black formatter

Author: tsmbland

.gitattributes

@@ -0,0 +1 @@
+*.ipynb -linguist-detectable

.gitignore

@@ -1,5 +1,18 @@
+# Bytecode
+__pycache__/
+
+# Distribution/packaging
+build/
 dist/
-saibr.egg-info/
-docs/build/
+*.egg-info/
+
+# Unit tests
+.coverage
+.pytest_cache/
+
+# OS
 .DS_Store
-__pycache__
+
+# IPython notebooks
+.ipynb_checkpoints
+

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+    - repo: https://github.com/psf/black
+      rev: 22.10.0
+      hooks:
+          - id: black

README.md

@@ -1,6 +1,9 @@
 # SAIBR (python implementation)
 
 [![CC BY 4.0][cc-by-shield]][cc-by]
+[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Tests](https://github.com/goehringlab/saibr_python/actions/workflows/test.yaml/badge.svg)](https://github.com/goehringlab/saibr_python/actions/workflows/test.yaml)
 [![PyPi version](https://badgen.net/pypi/v/saibr/)](https://pypi.org/project/saibr)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/goehringlab/saibr_python/HEAD?filepath=%2Fscripts/SAIBRdemonstration.ipynb)
 [![Documentation Status](https://readthedocs.org/projects/saibr/badge/?version=latest)](https://saibr.readthedocs.io/en/latest/?badge=latest)

docs/source/conf.py

@@ -1,6 +1,7 @@
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 # Configuration file for the Sphinx documentation builder.
 #
@@ -10,27 +11,24 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'saibr'
-copyright = '2023, Tom Bland'
-author = 'Tom Bland'
-release = '0.1.5'
+project = "saibr"
+copyright = "2023, Tom Bland"
+author = "Tom Bland"
+release = "0.1.5"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = [
-   'sphinx.ext.autodoc',
-   'sphinx.ext.napoleon'
-]
-autoapi_dirs = ['../../saibr']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+autoapi_dirs = ["../../saibr"]
 
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 exclude_patterns = []
 
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

saibr/__init__.py

@@ -4,4 +4,4 @@
 
 __all__ = []
 __all__.extend(saibr.__all__)
-__all__.extend(misc.__all__)
+__all__.extend(misc.__all__)

saibr/legacy.py

@@ -1,6 +1,18 @@
-from saibr import SaibrCalibrate, saibr_correlation, saibr_correlation_3channel, saibr_correct, saibr_correct_3channel
+from saibr import (
+    SaibrCalibrate,
+    saibr_correlation,
+    saibr_correlation_3channel,
+    saibr_correct,
+    saibr_correct_3channel,
+)
 
-__all__ = ['AfCorrelation', 'af_correlation', 'af_correlation_3channel', 'af_subtraction', 'af_subtraction_3channel']
+__all__ = [
+    "AfCorrelation",
+    "af_correlation",
+    "af_correlation_3channel",
+    "af_subtraction",
+    "af_subtraction_3channel",
+]
 
 AfCorrelation = SaibrCalibrate
 af_correlation = saibr_correlation

saibr/misc.py

@@ -5,7 +5,8 @@
 import matplotlib.pyplot as plt
 import copy
 
-__all__ = ['load_image', 'save_img', 'save_img_jpeg', 'direcslist']
+__all__ = ["load_image", "save_img", "save_img_jpeg", "direcslist"]
+
 
 def load_image(filename: str) -> np.ndarray:
     """
@@ -32,11 +33,16 @@ def save_img(img: np.ndarray, direc: str):
 
     """
 
-    io.imsave(direc, img.astype('float32'))
+    io.imsave(direc, img.astype("float32"))
 
 
-def save_img_jpeg(img: np.ndarray, direc: str, cmin: Optional[float] = None, cmax: Optional[float] = None,
-                  cmap: str = 'gray'):
+def save_img_jpeg(
+    img: np.ndarray,
+    direc: str,
+    cmin: Optional[float] = None,
+    cmax: Optional[float] = None,
+    cmap: str = "gray",
+):
     """
     Saves 2D array as jpeg, according to min and max pixel intensities
 
@@ -52,14 +58,18 @@ def save_img_jpeg(img: np.ndarray, direc: str, cmin: Optional[float] = None, cma
     plt.imsave(direc, img, vmin=cmin, vmax=cmax, cmap=cmap)
 
 
-def _direcslist(dest: str, levels: int = 0, exclude: Optional[tuple] = ('!',),
-                exclusive: Optional[tuple] = None) -> list:
-    lis = sorted(glob.glob(f'{dest}/*/'))
+def _direcslist(
+    dest: str,
+    levels: int = 0,
+    exclude: Optional[tuple] = ("!",),
+    exclusive: Optional[tuple] = None,
+) -> list:
+    lis = sorted(glob.glob(f"{dest}/*/"))
 
     for level in range(levels):
         newlis = []
         for e in lis:
-            newlis.extend(sorted(glob.glob(f'{e}/*/')))
+            newlis.extend(sorted(glob.glob(f"{e}/*/")))
         lis = newlis
         lis = [x[:-1] for x in lis]
 
@@ -85,8 +95,12 @@ def _direcslist(dest: str, levels: int = 0, exclude: Optional[tuple] = ('!',),
     return sorted(lis2)
 
 
-def direcslist(dest: str, levels: int = 0, exclude: Optional[tuple] = ('!',),
-               exclusive: Optional[tuple] = None) -> list:
+def direcslist(
+    dest: str,
+    levels: int = 0,
+    exclude: Optional[tuple] = ("!",),
+    exclusive: Optional[tuple] = None,
+) -> list:
     """
     Gives a list of directories within a given directory (full path)
     Todo: os.walk