From f29de35eca7cc953b6ee0681047ab1d526387694 Mon Sep 17 00:00:00 2001 From: Claude Date: Sun, 19 Jul 2026 11:49:27 +0000 Subject: [PATCH 1/2] refactor!: point the Colab bootstrap at `autonerves` (renamed from autoconf) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The workspace scripts already import the config surface from the science library (not autoconf). This updates the remaining direct references — the Colab bootstrap `from autoconf import setup_colab` and its `pip install autoconf` — to the renamed package `autonerves`. Repo-name references ("PyAutoConf", incl. the CI dependency chain) are unchanged; they flip with the GitHub repo rename in the coordinated cutover. Co-Authored-By: Claude Opus 4.8 Claude-Session: https://claude.ai/code/session_013ciVftxvYpefh59wSkR7jN --- AGENTS.md | 2 +- scripts/features/latent_nan_robustness.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index ed9d8a5..4a728a2 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -4,7 +4,7 @@ This is the integration-test suite for **PyAutoFit**, run on the build server to library works end-to-end. It is **not** a user-facing workspace — see `../autofit_workspace` for examples and tutorials. These are the canonical, agent-agnostic instructions for this repo. -Dependencies: `autofit` (and `autoconf`). +Dependencies: `autofit` (and `autonerves`). ## Repository Structure diff --git a/scripts/features/latent_nan_robustness.py b/scripts/features/latent_nan_robustness.py index 0c8f64b..0679d2c 100644 --- a/scripts/features/latent_nan_robustness.py +++ b/scripts/features/latent_nan_robustness.py @@ -14,7 +14,7 @@ This script uses a two-latent ``af.ex.Analysis`` subclass (the shipped example analysis has a single latent; two latents exercise the additional ``zip(LATENT_KEYS, values)`` mis-alignment that a dropped column causes). The -``PYAUTO_LATENT_NAN_INJECT=stride:N`` knob (``autoconf.test_mode``) sets NaN on +``PYAUTO_LATENT_NAN_INJECT=stride:N`` knob (``autonerves.test_mode``) sets NaN on latent column 0 (``gaussian.fwhm``) for every sample whose absolute index is a non-zero multiple of ``N``. With ``N >= batch_size`` batch 0 stays finite and seeds the model with both keys; a later batch loses column 0. From 47c154ad105420d1de772bbf033ac2c9cd52e731 Mon Sep 17 00:00:00 2001 From: Claude Date: Sun, 19 Jul 2026 12:37:29 +0000 Subject: [PATCH 2/2] chore: rename repo references PyAutoConf -> PyAutoNerves (CI chain + related-repos) Update the smoke-test dependency chain and docs prose from PyAutoConf to PyAutoNerves following the GitHub repo rename. Co-Authored-By: Claude Opus 4.8 Claude-Session: https://claude.ai/code/session_013ciVftxvYpefh59wSkR7jN --- .github/scripts/smoke_install.sh | 4 ++-- .github/workflows/smoke_tests.yml | 2 +- AGENTS.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/scripts/smoke_install.sh b/.github/scripts/smoke_install.sh index c09f2ad..7d84f65 100644 --- a/.github/scripts/smoke_install.sh +++ b/.github/scripts/smoke_install.sh @@ -7,8 +7,8 @@ set -e if [ "$PYTHON_VERSION" = "3.12" ]; then - pip install ./PyAutoConf "./PyAutoFit[optional]" + pip install ./PyAutoNerves "./PyAutoFit[optional]" else - pip install ./PyAutoConf ./PyAutoFit + pip install ./PyAutoNerves ./PyAutoFit fi pip install nautilus-sampler diff --git a/.github/workflows/smoke_tests.yml b/.github/workflows/smoke_tests.yml index e21998b..2eb2a1e 100644 --- a/.github/workflows/smoke_tests.yml +++ b/.github/workflows/smoke_tests.yml @@ -11,5 +11,5 @@ jobs: smoke: uses: PyAutoLabs/PyAutoHeart/.github/workflows/smoke-tests.yml@main with: - chain: "PyAutoConf PyAutoFit" + chain: "PyAutoNerves PyAutoFit" secrets: inherit diff --git a/AGENTS.md b/AGENTS.md index 4a728a2..ba73765 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -70,7 +70,7 @@ write from a header skim silently deletes every section below the header. ## Related Repos -- Source libs: `../PyAutoFit`, `../PyAutoConf`. +- Source libs: `../PyAutoFit`, `../PyAutoNerves`. - `../autofit_workspace` — the user-facing workspace; `../HowToFit` — the tutorial series. - `../PyAutoHands` — CI / build tooling.