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@summeraz

Andrew,

It was good meeting you at FOMMS a few weeks ago. I have finally gotten around to trying to implement mbuild and foyer. I successfully installed all the needed software to run the "Individual Tutorial Overview", except for visualize. I tried "pip install visualize" and searching for it online, but to no avail. Where can I find visualize? For now, I have just commented out everywhere that visualize is found in the jupyter notebook, but that is obviously not the ideal solution.

Thanks

Rich

we could use pytest plugin nbval to check our notebooks. Here is an actions yml from our notebook tutorials repo:

name: Test PR and Image
on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]
jobs:
  test:
    runs-on: ubuntu-latest
    container: 
      image: cmelab/notebook-tutorials
    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
    - uses: actions/checkout@v1
    - name: test notebooks
      shell: bash -l {0}
      run: python -m pytest -v --nbval-lax

mbuild-overview.ipynb contains AlkaneMonolayer which has since been moved to a separate repo mbuild-examples.

There are several warnings raised from pandas that appear throughout the tutorials, looking like:

/anaconda3/envs/mosdef-binder/lib/python3.5/site-packages/pandas/io/parsers.py:2230: FutureWarning: split() requires a non-empty pattern match.
  yield pat.split(line.strip())

These can easily be filtered out by adding warnings.filterwarnings("ignore", FutureWarning) at the top of each notebook.

In test_atomtyping the force field file the user has edited is found by the following line: FORCEFIELD_FILES = glob('*.xml'). Because mff_test1-MASTER.xml also exists in this directory, foyer attempts to load in both force field xmls. As a result, the test fails because multiple definitions are found for the same atom type.