Add fmt and lint checks

.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  run-hooks:
+    name: Run pre-commit hooks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out Git repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.7
+
+      - name: Install Python dependencies
+        run: pip install pre-commit
+
+      - name: Run pre-commit hooks
+        run: pre-commit run --all-files

.github/workflows/test.yml

@@ -25,4 +25,4 @@ jobs:
         run: coverage run -m unittest discover -v nrrd/tests
 
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v2

.gitignore

@@ -10,4 +10,4 @@ MANIFEST
 docs/build/
 
 # coverage.py files
-.coverage
+.coverage

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+exclude: "docs"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.34.0
+    hooks:
+      -  id: pyupgrade
+         args: [--py37-plus]
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+        args: ["--config=setup.cfg"]

MANIFEST.in

@@ -1,3 +1,3 @@
 include AUTHORS
 include README.md
-include LICENSE
+include LICENSE

README.rst

@@ -25,7 +25,7 @@
 
 pynrrd
 ======
-pynrrd is a pure-Python module for reading and writing `NRRD <http://teem.sourceforge.net/nrrd/>`_ files into and 
+pynrrd is a pure-Python module for reading and writing `NRRD <http://teem.sourceforge.net/nrrd/>`_ files into and
 from numpy arrays.
 
 Dependencies
@@ -46,7 +46,7 @@ Install via pip and GitHub
 .. code-block:: bash
 
     pip install git+https://github.com/mhe/pynrrd.git
-    
+
 Install from source (recommended for contributing to pynrrd)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 For developers that want to contribute to pynrrd, you can clone the pynrrd repository and install it using the following commands:
@@ -74,20 +74,24 @@ The tests can be run via the following command from the base directory:
 
     python -m unittest discover -v nrrd/tests
 
+**Format and Lint code**
+
+ This repository uses pre-commit hooks to run format and lint the code and they are enforced in CI. See [pre-commit](https://pre-commit.com)
+
 Example usage
 -------------
 .. code-block:: python
 
     import numpy as np
     import nrrd
-    
+
     # Some sample numpy data
     data = np.zeros((5,4,3,2))
     filename = 'testdata.nrrd'
-    
+
     # Write to a NRRD file
     nrrd.write(filename, data)
-    
+
     # Read the data back from file
     readdata, header = nrrd.read(filename)
     print(readdata.shape)

nrrd/formatters.py

@@ -31,7 +31,7 @@ def format_number(x):
         # floating point number.
         # The g option is used rather than f because g precision uses significant digits while f is just the number of
         # digits after the decimal. (NRRD C implementation uses g).
-        value = '{:.17g}'.format(x)
+        value = f'{x:.17g}'
     else:
         value = str(x)
 

nrrd/reader.py

@@ -1,4 +1,3 @@
-# encoding: utf-8
 import bz2
 import os
 import re
@@ -321,9 +320,9 @@ def read_data(header, fh=None, filename=None, index_order='F'):
         Filename of the header file. Only necessary if data is detached from the header. This is used to get the
         absolute data path.
     index_order : {'C', 'F'}, optional
-        Specifies the index order of the resulting data array. Either 'C' (C-order) where the dimensions are ordered from
-        slowest-varying to fastest-varying (e.g. (z, y, x)), or 'F' (Fortran-order) where the dimensions are ordered
-        from fastest-varying to slowest-varying (e.g. (x, y, z)).
+        Specifies the index order of the resulting data array. Either 'C' (C-order) where the dimensions are ordered
+        from slowest-varying to fastest-varying (e.g. (z, y, x)), or 'F' (Fortran-order) where the dimensions are
+        ordered from fastest-varying to slowest-varying (e.g. (x, y, z)).
 
     Returns
     -------
@@ -452,8 +451,8 @@ def read_data(header, fh=None, filename=None, index_order='F'):
     fh.close()
 
     if total_data_points != data.size:
-        raise NRRDError('Size of the data does not equal the product of all the dimensions: {0}-{1}={2}'
-                        .format(total_data_points, data.size, total_data_points - data.size))
+        raise NRRDError(f'Size of the data does not equal the product of all the dimensions: '
+                        f'{total_data_points}-{data.size}={total_data_points - data.size}')
 
     # In the NRRD header, the fields are specified in Fortran order, i.e, the first index is the one that changes
     # fastest and last index changes slowest. This needs to be taken into consideration since numpy uses C-order
@@ -475,7 +474,9 @@ def read(filename, custom_field_map=None, index_order='F'):
     See :ref:`user-guide:Reading NRRD files` for more information on reading NRRD files.
 
     .. note::
-            Users should be aware that the `index_order` argument needs to be consistent between `nrrd.read` and `nrrd.write`. I.e., reading an array with `index_order='F'` will result in a transposed version of the original data and hence the writer needs to be aware of this.
+            Users should be aware that the `index_order` argument needs to be consistent between `nrrd.read` and
+            `nrrd.write`. I.e., reading an array with `index_order='F'` will result in a transposed version of the
+            original data and hence the writer needs to be aware of this.
 
     Parameters
     ----------
@@ -485,9 +486,9 @@ def read(filename, custom_field_map=None, index_order='F'):
         Dictionary used for parsing custom field types where the key is the custom field name and the value is a
         string identifying datatype for the custom field.
     index_order : {'C', 'F'}, optional
-        Specifies the index order of the resulting data array. Either 'C' (C-order) where the dimensions are ordered from
-        slowest-varying to fastest-varying (e.g. (z, y, x)), or 'F' (Fortran-order) where the dimensions are ordered
-        from fastest-varying to slowest-varying (e.g. (x, y, z)).
+        Specifies the index order of the resulting data array. Either 'C' (C-order) where the dimensions are ordered
+        from slowest-varying to fastest-varying (e.g. (z, y, x)), or 'F' (Fortran-order) where the dimensions are
+        ordered from fastest-varying to slowest-varying (e.g. (x, y, z)).
 
     Returns
     -------

nrrd/tests/data/test1d_ascii.nrrd

@@ -35,4 +35,3 @@ encoding: ASCII
 25
 26
 27
-

nrrd/tests/data/test2d_ascii.nrrd

@@ -17,4 +17,3 @@ encoding: ASCII
 19 20 21
 22 23 24
 25 26 27
-

nrrd/tests/data/test_customFields.nrrd

@@ -45,4 +45,3 @@ double matrix:= (1.2,0.3,0) (0,1.5,0) (0,-0.55,1.6)
 25
 26
 27
-

nrrd/tests/test_formatting.py

@@ -1,12 +1,13 @@
 import os
 import sys
 
-# Required specifically in each module so that searches happen at the parent directory for importing modules
-sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
-
 import numpy as np
-from nrrd.tests.util import *
+
 import nrrd
+from nrrd.tests.util import *
+
+# Required specifically in each module so that searches happen at the parent directory for importing modules
+sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
 
 
 class TestFieldFormatting(unittest.TestCase):

nrrd/tests/test_parsing.py

@@ -1,11 +1,12 @@
 import os
 import sys
 
-sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
-
 import numpy as np
-from nrrd.tests.util import *
+
 import nrrd
+from nrrd.tests.util import *
+
+sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
 
 
 class TestFieldParsing(unittest.TestCase):