Add pre-commit job to CI

.github/workflows/ci.yml

@@ -10,6 +10,16 @@ on:
     branches: [ main, master ]
 
 jobs:
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8  # v5.0.0
+    - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5.6.0
+      with:
+        python-version: '3.12'
+    - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd  # v3.0.1
+
   build:
 
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-yaml
+        args: ["--unsafe"]
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: debug-statements
+      - id: detect-private-key
+      # - id: end-of-file-fixer
+      # - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.12.3'
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+      - id: ruff-format

.ruff.toml

@@ -0,0 +1,66 @@
+extend = "pyproject.toml"
+
+exclude = [
+    "docs",
+    ".tox",
+    ".eggs",
+    "build",
+    "*.ipynb",
+    "**/tests/**/__init__.py",
+]
+line-length = 100
+
+target-version = "py312"
+
+[format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+
+[lint]
+select = [
+    "F",      # Pyflakes (part of default flake8)
+    "E",      # pycodestyle (part of default flake8)
+    "W",      # pycodestyle (part of default flake8)
+    "D",      # docstrings, see also numpydoc pre-commit action
+    "N",      # pep8-naming (naming conventions)
+    "A",      # flake8-builtins (prevent shadowing of builtins)
+    "ARG",    # flake8-unused-arguments (prevent unused arguments)
+    "B",      # flake8-bugbear (miscellaneous best practices to avoid bugs)
+    "C4",     # flake8-comprehensions (best practices for comprehensions)
+    "I",      # isort
+    "ICN",    # flake8-import-conventions (enforce import conventions)
+    "INP",    # flake8-no-pep420 (prevent use of PEP420, i.e. implicit name spaces)
+    "ISC",    # flake8-implicit-str-concat (conventions for concatenating long strings)
+    "LOG",    # flake8-logging
+    "NPY",    # numpy-specific rules
+    "PGH",    # pygrep-hooks (ensure appropriate usage of noqa and type-ignore)
+    # "PTH",    # flake8-use-pathlib (enforce using Pathlib instead of os)
+    "S",      # flake8-bandit (security checks)
+    "SLF",    # flake8-self (prevent using private class members outside class)
+    "SLOT",   # flake8-slots (require __slots__ for immutable classes)
+    # "T20",    # flake8-print (prevent print statements in code)
+    "TRY",    # tryceratops (best practices for try/except blocks)
+    "UP",     # pyupgrade (simplified syntax allowed by newer Python versions)
+    "YTT",    # flake8-2020 (prevent some specific gotchas from sys.version)
+    "TID252"  # Checks for relative imports
+]
+ignore = ["D100", "D104", "TRY003"]
+
+[lint.per-file-ignores]
+"**/tests/test_*.py" = [
+    "D",
+    "S",
+]
+
+[lint.pydocstyle]
+convention = "numpy"
+
+[lint.flake8-annotations]
+ignore-fully-untyped = true  # Turn off annotation checking for fully untyped code
+
+[lint.flake8-tidy-imports]
+ban-relative-imports = "all"  # Disallow all relative imports.
+
+[lint.isort]
+known-first-party = ["nirc2_reduce"]

nirc2_reduce/_version.py

@@ -12,11 +12,8 @@
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
+    VERSION_TUPLE = tuple[int | str, ...]
+    COMMIT_ID = str | None
 else:
     VERSION_TUPLE = object
     COMMIT_ID = object
@@ -28,7 +25,7 @@
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.dev53+g310c26299.d20250816'
-__version_tuple__ = version_tuple = (0, 1, 'dev53', 'g310c26299.d20250816')
+__version__ = version = "0.1.dev55+g3741c605e.d20250817"
+__version_tuple__ = version_tuple = (0, 1, "dev55", "g3741c605e.d20250817")
 
-__commit_id__ = commit_id = 'g310c26299'
+__commit_id__ = commit_id = "g3741c605e"

nirc2_reduce/flats.py

@@ -1,24 +1,25 @@
-import numpy as np
-import matplotlib.pyplot as plt
-from astropy.io import fits
-from .image import Image
 import warnings
 
+import matplotlib.pyplot as plt
+import numpy as np
+
+from nirc2_reduce.image import Image
+
+
 class Flats:
-    """
-    class for dome flats
-    """
+    """Class for dome flats."""
 
     def __init__(self, fnames_off, fnames_on):
         """
-        subtract lights off from lights on,
-        divide by median value to center it around 1
-
+        Subtract lights off from lights on.
+
+        Divide by median value to center it around 1
+
         Parameters
         ----------
         fnames_off : list, required. fits files for dome flat OFF
         fnames_on : list, required. fits files for dome flat ON
-        
+
         Attributes
         ----------
         dummy_fits : Image object used to hijack header info
@@ -32,16 +33,23 @@ def __init__(self, fnames_off, fnames_on):
 
         off = np.nanmedian(self.frames_off, axis=0)
         on = np.nanmedian(self.frames_on, axis=0)
-        if (np.nanmean(on) - np.nanmean(off))/np.nanmean(on) < 0.01:
-            warnings.warn(f'brightness difference between domeflaton and domeflatoff is near zero for flat including fname {fnames_on[0]}. setting to off. if this is a thermal filter (lp, ms) then this is probably ok', stacklevel=2)
+        if (np.nanmean(on) - np.nanmean(off)) / np.nanmean(on) < 0.01:
+            warnings.warn(
+                "brightness difference between domeflaton and domeflatoff is near zero "
+                f"for flat including fname {fnames_on[0]}. setting to off. "
+                "if this is a thermal filter (lp, ms) then this is probably ok",
+                stacklevel=2,
+            )
             flat = off
         else:
             flat = on - off
-            
+
         self.flat = flat / np.nanmedian(flat)
 
     def write(self, outfile):
         """
+        Write the flat to fits.
+
         Parameters
         ----------
         outfile : str, required. output fits filename
@@ -53,23 +61,25 @@ def write(self, outfile):
         hdulist_out[0].writeto(outfile, overwrite=True)
 
     def plot(self):
+        """Make a simple plot of the flat."""
         plt.imshow(self.flat, origin="lower")
         plt.show()
 
     def make_badpx_map(self, outfile, tol=0.07, blocksize=6):
         """
-        Find pixels whose values are very far from the average of their neighbors
-        Bad pixel is defined as 
+        Find pixels whose values are very far from the average of their neighbors.
+
+        Bad pixel is defined as
         abs(pixel value / median of nearby pixels - 1) > tol
-        
+
         Parameters
         ----------
-        outfile : str, required. 
+        outfile : str, required.
             fits filename to write to
         tol : float, optional. default 0.07
-            fractional tolerance. 
+            fractional tolerance.
         blocksize : int, optional. default 6
-            number of pixels over which to average 
+            number of pixels over which to average
             in each direction
         """
         badpx_map = np.ones(self.flat.shape)
@@ -78,7 +88,7 @@ def make_badpx_map(self, outfile, tol=0.07, blocksize=6):
                 flatblock = self.flat[i : i + blocksize, j : j + blocksize]
                 mapblock = badpx_map[i : i + blocksize, j : j + blocksize]
                 with warnings.catch_warnings():
-                    warnings.filterwarnings('ignore', category=RuntimeWarning)
+                    warnings.filterwarnings("ignore", category=RuntimeWarning)
                     med = np.median(flatblock)
 
                     # if not within tolerance, set to NaN

nirc2_reduce/image.py

@@ -1,14 +1,13 @@
-import numpy as np
+import warnings
+
 import matplotlib.pyplot as plt
 from astropy.io import fits
-import warnings
 
 
 class Image:
     """
-    Thin wrapper to astropy.io.fits providing convenience functions
-    and suppression of warnings in fits.open
-
+    Thin wrapper to astropy.io.fits.
+
     To do
     -----
     make agnostic to specific .fits header keywords
@@ -17,10 +16,12 @@ class Image:
 
     def __init__(self, fname):
         """
+        Provide convenience function for opening fits files.
+
         Parameters
         ----------
         fname : str, required. input .fits filename
-        
+
         Attributes
         ----------
         hdulist: .fits format hdulist structure
@@ -31,15 +32,17 @@ def __init__(self, fname):
         """
         warnings.filterwarnings(
             "ignore",
-            "The following header keyword is invalid or follows an unrecognized non-standard convention",
+            "The following header keyword is invalid or follows an unrecognized "
+            "non-standard convention",
         )
         warnings.filterwarnings(
             "ignore",
             "non-ASCII characters are present in the FITS file header and have been replaced",
         )
         warnings.filterwarnings(
             "ignore",
-            "Header block contains null bytes instead of spaces for padding, and is not FITS-compliant",
+            "Header block contains null bytes instead of spaces for padding, "
+            "and is not FITS-compliant",
         )
         self.hdulist = fits.open(fname, ignore_missing_end=True)
         self.header = self.hdulist[0].header
@@ -51,7 +54,7 @@ def __init__(self, fname):
         try:
             targ = self.header["OBJECT"]
             self.target = targ.split()[0].strip(", \n").capitalize()
-        except:
+        except KeyError:
             self.target = "Unknown"
         try:
             fwi = self.header["FWINAME"].strip(", \n")
@@ -60,14 +63,25 @@ def __init__(self, fname):
                 self.filt = fwi
             elif fwi == "clear" or fwi == "PK50_1.5":
                 self.filt = fwo
-        except:
+            else:
+                self.filt = "Unknown"
+        except KeyError:
             self.filt = "Unknown"
 
     def plot(self):
+        """Make a simple plot of the data."""
         plt.imshow(self.data, origin="lower left")
         plt.show()
 
     def write(self, fname):
+        """
+        Write the image to fits.
+
+        Parameters
+        ----------
+        fname : str
+            Filename to write to.
+        """
         self.hdulist[0].header = self.header
         self.hdulist[0].data = self.data
         self.hdulist.writeto(fname, overwrite=True)