refactor: rename darnit-reproducibility to darnit-amber

.github/workflows/release.yml

@@ -222,7 +222,7 @@ jobs:
   # token). Migrate to project-scoped tokens once the projects exist on PyPI.
   #
   # Sequenced via `needs:` because darnit-baseline, darnit-gittuf,
-  # darnit-reproducibility, and darnit-mcp declare `darnit-core>=...` runtime
+  # darnit-amber, and darnit-mcp declare `darnit-core>=...` runtime
   # deps; darnit-mcp additionally depends on the other four. Publishing them
   # before the deps are on the index briefly produces unresolvable wheels.
 
@@ -289,8 +289,8 @@ jobs:
           password: ${{ secrets.PYPI_API_TOKEN }}
           skip-existing: true
 
-  publish-darnit-reproducibility:
-    name: Publish darnit-reproducibility to PyPI
+  publish-darnit-amber:
+    name: Publish darnit-amber to PyPI
     needs: [preflight, build, publish-darnit-core]
     runs-on: ubuntu-latest
     timeout-minutes: 10
@@ -303,10 +303,10 @@ jobs:
           name: dist
           path: dist/
 
-      - name: Publish darnit-reproducibility
+      - name: Publish darnit-amber
         uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # release/v1
         with:
-          packages-dir: dist/darnit-reproducibility/
+          packages-dir: dist/darnit-amber/
           password: ${{ secrets.PYPI_API_TOKEN }}
           skip-existing: true
 
@@ -317,7 +317,7 @@ jobs:
       - build
       - publish-darnit-baseline
       - publish-darnit-gittuf
-      - publish-darnit-reproducibility
+      - publish-darnit-amber
     runs-on: ubuntu-latest
     timeout-minutes: 10
     permissions:
@@ -482,7 +482,7 @@ jobs:
           ## Install
 
           - **MCP (Claude Code / Claude Desktop):** \`darnit install\` writes an \`uvx --from darnit-mcp\` config for you. See [docs/install/](https://github.com/${GITHUB_REPOSITORY}/tree/${TAG}/docs/install).
-          - **PyPI:** \`pip install darnit-mcp==${VERSION}\` (installs the meta-package plus \`darnit-core\`, \`darnit-baseline\`, \`darnit-gittuf\`, \`darnit-reproducibility\`).
+          - **PyPI:** \`pip install darnit-mcp==${VERSION}\` (installs the meta-package plus \`darnit-core\`, \`darnit-baseline\`, \`darnit-gittuf\`, \`darnit-amber\`).
           - **Container:** \`docker pull ghcr.io/${owner_lc}/darnit:${TAG}\`.
           - **Standalone binary / Homebrew:** not yet in this release. Tracked for follow-ups.
 
@@ -512,7 +512,7 @@ jobs:
       - publish-darnit-core
       - publish-darnit-baseline
       - publish-darnit-gittuf
-      - publish-darnit-reproducibility
+      - publish-darnit-amber
       - publish-darnit-mcp
       - container_build_push
       - release
@@ -527,7 +527,7 @@ jobs:
           PYPI_CORE: ${{ needs.publish-darnit-core.result }}
           PYPI_BASELINE: ${{ needs.publish-darnit-baseline.result }}
           PYPI_GITTUF: ${{ needs.publish-darnit-gittuf.result }}
-          PYPI_REPRO: ${{ needs.publish-darnit-reproducibility.result }}
+          PYPI_REPRO: ${{ needs.publish-darnit-amber.result }}
           PYPI_MCP: ${{ needs.publish-darnit-mcp.result }}
           CONTAINER: ${{ needs.container_build_push.result }}
           RELEASE: ${{ needs.release.result }}
@@ -540,7 +540,7 @@ jobs:
             echo "| pypi-darnit-core | $PYPI_CORE |"
             echo "| pypi-darnit-baseline | $PYPI_BASELINE |"
             echo "| pypi-darnit-gittuf | $PYPI_GITTUF |"
-            echo "| pypi-darnit-reproducibility | $PYPI_REPRO |"
+            echo "| pypi-darnit-amber | $PYPI_REPRO |"
             echo "| pypi-darnit-mcp | $PYPI_MCP |"
             echo "| container | $CONTAINER |"
             echo "| github-release | $RELEASE |"

CLAUDE.md

@@ -142,7 +142,7 @@ my-framework = "my_framework:register"
 
 ### Framework config resolution (feature 021)
 
-`get_framework_config_path()` MUST use `importlib.resources.files(__package__) / "<framework>.toml"` -- never `Path(__file__).parent.parent...`. The framework TOML MUST live INSIDE `src/<module>/` (alongside `implementation.py`), not sibling to `src/`, so hatchling's default `packages = ["src/<module>"]` includes it in the wheel and `importlib.resources` finds it under both editable and wheel installs. See `packages/darnit-baseline`, `packages/darnit-gittuf`, `packages/darnit-reproducibility` for reference layouts; `packages/darnit-hello` is the minimal template.
+`get_framework_config_path()` MUST use `importlib.resources.files(__package__) / "<framework>.toml"` -- never `Path(__file__).parent.parent...`. The framework TOML MUST live INSIDE `src/<module>/` (alongside `implementation.py`), not sibling to `src/`, so hatchling's default `packages = ["src/<module>"]` includes it in the wheel and `importlib.resources` finds it under both editable and wheel installs. See `packages/darnit-baseline`, `packages/darnit-gittuf`, `packages/darnit-amber` for reference layouts; `packages/darnit-hello` is the minimal template.
 
 ## Sieve Pattern
 
@@ -365,7 +365,7 @@ else:
 ## Active Technologies
 - Python 3.11/3.12 (workspace targets) plus bash for release scripts and GitHub Actions YAML + `shiv` (binary builder), `cosign` (image + binary signing), `syft` (SBOM generation), `docker buildx` (multi-arch images), `gh` CLI (release creation), Sigstore-action (PyPI wheel signing via `pypa/gh-action-pypi-publish`). No new runtime dependencies in any darnit Python package. (012-packaging-distribution)
 - External release surfaces only — PyPI, TestPyPI, GHCR, GitHub Releases (binary assets + attestations), `kusari-oss/homebrew-tap` repo (formula). Repo itself stores only build configs and workflow definitions. (012-packaging-distribution)
-- Python 3.11/3.12 (workspace targets — same as the rest of darnit) + `pydantic >= 2.0` (already used for `FrameworkConfig`); `packaging` for PEP 440 `SpecifierSet` (declared by `darnit-reproducibility` as of feature 037; darnit-core imports it at runtime without declaring it, which is tracked separately). `tomllib` from stdlib for TOML parsing. No new runtime dependencies. (013-plugin-composition)
+- Python 3.11/3.12 (workspace targets — same as the rest of darnit) + `pydantic >= 2.0` (already used for `FrameworkConfig`); `packaging` for PEP 440 `SpecifierSet` (declared by `darnit-amber` as of feature 037; darnit-core imports it at runtime without declaring it, which is tracked separately). `tomllib` from stdlib for TOML parsing. No new runtime dependencies. (013-plugin-composition)
 - Filesystem only. Composition is resolved in-memory at framework-config load time; no new persistent state. (013-plugin-composition)
 
 ## Recent Changes

docs/design/reproducibility-attestation-system.md → docs/design/amber-attestation-system.md

@@ -2,7 +2,7 @@
 
 ## Executive Summary
 
-This document describes a system design for **darnit-reproducibility**, an extension to the darnit compliance framework that enables automated reproducibility verification and attestation for computational research software. The system addresses a critical gap in scientific computing: the inability to reliably rebuild and re-execute research software (e.g., protein folding simulations, molecular dynamics, genomics pipelines) in deterministic ways.
+This document describes a system design for **darnit-amber**, an extension to the darnit compliance framework that enables automated reproducibility verification and attestation for computational research software. The system addresses a critical gap in scientific computing: the inability to reliably rebuild and re-execute research software (e.g., protein folding simulations, molecular dynamics, genomics pipelines) in deterministic ways.
 
 The system operates in two primary flows:
 
@@ -256,7 +256,7 @@ mutation {
     hasMetadata: {
       key: "https://darnit.dev/attestations/reproducibility/v1",
       value: "{...attestation JSON...}",
-      origin: "darnit-reproducibility",
+      origin: "darnit-amber",
       collector: "darnit"
     }
   )
@@ -514,7 +514,7 @@ witness_attestation_bundle:
 #### Ingestor Implementation
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/ingest/witness.py
+# packages/darnit-amber/src/darnit_amber/ingest/witness.py
 
 from dataclasses import dataclass
 from typing import Optional, List, Dict, Any
@@ -580,7 +580,7 @@ The Provenance Analyzer processes Witness data to understand the complete depend
 #### Analysis Pipeline
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/analysis/provenance.py
+# packages/darnit-amber/src/darnit_amber/analysis/provenance.py
 
 from dataclasses import dataclass, field
 from typing import List, Dict, Set, Optional
@@ -745,7 +745,7 @@ Generates environment definitions based on the provenance analysis.
 #### Generator Interface
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/generate/base.py
+# packages/darnit-amber/src/darnit_amber/generate/base.py
 
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
@@ -784,7 +784,7 @@ class EnvironmentGenerator(ABC):
 #### Container Generator (Docker/Singularity)
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/generate/container.py
+# packages/darnit-amber/src/darnit_amber/generate/container.py
 
 class ContainerGenerator(EnvironmentGenerator):
     """Generates Dockerfile or Singularity definition files."""
@@ -842,7 +842,7 @@ class ContainerGenerator(EnvironmentGenerator):
         hardware: HardwareRequirements
     ) -> str:
         lines = [
-            f"# Auto-generated by darnit-reproducibility",
+            f"# Auto-generated by darnit-amber",
             f"# Provenance: {self._provenance_comment()}",
             f"FROM {base_image}",
             "",
@@ -904,7 +904,7 @@ class ContainerGenerator(EnvironmentGenerator):
 #### HPC Generator (Slurm/PBS)
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/generate/hpc.py
+# packages/darnit-amber/src/darnit_amber/generate/hpc.py
 
 class HPCGenerator(EnvironmentGenerator):
     """Generates HPC job scripts and environment modules."""
@@ -993,7 +993,7 @@ class HPCGenerator(EnvironmentGenerator):
 #### Nix Generator
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/generate/nix.py
+# packages/darnit-amber/src/darnit_amber/generate/nix.py
 
 class NixGenerator(EnvironmentGenerator):
     """Generates Nix derivations for maximum reproducibility."""
@@ -1031,7 +1031,7 @@ class NixGenerator(EnvironmentGenerator):
         nix_deps: List["NixPackage"]
     ) -> str:
         return f'''{{
-  description = "Reproducible environment generated by darnit-reproducibility";
+  description = "Reproducible environment generated by darnit-amber";
 
   inputs = {{
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05";
@@ -1086,7 +1086,7 @@ class NixGenerator(EnvironmentGenerator):
 Executes builds in generated environments with Witness tracing.
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/execute/engine.py
+# packages/darnit-amber/src/darnit_amber/execute/engine.py
 
 from dataclasses import dataclass
 from typing import Optional, List
@@ -1224,7 +1224,7 @@ class ExecutionEngine:
 Generates reproducibility attestations in in-toto format.
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/attestation/reproducibility.py
+# packages/darnit-amber/src/darnit_amber/attestation/reproducibility.py
 
 from dataclasses import dataclass, field
 from typing import List, Dict, Any, Optional
@@ -1296,7 +1296,7 @@ class ReproducibilityAttestationGenerator:
             "predicateType": predicate.predicate_type,
             "predicate": {
                 "assessor": {
-                    "name": "darnit-reproducibility",
+                    "name": "darnit-amber",
                     "version": self.config.version,
                     "timestamp": datetime.utcnow().isoformat() + "Z"
                 },
@@ -1403,7 +1403,7 @@ class ReproducibilityAttestationGenerator:
 Publishes attestations to OpenSSF GUAC.
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/publish/guac.py
+# packages/darnit-amber/src/darnit_amber/publish/guac.py
 
 from dataclasses import dataclass
 from typing import Optional, List, Dict, Any
@@ -1554,7 +1554,7 @@ class GUACPublisher:
                 "value": json.dumps(attestation["predicate"]),
                 "timestamp": attestation["predicate"]["assessor"]["timestamp"],
                 "justification": "Reproducibility attestation from darnit",
-                "origin": "darnit-reproducibility",
+                "origin": "darnit-amber",
                 "collector": "darnit"
             }
         }
@@ -1632,7 +1632,7 @@ class GUACPublisher:
 ### Tool Definitions
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/server/tools.py
+# packages/darnit-amber/src/darnit_amber/server/tools.py
 
 REPRODUCIBILITY_TOOLS = [
     {
@@ -1874,12 +1874,12 @@ reproducibility:
 ### Plugin Registration
 
 ```python
-# packages/darnit-reproducibility/src/darnit_reproducibility/__init__.py
+# packages/darnit-amber/src/darnit_amber/__init__.py
 
 from darnit.core.plugin import ComplianceImplementation
 
 def register() -> ComplianceImplementation:
-    """Register darnit-reproducibility as a compliance implementation."""
+    """Register darnit-amber as a compliance implementation."""
     return ReproducibilityImplementation()
 
 class ReproducibilityImplementation:

packages/darnit-reproducibility/README.md → packages/darnit-amber/README.md

@@ -1,4 +1,4 @@
-# darnit-reproducibility
+# darnit-amber
 
 Scientific reproducibility checks plugin for darnit.
 

packages/darnit-reproducibility/pyproject.toml → packages/darnit-amber/pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "darnit-reproducibility"
+name = "darnit-amber"
 version = "0.1.0"
 description = "Scientific reproducibility checks plugin for darnit"
 readme = "README.md"
@@ -15,16 +15,16 @@ dependencies = [
 ]
 
 [project.entry-points."darnit.implementations"]
-reproducibility = "darnit_reproducibility:register"
+amber = "darnit_amber:register"
 
 [project.entry-points."darnit.frameworks"]
-reproducibility = "darnit_reproducibility:get_framework_path"
+amber = "darnit_amber:get_framework_path"
 
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/darnit_reproducibility"]
-# reproducibility.toml lives at src/darnit_reproducibility/reproducibility.toml
+packages = ["src/darnit_amber"]
+# amber.toml lives at src/darnit_amber/amber.toml
 # (feature 021) and is packaged automatically by the entry above.

packages/darnit-reproducibility/src/darnit_reproducibility/__init__.py → packages/darnit-amber/src/darnit_amber/__init__.py

@@ -2,12 +2,12 @@
 
 from pathlib import Path
 
-from .implementation import ReproducibilityImplementation
+from .implementation import AmberImplementation
 
 
-def register() -> ReproducibilityImplementation:
+def register() -> AmberImplementation:
     """Entry point called by darnit plugin discovery."""
-    impl = ReproducibilityImplementation()
+    impl = AmberImplementation()
     impl.register_controls()
     impl.register_sieve_handlers()
     return impl
@@ -19,7 +19,7 @@ def get_framework_path() -> Path:
     # and name lookup. The 'darnit.implementations' get_framework_config_path()
     # feeds the audit path instead; both entry points are required. Delegating
     # here ensures both paths use the same importlib.resources resolver.
-    return ReproducibilityImplementation().get_framework_config_path()
+    return AmberImplementation().get_framework_config_path()
 
 
-__all__ = ["ReproducibilityImplementation", "register", "get_framework_path"]
+__all__ = ["AmberImplementation", "register", "get_framework_path"]

packages/darnit-reproducibility/src/darnit_reproducibility/reproducibility.toml → packages/darnit-amber/src/darnit_amber/amber.toml

@@ -1,13 +1,13 @@
 [metadata]
 schema_version = "0.1.0-alpha"
-name = "reproducibility"
-display_name = "Scientific Reproducibility Checks"
+name = "amber"
+display_name = "Amber — Scientific Reproducibility Checks"
 version = "0.1.0"
 spec_version = "0.1.0"
 description = "Checks that builds are reproducible and verifiable"
 
 [mcp]
-name = "reproducibility"
+name = "amber"
 description = "Run scientific reproducibility checks on a repository"
 
 [mcp.tools.audit_reproducibility]

packages/darnit-reproducibility/src/darnit_reproducibility/handlers.py → packages/darnit-amber/src/darnit_amber/handlers.py

@@ -15,7 +15,7 @@
 
 from .witness_attestation import WitnessCheckResult, check_witness_attestation
 
-logger = get_logger("darnit_reproducibility.handlers")
+logger = get_logger("darnit_amber.handlers")
 
 
 _MAX_EVIDENCE_EXAMPLES = 10

packages/darnit-reproducibility/src/darnit_reproducibility/implementation.py → packages/darnit-amber/src/darnit_amber/implementation.py

@@ -4,10 +4,10 @@
 from typing import Any
 
 from darnit.core.plugin import ControlSpec
-from darnit_reproducibility import handlers
+from darnit_amber import handlers
 
 
-class ReproducibilityImplementation:
+class AmberImplementation:
     """Scientific reproducibility checks plugin.
 
     Provides checks for dependency pinning, build environment
@@ -17,11 +17,11 @@ class ReproducibilityImplementation:
 
     @property
     def name(self) -> str:
-        return "reproducibility"
+        return "amber"
 
     @property
     def display_name(self) -> str:
-        return "Scientific Reproducibility Checks"
+        return "Amber — Scientific Reproducibility Checks"
 
     @property
     def version(self) -> str:
@@ -93,11 +93,11 @@ def get_remediation_registry(self) -> dict[str, Any]:
     def get_framework_config_path(self) -> Path | None:
         from importlib.resources import files
 
-        resource = files(__package__) / "reproducibility.toml"
+        resource = files(__package__) / "amber.toml"
         path = Path(str(resource))
         if not path.is_file():
             raise FileNotFoundError(
-                f"reproducibility.toml not found in installed darnit_reproducibility "
+                f"amber.toml not found in installed darnit_amber "
                 f"package at {path}. This indicates a broken build; check the "
                 f"wheel's force-include configuration."
             )

packages/darnit-reproducibility/src/darnit_reproducibility/witness_attestation.py → packages/darnit-amber/src/darnit_amber/witness_attestation.py

@@ -41,7 +41,7 @@
 from darnit.core.logging import get_logger
 from darnit.sieve.handler_registry import HandlerContext
 
-logger = get_logger("darnit_reproducibility.witness_attestation")
+logger = get_logger("darnit_amber.witness_attestation")
 
 try:
     from sigstore.models import Bundle