chore: rename repo references PyAutoConf → PyAutoNerves

.claude/hooks/validate_pyauto_code.py

@@ -45,7 +45,7 @@
 # Mirrors ALIAS_TO_MODULE in autoassistant/audit_skill_apis.py.
 _ALIASES = (
     "aplt",
-    "autoconf",
+    "autonerves",
     "autofit",
     "af",
 )

.github/workflows/wiki-currency.yml

@@ -69,7 +69,7 @@ jobs:
           python -m pip install --upgrade pip
           VER="${{ inputs.stack_version }}"
           if [ -n "$VER" ]; then
-            echo "Installing autofit==$VER (pulls the pinned autoconf)."
+            echo "Installing autofit==$VER (pulls the pinned autonerves)."
             pip install "autofit==$VER"
           else
             echo "Installing the latest released autofit."
@@ -85,7 +85,7 @@ jobs:
       - name: Clone cited source trees (citation ground truth)
         run: |
           mkdir -p sources
-          for repo in PyAutoConf PyAutoFit; do
+          for repo in PyAutoNerves PyAutoFit; do
             git clone --quiet --depth 1 "https://github.com/PyAutoLabs/$repo" "sources/$repo"
           done
           git clone --quiet --depth 1 --filter=blob:none --sparse \

activate.sh

@@ -18,7 +18,7 @@ elif [ -n "${PYAUTO_HPC_BASE:-}" ] && [ -f "$PYAUTO_HPC_BASE/PyAuto/bin/activate
     BASE="$PYAUTO_HPC_BASE"
     source "$BASE/PyAuto/bin/activate"
     export PYTHONPATH=$BASE:\
-$BASE/PyAutoConf:\
+$BASE/PyAutoNerves:\
 $BASE/PyAutoFit
 else
     echo "No local .venv found (set PYAUTO_HPC_BASE for a shared/HPC PyAuto checkout)." >&2
@@ -30,5 +30,5 @@ fi
 #
 #   SRC=~/Code/PyAutoLabs
 #   export PYTHONPATH=$SRC:\
-#   $SRC/PyAutoConf:\
+#   $SRC/PyAutoNerves:\
 #   $SRC/PyAutoFit

autoassistant/audit_skill_apis.py

@@ -42,7 +42,7 @@
 
 try:
     import yaml
-except ImportError:  # pragma: no cover - yaml ships with the stack (autoconf dep)
+except ImportError:  # pragma: no cover - yaml ships with the stack (autonerves dep)
     yaml = None
 
 # ---------------------------------------------------------------------------
@@ -59,12 +59,12 @@
 # `__version__`; `autofit.plot` is hashed too (it is where the plot API lives)
 # but inherits the autofit version.
 BASELINE_MODULES: tuple[str, ...] = (
-    "autoconf",
+    "autonerves",
     "autofit",
     "autofit.plot",
 )
 VERSIONED_MODULES: tuple[str, ...] = (
-    "autoconf",
+    "autonerves",
     "autofit",
 )
 
@@ -79,7 +79,7 @@
 ALIAS_TO_MODULE: dict[str, str] = {
     "af": "autofit",
     "aplt": "autofit.plot",
-    "autoconf": "autoconf",
+    "autonerves": "autonerves",
     "autofit": "autofit",
 }
 
@@ -376,7 +376,7 @@ def _cross_module_candidates(leaf: str) -> list[str]:
     if leaf in _cross_cache:
         return _cross_cache[leaf]
     hits: list[str] = []
-    for mod_name in ("autoconf", "autofit"):
+    for mod_name in ("autonerves", "autofit"):
         root = _module_cache.get(mod_name)
         if root is None:
             try:
@@ -582,7 +582,7 @@ def render_report(
 # ---------------------------------------------------------------------------
 def gather_versions() -> dict[str, str]:
     out: dict[str, str] = {}
-    for name in ("autoconf", "autofit"):
+    for name in ("autonerves", "autofit"):
         try:
             mod = importlib.import_module(name)
         except Exception as e:  # noqa: BLE001
@@ -695,7 +695,7 @@ def render_installation_check(check: InstallationCheck) -> str:
         lines.append(f"  install type: {check.install_kind}")
     if check.missing:
         lines.append(f"  missing from this interpreter: {', '.join(check.missing)}")
-    # Group identical errors: with e.g. a workspace-version mismatch, autoconf
+    # Group identical errors: with e.g. a workspace-version mismatch, autonerves
     # and autofit fail with the same multi-paragraph message — print it once,
     # naming every module it applies to.
     grouped: dict[str, list[str]] = {}
@@ -890,7 +890,7 @@ def check_version(root: Path) -> int:
 # `main`-pinned pages that predate the discipline.
 # ---------------------------------------------------------------------------
 PROJECT_IMPORT: dict[str, str] = {
-    "PyAutoConf": "autoconf",
+    "PyAutoNerves": "autonerves",
     "PyAutoFit": "autofit",
 }
 _SHA_RE = re.compile(r"[0-9a-f]{7,40}\Z")

autoassistant/benchmark.py

@@ -18,7 +18,7 @@
 RUNS_DIRNAME = "runs"
 BENCHMARKS_DIRNAME = "benchmarks"
 
-STACK_PACKAGES = ("autofit", "autoconf")
+STACK_PACKAGES = ("autofit", "autonerves")
 
 FRONTMATTER = re.compile(r"\A---\n(.*?)\n---\n", re.DOTALL)
 RUBRIC_ROW = re.compile(r"^\|\s*(M\d+|J\d+)\s*\|\s*(.+?)\s*\|\s*(\d+)\s*\|\s*$")

autoassistant/mcp/tools.py

@@ -17,7 +17,7 @@
 import sys
 from pathlib import Path
 
-from autoconf.dictable import to_dict
+from autonerves.dictable import to_dict
 
 import autofit as af
 

autoassistant/refresh_api_docs.py

@@ -21,7 +21,7 @@
 
 
 MODULES = (
-    ("autoconf", "autoconf"),
+    ("autonerves", "autonerves"),
     ("autofit", "autofit"),
 )
 

autoassistant/tests/test_api_gate.py

@@ -30,7 +30,7 @@
 
 GOOD = "import autofit.plot as aplt; aplt.corner_cornerpy(samples=samples)"
 GOOD_SUBMODULE = "import autofit.jax.pytrees as pytrees"
-GOOD_AUTOCONF_SUBMODULE = "import autoconf.dictable"
+GOOD_AUTOCONF_SUBMODULE = "import autonerves.dictable"
 STALE_MODEL = "import autofit as af; af.PriorModel(SomeClass)"
 STALE_NEST = "from autofit.non_linear.nest.multi_nest import MultiNest"
 
@@ -91,7 +91,7 @@ def test_validator_passes_current_submodule_import():
     assert _run_validator("--code", GOOD_SUBMODULE).returncode == 0
 
 
-def test_validator_passes_autoconf_submodule_import():
+def test_validator_passes_autonerves_submodule_import():
     assert _run_validator("--code", GOOD_AUTOCONF_SUBMODULE).returncode == 0
 
 
@@ -275,14 +275,14 @@ def test_render_installation_check_groups_identical_errors():
     check = mod.InstallationCheck(
         status="import_failed", python="py", prefix="env",
         versions={}, locations={}, missing=[],
-        errors={name: "Boom: identical wall" for name in ("autoconf", "autofit")},
+        errors={name: "Boom: identical wall" for name in ("autonerves", "autofit")},
         install_kind="unknown", cache_defaults={},
     )
 
     text = mod.render_installation_check(check)
 
     assert text.count("Boom: identical wall") == 1
-    assert "autoconf, autofit import failed" in text
+    assert "autonerves, autofit import failed" in text
 
 
 if __name__ == "__main__":

autoassistant/tests/test_install_preflight.py

@@ -51,7 +51,7 @@ def test_install_preflight_distinguishes_absent_stack():
 
 
 def test_install_preflight_distinguishes_broken_import(tmp_path):
-    for package in ("autoconf", "autofit"):
+    for package in ("autonerves", "autofit"):
         package_path = tmp_path / package
         package_path.mkdir()
         body = (

autoassistant/tests/test_mcp_tools.py

@@ -15,7 +15,7 @@
 from PIL import Image
 
 import autofit as af
-from autoconf import conf
+from autonerves import conf
 
 from autoassistant.mcp import tools
 

hpc/template.py

@@ -51,11 +51,11 @@
 
 Anchor config and output to the project root (the directory holding this script's
 parent), so the script behaves identically from a local shell and from a SLURM batch
-working directory (`PyAutoConf:autoconf/conf.py`).
+working directory (`PyAutoNerves:autonerves/conf.py`).
 """
 PROJECT_PATH = Path(__file__).resolve().parents[1]
 
-from autoconf import conf
+from autonerves import conf
 
 conf.instance.push(
     new_path=str(PROJECT_PATH / "config"),

skills/_bootstrap_skill.md

@@ -47,7 +47,7 @@ touch. Common patterns:
 
 - Model composition, priors, searches, samples, aggregator, graphical models →
   `PyAutoFit`.
-- Configuration option → `PyAutoConf` + the config you're touching.
+- Configuration option → `PyAutoNerves` + the config you're touching.
 - Construction idioms and worked examples → `autofit_workspace` (read-only reference).
 
 If the new skill needs a repo not in `sources.yaml`, add it there first (with a `name`,

skills/af_adapt_to_domain.md

@@ -73,7 +73,7 @@ later.
 Run [`af_compose_model`](./af_compose_model.md) for their standard model(s). If a
 parametrisation is truly standard for them, offer to write its priors into
 `config/priors/` as project defaults (see
-[[../wiki/core/stack/autoconf]]) and to serialise the composed model to JSON — both make
+[[../wiki/core/stack/autonerves]]) and to serialise the composed model to JSON — both make
 "the usual model" a one-liner in every future script.
 
 ## Combine — proving and closing the loop

skills/af_audit_skill_apis.md

@@ -42,8 +42,8 @@ one with the PyAuto\* stack — source the project's `activate.sh` first.
 
 ```bash
 source activate.sh
-python -c "import autoconf, autofit; \
-print({m.__name__: getattr(m, '__version__', '?') for m in [autoconf, autofit]})"
+python -c "import autonerves, autofit; \
+print({m.__name__: getattr(m, '__version__', '?') for m in [autonerves, autofit]})"
 ```
 
 If those imports fail, stop and route the user to
@@ -226,7 +226,7 @@ A complete audit may surface ten or more misses. Don't try to fix all of them in
 push. Ask the user how they want to slice the work:
 
 - *"Fix the skill that triggered this audit first, then sweep the rest?"*
-- *"Group fixes by library — the autoconf drift in one pass, the PyAutoFit drift in
+- *"Group fixes by library — the autonerves drift in one pass, the PyAutoFit drift in
   another?"*
 - *"One file per commit, or batch?"*
 
@@ -323,7 +323,7 @@ complete.
 ## Agent procedural checklist
 
 1. Confirm scope (skills / wiki / scripts / all) and whether to apply fixes now.
-2. `source activate.sh`; verify autoconf + autofit import.
+2. `source activate.sh`; verify autonerves + autofit import.
 3. `python autoassistant/audit_skill_apis.py --check-version` — is the installed stack
    still on the pinned baseline? If it drifted, that's likely *why* you're here.
 4. `python autoassistant/audit_skill_apis.py --scope <scope>`.

skills/af_configure_search.md

@@ -102,7 +102,7 @@ telling the user before they wonder why a second run finishes instantly.
 
 Per-sampler defaults live in `config/non_linear/` — a project can retune a sampler
 globally there instead of repeating kwargs in every script
-(`PyAutoConf:autoconf/conf.py`).
+(`PyAutoNerves:autonerves/conf.py`).
 
 ## Combine
 

skills/af_refresh_api_docs.md

@@ -36,8 +36,8 @@ Start from an environment where the PyAuto* stack imports cleanly:
 
 ```bash
 source activate.sh
-python -c "import autoconf, autofit; \
-print({m.__name__: getattr(m, '__version__', '?') for m in [autoconf, autofit]})"
+python -c "import autonerves, autofit; \
+print({m.__name__: getattr(m, '__version__', '?') for m in [autonerves, autofit]})"
 ```
 
 If those imports fail, stop and route the user to
@@ -152,7 +152,7 @@ Then commit on the cadence they chose.
 ## Agent procedural checklist
 
 1. Confirm scope, reference point, and whether this is report-only or fix-and-commit.
-2. `source activate.sh`; verify autoconf + autofit import.
+2. `source activate.sh`; verify autonerves + autofit import.
 3. Run `python autoassistant/refresh_api_docs.py --scope <scope>` to do preflight and launch the audit.
 4. Read the audit report and fix symbol drift first.
 5. For wiki pages in scope, diff each page's pinned sources against the target repo HEAD and rewrite only changed sections.

skills/af_setup_environment.md

@@ -5,7 +5,7 @@ description: Detect, install, and configure a Python environment for the PyAutoF
 
 # Setting up an environment for the PyAuto\* stack
 
-This skill installs the libraries the workspace targets — PyAutoConf and PyAutoFit —
+This skill installs the libraries the workspace targets — PyAutoNerves and PyAutoFit —
 and prepares the sandbox so the rest of the skills will run. The user picks one of two
 install modes only if the active environment is not already usable: pip (fastest path to
 "import autofit works") or editable-clone (source-level access, slower but lets you read
@@ -57,7 +57,7 @@ For background on what each library does, point at `wiki/core/stack/overview.md`
 
 ## Branch — Pip install
 
-The simplest path. PyAutoFit declares autoconf as a transitive dep, so a single
+The simplest path. PyAutoFit declares autonerves as a transitive dep, so a single
 `pip install` pulls everything in.
 
 ```bash
@@ -79,7 +79,7 @@ protocol SDK (assistant-environment only — never a library requirement).
 Verify:
 
 ```bash
-python -c "import autofit, autoconf; print(autofit.__version__)"
+python -c "import autofit, autonerves; print(autofit.__version__)"
 ```
 
 If that prints a version (no traceback), the install is good.
@@ -96,7 +96,7 @@ mkdir -p sources && cd sources
 
 # Order matters — install from the bottom of the dependency chain up.
 # URLs come from ../sources.yaml.
-git clone https://github.com/PyAutoLabs/PyAutoConf.git
+git clone https://github.com/PyAutoLabs/PyAutoNerves.git
 git clone https://github.com/PyAutoLabs/PyAutoFit.git
 
 cd ..
@@ -105,7 +105,7 @@ python3.11 -m venv .venv
 source .venv/bin/activate
 pip install --upgrade pip
 
-for repo in PyAutoConf PyAutoFit; do
+for repo in PyAutoNerves PyAutoFit; do
     pip install -e "sources/$repo"
 done
 ```
@@ -117,7 +117,7 @@ than hand-editing this skill.
 Verify the same way as for pip:
 
 ```bash
-python -c "import autofit, autoconf; print(autofit.__version__)"
+python -c "import autofit, autonerves; print(autofit.__version__)"
 ```
 
 ## Sandbox / restricted-filesystem environments
@@ -139,10 +139,10 @@ real inference.
 Save this to `scripts/verify_environment.py` and run it:
 
 ```python
-import autoconf
+import autonerves
 import autofit as af
 
-print("autoconf :", autoconf.__version__)
+print("autonerves :", autonerves.__version__)
 print("autofit  :", af.__version__)
 
 # A minimal model composition — proves the inference stack is wired up.

skills/af_update_wiki.md

@@ -18,7 +18,7 @@ dumps go in the libraries' own docs/ folders — that's not what this wiki is fo
 
 Before starting, confirm with the user:
 
-- Which source repos to update against — both (PyAutoConf + PyAutoFit), or one?
+- Which source repos to update against — both (PyAutoNerves + PyAutoFit), or one?
 - Whether to update against `main` of each repo, or a tagged release.
 - Whether to commit changes incrementally per-page or in one batch at the end.
 

skills/start-new-project.md

@@ -95,7 +95,7 @@ reproducible-science subset; generate the thin assistant layer; refer back for e
 else.
 
 **Copy from the assistant into the project** (the science needs these to run):
-- `config/` (PyAutoConf YAML — search defaults, priors, output policy)
+- `config/` (PyAutoNerves YAML — search defaults, priors, output policy)
 - `activate.sh` (sourced locally and by HPC batch scripts)
 - `scripts/` (the chosen analysis scripts, or empty)
 - datasets (Step 3) into `data/<sample>/...`

sources.yaml

@@ -9,10 +9,10 @@
 # the reference branch.
 
 projects:
-  - name: PyAutoConf
-    import: autoconf
+  - name: PyAutoNerves
+    import: autonerves
     role: config           # YAML config loading, prior resolution
-    git: https://github.com/PyAutoLabs/PyAutoConf
+    git: https://github.com/PyAutoLabs/PyAutoNerves
 
   - name: PyAutoFit
     import: autofit
@@ -37,5 +37,5 @@ projects:
 # Dependency chain (top-to-bottom). Skills target the top; lower layers
 # surface in the wiki when the user needs to understand them.
 dependency_chain:
-  - PyAutoConf
+  - PyAutoNerves
   - PyAutoFit

wiki/core/README.md

@@ -11,7 +11,7 @@ the user's domain papers and a per-clone journal respectively (see
 
 - [`index.md`](./index.md) — top-level map; the entry point for an agent or human
   reader.
-- `stack/` — one page per source library (`autoconf`, `autofit`), plus an overview of
+- `stack/` — one page per source library (`autonerves`, `autofit`), plus an overview of
   how they fit together.
 - `concepts/` — statistics + framework explanations: priors, model composition,
   searches, samples, graphical models, evidence.