feat: add activate.sh + switch submit to PyAuto + PYTHONPATH model#35
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PyAuto* libraries are source trees on the HPC at /mnt/ral/jnightin/PyAuto/
that HPCPullPyAuto keeps current. Editable / non-editable pip installs into
a venv just duplicate that — and lock you to whatever was on main when you
last reinstalled. The correct pattern, already used by z_projects/euclid
and autolens_assistant, is:
- venv (PyAuto) carries only third-party deps (jax, nautilus, blackjax,
nss, fastprogress, jax_zero_contour, anesthetic, numpy, ...).
- PYTHONPATH points at the canonical source trees; import autolens etc.
resolves there, picking up whatever HPCPullPyAuto last pulled.
Adds autolens_profiling/activate.sh in the same shape, and switches the
A100 search submit script to ``source $AP_ROOT/activate.sh`` instead of
sourcing PyAutoNSS's venv directly. PyAutoNSS is no longer a hard
dependency for these submits — PyAuto's site-packages already carry
nautilus, the handley-lab blackjax fork, nss, fastprogress, and
jax_zero_contour (installed today as the last missing pieces), and
PYTHONPATH gives us current autofit/autolens/autogalaxy/autoarray/autoconf.
Future updates are a one-liner: ``HPCPullPyAuto``. No pip install of
PyAuto* into the venv, ever.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Adopts the project-activate.sh pattern already used by `z_projects/euclid` and `autolens_assistant`. The pip side handles only third-party deps; PyAuto* libraries resolve via PYTHONPATH from the canonical source trees at `/mnt/ral/jnightin/PyAuto/` that `HPCPullPyAuto` keeps current.
After this PR:
```bash
HPCPullPyAuto # source trees update
sbatch submit_imaging_mge_a100_hst_fp64 # submit sources $AP_ROOT/activate.sh
# activate.sh: PyAuto venv + PYTHONPATH
# imports resolve to current main
```
No pip install of PyAuto* into the venv, ever.
PyAutoNSS is no longer a hard dependency. PyAuto venv already carries everything the submits need (nautilus, blackjax fork, nss, fastprogress, jax_zero_contour, jax 0.4.38).
Test plan
🤖 Generated with Claude Code