viva-discovery-engine 0.1.0__tar.gz

viva_discovery_engine-0.1.0/.github/workflows/downstream.yml

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+name: downstream
+
+# The "in sync" guard: before a change to the engine lands (or releases), prove it
+# still satisfies its primary consumer's contract. viva-superpowers is a facade of
+# back-compat shims over discovery_engine — its tests/test_discovery_engine_facade.py
+# asserts viva_superpowers.<m> IS discovery_engine.<m> across the whole shim set. We
+# install viva-superpowers against THIS discovery-engine (not the pinned one) and run
+# that contract, so a breaking change here is caught before it propagates downstream.
+#
+# Cross-repo checkout needs a token with read access to viva-superpowers. Set a repo
+# secret DOWNSTREAM_TOKEN (a PAT or a fine-grained token scoped to the consumer repos);
+# until it is set, this job skips cleanly (stays green) rather than failing.
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+concurrency:
+  group: downstream-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  facade:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Is the downstream token configured?
+        id: tok
+        run: echo "has=${{ secrets.DOWNSTREAM_TOKEN != '' }}" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout discovery-engine (this ref)
+        if: steps.tok.outputs.has == 'true'
+        uses: actions/checkout@v4
+        with:
+          path: discovery-engine
+
+      - name: Checkout viva-superpowers (main)
+        if: steps.tok.outputs.has == 'true'
+        uses: actions/checkout@v4
+        with:
+          repository: vivarium-collective/viva-superpowers
+          ref: main
+          token: ${{ secrets.DOWNSTREAM_TOKEN }}
+          path: viva-superpowers
+
+      - name: Install uv
+        if: steps.tok.outputs.has == 'true'
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        if: steps.tok.outputs.has == 'true'
+        run: uv python install 3.12
+
+      - name: Install viva-superpowers, then override discovery-engine with THIS ref
+        if: steps.tok.outputs.has == 'true'
+        run: |
+          uv venv
+          uv pip install -e ./viva-superpowers pytest
+          # editable local engine shadows the git-pinned one (same dist name)
+          uv pip install -e ./discovery-engine
+
+      - name: Run the shim-facade contract against this discovery-engine
+        if: steps.tok.outputs.has == 'true'
+        run: uv run python -m pytest -q viva-superpowers/tests/test_discovery_engine_facade.py
+
+      - name: Note when skipped
+        if: steps.tok.outputs.has != 'true'
+        run: echo "DOWNSTREAM_TOKEN not set — skipping the downstream facade check. Add the secret to enable it."

viva_discovery_engine-0.1.0/.github/workflows/release.yml

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+name: release
+
+# Cut a release whenever a semver tag is pushed. This turns the engine's
+# `branch=main` consumption into tagged, PyPI-published releases, so consumers can
+# pin a VERSION (`discovery-engine>=X.Y`) instead of a moving branch or a git commit
+# — the foundation of keeping the repos decoupled but reproducibly in sync.
+#
+# discovery-engine is the one core package still unpublished (v0.1.0, git `branch=main`
+# only): every consumer is forced onto `branch=main` for it, which cascades the whole
+# git-main dependency chain and the silent drift. Publishing it to PyPI (like
+# bigraph-schema / process-bigraph / viva-superpowers already do) lets consumers pin
+# semver and lets GitHub users `pip install` a coherent released set.
+#
+# Trusted publishing (OIDC) — no stored token. Requires a one-time PyPI setup:
+# register the `discovery-engine` project and add this repo + workflow + the `release`
+# environment as a trusted publisher (https://docs.pypi.org/trusted-publishers/).
+on:
+  push:
+    tags: ["v*"]
+
+permissions:
+  contents: read
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write   # required for OIDC trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up uv and Python
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.12"
+          enable-cache: true
+          cache-dependency-glob: "**/uv.lock"
+
+      - name: Verify the tag matches pyproject version
+        run: |
+          tag_version="${GITHUB_REF_NAME#v}"
+          pyproject_version=$(uv version --short)
+          if [ "$tag_version" != "$pyproject_version" ]; then
+            echo "Tag ($tag_version) != pyproject.toml version ($pyproject_version)"
+            exit 1
+          fi
+
+      - name: Build distributions
+        run: uv build
+
+      - name: Publish to PyPI via trusted publisher
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    needs: publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Create the GitHub Release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh release create "${{ github.ref_name }}" --generate-notes --verify-tag

viva_discovery_engine-0.1.0/.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: test-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Create venv + install (with dev extras)
+        run: |
+          uv venv
+          uv pip install -e '.[dev]'
+
+      - name: Check import contracts (no back-edge to consumers)
+        run: uv run lint-imports
+
+      - name: Run the test suite
+        run: uv run python -m pytest -q

viva_discovery_engine-0.1.0/.gitignore

@@ -0,0 +1,16 @@
+__pycache__/
+*.py[cod]
+*.egg-info/
+.eggs/
+build/
+dist/
+.venv/
+venv/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.DS_Store
+*.so
+.coverage
+htmlcov/
+uv.lock

viva_discovery_engine-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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viva_discovery_engine-0.1.0/PKG-INFO

@@ -0,0 +1,199 @@
+Metadata-Version: 2.5
+Name: viva-discovery-engine
+Version: 0.1.0
+Summary: A derive-first scientific-investigation discovery cycle engine for the Vivarium ecosystem.
+Project-URL: Homepage, https://github.com/vivarium-collective/discovery-engine
+Project-URL: Repository, https://github.com/vivarium-collective/discovery-engine
+Author: Vivarium Collective
+License: MIT
+License-File: LICENSE
+Keywords: discovery,process-bigraph,scientific-investigation,vivarium
+Requires-Python: >=3.11
+Requires-Dist: bigraph-schema
+Requires-Dist: click>=8.1
+Requires-Dist: filelock>=3.12
+Requires-Dist: jinja2>=3.1
+Requires-Dist: jsonschema[format-nongpl]>=4.21
+Requires-Dist: numpy>=1.24
+Requires-Dist: polars>=0.20
+Requires-Dist: process-bigraph
+Requires-Dist: psutil>=5.9
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0
+Requires-Dist: ruamel-yaml>=0.18
+Requires-Dist: scipy>=1.11
+Requires-Dist: typer>=0.12
+Requires-Dist: viva-emitters[parquet]>=0.2.3
+Requires-Dist: viva-workspace
+Provides-Extra: dev
+Requires-Dist: import-linter>=2.0; extra == 'dev'
+Requires-Dist: pytest>=7; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# discovery-engine
+
+<p align="center">
+  <img src="docs/discovery-engine-cycle.png" alt="The Discovery Engine discovery cycle" width="640">
+</p>
+
+The **investigation/study framework + the derive-first discovery cycle** for the
+Vivarium ecosystem. It owns the investigation/study data model, its lifecycle
+(canonicalize, contracts, scaffold, seed, migrate, audit), report/card
+generation — and the discovery cycle itself: it turns an investigation (an
+`investigation.yaml` plus its member `study.yaml` files) into a structured,
+reproducible view of what is known, what is unresolved, what is most valuable to
+do next, whether a study is materially ready to run, and how to cycle it forward
+— and now also **drives that cycle**: reconcile evidence, plan, design
+discriminating studies, acquire models, evaluate and promote claims, compose a
+transition model, and grow the investigation by seeding and refining studies —
+all without performing the science itself.
+
+It is a standalone library, consumed by:
+
+- **[viva-superpowers](https://github.com/vivarium-collective/viva-superpowers)** — the AI-agent skills that drive the engine and the workbench.
+- **[vivarium-workbench](https://github.com/vivarium-collective/vivarium-workbench)** — the UI/server for investigations and studies.
+
+## Two layers
+
+The engine has two cooperating layers over the same inputs. See
+[`docs/architecture.md`](docs/architecture.md) for the full reference.
+
+**Layer 1 — the pure projection** (assess + gate-readiness + execute + persist):
+
+```
+run_cycle        → knowledge / argument / narrative / gates / validators / suggestions
+frontier/closure → the prioritized unresolved work + the machine-checkable closure test
+opportunities    → value-ranked frontier (info·impact·enable·closure − cost)
+run_readiness    → is a study materially ready to produce an evaluable, rendered result?
+execute_action   → carry out the next move, gated by consequence
+advance_cycle    → build-if-needed and run the open questions
+persist_cycle    → the slim regenerable cycle_state + persist-time narrative renewal
+```
+
+It is **pure** (no disk I/O) and **derive-first**: every view is computed from
+the studies, then merged over any authored override — authored wins, an empty
+authored value never clobbers a derived one. Same inputs always yield the same
+bundle.
+
+**Layer 2 — the phased discovery cycle** (the generative, evidence-integrity
+half). Each phase produces a typed contract and is driven by one CLI verb:
+
+| Phase | What it decides | CLI verb | Module |
+|---|---|---|---|
+| **A** reconcile | classify each finding's evidence: verified / provisional / contradicted / unsupported | `reconcile-evidence` | `evidence_integrity` |
+| **B** plan | one ranked, dependency-ordered portfolio: REPAIR · RESOLVE · EXTEND | `plan` | `candidate_action` |
+| **C** design | a discriminating study: contrast, controls, registered predictions, committed decision rule | `design` | `experiment_design` |
+| **D** build | capability-driven model acquisition (reuse / wrap / build); immutable `ModelVersion` | `build-model` | `model_architect` |
+| **E** execute | run the designed studies, consequence- and autonomy-gated | `advance` / `execute` | (Layer 1) |
+| **F** evaluate | promote or reject claims (support × evidence integrity); emit a `DiscoveryDelta` | `evaluate` / `delta` | `evaluation` |
+
+**Growth ops** close the loop — propose → seed → run → promote → refine — gated
+by a `human_in_the_loop` (default) vs `autonomous` policy:
+
+| Op | What it does | CLI verb | Module |
+|---|---|---|---|
+| suggest | propose new studies (followups, narrative gaps, gated decisions) | `suggest` | `discover` |
+| seed | author a complete, run-ready `study.yaml` from a parent + proposal/finding | `seed-study` | `study_seeding` |
+| refine | deepen an existing study — add seeds, sweep variants, raise model fidelity | `refine-study` | `study_refinement` |
+
+## Install
+
+Use it as a **git dependency** (not published to a package index). In the
+Vivarium ecosystem it's wired as a git source in the consumer's `pyproject.toml`,
+e.g. in viva-superpowers / vivarium-workbench:
+
+```toml
+dependencies = ["discovery-engine", ...]
+
+[tool.uv.sources]
+discovery-engine = { git = "https://github.com/vivarium-collective/discovery-engine.git", branch = "main" }
+```
+
+Then `uv lock` / `uv sync` resolves it. To work on this repo directly, clone it
+and run `uv sync`.
+
+Depends on `viva-emitters` (reads run results) and `viva-workspace` (resolves a
+workspace's layout); plus process-bigraph, bigraph-schema, numpy, polars,
+ruamel.yaml, pyyaml, click.
+
+## Use — library
+
+```python
+import discovery_engine as de
+
+inv = {"studies": ["s1"], "acceptance_criteria": [{"study": "s1", "behavior": "b"}]}
+studies = {"s1": {"name": "s1", "behavior_tests": [{"name": "b"}], "runs": []}}
+
+bundle = de.run_cycle(inv, studies)          # pure projection
+front  = de.frontier(bundle, inv)            # prioritized unresolved items
+clo    = de.closure(bundle, inv)             # {closed, open_items, ...}
+opps   = de.opportunities(bundle, inv)       # value-ranked
+```
+
+## Use — CLI
+
+Drive a workspace on disk with `discover <verb> <investigation>`.
+
+```bash
+# Assess
+discover status <inv>                 # project one cycle, print the summary
+discover crank <inv>                   # frontier + next action + closure
+discover complete <inv>                # the completion map (+ publishable axis)
+discover diagnose <inv>                # classify the crank's productivity bottlenecks
+discover hypotheses <inv>              # the competing-hypothesis support rollup
+discover opportunities <inv>           # value-ranked frontier
+discover suggest <inv>                 # new studies to run next
+
+# Cycle N+1 — the phased discovery cycle
+discover reconcile-evidence <inv>      # A: evidence integrity per finding
+discover plan <inv>                    # B: the CandidateAction portfolio
+discover design <inv> <study>          # C: a discriminating study design
+discover build-model <inv> --mechanism …   # D: reuse/wrap/build model acquisition
+discover evaluate <inv>                # F: claim verdicts (support × integrity)
+discover delta <inv>                   # F: the per-cycle DiscoveryDelta
+
+# Cycle N+2
+
+# Grow — propose · seed · refine (autonomy-gated)
+discover seed-study <inv> <parent> --slug … [--autonomy …] [--write]
+discover refine-study <inv> <study> [--composite …] [--autonomy …] [--write]
+
+# Advance / author
+discover advance <inv> [--autonomous]
+discover execute <inv> [--execute] [--autonomous] [--ai-decide]
+discover set-verdict <study> <verdict> [--rationale …]
+discover relate <downstream> <upstream> [--relation …]
+discover connect <inv> [--relation …]
+discover resolve <inv> <kind> <target> --rationale …
+
+# Maintenance
+discover cycle <inv>                   # the full cycle bundle (JSON)
+discover snapshot-validations <inv>
+```
+
+Every subcommand is self-describing via `discover <verb> -h`.
+
+## Design invariants
+
+- **Progress ⊥ verdict** — a failed execution is not a refuted hypothesis.
+- **Closure ⊥ frontier** — a settled argument can still carry non-blocking work.
+- **Publishable ⊥ closure** — presentation-completeness is its own axis.
+- **Evidence integrity ⊥ support** — whether a claim is backed is distinct from
+  whether its evidence is a registered run; a provisional-backed claim is
+  provisionally-supported, never promoted.
+- **Specify before run** — a discriminating study's predictions and decision
+  rule are committed before any run.
+- **Declaration ⇒ materialization** — a run is gated unless its composite
+  imports, observables are emittable, measures resolve and viz is rendered.
+- **Epistemic separation** — a validator's execution status never implies its
+  scientific judgment.
+
+## Architecture & roadmap
+
+- **[`docs/architecture.md`](docs/architecture.md)** — the full discovery-cycle
+  reference: the two layers, the Phase A–F + N+2 model, the typed contracts
+  (Hypothesis, Prediction, Evidence, ExperimentDesign, ModelVersion,
+  DiscoveryDelta, CandidateAction), and the propose→seed→run→promote→refine loop.
+- **[`docs/roadmap.md`](docs/roadmap.md)** — what has shipped and the remaining
+  backlog (EIG over calibrated distributions, figure critique, Bayesian belief
+  updates, autonomy budgets + per-decision logs, scientific quality metrics).