[MAINT] update packaging and testing

.flake8

@@ -0,0 +1,18 @@
+[flake8]
+max-line-length = 110
+max-complexity = 10
+max_function_length = 105
+max_parameters_amount = 7
+max_returns_amount = 5
+count = True
+show-source = True
+statistics = True
+exclude =
+    *build
+    .git
+    __pycache__
+    tests/*
+    _version.py
+    docs/**
+per-file-ignores =
+    __init__.py: D104

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,97 +1,95 @@
+---
 name: Bug report
 
 # See the json schema to help you create / update this form
 # https://json.schemastore.org/github-issue-forms.json
 
 description: Fill in this template to report a bug
 
-title: "[BUG]"
+title: '[BUG]'
 
-labels: ["bug :bug:"]
+labels: ['bug :bug:']
 
 body:
 
-  - type: markdown
+-   type: markdown
     attributes:
-      value: |
-        Thanks for taking the time to fill out this bug report!
+        value: |
+            Thanks for taking the time to fill out this bug report!
 
-        To maximize chances for a quick fix make sure you know
-        [How to Report Bugs Effectively](https://www.chiark.greenend.org.uk/~sgtatham/bugs.html)
+            To maximize chances for a quick fix make sure you know
+            [How to Report Bugs Effectively](https://www.chiark.greenend.org.uk/~sgtatham/bugs.html)
 
-  - type: checkboxes
+-   type: checkboxes
     attributes:
-      label: Is there an existing issue for this?
-      description:
-        Please search to see if an issue already exists for the bug you
-        encountered.
-      options:
-        - label: I have searched the existing issues
-          required: true
-
-  - type: checkboxes
+        label: Is there an existing issue for this?
+        description: Please search to see if an issue already exists for the bug you encountered.
+        options:
+        -   label: I have searched the existing issues
+            required: true
+
+-   type: checkboxes
     attributes:
-      label: Operating system
-      description:
-        What operating system are you using?
-      options:
-        - label: Linux
-        - label: Mac
-        - label: Windows
-
-  - type: textarea
+        label: Operating system
+        description: What operating system are you using?
+        options:
+        -   label: Linux
+        -   label: Mac
+        -   label: Windows
+
+-   type: textarea
     attributes:
-      label: Operating system version
-      render: markdown
-      value: |
-        - Linux Ubuntu 18.04 "bionic beaver"
-        - Mac OS Version 12 "monterey"
+        label: Operating system version
+        render: markdown
+        value: |
+            - Linux Ubuntu 18.04 "bionic beaver"
+            - Mac OS Version 12 "monterey"
     validations:
-      required: true
+        required: true
 
-  - type: textarea
+-   type: textarea
     attributes:
-      label: bids2cite version
-      description: |
-        In the command line, try:
-          - `bids2cite --version`
+        label: bids2cite version
+        description: |
+            In the command line, try:
+              - `bids2cite --version`
     validations:
-      required: true
+        required: true
 
-  - type: textarea
+-   type: textarea
     attributes:
-      label: Expected Behavior
-      description: Describe what outcome you expected.
-      placeholder: Describe what outcome you expected.
+        label: Expected Behavior
+        description: Describe what outcome you expected.
+        placeholder: Describe what outcome you expected.
     validations:
-      required: false
+        required: false
 
-  - type: textarea
+-   type: textarea
     attributes:
-      label: Current Behavior
-      description: Describe what you got instead.
-      placeholder: Describe what you got instead
+        label: Current Behavior
+        description: Describe what you got instead.
+        placeholder: Describe what you got instead
     validations:
-      required: true
+        required: true
 
-  - type: textarea
+-   type: textarea
     attributes:
-      label: Error message
-      description: If possible paste below the error message you encountered.
+        label: Error message
+        description: If possible paste below the error message you encountered.
     validations:
-      required: false
-      value: |
-        ```matlab
-        % this is the error I got
+        required: false
+        value: |
+            ```matlab
+            % this is the error I got
 
-        ```
+            ```
 
-  - type: textarea
+-   type: textarea
     attributes:
-      label: Anything else?
-      description: |
-        Links? References? Anything that will give us more context about the issue you are encountering!
+        label: Anything else?
+        description: |
+            Links? References? Anything that will give us more context about the issue you are encountering!
 
-        Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
+            Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
     validations:
-      required: false
+        required: false

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,44 +1,43 @@
+---
 name: Feature request
 
 # See the json schema to help you create / update this form
 # https://json.schemastore.org/github-issue-forms.json
 
 description: Suggest an idea for this project
 
-title: "[ENH]: "
+title: '[ENH]: '
 
 body:
-  - type: checkboxes
+-   type: checkboxes
     attributes:
-      label: Is there an existing issue for this?
-      description:
-        Please search to see if an issue already exists for the feature you
-        want.
-      options:
-        - label: I have searched the existing issues
-          required: true
-
-  - type: textarea
+        label: Is there an existing issue for this?
+        description: Please search to see if an issue already exists for the feature you want.
+        options:
+        -   label: I have searched the existing issues
+            required: true
+
+-   type: textarea
     attributes:
-      label: New feature
-      description: You think / need this code to do...
-      render: markdown
-      placeholder: Insert here your cool idea.
+        label: New feature
+        description: You think / need this code to do...
+        render: markdown
+        placeholder: Insert here your cool idea.
     validations:
-      required: false
+        required: false
 
-  - type: textarea
+-   type: textarea
     attributes:
-      label: Unclear documentation
-      description: |
-        Something is missing / unclear about **X**.
+        label: Unclear documentation
+        description: |
+            Something is missing / unclear about **X**.
 
-        You are confused about how to do **Y**.
+            You are confused about how to do **Y**.
 
-        It is not clear how / why the code does **Z**.
+            It is not clear how / why the code does **Z**.
 
-        That means that we can improve the code or the documentation.
-      render: markdown
-      placeholder: Tell us more.
+            That means that we can improve the code or the documentation.
+        render: markdown
+        placeholder: Tell us more.
     validations:
-      required: false
+        required: false

.github/dependabot.yml

@@ -1,14 +1,14 @@
-
+---
 # 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: '/'
+-   package-ecosystem: github-actions
+    directory: /
     schedule:
-      interval: 'monthly'
+        interval: monthly
 
-  - package-ecosystem: 'gitsubmodule'
-    directory: '/'
+-   package-ecosystem: gitsubmodule
+    directory: /
     schedule:
-      interval: 'monthly'
+        interval: monthly

.github/workflows/check_md_links.yml

@@ -1,22 +1,22 @@
+---
 name: Check Markdown links
 
 # checking for any dead links in markdown files
 
 on:
-  push:
-    branches:
-      - main
-      - dev
-  pull_request:
-    branches: ['*']
+    push:
+        branches:
+        -   main
+        -   dev
+    pull_request:
+        branches: ['*']
 
 jobs:
-  markdown-link-check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@master
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
-      with:
-        use-quiet-mode: 'yes'
-        use-verbose-mode: 'yes'
-        # config-file: '.github/workflows/mlc_config.json'
+    markdown-link-check:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@master
+        -   uses: gaurav-nelson/github-action-markdown-link-check@v1
+            with:
+                use-quiet-mode: yes
+                use-verbose-mode: yes