Add CI and mybinder to Example Notebooks

.binder/environment.yml

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+name: openfe-notebooks
+channels:
+  - jaimergp/label/unsupported-cudatoolkit-shim
+  - conda-forge
+dependencies:
+  # setup
+  - openmm
+  - openmmforcefields
+  - openff-toolkit
+  # CI
+  - pytest
+  - pytest-xdist
+  - nbval

.github/workflows/CI.yml

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+name: full_tests
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+  schedule:
+    # nightly tests, 2 am
+    - cron: "0 2 * * *"
+
+concurrency:
+  # Probably overly cautious group naming.
+  # Commits to develop/master will cancel each other, but PRs will only cancel
+  # commits within the same PR
+  group: "${{ github.ref }}-${{ github.head_ref }}"
+  cancel-in-progress: true
+
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-10.15, macos-11]
+        python-version: ["3.9",]
+
+    steps:
+    - uses: actions/checkout@v2.4.0
+
+    - uses: conda-incubator/setup-miniconda@v2.1.1
+      with:
+        python-version: "${{ matrix.python-version }}"
+        environment-file: .binder/environment.yml
+        activate-environment: test
+        auto-activate-base: false
+        mamba-version: "*"
+        miniforge-version: latest
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        channel-priority: true
+
+    - name: Additional info about the build
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - name: Environment Information
+      run: |
+        conda info
+        conda list
+
+    - name: Run example notebooks
+      run: |
+        python -m pytest -v setup/ --nbval-lax -n auto --dist loadscope

.github/workflows/binder-badge.yaml

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+#./.github/workflows/binder-badge.yaml
+name: Binder Badge
+on: 
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  binder:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+    - name: comment on PR with Binder link
+      uses: actions/github-script@v3
+      with:
+        github-token: ${{secrets.GITHUB_TOKEN}}
+        script: |
+          var PR_HEAD_USERREPO = process.env.PR_HEAD_USERREPO;
+          var PR_HEAD_REF = process.env.PR_HEAD_REF;
+          github.issues.createComment({
+            issue_number: context.issue.number,
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            body: `[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/${PR_HEAD_USERREPO}/${PR_HEAD_REF}) :point_left: Launch a binder notebook on branch _${PR_HEAD_USERREPO}/${PR_HEAD_REF}_`
+          })
+      env:
+        PR_HEAD_REF: ${{ github.event.pull_request.head.ref }}
+        PR_HEAD_USERREPO: ${{ github.event.pull_request.head.repo.full_name }}

.github/workflows/build-image.yml

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+name: Build container image
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: checkout files in repo
+      uses: actions/checkout@main
+
+    - name: update jupyter dependencies with repo2docker
+      uses: jupyterhub/repo2docker-action@master
+      with: # make sure username & password/token matches your registry
+        DOCKER_USERNAME: ${{ secrets.QUAY_USERNAME }}
+        DOCKER_PASSWORD: ${{ secrets.QUAY_PASSWORD }}
+        DOCKER_REGISTRY: "quay.io"
+        IMAGE_NAME: "mikemhenry/openfe-notebooks"
+        MYBINDERORG_CACHE: true

.gitignore

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+# Files created by notebooks
+
+*.gro
+*.top
+
+# Created by https://www.toptal.com/developers/gitignore/api/osx,python,jupyternotebooks,windows,linux
+# Edit at https://www.toptal.com/developers/gitignore?templates=osx,python,jupyternotebooks,windows,linux
+
+### JupyterNotebooks ###
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### OSX ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+
+# IPython
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.toptal.com/developers/gitignore/api/osx,python,jupyternotebooks,windows,linux

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+ci:
+  autoupdate_schedule: quarterly
+
+files: (^notebooks)
+repos:
+  - repo: https://github.com/psf/black
+    rev: 21.12b0
+    hooks:
+      - id: black
+  - repo: https://github.com/psf/black
+    rev: 21.12b0
+    hooks:
+      - id: black-jupyter

README.md

@@ -0,0 +1,7 @@
+[![full_tests](https://github.com/mikemhenry/openfe-notebooks/actions/workflows/CI.yml/badge.svg)](https://github.com/mikemhenry/openfe-notebooks/actions/workflows/CI.yml)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/mikemhenry/openfe-notebooks/main.svg)](https://results.pre-commit.ci/latest/github/mikemhenry/openfe-notebooks/main)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mikemhenry/openfe-notebooks/HEAD)
+
+# OpenFE Notebooks
+
+Collection of notebooks for the Open FreeEnergy project.