p5rem

Remote HDF5/NetCDF access over SSH stdio, using a small remote pyfive-based server and a local proxy API.

Usage

For a minimal non-GUI example that defines the remote host and Python command directly in the script, see:

• examples/read_remote_slice.py
• doc/user-guide.md

Testing

The test suite is split into two groups:

• Default tests: pure unit and loopback tests that do not require a real SSH target.
• Integration tests: real SSH-backed tests marked with @pytest.mark.integration.

The integration marker exists so the normal test run can stay fast and self-contained, while the real SSH path is still exercised explicitly when credentials and a remote test directory are available.

Default test run

/Users/bnl28/miniforge3/envs/work26/bin/python -m pytest -m "not integration"
# or
make test

Real SSH integration run

Create a local environment override file such as tests/testenv.sh:

#!/usr/bin/env sh

export P5REM_SSH_HOST_ALIAS="xfer1"
export P5REM_SSH_PYTHON="conda run -n jas26 python"
export P5REM_SSH_LOGIN_SHELL="1"
export P5REM_SSH_REMOTE_DIR="p5test"

Then run:

source tests/testenv.sh
/Users/bnl28/miniforge3/envs/work26/bin/python -m pytest -m integration
# or
make test-integration

Notes:

• P5REM_SSH_PYTHON may be set to conda run -n <env> python; p5rem automatically adds --no-capture-output when bootstrapping the remote server so the SSH stdio protocol remains binary-clean.
• P5REM_SSH_LOGIN_SHELL=1 wraps the remote command with bash -lc, which is useful on HPC systems where conda is only initialized in login-shell startup files.
• The remote round-trip test reuses the same file-comparison assertions as the loopback tests.

Standalone acid test

There is also a CLI wrapper for the same shared SSH round-trip assertions:

source tests/testenv.sh
/Users/bnl28/miniforge3/envs/work26/bin/python tests/acid_test.py
# or
make acid-test

This is useful for manual debugging, but the canonical automated SSH test path is the pytest -m integration run above.