Merge pull request #2 from sef43/cookiecutter

Switch to cookiecutter template

.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:
+  - "openmm-mdanalysis-reporter/_version.py"

.gitattributes

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+openmm-mdanalysis-reporter/_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 openmm-mdanalysis-reporter
+
+...
+
+```
+
+## Current environment ##
+
+- Which version are you using? (run `python -c "import openmm-mdanalysis-reporter; print(openmm-mdanalysis-reporter.__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
+  pull_request:
+    branches:
+      - main
+  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:
+  environment-config:
+    runs-on: ubuntu-latest
+    outputs:
+      stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
+      python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }}
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - id: get-compatible-python
+        uses: MDAnalysis/mdanalysis-compatible-python@main
+
+  main-tests:
+    if: "github.repository == 'sef43/openmm-mdanalysis-reporter'"
+    needs: environment-config
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [macOS-latest, ubuntu-latest]
+          python-version: ${{ fromJSON(needs.environment-config.outputs.python-matrix) }}
+          mdanalysis-version: ["latest", "develop"]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - 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@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/test_env.yaml
+        add-pip-as-python-dependency: true
+        architecture: x64
+
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        channels: conda-forge, defaults
+
+        activate-environment: openmm-mdanalysis-reporter-test
+        auto-update-conda: true
+        auto-activate-base: false
+        show-channel-urls: true
+
+
+    - name: Install MDAnalysis version
+      uses: MDAnalysis/install-mdanalysis@main
+      with:
+        version: ${{ matrix.mdanalysis-version }}
+        install-tests: false
+        installer:  mamba 
+        shell: bash  -l {0} 
+
+    - name: Install package
+      run: |
+        python --version
+        python -m pip install .  --no-deps 
+
+    - name: Python information
+      run: |
+        which python
+        which pip
+        pip list
+
+        conda info
+        conda list
+
+
+    - name: Run tests
+      run: |
+        pytest -n 2 -v --cov=mdareporter --cov-report=xml --color=yes mdareporter/tests/
+
+    - name: codecov
+      if: github.repository == 'sef43/openmm-mdanalysis-reporter' && github.event_name != 'schedule'
+      uses: codecov/codecov-action@v3
+      with:
+        file: coverage.xml
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+        verbose: True
+
+
+  pylint_check:
+    if: "github.repository == 'sef43/openmm-mdanalysis-reporter'"
+    needs: environment-config
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+
+    - name: Install Pylint
+      run: |
+        which pip
+        which python
+        pip install pylint mdanalysis
+
+    - name: Run Pylint
+      env:
+        PYLINTRC: .pylintrc
+      run: |
+        pylint openmm-mdanalysis-reporter
+
+
+  # pypi_check:
+  #   if: "github.repository == 'sef43/openmm-mdanalysis-reporter'"
+  #   needs: environment-config
+  #   runs-on: ubuntu-latest
+
+  #   steps:
+  #   - uses: actions/checkout@v3
+
+  #   - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
+  #     uses: actions/setup-python@v4
+  #     with:
+  #       python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+
+  #   - name: Install dependencies
+  #     run: |
+  #       pip install setuptools cython numpy twine
+
+  #   - name: Build package
+  #     run: |
+  #       python setup.py sdist
+
+  #   - name: Check package build
+  #     run: |
+  #       DISTRIBUTION=$(ls -t1 dist/mdareporter-*.tar.gz | head -n 1)
+  #       test -n "${DISTRIBUTION}" || { echo "no distribution dist/mdareporter-*.tar.gz found"; exit 1; }
+  #       echo "twine check $DISTRIBUTION"
+  #       twine check $DISTRIBUTION