Merge pull request #13 from Remi-Gau/lint

[STY] set up linting, formatting and apply

.flake8

@@ -0,0 +1,37 @@
+[flake8]
+; exclude =
+    ; .git,
+    ; __pycache__,
+    ; build,
+    ; dist,
+	; env,
+	; venv,
+	; doc/_build
+--select = A,B,C,D,E,F,W,C90,FS
+; docstring-convention = numpy
+max-line-length = 100
+# For PEP8 error codes see
+# http://pep8.readthedocs.org/en/latest/intro.html#error-codes
+; per-file-ignores =
+	; **/__init__.py: D104
+ignore =
+	D100,
+	D101,
+	D102,
+	D103,
+	D105,
+	D107,
+	E501,
+	E711,
+	E712,
+	E713,
+	E721,
+	E741,
+	F821,
+	F841,
+	FS002,
+	FS001,
+	W503
+# for compatibility with black
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
+extend-ignore = E203

.github/dependabot.yml

@@ -0,0 +1,9 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+-   package-ecosystem: github-actions
+    directory: /
+    schedule:
+        interval: monthly

.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

@@ -0,0 +1,20 @@
+---
+name: Codespell
+
+on:
+    push:
+        branches:
+        -   master
+    pull_request:
+        branches:
+        -   '*'
+
+jobs:
+    codespell:
+        name: Check for spelling errors
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Run codespell
+            uses: codespell-project/actions-codespell@master

.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/update_precommit_hooks.yml

@@ -0,0 +1,53 @@
+---
+name: Update precommit hooks
+
+
+on:
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#            ┌───────────── minute (0 - 59)
+#            │ ┌───────────── hour (0 - 23)
+#            │ │ ┌───────────── day of the month (1 - 31)
+#            │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+#            │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            * * * * *
+    schedule:
+    -   cron: 0 0 1 1,4,7,10 * # every 3 months
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    update_precommit_hooks:
+
+    # only run on upstream repo
+        if: github.repository_owner == 'neuropower'
+
+        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 pre-commit
+            run: pip install pre-commit
+        -   name: Update pre-commit hooks
+            run: pre-commit autoupdate
+        -   name: Create Pull Request
+            uses: peter-evans/create-pull-request@v6
+            with:
+                commit-message: pre-commit hooks auto-update
+                base: main
+                token: ${{ secrets.GITHUB_TOKEN }}
+                delete-branch: true
+                title: '[BOT] update pre-commit hooks'
+                body: done via this [GitHub Action](https://github.com/${{ github.repository_owner }}/neuropower/blob/master/.github/workflows/update_precommit_hooks.yml)

.pre-commit-config.yaml

@@ -0,0 +1,68 @@
+---
+# See https://pre-commit.com for more information
+# 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/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/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/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell
+        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/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.12.0
+    hooks:
+    -   id: pretty-format-toml
+        args: [--autofix, --indent, '4']
+
+-   repo: https://github.com/pyCQA/flake8
+    rev: 7.0.0
+    hooks:
+    -   id: flake8
+        args: [--config, .flake8, --verbose, neurodesign, examples]
+        additional_dependencies: [flake8-docstrings, flake8-use-fstring]

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2016 
+Copyright (c) 2016
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -17,5 +17,4 @@ The documentation of neurodesign is available at [ReadTheDocs](http://neurodesig
     |---- source            Folder with the source code of the python package
     |       |
     |       |---- media     Folder contains the logo of neurodesign, which is used
-                            in the reports.       
-
+                            in the reports.