From 8d22838f11ba1a73e505337eff71f8aaf8f5e1e5 Mon Sep 17 00:00:00 2001
From: Jammy2211 <JNightingale2211@gmail.com>
Date: Thu, 28 May 2026 17:17:50 +0100
Subject: [PATCH] feat: add activate.sh + switch submit to PyAuto + PYTHONPATH
 model
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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>
---
 activate.sh                                   | 26 +++++++++++++++++++
 .../submit_imaging_mge_a100_hst_fp64          |  2 +-
 2 files changed, 27 insertions(+), 1 deletion(-)
 create mode 100755 activate.sh

diff --git a/activate.sh b/activate.sh
new file mode 100755
index 0000000..d918013
--- /dev/null
+++ b/activate.sh
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+# Activate the shared PyAuto venv and point PYTHONPATH at the canonical
+# PyAuto* source checkouts on the HPC.
+#
+# Mirrors the pattern used by z_projects/euclid/activate.sh and
+# autolens_assistant/activate.sh: pip handles only third-party deps in
+# the venv, while the five PyAuto* libraries are resolved via PYTHONPATH
+# directly from /mnt/ral/jnightin/PyAuto/<repo>. ``HPCPullPyAuto`` then
+# becomes the only mechanism needed to keep PyAuto* current — no pip
+# install of PyAuto* into the venv ever.
+#
+# Usage (inside a SLURM submit or interactive shell):
+#
+#     source /mnt/ral/jnightin/autolens_profiling/activate.sh
+#     python3 searches/nautilus/imaging/mge.py ...
+
+BASE=/mnt/ral/jnightin/PyAuto
+
+source "$BASE/PyAuto/bin/activate"
+
+export PYTHONPATH=$BASE:\
+$BASE/PyAutoConf:\
+$BASE/PyAutoFit:\
+$BASE/PyAutoArray:\
+$BASE/PyAutoGalaxy:\
+$BASE/PyAutoLens
diff --git a/hpc/batch_gpu/submit_imaging_mge_a100_hst_fp64 b/hpc/batch_gpu/submit_imaging_mge_a100_hst_fp64
index 5f0f3ee..babf3f4 100755
--- a/hpc/batch_gpu/submit_imaging_mge_a100_hst_fp64
+++ b/hpc/batch_gpu/submit_imaging_mge_a100_hst_fp64
@@ -22,7 +22,7 @@
 #SBATCH --mail-user=james.w.nightingale@durham.ac.uk
 
 export AP_ROOT=/mnt/ral/jnightin/autolens_profiling
-source /mnt/ral/jnightin/PyAutoNSS/PyAutoNSS/bin/activate
+source $AP_ROOT/activate.sh
 
 export JAX_PLATFORM_NAME=cuda
 export JAX_PLATFORMS=cuda,cpu