refactor: separate PYAUTOFIT_TEST_MODE into distinct PYAUTO_* env vars

[Jammy2211]

Overview

PYAUTOFIT_TEST_MODE has become a catch-all that controls sampler speedup, visualization, fit I/O, and validation checks. This task separates it into distinct, purpose-specific environment variables under a unified PYAUTO_* prefix. Also renames PYAUTOARRAY_OUTPUT_MODE → PYAUTO_OUTPUT_MODE and PYAUTO_WORKSPACE_SMALL_DATASETS → PYAUTO_SMALL_DATASETS.

Plan

• Add new env var accessor functions to PyAutoConf test_mode.py (skip_fit_output, skip_visualization, skip_checks)
• Rename PYAUTOFIT_TEST_MODE → PYAUTO_TEST_MODE (sampler-only, levels 0-3)
• Update every call site in PyAutoFit, PyAutoArray, PyAutoGalaxy, and PyAutoLens to use the correct new function
• Rename PYAUTOARRAY_OUTPUT_MODE → PYAUTO_OUTPUT_MODE and PYAUTO_WORKSPACE_SMALL_DATASETS → PYAUTO_SMALL_DATASETS
• Update all workspace env_vars.yaml files and shell scripts to set the new variables explicitly
• Update CLAUDE.md documentation across repos

Detailed implementation plan

Affected Repositories

• PyAutoConf (primary — defines env var functions)
• PyAutoFit (most call sites)
• PyAutoArray (hilbert checks, output_mode rename, small_datasets rename)
• PyAutoGalaxy (small_datasets rename)
• PyAutoLens (position checks, visualization)
• autofit_workspace (env_vars.yaml, run_scripts.sh)
• autogalaxy_workspace (env_vars.yaml, run_all_scripts.sh)
• autolens_workspace (env_vars.yaml, run_all_scripts.sh)

Work Classification

Library (then workspace follow-up)

Branch Survey

Repository	Current Branch	Dirty?
PyAutoConf	main	clean
PyAutoFit	main	clean
PyAutoArray	main	clean
PyAutoGalaxy	main	clean
PyAutoLens	main	clean
autofit_workspace	main	dirty (datasets)
autogalaxy_workspace	main	dirty (datasets)
autolens_workspace	main	dirty (datasets)

Suggested branch: feature/test-mode-separate
Worktree root: ~/Code/PyAutoLabs-wt/test-mode-separate/

New Environment Variables

New env var	Replaces	Type	What it controls
PYAUTO_TEST_MODE	PYAUTOFIT_TEST_MODE	int 0-3	Sampler speedup only
PYAUTO_SKIP_FIT_OUTPUT	(was in test_mode)	bool	Pre/post-fit I/O, VRAM, result text, likelihood check
PYAUTO_SKIP_VISUALIZATION	(was in test_mode)	bool	Fit visualization and plotting
PYAUTO_SKIP_CHECKS	(was in test_mode)	bool	Mesh validation, position resampling, weight thresholds
PYAUTO_OUTPUT_MODE	PYAUTOARRAY_OUTPUT_MODE	bool	Save all plots as numbered PNGs
PYAUTO_SMALL_DATASETS	PYAUTO_WORKSPACE_SMALL_DATASETS	bool	Cap grids to 15x15

Implementation Steps

Step 1: PyAutoConf — extend test_mode.py

Add new functions alongside existing test_mode_level() / is_test_mode():

• skip_fit_output() → reads PYAUTO_SKIP_FIT_OUTPUT
• skip_visualization() → reads PYAUTO_SKIP_VISUALIZATION
• skip_checks() → reads PYAUTO_SKIP_CHECKS

Rename env var from PYAUTOFIT_TEST_MODE to PYAUTO_TEST_MODE.

Export all new functions from autoconf/__init__.py.

Step 2: PyAutoFit — update call sites

Sampler speedup (keep test_mode_level() / is_test_mode()):

• non_linear/initializer.py:65 — is_test_mode()
• non_linear/search/abstract_search.py:668-674 — test_mode_level() >= 2
• non_linear/search/abstract_search.py:829-874 — _fit_bypass_test_mode()
• non_linear/search/mcmc/emcee/search.py:270-284 — is_test_mode()
• non_linear/search/mcmc/zeus/search.py:289-304 — is_test_mode()
• non_linear/search/mcmc/auto_correlations.py:52-53 — is_test_mode()

Change to skip_fit_output():

• non_linear/search/abstract_search.py:500-518 — pre-fit output
• non_linear/search/abstract_search.py:530-537 — post-fit output
• non_linear/analysis/analysis.py:331-334 — print_vram_use
• non_linear/fitness.py:459-461 — check_likelihood_function
• text/text_util.py:60-61 — model_text_from

Change to skip_visualization():

• non_linear/analysis/visualize.py:44-45 — should_visualize
• non_linear/plot/plot_util.py:16-18 — skip_in_test_mode decorator

Change to skip_checks():

• non_linear/samples/samples.py:382-383 — weight threshold

Step 3: PyAutoArray — update call sites + renames

Change to skip_checks():

• inversion/mesh/image_mesh/hilbert.py:334-335 — check_adapt_pixelisation
• inversion/mesh/image_mesh/hilbert.py:401-402 — check_adapt_background_pixels

Rename PYAUTOARRAY_OUTPUT_MODE → PYAUTO_OUTPUT_MODE:

• plot/output.py:196,225
• plot/utils.py:308

Rename PYAUTO_WORKSPACE_SMALL_DATASETS → PYAUTO_SMALL_DATASETS:

• structures/grids/uniform_2d.py:174,493
• mask/mask_2d.py:363
• operators/over_sampling/over_sample_util.py:272
• util/dataset_util.py:20

Step 4: PyAutoGalaxy — renames

Rename PYAUTO_WORKSPACE_SMALL_DATASETS → PYAUTO_SMALL_DATASETS:

• autogalaxy/analysis/model_util.py:93

Step 5: PyAutoLens — update call sites

Change to skip_checks():

• autolens/analysis/result.py:307-308 — position resampling
• autolens/analysis/analysis/dataset.py:113-114 — inversion position exception

Change to skip_visualization():

• autolens/quantity/model/visualizer.py:43-44

Step 6: Workspace env_vars.yaml and shell scripts

Update all env_vars.yaml files to set all new vars explicitly:

PYAUTO_TEST_MODE: "2"
PYAUTO_SKIP_FIT_OUTPUT: "1"
PYAUTO_SKIP_VISUALIZATION: "1"
PYAUTO_SKIP_CHECKS: "1"
PYAUTO_SMALL_DATASETS: "1"

Update run_scripts.sh / run_all_scripts.sh to export all new vars.

Update any unset: overrides that referenced old names.

Step 7: Update CLAUDE.md and documentation

Update env var references in CLAUDE.md across all repos.

Key Files

• PyAutoConf/autoconf/test_mode.py — central definition
• PyAutoConf/autoconf/__init__.py — exports
• PyAutoFit/autofit/non_linear/search/abstract_search.py — most call sites
• PyAutoArray/autoarray/plot/output.py — output_mode rename
• All workspace config/build/env_vars.yaml files

Original Prompt

Click to expand starting prompt

PYAUTOFIT_TEST_MODE has become a bit of a catch all term for things I dont want to run when testing,
it incldues disable some visualization and posiition resmapling in autolens as opposed to just
making the sampler run faster.

Furthermore, there is also PYAUTOARRAY_OUTPUT_MODE which outputs images to hard disk, which si use.

Can you look at all PYAUTOFIT_TEST_MODE clauses and work out which are not doing a sampler speed up.
Can you then suggest names for us to use for them all.

I also want us to move to environment variables just being PYAUTO, so PYAUTO_TEST_MODE, PYAUTO_OUTPUT_MODE,
we will also rename PYAUTO_WORKSPACE_SMALL_DATASETS to PYAUTO_SMALL_DATASETS.

[Jammy2211]

Library PRs Created — 2026-04-12

PRs

• refactor: separate PYAUTOFIT_TEST_MODE into distinct PYAUTO_* env vars PyAutoConf#86
• refactor: separate PYAUTOFIT_TEST_MODE into distinct PYAUTO_* env vars #1195
• refactor: rename env vars to PYAUTO_* prefix PyAutoArray#265
• refactor: rename env vars to PYAUTO_* prefix PyAutoGalaxy#343
• refactor: use PYAUTO_SKIP_CHECKS and PYAUTO_SKIP_VISUALIZATION PyAutoLens#432

Status

Workspace changes needed. Next: /start_workspace

API Changes

• PYAUTOFIT_TEST_MODE → PYAUTO_TEST_MODE
• PYAUTOARRAY_OUTPUT_MODE → PYAUTO_OUTPUT_MODE
• PYAUTO_WORKSPACE_SMALL_DATASETS → PYAUTO_SMALL_DATASETS
• New vars: PYAUTO_SKIP_FIT_OUTPUT, PYAUTO_SKIP_VISUALIZATION, PYAUTO_SKIP_CHECKS
• All workspace env_vars.yaml, shell scripts, and 2 Python scripts need updating

[Jammy2211]

Shipped — 2026-04-12

Library PRs

• refactor: separate PYAUTOFIT_TEST_MODE into distinct PYAUTO_* env vars PyAutoConf#86
• refactor: separate PYAUTOFIT_TEST_MODE into distinct PYAUTO_* env vars #1195
• refactor: rename env vars to PYAUTO_* prefix PyAutoArray#265
• refactor: rename env vars to PYAUTO_* prefix PyAutoGalaxy#343
• refactor: use PYAUTO_SKIP_CHECKS and PYAUTO_SKIP_VISUALIZATION PyAutoLens#432

Workspace PRs

• refactor: rename env vars to PYAUTO_* prefix autofit_workspace#29
• refactor: rename env vars to PYAUTO_* prefix autogalaxy_workspace#25
• refactor: rename env vars to PYAUTO_* prefix autolens_workspace#51

Summary

Separated the catch-all PYAUTOFIT_TEST_MODE into purpose-specific environment variables: PYAUTO_TEST_MODE (sampler), PYAUTO_SKIP_FIT_OUTPUT, PYAUTO_SKIP_VISUALIZATION, PYAUTO_SKIP_CHECKS. Also renamed PYAUTOARRAY_OUTPUT_MODE → PYAUTO_OUTPUT_MODE and PYAUTO_WORKSPACE_SMALL_DATASETS → PYAUTO_SMALL_DATASETS. Updated all 8 repos (5 libraries + 3 workspaces).

Session Notes

• The categorisation was: sampler speedup (6 call sites stay as test_mode), fit I/O (5 sites → skip_fit_output), visualization (3 sites → skip_visualization), validation checks (5 sites → skip_checks).
• Workspace env_vars.yaml now sets all new skip vars explicitly rather than having test_mode imply them.
• Pre-existing smoke test failure in autofit_workspace/scripts/cookbooks/samples.py (bypass mode generates 2 samples but script indexes [4]) — unrelated to this change.