Updated examples from cookiecutter-mdakit at 99b1fb9

.codecov.yml

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+# Codecov configuration to make it a bit less noisy
+coverage:
+  status:
+    patch: false
+    project:
+      default:
+        threshold: 50%
+comment:
+  layout: "header"
+  require_changes: false
+  branches: null
+  behavior: default
+  flags: null
+  paths: null
+ignore:
+  - "mdakit-Cookie/_version.py"

.gitattributes

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+mdakit-Cookie/_version.py export-subst

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+## Expected behavior ##
+
+<!-- A clear and concise description of what you want to do and what you think should happen. (Code to reproduce the behavior can be added below). -->
+
+
+## Actual behavior ##
+
+<!-- What happened instead. Add as much detail as you can. Include (copy and paste) stack traces and any output. -->
+
+
+## Code to reproduce the behavior ##
+
+<!-- Show us how to reproduce the failure. If you can, use trajectory files from the test data. Use the code snipped below as a starting point. -->
+
+``` python
+import mdakit-Cookie
+
+...
+
+```
+
+## Current environment ##
+
+- Which version are you using? (run `python -c "import mdakit-Cookie; print(mdakit-Cookie.__version__)"`)
+- Which version of Python (`python -V`)?
+- Which operating system?
+- What is the output of `pip list`?
+- If you use conda, what is the output of `conda list`?

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+## Is your feature request related to a problem? ##
+<!-- A clear and concise description of what the problem is. For example, I'm always frustrated when [...] -->
+
+
+## Describe the solution you'd like ##
+<!-- A description of what you want to happen. For example, I'd like to be able to do [...] -->
+
+
+## Describe alternatives you've considered ##
+<!-- A description of any alternative solutions or features you've considered or possible solutions that you've seen elsewhere. -->
+
+
+## Additional context ##
+<!-- Add any other context or screenshots about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

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+
+<!-- Does this PR fix an issue or relate to an existing discussion? Please link it below after "Fixes #" -->
+
+Fixes #
+
+Changes made in this Pull Request:
+<!-- Summarise changes made with dot points below -->
+ - 
+ - 
+
+
+PR Checklist
+------------
+ - [ ] Tests?
+ - [ ] Docs?
+ - [ ] CHANGELOG updated?
+ - [ ] Issue raised/referenced?

.github/workflows/gh-ci.yaml

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+name: GH Actions CI
+on:
+  push:
+    branches:
+      - "**" # main   -- replaced main to allow CI to run in example cookie repo
+  pull_request:
+    branches:
+      - "**" # main   -- replaced main to allow CI to run in example cookie repo
+  schedule:
+    # Weekly tests at midnight on Sundays run on main by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * 0"
+
+concurrency:
+  # Specific group naming so CI is only cancelled
+  # within same PR or on merge to main
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash  -l {0} 
+
+jobs:
+  main-tests:
+    if: "github.repository == 'other/mdakit-Cookie'"
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [ubuntu-latest, macOS-latest, windows-latest]
+          mdanalysis-version: ["latest", "develop"]
+          python-version: ["3.10", "3.11", "3.12"]
+          exclude:
+            # Entries here exclude particular combinations of the matrix
+            # Edit or remove as particular combinations come into or out of date
+            # Below we exclude runs with the latest release and Python 3.12
+            - mdanalysis-version: "latest"
+              python-version: "3.12"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build information
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+
+    # More info on options: https://github.com/conda-incubator/setup-miniconda
+    - name: Install conda dependencies
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/test_env.yaml
+        add-pip-as-python-dependency: true
+
+        channels: defaults
+
+        activate-environment: mdakit-Cookie-test
+        auto-update-conda: true
+        auto-activate-base: false
+        show-channel-urls: true
+
+
+    - name: Install MDAnalysis version
+      uses: MDAnalysis/install-mdanalysis@main
+      with:
+        version: ${{ matrix.mdanalysis-version }}
+        install-tests: false
+        installer:  pip 
+        shell: bash  -l {0} 
+
+    - name: Install package
+      run: |
+        python --version
+        python -m pip install .  --no-deps 
+
+    - name: Python information
+      run: |
+        which python
+        which pip
+        pip list
+
+        conda info
+        conda list
+
+
+    - name: Run tests
+      run: |
+        pytest -n 2 -v --cov=cookieKit --cov-report=xml --color=yes cookieKit/tests/
+
+    - name: codecov
+      if: github.repository == 'other/mdakit-Cookie' && github.event_name != 'schedule'
+      uses: codecov/codecov-action@v4
+      with:
+        file: coverage.xml
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+        verbose: True
+        # to upload coverage reports, set a secret called CODECOV_TOKEN
+        # in the repository settings
+        # (Obtain this from the Codecov website after setting up the repository there)
+        token: ${{ secrets.CODECOV_TOKEN }}
+        # To fail the CI if there's an error, keep this set to true
+        # If repository forks need to run CI, you may need to set this to false
+        # Forks can't access the CODECOV_TOKEN secret,
+        # and a failed upload registers as an error
+        fail_ci_if_error: true
+
+
+  pylint_check:
+    if: "github.repository == 'other/mdakit-Cookie'"
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install Pylint
+      run: |
+        which pip
+        which python
+        pip install pylint mdanalysis
+
+    - name: Run Pylint
+      env:
+        PYLINTRC: .pylintrc
+      run: |
+        pylint mdakit-Cookie
+
+
+  pypi_check:
+    if: "github.repository == 'other/mdakit-Cookie'"
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install dependencies
+      run: |
+        pip install pipx twine
+
+    - name: Build package
+      run: |
+        python -m pipx run build --sdist
+
+    - name: Check package build
+      run: |
+        DISTRIBUTION=$(ls -t1 dist/mdakit_cookie-*.tar.gz | head -n 1)
+        test -n "${DISTRIBUTION}" || { echo "no distribution dist/mdakit-Cookie-*.tar.gz found"; exit 1; }
+        echo "twine check $DISTRIBUTION"
+        twine check $DISTRIBUTION

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# VS Code
+.vscode/
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.DS_Store
+
+# poetry
+poetry.lock

.pre-commit-config.yaml

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+
+# To install the git pre-commit hook run:
+#   pre-commit install
+# To update the pre-commit hooks run:
+#   pre-commit install-hooks
+exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg)(/|$)'
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: master
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: debug-statements
+  - repo: https://github.com/timothycrosley/isort
+    rev: master
+    hooks:
+      - id: isort
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: master
+    hooks:
+      - id: flake8