Force bool to float32, add explicit error message

.pre-commit-config.yaml

@@ -1,16 +1,13 @@
 ci:
-  autoupdate_commit_msg: "chore(deps): update pre-commit hooks"
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
-  autoupdate_schedule: "monthly"
-
-exclude: ^.cruft.json|.copier-answers.yml$
 
 repos:
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.20.0"
     hooks:
       - id: blacken-docs
-        additional_dependencies: [black==25.*]
+        additional_dependencies: [black==24.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: "v6.0.0"
@@ -28,44 +25,46 @@ repos:
       - id: requirements-txt-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: "v1.10.0"
-    hooks:
-      - id: rst-backticks
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
+  # - repo: https://github.com/pre-commit/pygrep-hooks
+  #   rev: "v1.10.0"
+  #   hooks:
+  #     - id: rst-backticks
+  #     - id: rst-directive-colons
+  #     - id: rst-inline-touching-normal
 
-  - repo: https://github.com/rbubley/mirrors-prettier
-    rev: "v3.8.3"
-    hooks:
-      - id: prettier
-        types_or: [yaml, markdown, html, css, scss, javascript, json]
-        args: [--prose-wrap=always]
+  # - repo: https://github.com/pre-commit/mirrors-prettier
+  #   rev: "v4.0.0-alpha.8"
+  #   hooks:
+  #     - id: prettier
+  #       types_or: [yaml, markdown, html, css, scss, javascript, json]
+  #       args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: "v0.15.12"
     hooks:
-      - id: ruff-check
+      - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v2.0.0"
     hooks:
       - id: mypy
-        files: eye_patch|tests
+        files: flint|tests
         args: ["--ignore-missing-imports"]
         additional_dependencies:
-          - numpy
-          - capn-crunch
-          - pytest-stub
+          - pytest
+          - types-PyYAML
+
+  - repo: https://github.com/crate-ci/typos
+    rev: "v1.46.0"
+    hooks:
+      - id: typos
 
   - repo: https://github.com/codespell-project/codespell
     rev: "v2.4.2"
     hooks:
       - id: codespell
-        additional_dependencies:
-          - tomli; python_version<'3.11'
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
     rev: "v0.11.0.1"

eye_patch/logging.py

@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+import logging
+
+# Create logger
+logging.captureWarnings(True)
+logger = logging.getLogger("eye-patch")
+logger.setLevel(logging.INFO)
+
+# Create console handler and set level to debug
+ch = logging.StreamHandler()
+ch.setLevel(logging.INFO)
+
+
+class CustomFormatter(logging.Formatter):
+    """A custom logger formatter"""
+
+    grey = "\x1b[38;20m"
+    blue = "\x1b[34;20m"
+    green = "\x1b[32;20m"
+    yellow = "\x1b[33;20m"
+    red = "\x1b[31;20m"
+    bold_red = "\x1b[31;1m"
+    reset = "\x1b[0m"
+    format_str = "%(asctime)s.%(msecs)03d %(module)s - %(funcName)s: %(message)s"
+
+    FORMATS = {  # noqa: RUF012
+        logging.DEBUG: f"{blue}%(levelname)s{reset} {format_str}",
+        logging.INFO: f"{green}%(levelname)s{reset} {format_str}",
+        logging.WARNING: f"{yellow}%(levelname)s{reset} {format_str}",
+        logging.ERROR: f"{red}%(levelname)s{reset} {format_str}",
+        logging.CRITICAL: f"{bold_red}%(levelname)s{reset} {format_str}",
+    }
+
+    def format(self, record):
+        log_fmt = self.FORMATS.get(record.levelno)
+        formatter = logging.Formatter(log_fmt, "%Y-%m-%d %H:%M:%S")
+        return formatter.format(record)
+
+
+# Add formatter to ch
+ch.setFormatter(CustomFormatter())
+
+# Add ch to logger
+logger.addHandler(ch)

eye_patch/masking.py

@@ -4,7 +4,6 @@
 
 from __future__ import annotations
 
-import logging
 from argparse import ArgumentParser
 from pathlib import Path
 from typing import NamedTuple, TypeAlias
@@ -26,6 +25,7 @@
 from scipy.ndimage import binary_fill_holes, label, maximum_filter, minimum_filter
 from scipy.signal import fftconvolve
 
+from eye_patch.logging import logger
 from eye_patch.naming import FITSMaskNames, create_fits_mask_names
 
 # Add explicit export so mypy on tests is ok
@@ -37,8 +37,6 @@
 # during fits file creation.
 MaskLike: TypeAlias = NDArray[np.floating]
 
-logger = logging.getLogger("__name__")
-
 
 class MaskingOptions(BaseOptions):
     """Contains options for the creation of clean masks from some subject
@@ -916,7 +914,7 @@ def create_snr_mask_from_fits(
     logger.info(f"Writing {mask_names.mask_fits}")
     fits.writeto(
         filename=mask_names.mask_fits,
-        data=mask_data,
+        data=mask_data.astype(np.float32),
         header=fits_header,
         overwrite=overwrite,
     )
@@ -965,6 +963,12 @@ def convolve_image_by_scale(
     logger.info(f"Generating gaussian kernel for {scale=} {fwhm=:.3f} {sigma=:.3f}")
 
     pix_sigma = int(sigma * 5)
+    if pix_sigma < 1:
+        # linspace can only take integer inputs, and if sigma is too small then this array comes
+        # out as length zero.
+        msg = f"{scale=} is too small and an appropriately sized kernel can not be formed. Consider removing it. "
+        raise ValueError(msg)
+
     x = np.linspace(0, pix_sigma, pix_sigma)
     y = np.linspace(0, pix_sigma, pix_sigma)