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fix: install emcee and dynesty in the Colab bootstrap - #164
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The Colab setup installs the PyAuto stack with `--no-deps`, on the premise that Colab already ships the scientific stack. `emcee` and `dynesty` are real `autofit` dependencies (PyAutoFit/pyproject.toml) that Colab does not ship and `_SHARED_EXTRAS` did not name, so they never landed: every Colab notebook that runs `af.Emcee` or `af.DynestyStatic` died with `ModuleNotFoundError` at the fit. Reported against HowToFit tutorial 3. Both are now named in `_SHARED_EXTRAS` with the specifiers autofit declares, and a comment records why a `--no-deps` install has to list them. Refs PyAutoLabs/HowToFit#57 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0132v5TNVbbvBBESAefHwnwG
This was referenced Sep 14, 2026
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Refs PyAutoLabs/HowToFit#57.
The failure
A reader working through HowToFit tutorial 3 on Colab hit:
Cause
_colab_setupinstalls the project stack with--no-deps, on the premise that Colab already ships the scientific stack. That premise holds for numpy, scipy and matplotlib. It does not hold foremcee>=3.1.6anddynesty==2.1.5, which are declareddependenciesofautofit(PyAutoFit/pyproject.toml) and are not installed by Colab — and neither was named in_SHARED_EXTRAS, so neither ever landed.Every Colab notebook that runs
af.Emceetherefore dies at the fit, and would die again ataf.DynestyStatic. That is all six Colab-enabled projects (autofit, autogalaxy, autolens, howtofit, howtogalaxy, howtolens), sinceautofitis in every stack.Change
Adds
emcee>=3.1.6anddynesty==2.1.5to_SHARED_EXTRAS, matching the specifiers autofit declares, plus a comment recording why a--no-depsinstall has to name its siblings' real dependencies.Testing
pytest test_autonerves— 183 passed.test_setup_colab.pyalone: 20 passed. (It assertspackages[0] == "autonerves", which the append preserves.)Note
This reaches users on the next
autonervesrelease, not on merge — the Colab cell installsautonervesfrom PyPI.black --checkreports one pre-existing reformat in_clone_workspace, untouched by this change and not gated by CI; left alone rather than mixed into this diff.🤖 Generated with Claude Code
https://claude.ai/code/session_0132v5TNVbbvBBESAefHwnwG