Consistent styling, formatting, and linting for all python code in the repo (#1626)

* bump version for isort, include all python source code files in styling, formatting, and linting, add precommit script

* Update README with linting tools details

Added information about linting tools used in the project.

---------

Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>
Co-authored-by: Aaron S. Brewster <asbrewster@lbl.gov>

Author: 3 people

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 26.3.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/pycqa/isort
+    rev: 8.0.0
+    hooks:
+      - id: isort
+
+  # - repo: https://github.com/streetsidesoftware/cspell-cli
+  #   rev: v9.7.0
+  #   hooks:
+  #     - id: cspell  # spellchecking
+  #       pass_filenames: false
+  #       args:
+  #         - --config
+  #         - cspell.json
+  #         - applications/**/*
+  #         - base_classes/**/*
+  #         - contributed_definitions/**/*

Makefile

@@ -47,13 +47,13 @@ install ::
 	$(PYTHON) -m pip install -r requirements.txt
 
 style ::
-	$(PYTHON) -m black --check dev_tools
-	$(PYTHON) -m flake8 dev_tools
-	$(PYTHON) -m isort --check dev_tools
+	$(PYTHON) -m black --check .
+	$(PYTHON) -m flake8 .
+	$(PYTHON) -m isort --check .
 
 autoformat ::
-	$(PYTHON) -m black dev_tools
-	$(PYTHON) -m isort dev_tools
+	$(PYTHON) -m black .
+	$(PYTHON) -m isort .
 
 test ::
 	$(PYTHON) -m pytest dev_tools

README.md

@@ -13,7 +13,7 @@ to be made before commiting the change:
  1. check whether the change does not violate any syntax rules
  2. verify whether the change looks as intended in the HTML documentation
 
-First install the test and build requirements with this command (only run once)
+First install the test and build requirements with this command (only run once).  This will install linting tools such as black and flake8 as well.
 
     make install
 
@@ -75,4 +75,8 @@ package/                       | directory for packaging this content
 utils/                         | various tools used in the definitions tree
 www/                           | launch (home) page of NeXus WWW site
 xslt/                          | various XML stylesheet transformations
-dev_tools/                     | developer tools for testing and building
+dev_tools/                     | developer tools for testing and building
+
+## Linting
+
+We use flake8 and black for linting our Python code.  When running `git commit` these tools will automatically apply formatting.

applications/stress/gauge_volume.py

@@ -1,7 +1,7 @@
 import os
-import numpy as np
 
 import matplotlib.pyplot as plt
+import numpy as np
 from mpl_toolkits.mplot3d.art3d import Poly3DCollection
 
 fig = plt.figure(figsize=(10, 10))

galleries/nxdata/plot_hist1d.py

@@ -35,9 +35,10 @@
 x = [0.5, 1.5, 2.5, 4, 5, 6.5, 7, 8]
 y = [4.8, 5.5, 3.5, 4.6, 6.5, 6.6, 2.6]
 
+import matplotlib.pyplot as plt  # noqa E402
+
 # Plot
 import numpy as np  # noqa E402
-import matplotlib.pyplot as plt  # noqa E402
 
 plt.style.use("_mpl-gallery")