[STY] format and lint code

.flake8

@@ -0,0 +1,40 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+--select = D,E,F,W
+docstring-convention = numpy
+max-line-length = 240
+# 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,
+    F821,
+    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/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/test.yml

@@ -1,88 +1,89 @@
+---
 name: Build and test
 
 on:
-  push:
-    branches:
-      - main
-    tags:
-      - "*"
-  pull_request:
-    branches:
-      - main
+    push:
+        branches:
+        -   main
+        tags:
+        -   '*'
+    pull_request:
+        branches:
+        -   main
   # Run weekly to avoid missing deprecations during low activity
-  schedule:
-    - cron: '0 0 * * 1'
+    schedule:
+    -   cron: 0 0 * * 1
   # Allow job to be triggered manually from GitHub interface
-  workflow_dispatch:
+    workflow_dispatch:
 
 defaults:
-  run:
-    shell: bash
+    run:
+        shell: bash
 
 # Force tox and pytest to use color
 env:
-  FORCE_COLOR: true
+    FORCE_COLOR: true
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
 
 permissions:
-  contents: read
+    contents: read
 
 jobs:
-  test:
+    test:
     # Check each OS, all supported Python, minimum versions and latest releases
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ['ubuntu-latest']
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        include:
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest]
+                python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+                include:
           # Basic dependencies only
-          - os: ubuntu-latest
-            python-version: 3.8
-            dependencies: 'min'
+                -   os: ubuntu-latest
+                    python-version: 3.8
+                    dependencies: min
 
-    env:
-      DEPENDS: ${{ matrix.dependencies }}
-      ARCH: ${{ !contains(fromJSON('["none", "min"]'), matrix.dependencies) && matrix.architecture }}
+        env:
+            DEPENDS: ${{ matrix.dependencies }}
+            ARCH: ${{ !contains(fromJSON('["none", "min"]'), matrix.dependencies) && matrix.architecture }}
 
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          fetch-depth: 0
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          architecture: ${{ matrix.architecture }}
-          allow-prereleases: true
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Install tox
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
-      - name: Show tox config
-        run: tox c
-      - name: Run tox
-        run: tox -v --exit-and-dump-after 1200
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+        -   name: Set up Python ${{ matrix.python-version }}
+            uses: actions/setup-python@v5
+            with:
+                python-version: ${{ matrix.python-version }}
+                architecture: ${{ matrix.architecture }}
+                allow-prereleases: true
+        -   name: Display Python version
+            run: python -c "import sys; print(sys.version)"
+        -   name: Install tox
+            run: |
+                python -m pip install --upgrade pip
+                python -m pip install tox tox-gh-actions
+        -   name: Show tox config
+            run: tox c
+        -   name: Run tox
+            run: tox -v --exit-and-dump-after 1200
 
-  publish:
-    runs-on: ubuntu-latest
-    environment: "Package deployment"
-    needs: [test]
-    permissions:
+    publish:
+        runs-on: ubuntu-latest
+        environment: Package deployment
+        needs: [test]
+        permissions:
       # Required for trusted publishing
-      id-token: write
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          fetch-depth: 0
-      - run: pipx run build
-      - uses: pypa/gh-action-pypi-publish@release/v1
+            id-token: write
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+        -   run: pipx run build
+        -   uses: pypa/gh-action-pypi-publish@release/v1

.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

@@ -1,19 +1,14 @@
 **/.DS_Store
+
 __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
+
+.vscode
+
+sample_data/
 
 # build related
 pydfc.egg-info
 build
-dist/
+dist/

.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: 24.2.0
+    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, HCP_resting_state_analysis, task_dFC]
+        additional_dependencies: [flake8-use-fstring]