chore: update pre-commit hooks

.pre-commit-config.yaml

@@ -40,14 +40,14 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.8.2"
+    rev: "v0.9.1"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.13.0"
+    rev: "v1.14.1"
     hooks:
       - id: mypy
         files: flint|tests
@@ -57,7 +57,7 @@ repos:
           - types-PyYAML
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.29.4
+    rev: dictgen-v0.3.1
     hooks:
       - id: typos
 
@@ -87,7 +87,7 @@ repos:
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.30.0"
+    rev: "0.31.0"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

flint/archive.py

@@ -77,11 +77,11 @@
     logger.info(f"Copying {total} files into {copy_out_path}")
     for count, file in enumerate(files_to_copy):
         if file.is_file():
-            logger.info(f"{count+1} of {total}, copying file {file}")
+            logger.info(f"{count + 1} of {total}, copying file {file}")
             shutil.copy(file, copy_out_path)
         elif file.is_dir():
             # TODO: Add an option to tar folders into the final location
-            logger.info(f"{count+1} of {total}, copying folder {file}")
+            logger.info(f"{count + 1} of {total}, copying folder {file}")
             shutil.copytree(file, copy_out_path / file.name)
         else:
             not_copied.append(file)
@@ -108,9 +108,9 @@
         bool: True if the ``tar``s exit code is 0, False otherwise
     """
     tarball = Path(tarball)  # trust nothing
-    assert (
-        tarball.exists() and tarball.is_file()
-    ), f"{tarball} is not a file or does not exist"
+    assert tarball.exists() and tarball.is_file(), (
+        f"{tarball} is not a file or does not exist"
+    )
     assert tarball.suffix == ".tar", f"{tarball=} appears to not have a .tar extension"
 
     cmd = f"tar -tvf {tarball!s}"
@@ -155,7 +155,7 @@
     logger.info(f"Opening {tar_out_path}")
     with tarfile.open(tar_out_path, "w") as tar:
         for count, file in enumerate(files_to_tar):
-            logger.info(f"{count+1} of {total}, adding {file!s}")
+            logger.info(f"{count + 1} of {total}, adding {file!s}")
             tar.add(file, arcname=file.name)
 
     logger.info(f"Created {tar_out_path}")

flint/bandpass.py

@@ -67,9 +67,9 @@
         field_names = tab.getcol("NAME")
         field_idx = np.argwhere([fn == good_field_name for fn in field_names])[0]
 
-        assert (
-            len(field_idx) == 1
-        ), f"More than one matching field name found. This should not happen. {good_field_name=} {field_names=}"
+        assert len(field_idx) == 1, (
+            f"More than one matching field name found. This should not happen. {good_field_name=} {field_names=}"
+        )
 
         field_idx = field_idx[0]
         logger.info(f"{good_field_name} FIELD_ID is {field_idx}")

flint/bptools/preflagger.py

@@ -312,9 +312,9 @@ def flags_over_threshold(
         bool: Whether the number of flags has reached a threshold
     """
 
-    assert (
-        0.0 <= thresh <= 1.0
-    ), f"The provided {thresh=} should be a fraction between 0 to 1. "
+    assert 0.0 <= thresh <= 1.0, (
+        f"The provided {thresh=} should be a fraction between 0 to 1. "
+    )
 
     number_flagged = np.sum(flags)
     # Use the shape in case multi-dimensional array passed in
@@ -468,9 +468,9 @@ def flag_mean_xxyy_amplitude_ratio(
         bool: Whether data should be flagged (True) or not (False)
     """
 
-    assert (
-        xx_complex_gains.shape == yy_complex_gains.shape
-    ), f"Input xx and yy shapes do not match. {xx_complex_gains.shape=} {yy_complex_gains.shape=}"
+    assert xx_complex_gains.shape == yy_complex_gains.shape, (
+        f"Input xx and yy shapes do not match. {xx_complex_gains.shape=} {yy_complex_gains.shape=}"
+    )
     logger.info("Calculating mean ratios. ")
 
     xx_amplitudes = np.abs(xx_complex_gains)
@@ -514,9 +514,9 @@ def construct_mesh_ant_flags(mask: np.ndarray) -> np.ndarray:
         np.ndarray: Output array where antennas have common sets of flags
     """
 
-    assert (
-        len(mask.shape) == 3
-    ), f"Expect array of shape (ant, channel, pol), received {mask.shape=}"
+    assert len(mask.shape) == 3, (
+        f"Expect array of shape (ant, channel, pol), received {mask.shape=}"
+    )
     accumulate_mask = np.zeros_like(mask[0], dtype=bool)
 
     nant = mask.shape[0]
@@ -562,9 +562,9 @@ def construct_jones_over_max_amp_flags(
         np.ndarray: Boolean array of equal shape to `complex_gains`, with `True` indicating a flag
     """
 
-    assert (
-        complex_gains.shape[-1] == 4
-    ), f"Expected last dimension to be length 4, received {complex_gains.shape=}"
+    assert complex_gains.shape[-1] == 4, (
+        f"Expected last dimension to be length 4, received {complex_gains.shape=}"
+    )
 
     logger.info(f"Creating mask for Jones with amplitudes of {max_amplitude=}")
     complex_gains = complex_gains.copy()

flint/bptools/smoother.py

@@ -43,9 +43,9 @@ def divide_bandpass_by_ref_ant_preserve_phase(
     Returns:
         np.ndarray: The normalised bandpass solutions
     """
-    assert (
-        len(complex_gains.shape) == 3
-    ), f"The shape of the input complex gains should be of rank 3 in form (ant, chan, pol). Received {complex_gains.shape}"
+    assert len(complex_gains.shape) == 3, (
+        f"The shape of the input complex gains should be of rank 3 in form (ant, chan, pol). Received {complex_gains.shape}"
+    )
 
     logger.info(
         f"Dividing bandpass gain solutions using reference antenna={ref_ant}, using correct phasor"
@@ -113,9 +113,9 @@ def divide_bandpass_by_ref_ant(complex_gains: np.ndarray, ref_ant: int) -> np.nd
     Returns:
         np.ndarray: The normalised bandpass solutions
     """
-    assert (
-        len(complex_gains.shape) == 3
-    ), f"The shape of the input complex gains should be of rank 3 in form (ant, chan, pol). Received {complex_gains.shape}"
+    assert len(complex_gains.shape) == 3, (
+        f"The shape of the input complex gains should be of rank 3 in form (ant, chan, pol). Received {complex_gains.shape}"
+    )
 
     logger.info(
         f"Dividing bandpass gain solutions using reference antenna={ref_ant} with shifted phasor"
@@ -234,9 +234,9 @@ def smooth_bandpass_complex_gains(
         np.ndarray: Smoothed complex gains
     """
 
-    assert (
-        len(complex_gains.shape) == 3
-    ), f"The shape of the input complex gains should be of rank 3 in form (ant, chan, pol). Received {complex_gains.shape}"
+    assert len(complex_gains.shape) == 3, (
+        f"The shape of the input complex gains should be of rank 3 in form (ant, chan, pol). Received {complex_gains.shape}"
+    )
 
     # Duplicate the original, ya filthy pirate
     smoothed_complex_gains = complex_gains.copy()

flint/calibrate/aocalibrate.py

@@ -393,9 +393,9 @@
         AOSolutions: Structure container the deserialized solutions file
     """
 
-    assert (
-        solutions_path.exists() and solutions_path.is_file()
-    ), f"{solutions_path!s} either does not exist or is not a file. "
+    assert solutions_path.exists() and solutions_path.is_file(), (
+        f"{solutions_path!s} either does not exist or is not a file. "
+    )
     logger.info(f"Loading {solutions_path}")
 
     with open(solutions_path) as in_file:
@@ -470,9 +470,9 @@
 
     # If not all the treasure could be found. At the moment this function will only
     # work if the bandpass solutions were made using the default values.
-    assert all(
-        [solution_path.exists() for solution_path in solution_paths]
-    ), f"Missing solution file constructed from scanning {bandpass_directory}. Check the directory. "
+    assert all([solution_path.exists() for solution_path in solution_paths]), (
+        f"Missing solution file constructed from scanning {bandpass_directory}. Check the directory. "
+    )
 
     calibrate_cmds = [
         CalibrateCommand(
@@ -556,9 +556,9 @@
         else:
             unknowns.append((key, value))
 
-    assert (
-        len(unknowns) == 0
-    ), f"Unknown types when generating calibrate command: {unknowns}"
+    assert len(unknowns) == 0, (
+        f"Unknown types when generating calibrate command: {unknowns}"
+    )
 
     cmd += f"{ms_path!s} {solutions_path!s}"
 
@@ -670,9 +670,9 @@
 
     assert ms.path.exists(), f"The measurement set {ms} was not found. "
     assert ms.column is not None, f"{ms} does not have a nominated data_column. "
-    assert (
-        solutions_file.exists()
-    ), f"The solutions file {solutions_file} does not exists. "
+    assert solutions_file.exists(), (
+        f"The solutions file {solutions_file} does not exists. "
+    )
 
     input_column = ms.column
     copy_mode = "-nocopy" if input_column == output_column else "-copy"
@@ -714,9 +714,9 @@
     """
 
     assert container.exists(), f"The calibrate container {container} does not exist. "
-    assert (
-        calibrate_cmd.ms is not None
-    ), "When calibrating the 'ms' field attribute must be defined. "
+    assert calibrate_cmd.ms is not None, (
+        "When calibrating the 'ms' field attribute must be defined. "
+    )
 
     run_singularity_command(
         image=container,
@@ -738,12 +738,12 @@
         container (Path): Location of the existing solutions file
     """
 
-    assert (
-        container.exists()
-    ), f"The applysolutions container {container} does not exist. "
-    assert (
-        apply_solutions_cmd.ms.path.exists()
-    ), f"The measurement set {apply_solutions_cmd.ms} was not found. "
+    assert container.exists(), (
+        f"The applysolutions container {container} does not exist. "
+    )
+    assert apply_solutions_cmd.ms.path.exists(), (
+        f"The measurement set {apply_solutions_cmd.ms} was not found. "
+    )
 
     run_singularity_command(
         image=container,
@@ -828,9 +828,9 @@
         int: The index of the reference antenna that should be used.
     """
 
-    assert (
-        len(bandpass.shape) == 4
-    ), f"Expected a bandpass of shape (times, ant, channels, pol), received {bandpass.shape=}"
+    assert len(bandpass.shape) == 4, (
+        f"Expected a bandpass of shape (times, ant, channels, pol), received {bandpass.shape=}"
+    )
 
     # create the mask of valid solutions
     mask = np.isfinite(bandpass)
@@ -1019,7 +1019,7 @@
 
                 flagged = ~np.isfinite(bandpass[time, ant, :, pol])
                 logger.info(
-                    f"{ant=:02d}, pol={pols[pol]}, flagged {np.sum(flagged) / ant_gains.shape[0] * 100.:.2f}%"
+                    f"{ant=:02d}, pol={pols[pol]}, flagged {np.sum(flagged) / ant_gains.shape[0] * 100.0:.2f}%"
                 )
 
     for time in range(solutions.nsol):
@@ -1070,7 +1070,7 @@
     total_flagged = np.sum(~np.isfinite(bandpass)) / np.prod(bandpass.shape)
     if total_flagged > 0.8:
         msg = (
-            f"{total_flagged*100.:.2f}% of {(solutions_path)!s} is flagged after running the preflagger. "
+            f"{total_flagged * 100.0:.2f}% of {(solutions_path)!s} is flagged after running the preflagger. "
             "That is over 90%. "
             f"This surely can not be correct. Likely something has gone very wrong. "
         )

flint/catalogue.py

@@ -288,9 +288,9 @@ def download_vizier_catalogue(
     logger.info(f"catalogue downloaded, contains {len(tablelist[0])} rows")
     logger.info(f"Writing {vizier_id=} to {output_path=}")
 
-    assert (
-        len(tablelist) == 1
-    ), f"Table list for {vizier_id=} has unexpected length of {len(tablelist)}"
+    assert len(tablelist) == 1, (
+        f"Table list for {vizier_id=} has unexpected length of {len(tablelist)}"
+    )
 
     # Note all pirates respect the FITS standard@
     if description := tablelist[0].meta.get("description", None):