apbs-binary 3.4.1.1

Install apbs with pip

pip install apbs-binary (Unofficial binary distribution of APBS)

Install and use APBS with ease in Python.

pip install apbs-binary

from apbs_binary import run_apbs, popen_apbs, run_multivalue, popen_multivalue

run_apbs("--help")  # like subprocess.run(["apbs", "-h"])
popen_apbs("--help")  # like subprocess.Popen(["apbs", "-h"])

# For no-argument case, pass an empty string
run_apbs("")  # like subprocess.run(["apbs"])

# Pass a list of arguments
run_apbs(["-Trim", "input.pdb"])

# Run multivalue
run_multivalue(...)
popen_multivalue(...)

The other tools are also available. Use as apbs_binary.run_analysis("--help") for example.

Supported platforms:

• Linux x86_64 (Ubuntu 20.04 +)
• MacOS x86_64 (11.6+), arm64 (12.0+)

[!NOTE] Installing the package does NOT put the binary in $PATH.
If you need to directly execute the binary, you can execute apbs_binary.APBS_BIN_PATH on Linux. For macOS, the environment variable DYLD_LIBRARY_PATH must be set to apbs_binary.LIB_DIR.

👨‍💻️ Maintenance Notes

Releasing a new version with CI (recommended)

Go to Github Actions and run the Build and Release workflow.

Version rule:

3.4.1.2:

• 3.4.1 is the APBS version
• the last digit (.2) is the patch/build number. It increases as we rebuild the wheels with different configurations or update the python API.

Running locally

This section describes how it works.

To run it locally, first install the dependencies:

pip install uv --user --break-system-packages
uv tool install wheel
uv tool install build
uv tool install huggingface_hub

# Mac
brew install gnu-sed

Download the built binaries into data/:

huggingface-cli download --repo-type dataset --local-dir data Deargen/py-apbs-binary

Build four wheels on all platforms. Basically it will put the binaries in the src/apbs_binary/bin/ folder and then build the wheels in a temp directory, outputting the wheels to dist/.

# first arg: APBS version to find in `data/` (i.e. data/apbs-3.4.1/APBS-3.4.1.Linux)
# second arg: wheel version
bash build_python.sh 3.4.1 3.4.1.2

Test the wheel

uv venv
source .venv/bin/activate
uv pip install -r requirements_test.txt
uv pip install build_python/dist/*.whl    # choose the wheel for your platform only.
pytest

Notes

• The official 3.4.1 binary is not static and depends on python39.dll, libpython3.9.so.1.0, etc. on Windows and Mac (Linux seems fine)
• brew install brewsci/bio/apbs is not static either and depends on libmetis.dylib.
• In this repository, we use the brew-created binary for macOS and the official binary for Linux. We don't support Windows yet.