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PyAutoHands — internals

Operational detail for working inside this repo: the autohands CLI, the pre-build steps, workspace folder structure, config files, and release.yml. What PyAutoHands is and the Brain/Heart/Build boundary live in AGENTS.md — read that first; read this only when changing the build pipeline itself.

What the pipeline automates

PyAutoHands runs no release-readiness checks of its own (that is PyAutoHeart's job). It automates:

  1. Building and releasing packages to TestPyPI, then PyPI
  2. Running workspace Python scripts (integration tests)
  3. Converting Python scripts to Jupyter notebooks and executing them
  4. Committing generated notebooks to workspace main branches and tagging each workspace with a version matching the released library

The pipeline is triggered via GitHub Actions (release.yml) and is manually dispatched with configurable options. Release-readiness gating happens upstream: the PyAutoBrain release agent calls pyauto-heart readiness and only dispatches release.yml on a green verdict.

Bash CLI

Every operation in this repo is invokable from the shell via the autohands dispatcher at bin/autohands. List subcommands with autohands help; print the docstring for one with autohands help <subcommand> (or autohands <subcommand> --help).

Recommended alias for ~/.bashrc:

alias autohands-help='$HOME/Code/PyAutoLabs/PyAutoHands/bin/autohands help'

The dispatcher routes to the underlying bash script directly, or to the Python tool with PYTHONPATH already set so the internal build_util / result_collector / env_config imports resolve. The same operations remain callable as Claude skills (/pre_build, /verify_install, /review_release); use the skill when you want the validation + summary wrapper, the CLI when you just want to fire the underlying tool.

Pre-Build Steps

Before triggering a build, run:

bash $HOME/Code/PyAutoLabs/PyAutoHands/bin/autohands pre_build [minor_version]
# minor_version defaults to 1
# (equivalent to: bash $HOME/Code/PyAutoLabs/PyAutoHands/pre_build.sh [minor_version])

This script does the following for each repo:

Repo black generate.py commit & push
autofit_workspace yes yes (autofit) yes
autogalaxy_workspace yes yes (autogalaxy) yes
autolens_workspace yes yes (autolens) yes
autofit_workspace_test yes no yes
autogalaxy_workspace_test yes no yes
autolens_workspace_test yes no yes
euclid_strong_lens_modeling_pipeline yes no yes
HowToGalaxy yes yes (howtogalaxy) yes
HowToLens yes yes (howtolens) yes
HowToFit yes yes (howtofit) yes

Before the per-repo loop, pre_build.sh invokes PyAutoBrain/bin/ensure_workspace_labels.sh to assert the canonical pending-release label across every release-window repo (idempotent — a no-op when nothing has drifted).

Release-readiness checking is not Build's job — PyAutoHands is a pure executor. The version-skew check that used to live here (verify_workspace_versions.sh, a fail-fast guard against a workspace pinned ahead of its installed library, or a config/general.yaml ↔ version.txt disagreement) now lives in PyAutoHeart as the version_skew check feeding pyauto-heart readiness. The PyAutoBrain release agent gates on pyauto-heart readiness before invoking pre_build; a human running pre_build directly is trusted to have checked readiness first. See PyAutoHeart for the resolution precedence (config/general.yaml:version.workspace_version, then version.txt) — mirroring autoconf.workspace.check_version. Since PyAutoBuild#120, releases no longer write workspace version pins or commit __init__.py stamps back to library mains (wheels are stamped at build time; tags are the release anchor): the runtime check enforces a compatibility floor (version.minimum_library_version, bumped deliberately — PyAutoNerves#118), and Heart's version_skew check needs a follow-up rework to compare floors against release tags rather than stamp-vs-pin.

generate.py is run from the workspace root with PYTHONPATH pointing at PyAutoHands/autohands/. Only specific safe directories are committed — never output/, output_model/, or run-generated artefacts. After all workspaces are done, PyAutoHands itself is committed and pushed, then gh workflow run release.yml dispatches the GitHub Actions release.

Workspace Folder Structure

Each workspace repo (autofit_workspace, autogalaxy_workspace, autolens_workspace, their _test variants, and the lecture repos HowToGalaxy/HowToLens) has the following expected structure. Only these paths should ever be committed.

Folder / file autofit autogalaxy autolens Notes
config/ yes yes yes PyAutoNerves config files
dataset/ yes yes yes Allowlisted real observational data only; simulated datasets are never committed (#126/#150)
notebooks/ yes yes yes Generated from scripts/ by generate.py
scripts/ yes yes yes Source Python scripts
slam_pipeline/ no no yes autolens only
output/ — — — Always empty — kept under git with a .gitignore only
Root-level files yes yes yes README.md, llms-full.txt, workspace_index.json, requirements.txt, LICENSE* — committed by release.yml on the runner, not by pre_build.sh (#156)

Paths that must NEVER be committed

  • output/ contents — run results; the folder itself exists only via .gitignore
  • output_model/ — model JSON/pickle artefacts written during script execution
  • path/to/model/ or any nested model JSON files written at runtime
  • .fits files outside dataset/ (e.g. image.fits, dataset.fits generated by simulators into scripts/ or other subdirectories)

Running Tests

# Run all tests
pytest

# Run a single test
pytest tests/test_files_to_run.py::test_script_order

Codex / sandboxed runs

When running Python from Codex or any restricted environment, set writable cache directories so numba and matplotlib do not fail on unwritable home or source-tree paths:

NUMBA_CACHE_DIR=/tmp/numba_cache MPLCONFIGDIR=/tmp/matplotlib pytest

This workspace is often imported from /mnt/c/... and Codex may not be able to write to module __pycache__ directories or /home/jammy/.cache, which can cause import-time numba caching failures without this override.

Key Scripts

All scripts in autohands/ are run from within a checked-out workspace directory (not from this repo root). They rely on PYTHONPATH including the PyAutoHands directory.

  • run_python.py <project> <directory> — Executes Python scripts in a workspace folder, skipping files listed in config/no_run.yaml
  • run.py <project> <directory> [--visualise] — Executes Jupyter notebooks in a workspace folder, skipping files in config/no_run.yaml
  • generate.py <project> — Converts Python scripts in scripts/ to .ipynb notebooks in notebooks/, run from within the workspace root
  • generate_markdown.py <project> [--only <substring>] — Renders the curated scripts listed in the workspace's config/build/markdown_examples.yaml to executed markdown pages with output images under markdown/, plus an index, committed so examples are readable on GitHub. Manual / at-release only, never per-commit; refuses PYAUTO_TEST_MODE (truncated searches make wrong images — model-fit reruns instead resume from the completed output/ cache); never renders features/ scripts; restores tracked files a script modifies (e.g. simulators rewriting dataset/). Rules and rationale in the module docstring.
  • script_matrix.py <project1> [project2 ...] — Outputs a JSON matrix of {name, directory} pairs for GitHub Actions matrix strategy
  • tag_and_merge.sh --version <version> — Commits pending changes and tags library repos (PyAutoNerves, PyAutoFit, PyAutoArray, PyAutoGalaxy, PyAutoLens) for release
  • url_check — URL hygiene moved to PyAutoHeart (Heart owns all health checking). autohands url_check is now a thin shim to pyauto-heart url_check; the ecosystem-wide sweep runs from PyAutoHeart's central url-check.yml workflow (replacing the old per-repo url_check.yml workflows). The runnable scripts live at PyAutoHeart/heart/checks/url_check*.{sh,py}.
  • bump_colab_urls.sh <new-tag> — Rewrites every colab.research.google.com/github/PyAutoLabs/<repo>/blob/<old-tag>/... URL in cwd to use <new-tag>, where <repo> is one of autofit_workspace, autogalaxy_workspace, autolens_workspace, HowToFit, HowToGalaxy, HowToLens. Called by the release_workspaces and bump_library_colab_urls jobs in release.yml so README/docs Colab links always pin to the just-released tag. Idempotent; skips URLs not in canonical PyAutoLabs/date-tagged form.

Architecture

Script-to-Notebook Conversion Pipeline

generate.py → generate_autofit.py + build_util.py:

  1. add_notebook_quotes.py transforms triple-quoted docstrings into # %% cell markers in a temp .py file
  2. ipynb-py-convert converts the temp file to .ipynb
  3. build_util.uncomment_jupyter_magic() restores commented-out Jupyter magic commands (e.g. # %matplotlib → %matplotlib)
  4. build_util.inject_colab_setup() prepends the standard Google Colab setup cell pair (see "Google Colab architecture" below)
  5. Generated notebooks are git add -fed directly

Optional-dependency skip guards in notebooks

The workspaces guard optional-dependency examples with the script idiom

if importlib.util.find_spec("<optional-dep>") is None:
    print("Skipping ...")
    sys.exit(0)

As a .py script that is a clean exit 0. In a Jupyter kernel the same call raises SystemExit, nbclient marks the cell as errored and jupyter nbconvert --execute exits non-zero — so an intended skip is reported as a notebook failure. CI never sees it (its matrices install the optional extras); users and local runs without them do.

The fix is classification at the point of execution, not a source rewrite: build_util.is_clean_skip_exit(output) inspects the combined stdout/stderr of an nbconvert run and returns True only when the run's single CellExecutionError terminates in SystemExit: 0 (ANSI escapes stripped first — IPython colours the traceback). SystemExit: 1 and every other exception stay failures. build_util.execute_notebook consults it in its CalledProcessError branch and records a PASS, alongside the existing InversionException exemption.

Rewriting the guard at generation time was rejected: it would need a source-level transform of arbitrary "skip the rest of the notebook" control flow, would diverge notebook semantics from the script the user reads, and would require regenerating and committing notebooks across every workspace.

Propagation. Each workspace repo carries its own .github/scripts/run_smoke.py (no template sync — PyAutoHeart's reusable smoke-tests.yml deliberately leaves the runner in the workspace), and that copy has its own execute_notebook used by the PR smoke gate. It already imports from PyAutoHands (env_config, build_util.py_to_notebook, with PyAutoHands/autohands on PYTHONPATH), so adoption is a two-line change per workspace:

from build_util import is_clean_skip_exit
...
rc, output = execute_notebook(nb_path, env)
if rc != 0 and is_clean_skip_exit(output):
    rc = 0

Workspaces carrying a run_smoke.py copy: autofit_workspace, autogalaxy_workspace, autolens_workspace, autofit_workspace_test, autogalaxy_workspace_test, autolens_workspace_test, autocti_workspace_test, HowToGalaxy, HowToLens (nine copies, five distinct revisions — they have drifted). Only the three user-facing workspaces (autofit_workspace, autogalaxy_workspace, autolens_workspace) have a notebook execution leg, so only those three needed the edit — applied 2026-07-25. The HowTo and *_test runners are scripts-only (no smoke_notebooks.txt, no nbconvert path) and require nothing.

Google Colab architecture

Every published notebook must be runnable on Google Colab with zero local installation. Four pieces, spread over three organs plus PyAutoNerves:

  1. Runtime bootstrap — PyAutoNerves/autoconf/setup_colab.py. A _PROJECTS registry (autofit, autogalaxy, autolens, howtofit, howtogalaxy, howtolens) maps each notebook repo to its package stack, workspace repo and Colab directory. setup_colab.setup("<project>") is a no-op outside Colab; on Colab it pip-installs the stack (--no-deps — Colab ships the scientific base), shallow-clones the workspace at the tag matching the installed release (default branch as fallback) and points autoconf's config/output paths at it.
  2. Generation-time injection — build_util.inject_colab_setup(notebook, project), called by generate.py / generate_autofit.py after every py→ipynb conversion. It prepends a markdown explainer + code cell calling setup_colab.setup("<project>"), immediately after the notebook's title cell. Notebooks whose script already hand-writes a setup_colab call are left untouched. build_util.COLAB_PROJECTS must stay in sync with the PyAutoNerves registry; an unknown project fails generation loudly. Coverage is therefore guaranteed by construction — every generated notebook is Colab-ready, with no per-script maintenance.
  3. Release maintenance — bump_colab_urls.sh (above) re-pins every canonical Colab URL in READMEs/docs/notebooks to the just-released tag, from the release_workspaces and bump_library_colab_urls jobs. Only date-tagged PyAutoLabs/<repo> URLs are bumped — unpinned or wrong-owner URLs are invisible to it, which is why Heart forbids them (next item).
  4. Monitoring — PyAutoHeart's central url-check.yml (weekly): the offline guard (heart/checks/url_check.sh) forbids Colab URL forms that rot (Binder, Jammy2211 owner, /blob/release/, unpinned /blob/main/, chapter paths pointing at workspace repos instead of the HowTo repos); the live audit (url_check_live.py) converts Colab URLs to raw-GitHub form and 404-checks that each linked notebook actually exists at its pinned tag.

Script Execution Order

build_util.find_scripts_in_folder() enforces a specific ordering:

  1. Scripts with "simulator" in the path (data must be generated first)
  2. Scripts named start_here.py
  3. All other scripts

Config Files

Each workspace owns its own build config under <workspace>/config/build/:

  • no_run.yaml — flat list of script/notebook patterns to skip during execution. Required: every build target must own one (an empty file is valid and skips nothing). run.py raises FileNotFoundError if it is missing.
  • profile_smoke.yaml / profile_release.yaml — defaults + per-pattern overrides for environment variables
  • visualise_notebooks.yaml — flat list of notebook stems to run when the --visualise flag is used. Optional: a workspace without one simply has nothing marked for visualisation.

config/build/ is the single source of truth — autohands/config/ holds no per-project config fallbacks. The keyed-dict fallbacks (no_run.yaml, copy_files.yaml, visualise_notebooks.yaml) were removed once every build target owned its own files; the only file left in autohands/config/ is workspaces.yaml, which is build policy (the run matrix), not workspace config.

The copy_files.yaml mechanism — which copied listed scripts verbatim into notebooks/ instead of converting them — was removed entirely. It resolved to an empty list in every workspace and had produced no output in any build.

Environment Variables

  • BUILD_PYTHON_INTERPRETER — Python interpreter to use for script execution (defaults to python3)
  • PYAUTO_TEST_MODE — Set to 1 for workspace runs, 0 for *_test workspace runs
  • PYAUTO_SMALL_DATASETS — Set to 1 for workspace runs (caps grids to 15x15), not set for *_test runs
  • PYAUTO_FAST_PLOTS — Set to 1 for workspace runs (skips tight_layout() in subplots and critical curve/caustic overlays in plots), not set for *_test runs
  • JAX_ENABLE_X64 — Set to True during CI runs

GitHub Actions Workflow

The workflow (release.yml) is manually dispatched with inputs:

  • minor_version — appended to date-based version (format: YYYY.M.D.minor)
  • rehearsal — the one mode switch (default false = full real release). When true, it is TestPyPI-only rehearsal mode: build every package from source, publish to TestPyPI, emit the resolved version as the testpypi-rehearsal-version artifact, then STOP (no PyPI upload, no git tag, no notebook/version commits, no Colab bumps). This is the mode the Heart/Brain release-validation gate dispatches so it can install and validate the built wheels.

(The legacy skip_scripts / skip_notebooks / skip_release force-through knobs and the update_notebook_visualisations path were removed with the Heart/Build split — Build is a pure executor with no ad-hoc skip levers or inline notebook-visualisation job. "Build without releasing" is now exactly what rehearsal mode is for.)

release.yml is a pure executor: it builds, tests-the-install, publishes to PyPI, tags every library and workspace, and commits generated notebooks + Colab URL bumps to the workspaces (version stamps are build-tree-only since #120 — no __init__.py commit-backs to library mains, no workspace version pins). Workspace-integration validation (the old find_scripts / generate_notebooks / run_scripts / run_notebooks / analyze_results jobs) moved to PyAutoHeart's workspace-validation.yml; release readiness is gated upstream by the PyAutoBrain release agent via pyauto-heart readiness before this workflow is dispatched. The script_matrix.py / run_python.py / run.py / aggregate_results.py primitives remain here and are checked out + reused by the Heart workflow. The never-rewrite-history rules live in AGENTS.md and apply here as everywhere.