[STY] apply black, isort, flake8

.flake8

@@ -0,0 +1,20 @@
+[flake8]
+--select = A,B,C,D,E,F,W,C90,FS
+max-line-length = 93
+# For PEP8 error codes see
+# http://pep8.readthedocs.org/en/latest/intro.html#error-codes
+ignore =
+	D101,
+	D102,
+	D103,
+	D104,
+	D105,
+	D107,
+	F403,
+	F405,
+	F841,
+	FS,
+	W503
+# for compatibility with black
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
+extend-ignore = E203

.github/workflows/black.yml

@@ -0,0 +1,30 @@
+---
+name: black
+
+on:
+    push:
+        branches:
+        -   master
+    pull_request:
+        branches:
+        -   '*'
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    black:
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install black
+            run: python -m pip install --upgrade pip black
+        -   name: Run Black
+            run: black --check --diff --color .

.github/workflows/codespell.yml

@@ -2,21 +2,21 @@
 name: Codespell
 
 on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
+    push:
+        branches: [master]
+    pull_request:
+        branches: [master]
 
 permissions:
-  contents: read
+    contents: read
 
 jobs:
-  codespell:
-    name: Check for spelling errors
-    runs-on: ubuntu-latest
+    codespell:
+        name: Check for spelling errors
+        runs-on: ubuntu-latest
 
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Codespell
-        uses: codespell-project/actions-codespell@v2
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Codespell
+            uses: codespell-project/actions-codespell@v2

.github/workflows/flake8.yml

@@ -0,0 +1,31 @@
+---
+name: flake8
+
+on:
+    push:
+        branches:
+        -   master
+    pull_request:
+        branches:
+        -   '*'
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    flake8:
+        name: run flake8
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Setup python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install tox
+            run: python -m pip install --upgrade tox
+        -   name: Run Flake8
+            run: tox run -e flake8

.github/workflows/isort.yml

@@ -0,0 +1,31 @@
+---
+name: isort
+
+on:
+    push:
+        branches:
+        -   master
+    pull_request:
+        branches:
+        -   '*'
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    isort:
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install isort
+            shell: bash {0}
+            run: python -m pip install --upgrade pip isort
+        -   name: Run isort
+            run: isort --diff --check --settings-path pyproject.toml .

.github/workflows/test.yml

@@ -3,7 +3,7 @@ name: Test
 
 on:
     push:
-        branches: ['master']
+        branches: [master]
     pull_request:
         branches: ['*']
 
@@ -16,7 +16,7 @@ jobs:
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
-                os: [ubuntu-latest, macOS-latest, windows-latest] 
+                os: [ubuntu-latest, macOS-latest, windows-latest]
                 python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
             fail-fast: false
         steps:
@@ -30,4 +30,3 @@ jobs:
             run: pip install tox
         -   name: Run tests
             run: tox run -e tests
-

.gitignore

@@ -21,4 +21,4 @@ debug.log
 
 test/data
 
-.tox
+.tox

.pre-commit-config.yaml

@@ -3,43 +3,43 @@
 # See https://pre-commit.com/hooks.html for more hooks
 
 repos:
-# -   repo: https://github.com/pre-commit/pre-commit-hooks
-#     rev: v4.5.0
-#     hooks:
-#     -   id: check-ast
-#     -   id: check-case-conflict
-#     -   id: check-json
-#     -   id: check-merge-conflict
-#     -   id: check-toml
-#     -   id: check-yaml
-#     -   id: end-of-file-fixer
-#     -   id: mixed-line-ending
-#     -   id: trailing-whitespace
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: check-ast
+    -   id: check-case-conflict
+    -   id: check-json
+    -   id: check-merge-conflict
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
 
-# -   repo: https://github.com/pycqa/isort
-#     rev: 5.13.2
-#     hooks:
-#     -   id: isort
-#         args: [--profile, black, --settings-path, pyproject.toml]
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: [--profile, black, --settings-path, pyproject.toml]
 
-# -   repo: https://github.com/asottile/pyupgrade
-#     rev: v3.15.0
-#     hooks:
-#     -   id: pyupgrade
-#         args: [--py38-plus]
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    -   id: pyupgrade
+        args: [--py38-plus]
 
-# -   repo: https://github.com/psf/black-pre-commit-mirror
-#     rev: 24.1.1
-#     hooks:
-#     -   id: black
-#         args: [--config, pyproject.toml]
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.1.1
+    hooks:
+    -   id: black
+        args: [--config, pyproject.toml]
 
-# -   repo: https://github.com/adamchainz/blacken-docs
-#     rev: 1.16.0
-#     hooks:
-#     -   id: blacken-docs
-#         additional_dependencies:
-#         -   black==23.9.1
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies:
+        -   black==23.9.1
 
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
@@ -48,26 +48,26 @@ repos:
         args: [--toml, pyproject.toml]
         additional_dependencies: [tomli]
 
-# -   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
-#     rev: 0.2.3
-#     hooks:
-#     -   id: yamlfmt
-#         args: [--mapping, '4', --sequence, '4', --offset, '0']
+-   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+    -   id: yamlfmt
+        args: [--mapping, '4', --sequence, '4', --offset, '0']
 
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
     rev: v2.12.0
     hooks:
     -   id: pretty-format-toml
         args: [--autofix, --indent, '4']
 
-# -   repo: https://github.com/pre-commit/pygrep-hooks
-#     rev: v1.10.0
-#     hooks:
-#     -   id: rst-backticks
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+    -   id: rst-backticks
 
-# -   repo: https://github.com/pyCQA/flake8
-#     rev: 7.0.0
-#     hooks:
-#     -   id: flake8
-#         args: [--config, .flake8, --verbose, nilearn, examples, maint_tools]
-#         additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions]
+-   repo: https://github.com/pyCQA/flake8
+    rev: 7.0.0
+    hooks:
+    -   id: flake8
+        args: [--config, .flake8, --verbose, nidmresults, examples]
+        additional_dependencies: [flake8-docstrings, flake8-use-fstring]

README.md

@@ -23,5 +23,3 @@ Examples are available in the [examples](examples) folder.
 
 ## Contributing
 Thanks for your interest in contributing to nidmresults. All contributions are very welcome! If you experience difficulties using the library, please [open an issue](https://github.com/incf-nidash/nidmresults/issues/new) describing the problem. See the list of [current issues](https://github.com/incf-nidash/nidmresults/issues).
-
-

examples/ex_read_nidm.py

@@ -1,22 +1,24 @@
-# Example: reading a NIDM pack available on NeuroVault
-import os
+"""Example: reading a NIDM pack available on NeuroVault."""
+
 import json
-import nidmresults as nidm
+import os
 import urllib.request
 
+import nidmresults as nidm
+
 # Download the NIDM pack locally
-nidm_url = 'https://neurovault.org/collections/2210/fsl_default_130.nidm.zip'
+nidm_url = "https://neurovault.org/collections/2210/fsl_default_130.nidm.zip"
 nidmpack = "2210_fsl_default_130.nidm.zip"
 
 if not os.path.isfile(nidmpack):
-    print(f'Downloading {nidmpack}')
+    print(f"Downloading {nidmpack}")
     urllib.request.urlretrieve(nidm_url, nidmpack)
 
 # Known issues with NIDM packs in collection 2210
 to_replace = {
-    ' \\ntask': '\\\\n task',
-    ';\n    nidm_coordinateVectorInVoxels: "null"^^xsd:string .':
-    '.'}
+    " \\ntask": "\\\\n task",
+    ';\n    nidm_coordinateVectorInVoxels: "null"^^xsd:string .': ".",
+}
 
 # Read the NIDM pack
 nres = nidm.load(nidmpack, to_replace=to_replace)

nidmresults/__init__.py

@@ -1,11 +1,13 @@
 import os
 
+from nidmresults._version import __version__  # noqa
 from nidmresults.load import load
 
-from nidmresults._version import __version__
-
 latest_owlfile = os.path.join(
-    os.path.dirname(os.path.dirname(__file__)), 'nidmresults', 'owl',
-    "nidm-results_130.owl")
+    os.path.dirname(os.path.dirname(__file__)),
+    "nidmresults",
+    "owl",
+    "nidm-results_130.owl",
+)
 
-__all__ = ["load"]
+__all__ = ["load"]

nidmresults/cli/nidm_mkda_convert.py

@@ -5,7 +5,6 @@
 @copyright: University of Warwick 2013-2014
 """
 
-from __future__ import absolute_import, division, print_function
 
 import argparse
 import os
@@ -29,7 +28,7 @@ def main(argv=sys.argv):
         nargs="+",
     )
     parser.add_argument(
-        "--version", action="version", version="{version}".format(version=__version__)
+        "--version", action="version", version=f"{__version__}"
     )
 
     args = parser.parse_args(argv[1:])
@@ -56,7 +55,10 @@ def main(argv=sys.argv):
 
         nidmgraph = Graph(nidm_zip=nidmpack)
         con_ids = nidmgraph.serialize(
-            outfile, "mkda", overwrite=overwrite, last_used_con_id=max(con_ids.values())
+            outfile,
+            "mkda",
+            overwrite=overwrite,
+            last_used_con_id=max(con_ids.values()),
         )