set up config for precommit, black, flake8, codespell, isort and run

.flake8

@@ -0,0 +1,42 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+--select = D,E,F,W
+docstring-convention = numpy
+max-line-length = 250
+# For PEP8 error codes see
+# http://pep8.readthedocs.org/en/latest/intro.html#error-codes
+	# D100-D104: missing docstring
+	# D105: missing docstring in magic method
+	# D107: missing docstring in __init__
+	# W504: line break after binary operator
+per-file-ignores =
+	**/__init__.py: D104
+ignore =
+    BLK100,
+    D105
+    D107,
+    E402,
+    E266,
+    E721,
+    E731,
+    E713,
+    E714,
+    E741,
+    F403,
+    F405,
+    E401,
+    F401,
+    F811,
+    F841,
+    F821,
+    FS001
+    W503,
+    W504,
+    W605,
+# 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/run_precommit.yml

@@ -0,0 +1,15 @@
+---
+name: pre-commit
+
+on:
+    pull_request:
+    push:
+        branches: [main]
+
+jobs:
+    pre-commit:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: actions/setup-python@v5
+        -   uses: pre-commit/[email protected]

.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 # every monday
+
+  # 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 == 'SIMEXP'
+
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout repo
+            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@v5
+            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 }}/giga_connectome/blob/main/.github/workflows/update_precommit_hooks.yml)

.gitignore

@@ -2,14 +2,4 @@
 __pycache__
 *.pyc
 *.cpython
-sample_data/sub-0001_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
-sample_data/sub-0001_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
-sample_data/sub-0002_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
-sample_data/sub-0002_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
-sample_data/sub-0003_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
-sample_data/sub-0003_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
-sample_data/sub-0004_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
-sample_data/sub-0004_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
-sample_data/sub-0005_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
-sample_data/sub-0005_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
-
+sample_data/

.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+---
+# 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/ikamensh/flynt/
+    rev: 1.0.1
+    hooks:
+    -   id: flynt
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: [--profile, black]
+
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.12.1
+    hooks:
+    -   id: black-jupyter
+        args: [--config, pyproject.toml]
+
+-   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, pydfc, rest_dFC, task_dFC]
+        additional_dependencies: [flake8-use-fstring]

README.rst

@@ -1,6 +1,6 @@
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10211966.svg
     :target: https://doi.org/10.5281/zenodo.10211966
-    
+
 pydfc
 =======
 An implementation of several well-known dynamic Functional Connectivity (dFC) assessment methods.
@@ -16,4 +16,4 @@ The ``multi_analysis_demo.ipynb`` illustrates how to use the ``pydfc`` toolbox t
 
 For more details about the implemented methods and the comparison analysis see `our paper <https://www.biorxiv.org/content/10.1101/2023.07.13.548883v2>`_.
 
-  * Torabi M, Mitsis GD, Poline JB. On the variability of dynamic functional connectivity assessment methods. bioRxiv. 2023:2023-07. 
+  * Torabi M, Mitsis GD, Poline JB. On the variability of dynamic functional connectivity assessment methods. bioRxiv. 2023:2023-07.