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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

What This Project Does

PyAutoBuild is a CI/CD build server for the PyAuto software family (PyAutoConf, PyAutoFit, PyAutoArray, PyAutoGalaxy, PyAutoLens). 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.

Bash CLI

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

Recommended alias for ~/.bashrc:

alias autobuild-help='$HOME/Code/PyAutoLabs/PyAutoBuild/bin/autobuild 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/PyAutoBuild/bin/autobuild pre_build [minor_version]
# minor_version defaults to 1
# (equivalent to: bash $HOME/Code/PyAutoLabs/PyAutoBuild/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 admin_jammy/software/ensure_workspace_labels.sh to assert the canonical pending-release label across every release-window repo (idempotent — a no-op when nothing has drifted).

After the loop, before dispatching the workflow, pre_build.sh invokes verify_workspace_versions.sh — a fail-fast check that blocks the release if any workspace's pinned version is ahead of the currently-installed library version. This guards against bootstrap commits that set an aspirational version, which would otherwise crash every script run with WorkspaceVersionMismatchError until the next release lands.

The pinned workspace version is resolved with the same precedence as autoconf.workspace.check_version:

  1. config/general.yaml — version.workspace_version key (canonical, written by release.yml).
  2. version.txt at the workspace root (legacy fallback, also written by release.yml).

Both sources are written atomically by the Write workspace version step in release.yml; if they ever disagree on a checked-out workspace, verify_workspace_versions.sh fails before dispatch. The runtime check in autoconf.workspace.check_version (called from every library's __init__.py) reads the same precedence, so workspace/library mismatches surface on every script run, not just welcome.py.

generate.py is run from the workspace root with PYTHONPATH pointing at PyAutoBuild/autobuild/. Only specific safe directories are committed — never output/, output_model/, or run-generated artefacts. After all workspaces are done, PyAutoBuild 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 PyAutoConf config files
dataset/ yes yes yes Input data; force-added with git add -f
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, setup.py, pyproject.toml, requirements.txt, *.cfg, *.ini, *.yml, *.yaml, LICENSE*

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 autobuild/ are run from within a checked-out workspace directory (not from this repo root). They rely on PYTHONPATH including the PyAutoBuild 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
  • 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 (PyAutoConf, PyAutoFit, PyAutoArray, PyAutoGalaxy, PyAutoLens) for release
  • url_check.sh [directory] — Fails if any forbidden Binder/Colab URL pattern appears in *.rst, *.md, *.ipynb, or *.py under the directory. Forbidden: any mybinder.org URL, Colab URLs with Jammy2211/ owner, and Colab URLs pinned to /blob/release/. Each affected workspace and library repo runs this in CI to prevent regressions.
  • 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, 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. Generated notebooks are git add -fed directly

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
  • env_vars.yaml — defaults + per-pattern overrides for environment variables
  • copy_files.yaml — flat list of script paths to copy as-is to notebooks/ instead of converting
  • visualise_notebooks.yaml — flat list of notebook stems to run when --visualise flag is used

autobuild/config/ retains keyed-dict copies of no_run.yaml, copy_files.yaml, and visualise_notebooks.yaml as fallbacks for legacy workspaces (HowTo*, BSc_Galaxies_Project) that have not been migrated yet. The 6 main workspaces (autofit/autogalaxy/autolens and their _test variants) own their own configs and do not consult these fallbacks.

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)
  • skip_scripts / skip_notebooks / skip_release — flags to skip pipeline stages
  • update_notebook_visualisations — runs notebooks with --visualise and pushes the rendered output to main

The find_scripts job uses script_matrix.py to dynamically generate the matrix for parallel run_scripts and run_notebooks jobs.

Never rewrite history

NEVER perform these operations on any repo with a remote:

  • git init in a directory already tracked by git
  • rm -rf .git && git init
  • Commit with subject "Initial commit", "Fresh start", "Start fresh", "Reset for AI workflow", or any equivalent message on a branch with a remote
  • git push --force to main (or any branch tracked as origin/HEAD)
  • git filter-repo / git filter-branch on shared branches
  • git rebase -i rewriting commits already pushed to a shared branch

If the working tree needs a clean state, the only correct sequence is:

git fetch origin
git reset --hard origin/main
git clean -fd

This applies equally to humans, local Claude Code, cloud Claude agents, Codex, and any other agent. The "Initial commit — fresh start for AI workflow" pattern that appeared independently on origin and local for three workspace repos is exactly what this rule prevents — it costs ~40 commits of redundant local work every time it happens.