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Instructions for setting up a development environment

For Coding

If using Linux with Intel processors, you can skip the conda step and directly to Setting ACPYPE. Otherwise:

Setting conda

For Linux (Ubuntu 20 recommended) and macOS. Anyway, CONDA is strongly recommended. Also recommended is GPG key, so do accordingly in GitHub.

curl -sSL https://install.python-poetry.org | python3 -

conda create -n acpype python=3.9 ambertools openbabel ocl-icd-system ipython gromacs=2019.1 -y
# ocl-icd-system: case you have GPU

conda activate acpype

Setting ACPYPE

git clone https://github.com/alanwilter/acpype.git

cd acpype

poetry install

pre-commit install

pre-commit run -a

sys=$(perl -e '`uname` eq "Darwin\n" ? print "macos" : print "linux"')
cp ./acpype/amber_${sys}/bin/charmmgen $(dirname $(which antechamber))

git config user.email _email_ # as seen in 'gpg --list-secret-keys --keyid-format=long'

git config user.signingkey _singing_key_ # as seen in 'gpg --list-secret-keys --keyid-format=long'

git config commit.gpgsign true

pytest --cov=tests --cov=acpype --cov-report=term-missing:skip-covered --cov-report=xml

If using VSCode:

  • Enable enableCommitSigning in settings.json (Workspace recommended):

    "git.enableCommitSigning": true,

  • Another VSCode nuisance, if using its graphic buttons for commit etc.: its environment won't necessarily recognise the dependencies installed via poetry under conda environment named acpype (unless you have started VSCode from folder repository with command code .). To avoid troubles do:

    conda deactivate
poetry install # it will create its own virtualenv

    You could use this poetry virtualenv as the Python Interpreter for VSCode, however ambertools, gromacs and openbabel won't be available (unless you've had installed them system wide by other means rather than conda). To avoid further troubles, go back to conda activate acpype and remember to do the instructions above if you add new dependencies to the project via poetry.

For Documenting

Using Sphinx with theme from pip install sphinx-rtd-theme.

Online documentation provided by Read the Docs.

To test it locally:

cd docs/
make clean
make html

Then open _build/html/index.html in a browser.