read_exchange  # noqa: F401
@@ -18,7 +18,7 @@ def logger(msg):
 
 class DisplaylHandler(logging.Handler):
     def emit(self, record) -> None:
-        logger(self.formatter.format(record))  # type: ignore
+        logger(self.formatter.format(record))
 
 
 root = logging.getLogger()

pyproject.toml

@@ -68,7 +68,7 @@ dev = [
     "pre-commit>=4.1.0",
     "pytest-cov>=6.0.0",
     "pytest-xdist>=3.6.1",
-    "ruff>=0.9.7",
+    "ruff>=0.12.0",
     "types-requests>=2.32.0.20241016",
 ]
 docs = [

src/cchdo/hydro/__main__.py

@@ -268,9 +268,7 @@ def status_exchange(
 
     out_path = Path(out_dir)
     cruises, files = cchdo_loader(dtype)
-    file_paths = []
-    for file in track(files, description="Loading data files"):
-        file_paths.append((cached_file_loader(file), file))
+    file_paths = [(cached_file_loader(file), file) for file in track(files, description="Loading data files")]
 
     results = []
     all_unknown_params = {}

src/cchdo/hydro/__main_helpers.py

@@ -4,7 +4,7 @@
 
 import xarray as xr
 
-from cchdo.hydro import accessors  # noqa
+from cchdo.hydro import accessors  # noqa: F401
 from cchdo.hydro.exchange import read_exchange
 from cchdo.hydro.exchange.exceptions import (
     ExchangeDataFlagPairError,

src/cchdo/hydro/accessors.py

@@ -544,8 +544,8 @@ def compact_profile(self):
             )
         return self._obj.isel(N_LEVELS=(self._obj.sample != "")[0])
 
-    date_names = {WHPNames["DATE"], WHPNames["BTL_DATE"]}
-    time_names = {WHPNames["TIME"], WHPNames["BTL_TIME"]}
+    date_names = frozenset((WHPNames["DATE"], WHPNames["BTL_DATE"]))
+    time_names = frozenset((WHPNames["TIME"], WHPNames["BTL_TIME"]))
 
     @property
     def file_type(self):

src/cchdo/hydro/checks.py

@@ -131,7 +131,7 @@ def check_flags(dataset: xr.Dataset, raises=True):
             # TODO deal with strs
 
             if np.issubdtype(data.values.dtype, np.number):
-                fill_value_mismatch: xr.DataArray = ~(np.isfinite(data) ^ has_fill)  # type: ignore # numpy doesn't support __array_ufunc__ types yet
+                fill_value_mismatch: xr.DataArray = ~(np.isfinite(data) ^ has_fill)  #type: ignore[assignment]
                 if np.any(fill_value_mismatch):
                     fill_value_mismatch.attrs["comments"] = (
                         f"This is a boolean array in the same shape as '{data.name}' which is truthy where invalid values exist"

src/cchdo/hydro/exchange/__init__.py

@@ -837,8 +837,7 @@ def _load_raw_exchange(
     # lets just try "reading"
     elif hasattr(filename_or_obj, "read"):
         log.info("Loading object open file object")
-        # https://github.com/python/mypy/issues/1424
-        data_raw = io.BytesIO(filename_or_obj.read())  # type: ignore
+        data_raw = io.BytesIO(filename_or_obj.read())
 
     elif isinstance(filename_or_obj, bytes | bytearray):
         log.info("Loading raw data bytes")

src/cchdo/hydro/legacy/coards/__init__.py

@@ -307,8 +307,9 @@ def get_dataarrays(ds: xr.Dataset):
 
         if data.dtype.kind in "iuf":
             if np.all(np.isnan(data)):
-                attrs["data_min"] = float("-inf")  # type: ignore
-                attrs["data_max"] = float("inf")  # type: ignore
+                # the proper fix here would be to make a type dict that knows what is going on with each key
+                attrs["data_min"] = float("-inf")  # type: ignore[assignment]
+                attrs["data_max"] = float("inf")  # type: ignore[assignment]
             else:
                 attrs["data_min"] = np.nanmin(data)
                 attrs["data_max"] = np.nanmax(data)