amberflow 0.8.0

Python workflow to run Free Energy calculations

• Free software: MIT license

• Documentation: not yet publicly available.

Documentation

If you just want to check the documentation, it’s currentl being hosted on chardonnay. Just forward it using ssh:

ssh -L 8888:127.0.0.1:8000 [e-mail]

And then go to localhost:8888 on your browser.

Install

Clone this repo:

git clone [e-mail]:/pgbarletta/amberflow

Change dir into the project and create conda environment:

mamba env create -f conda/dev_environment.yaml

Install this project:

git clone [e-mail]:/pgbarletta/amberflow

Build it in editable mode using pip:

pip install -e .

Build the documentation:

sphinx-build -b html docs/source/ docs/build/html/

Access the docs locally on your browser:

PATH/amberflow/docs/build/html/index.html

Development

To release a new version, just tag the main brand and push:

git tag 0.2.8
git push --tags

Testing

Run tests from the amberflow/ worktree root.

Run the default validation steps directly:

pytest -n 12

Run a single test:

pytest -n 12 tests/integration/test_build_edges_pipeline.py::TestBuildEdgesIntegration::test_antechamber_build_edges_trunctyk2

Run all integration tests:

TEST_AF_INTEGRATION=1 pytest -n 12 tests/integration

Run all campaign tests:

TEST_AF_CAMPAIGN=1 pytest -n 12 tests/campaign

Keep generated test files for inspection (works with any test selection):

pytest tests/foo.py::test_bar --keep=./my_temp_dir
pytest -n 12 --keep=./my_temp_dir
TEST_AF_INTEGRATION=1 pytest -n 12 tests/integration --keep=./my_temp_dir

Each test’s workspace is moved into <dir>/<sanitized_test_name>/ after the session finishes. If the directory does not exist, it is created.

For sequential debugging, reduce the worker count:

pytest -n 1