refactor: remove duplicated POD scientific modules

.github/workflows/ci.yml

@@ -127,24 +127,82 @@ jobs:
       - uses: Swatinem/rust-cache@v2
       - run: cargo build --bins
       - run: cargo run --quiet --bin spod -- --help
-      - name: Start REST server and query health
+      - name: Start REST server and verify job provenance
         shell: bash
         run: |
           set -euo pipefail
           port=18080
           cargo run --quiet --bin spod-rest &
           server_pid=$!
           trap 'kill "$server_pid" 2>/dev/null || true' EXIT
+
+          ready=false
           for attempt in {1..30}; do
-            if curl --fail --silent "http://127.0.0.1:${port}/healthz"; then
-              exit 0
+            if curl --fail --silent "http://127.0.0.1:${port}/healthz" >/dev/null; then
+              ready=true
+              break
+            fi
+            sleep 1
+          done
+          if [[ "$ready" != true ]]; then
+            echo "REST server did not become ready" >&2
+            exit 1
+          fi
+
+          job_id="$(
+            curl --fail --silent \
+              -H 'content-type: application/json' \
+              -d '{"enable_j2":false}' \
+              "http://127.0.0.1:${port}/jobs" \
+              | python3 -c 'import json,sys; print(json.load(sys.stdin)["id"])'
+          )"
+
+          status_json=
+          for attempt in {1..60}; do
+            status_json="$(curl --fail --silent "http://127.0.0.1:${port}/jobs/${job_id}")"
+            state="$(printf '%s' "$status_json" | python3 -c 'import json,sys; print(json.load(sys.stdin)["state"])')"
+            if [[ "$state" == "finished" ]]; then
+              break
+            fi
+            if [[ "$state" == "failed" ]]; then
+              echo "$status_json" >&2
+              exit 1
             fi
             sleep 1
           done
-          echo "REST server did not become ready" >&2
-          exit 1
+
+          state="$(printf '%s' "$status_json" | python3 -c 'import json,sys; print(json.load(sys.stdin)["state"])')"
+          [[ "$state" == "finished" ]]
+
+          run_dir="$SPOD_REST_OUT/$job_id"
+          request_path="$run_dir/request.json"
+          manifest_path="$run_dir/run.manifest.json"
+          test -f "$request_path"
+          test -f "$manifest_path"
+
+          python3 - "$manifest_path" "$request_path" <<'PY'
+          import hashlib
+          import json
+          import pathlib
+          import sys
+
+          manifest_path = pathlib.Path(sys.argv[1])
+          request_path = pathlib.Path(sys.argv[2])
+          manifest = json.loads(manifest_path.read_text())
+          payload = request_path.read_bytes()
+
+          assert len(manifest["inputs"]) == 1
+          input_ref = manifest["inputs"][0]
+          assert pathlib.Path(input_ref["path"]) == request_path
+          assert input_ref["kind"] == "configuration"
+          assert input_ref["bytes"] == len(payload)
+          digest = hashlib.sha256(payload).hexdigest()
+          assert input_ref["sha256"] == digest
+          assert manifest["config_sha256"] == digest
+          PY
         env:
           SPOD_REST_BIND: 127.0.0.1:18080
+          SPOD_REST_OUT: ${{ runner.temp }}/spod-rest-smoke
 
   docker:
     name: Docker image and compatibility smoke tests
@@ -160,7 +218,7 @@ jobs:
         run: |
           set -euo pipefail
           cleanup() {
-            docker rm -f spod-ci-default spod-ci-new spod-ci-legacy >/dev/null 2>&1 || true
+            docker rm -f spod-ci-default spod-ci-new >/dev/null 2>&1 || true
           }
           trap cleanup EXIT
 
@@ -183,16 +241,6 @@ jobs:
             sleep 1
           done
 
-          docker run -d --name spod-ci-legacy -p 18081:8080 \
-            -e SIDERUST_POD_REST_BIND=0.0.0.0:8080 spod:ci >/dev/null
-          for attempt in {1..30}; do
-            if curl --fail --silent "http://127.0.0.1:18081/healthz"; then
-              exit 0
-            fi
-            [[ "$attempt" -eq 30 ]] && exit 1
-            sleep 1
-          done
-
   coverage:
     name: Coverage
     runs-on: ubuntu-latest

CHANGELOG.md

@@ -1,162 +1,65 @@
 # Changelog
 
-All notable changes to this workspace are documented here. Format follows
+All notable changes to this repository are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and the project
-follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html) per
-crate (independent versioning).
+follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
-### Migration
-
-* Renamed the project to `spod`, including the Cargo package/library, the
-  `spod` and `spod-rest` binaries, repository URLs, and Docker image examples.
-* Renamed REST configuration variables to `SPOD_REST_BIND` and
-  `SPOD_REST_OUT`. The former `SIDERUST_POD_REST_BIND` and
-  `SIDERUST_POD_REST_OUT` names remain supported as deprecated fallbacks.
-  Update scripts and deployments to use the `SPOD_*` namespace.
-* Raised the MSRV to Rust 1.89 because the released `siderust` dependency
-  graph requires it. The Docker builder and CI MSRV job use the same version.
-* Split CI into blocking format, build, lint, feature-test, doctest,
-  documentation, service-smoke, Docker, coverage, guard, MSRV, and
-  supply-chain jobs.
-
-### Workspace
+### Changed
 
-* Consolidated the former multi-crate implementation into the current
-  `spod` package and migrated its Siderust ecosystem dependencies to
-  released crates.io versions.
-* Added a `[workspace.lints]` table (`unsafe_code = forbid`,
-  `missing_docs = deny`, `clippy::all = deny`,
-  `clippy::{todo,unimplemented,dbg_macro} = deny`,
-  `rustdoc::broken_intra_doc_links = deny`) and wired every workspace
-  member to inherit it via `[lints] workspace = true`. The full
-  workspace now builds clean under `cargo clippy --all-targets -- -D
-  warnings` and `cargo doc -- -D rustdoc::broken-intra-doc-links`.
-* CI scripts under `scripts/`:
-  * `check_no_todos.sh` (gates `todo!`/`unimplemented!`/TODO/FIXME/XXX
-    comments — currently passes with zero hits in the source tree).
-  * `snapshot_public_api.sh` (commits `crates/<crate>/api.snapshot`
-    baselines for all 14 library crates via `cargo public-api`; runs
-    in `--update` mode locally and as a diff in CI).
-* `.github/workflows/ci.yml`: extended the `build-test` job with
-  default / no-default-features / all-features test matrices and the
-  new `todo-sweep` step, and added an advisory `public-api` job that
-  diffs against the committed snapshots.
-* Per-crate library-hygiene baseline: every flagged `missing_docs`
-  warning across `siderust-{tle,dynamics,lambert,sgp4,spice}` and
-  `siderust-pod-{core,dynamics}` was resolved (120 warnings → 0)
-  with informative rustdoc covering items, fields, variants, and
-  units/encoding.
-* `siderust-pod-estimation::WlsSolverError`: new `Other(String)` variant
-  + `WlsSolverError::other()` constructor so callers can wrap upstream
-  propagation/STM failures during normal-equation assembly.
-* `siderust-pod-service::pipeline`: scoped `#[allow(deprecated)]`
-  around the legacy `finite_diff_stm_series` call site (upstream notes
-  explicitly preserve the series API for batch-LS use, since
-  `propagate_stm` only returns Φ at the terminal epoch).
+- Renamed the project and Cargo package to `spod`, including the `spod` and
+  `spod-rest` binaries, repository metadata, Docker examples, and REST
+  configuration variables.
+- Consolidated `spod` into a service/application built on the canonical
+  `siderust 0.12` POD APIs instead of maintaining a second POD scientific
+  implementation.
+- The synthetic POD pipeline now uses
+  `siderust::pod::propagation::VariationalPropagator` for aligned per-epoch
+  states and state-transition matrices.
+- CLI runs hash the executed YAML configuration with Siderust `DatasetRef`;
+  REST jobs hash a deterministic serialized request representation.
+- The service now rejects every real-data input while real-data ingestion is
+  not implemented, preventing unused files from being recorded as scientific
+  provenance.
+- The synthetic-only configuration rejects unsupported third-body gravity
+  instead of silently ignoring the requested force model.
+- REST jobs persist their canonical request document inside the run directory
+  before hashing it, so every manifest input path names a real auditable file.
+- Reusable scientific types and low-level SPICE parser APIs are imported
+  directly from Siderust rather than re-exported through compatibility
+  façades.
+- Raised the MSRV to Rust 1.89 to match the released Siderust dependency graph.
 
 ### Fixed
 
-* `siderust-pod-observations::gnss::sagnac_km`: convert the typed
-  `OMEGA_EARTH_RAD_S` (`InverseSeconds`) to its scalar value before the
-  km/(km·s⁻¹) division, restoring `cargo check` after the upstream
-  `siderust` typed-constant migration.
-* `siderust-pod-service`: pipeline & synthetic-arc generation updated
-  to the new five-argument `rk4_propagate_series`/`finite_diff_stm_series`
-  signatures (which now take a `&DynamicsContext` and return
-  `Result<_, DynamicsError>`); errors are wrapped through
-  `WlsSolverError::Other`. EKF replay test migrated to the
-  `EncodedTime`-based `OrbitState::new` and to
-  `StateCovariance::diagonal_from_sigmas` with typed
-  `Kilometers`/`KmPerSecond` arguments.
+- Run manifests now contain a real configuration SHA-256, canonical hashed
+  dataset references, and RFC3339 start/finish timestamps.
+- Removed unsupported synthetic carrier-ambiguity injection from the MVP,
+  whose estimated parameters are the six state components plus receiver
+  clock.
+- Synthetic state/STM indexing explicitly maps epoch zero to the identity STM
+  and subsequent epochs to the corresponding cumulative variational STM.
+- Runtime diagnostics no longer reference deleted implementation-plan
+  documents.
 
 ### Added
 
-* `siderust_pod_io::oem::{read_oem, OemFile, OemSegment}` — CCSDS OEM
-  KVN reader with full round-trip support (`write_oem` ↔ `read_oem`),
-  multi-segment parsing, tolerant skipping of `COVARIANCE_*` and
-  `MAN_*` sub-blocks, structured `PodIoError::Format` diagnostics with
-  line numbers, and a documented inverse `iso8601_to_jd`. Closes the
-  long-standing `todo!()` in `tests/functional/oem.rs` (replaced by a
-  proper round-trip functional test).
-
-* `siderust-pod-core::manifest`: shipped JSON-Schema (draft-07) for the
-  `RunManifest` and QC report formats as `schema/run_manifest.v1.json` and
-  `schema/qc.v1.json`, embedded at compile time as `RUN_MANIFEST_SCHEMA_V1`
-  and `QC_SCHEMA_V1` constants. Two new tests assert the embedded manifest
-  schema matches the actual serialised field set and that the QC schema
-  declares `schema = "qc.v1"`. Total `siderust-pod-core` test count: 8.
-* `siderust-pod-qc::orbit_compare`: RTN comparison adapter migrated to the
-  `siderust 0.7` API (`OrbitState::epoch_jd()`, `LocalOrbitalFrame::try_from_state`).
-  Existing tests still pass.
-
-### Changed
-
-* `siderust-pod-{io,observations,estimation,qc,products}`: migrated to the
-  upstream `siderust` API rename (`OrbitState.epoch_tt → epoch`,
-  `OrbitState::new(JulianDate, …) → OrbitState::new_at_jd(JulianDate, …)`,
-  `StateCovariance::from_stddevs([f64;3], [f64;3]) →
-  StateCovariance::diagonal_from_sigmas([Kilometers;3], [KmPerSeconds;3])`,
-  `LocalOrbitalFrame::from_state → try_from_state`). Public APIs of pod
-  crates unchanged.
-
-* Reserved sibling reusable crates under `rust/`:
-  `siderust-dynamics` (variational/STM, force-model composition,
-  thrust-arc physics), `siderust-sgp4` (SGP4 propagator producing typed
-  TEME states), `siderust-tle` (TLE/3LE/OMM parser),
-  `siderust-spice` (DAF/SPK reader extending `siderust::data::{daf,spk}`
-  to Type 3/9/13), and `siderust-lambert` (0/N-revolution Lambert
-  solver). Each crate ships with a README defining ownership boundaries
-  and a `CHANGELOG.md`. Implementation lands in plan Phases 3–5; the
-  scaffolds today only declare crate identity, dependencies on `qtty` /
-  `tempoch` / `affn[astro]` / `cheby` / `siderust`, an `AGPL-3.0-or-later`
-  license, and `#![forbid(unsafe_code)]`. None of these crates depend on
-  `siderust-pod-*`.
-* `siderust-pod-core`: new crate scaffolding the POD domain primitives
-  referenced by the existing design plan (`error::PodError`,
-  `dataset::DatasetRef`, `manifest::RunManifest` with deterministic JSON,
-  `parameter::{ParameterKind, Parameter, ParameterOrdering}`,
-  `covariance::ParameterCovariance` with symmetry/diagonal validators,
-  `providers::{EphemerisProvider, EarthOrientationProvider,
-  FrameTransformProvider}` traits). Closes the long-standing gap where
-  the workspace plan and changelog referenced this crate but it did not
-  exist on disk.
-* `siderust-pod-dynamics`: new crate scaffolding the POD-specific
-  dynamics composition layer (`force_config::ForceModelConfig`,
-  `thrust_arc::ThrustArcConfig` emitting estimable parameters,
-  `process_noise::ProcessNoiseConfig`). Numerical propagation and
-  analytic STM remain in `siderust` (today) and the future reusable
-  `siderust-dynamics` crate; this layer only owns POD-specific
-  composition.
-* `siderust-pod-dynamics`: cannonball solar-radiation-pressure force
-  (`forces::CannonballSrp`) and exponential-density atmospheric drag
-  (`forces::ExponentialDrag`). (audit fixes A-09, A-10)
-* `siderust-pod-core`: `PodError::NotImplemented` variant for
-  capabilities that are scoped to a future milestone.
-* `siderust-pod-service`: integration test verifying the runner refuses
-  real-input runs with a structured `Unsupported` error rather than
-  silently propagating-and-ignoring the inputs (audit fix A-03).
-* Top-level `SECURITY.md`, `SUPPORT.md`, `CHANGELOG.md`, and
-  `deny.toml` for cargo-deny gating in CI.
-* `crates/siderust-pod-dynamics/benches/propagation.rs`: criterion
-  bench skeleton for two-body and two-body+J2 RK4 propagation
-  (audit fix A-13 starter).
-
-### Changed
-
-* `siderust-pod-service::runner::run`: when real inputs are supplied
-  the runner now returns
-  `std::io::ErrorKind::Unsupported` carrying the
-  `PodError::NotImplemented` message instead of silently invoking the
-  legacy propagation-only stub. This closes audit finding C-01.
-
-### Documentation
-
-* `spod/docs/architecture/dependency-rules.md`: extended forbidden
-  edges to include reusable foundational crates (`qtty`, `tempoch`,
-  `affn`, `cheby`, `siderust`) which must not depend on any
-  `spod-*` crate. Enforced by `scripts/check_dep_graph.sh`.
-* `plan.md` §13 records the post-M7 technical audit (six 🔴 critical,
-  nine 🟠 high, ten 🟡 medium, five 🟢 low findings) and the M8–M12
-  remediation roadmap.
+- End-to-end synthetic service coverage from `RunConfig` through Siderust
+  propagation/estimation to orbit, residual, QC, and run-manifest artifacts.
+- Regression coverage ensuring every unsupported real-data input is rejected
+  rather than hashed and ignored.
+- CI guards for formatting, Clippy, feature combinations, documentation,
+  dependency direction, legacy project namespaces, MSRV, coverage, Docker,
+  REST/CLI smoke tests, and supply-chain policy.
+
+### Removed
+
+- Duplicated local POD scientific modules for dynamics, observations,
+  estimation, products, quality control, parameters, covariance, and run
+  metadata.
+- Deprecated finite-difference STM compatibility code and its deprecation
+  allowance.
+- Deprecated pre-rename REST environment aliases.
+- Obsolete compatibility reexports, stale architecture documents, and
+  dependencies used only by the removed scientific implementation.