scientific-workflow
This README is the public API documentation for the crates.io publication of
scientific-workflow.
For repository context, private crate boundaries, and runnable example
guidance, see the repository README.
scientific-workflow provides Rust primitives for representing scientific
system states and building reproducible simulation workflows.
The crate provides SystemState, a fixed-layout heterogeneous state container,
and StateSeries, an ordered growable collection of complete states for
in-memory analysis. Concrete payloads move through both layers without cloning,
making them suitable for large arrays and tensors.
Features
- Standard
config/{fixed,sweep,paths}.jsontask definition with either a project-owned or model-owned state schema. - Deterministic Cartesian and correlated explicit-case task expansion.
- Lazy complete
TaskConfighandles combining parameters and shared paths. - Exact sweep-value filtering and ambiguity-safe unique task selection.
- Clone-free dict-like resolved task views over shared JSON values.
- Named project-root-relative path resolution and byte-exact source export.
- JSON-defined state fields with deterministic order and optional descriptions.
- Dictionary-like typed access to heterogeneous Rust payloads.
- Coordinated immutable and mutable tuple borrowing for coupled kernels.
- Assembly-established field types retained across extraction and blank-state derivation.
- Clone-free payload insertion, in-place mutation, and owned extraction.
- Explicit deep cloning of complete states.
- Shared immutable state specifications.
- Integer and optional finite physical time coordinates.
- Strict template validation and semantic JSON round trips.
- Compatibility with owned scientific payloads such as
physics_in_paralleltensors. - Ordered state-series collection with strict shared-layout identity.
- Lightweight copyable series views and field-level analysis mutation.
- Borrowed JSON encoding without payload cloning.
- Writer-owned typed sampling intervals with no payload access for skipped states.
- Human-friendly numeric sampling-interval decoding with tagged-format compatibility.
- Automatic exactly-once final-state sampling across sampling-interval boundaries.
- Exact finite-
f64JSON reconstruction through Serde JSON's round-trip parser. - Finite byte- and record-bounded asynchronous writers.
- Exact-byte automatic chunking with indivisible JSONL records and reusable userspace accumulation buffers.
- Durable whole-chunk publication through one payload write, file sync, descriptor preparation, atomic lifecycle rename, and stream-directory sync.
- Explicit interrupted-run append and complete typed checkpoint recovery.
- RNG-agnostic method, version, key-encoding, key, and parameter provenance.
- SHA-256-verified eager reconstruction through per-key payload decoders.
- Efficient latest-state reconstruction without loading earlier chunks.
- Automatic UTC lifecycle timestamps and monotonic active durations.
- Collision-resistant generated or caller-named execution scopes.
- Atomic content-addressed input artifacts with verified execution-relative loading.
- Structurally separate terminal metadata and immutable completed-recording handles.
- Parameter-identified, parallel-safe centralized progress reporting.
- One exclusive terminal renderer with interactive, CI, and hidden modes.
API Design Rules
- Add a public type or trait only when an existing Workflow owner cannot express the behavior.
- Extend the existing API instead of creating a parallel replacement whenever the concepts are the same.
- Optional behavior uses one interface with explicit defaults. This applies to stream limits, continuation reasons, and RNG-record parameters.
- Workflow records RNG provenance but never implements scientific randomness.
Supported public API
This is the exhaustive supported API allowlist for scientific-workflow.
Users may rely on these items, their public enum variants, and their documented
public methods. prelude::basics::* imports scientific configuration, state,
storage, execution, and artifact APIs; prelude::runtime::* imports the opt-in
task/phase/runtime surface. Compiler-visible implementation paths not listed
here are not compatibility promises.
- Artifacts:
ArtifactDescriptor,ArtifactDisposition,ArtifactError,ArtifactLoadError,PersistedArtifact,VerifiedArtifact,persist_artifact, andload_verified_artifact. - Configuration:
ConfigurationError,MatchingTaskConfigIter,ParameterSpace,ProjectConfig,ProjectPaths,TaskConfig,TaskConfigIter,TaskParameters, andTaskParametersIter. - Projects and execution:
ScientificProject,ScientificProjectError,ExecutionScope, andExecutionScopeError. - Runtime:
WorkflowRuntime,WorkflowRuntimeBuilder,RuntimeError,RuntimeSummary,PhaseSummary,Phase,PhaseBuilder,PhaseFailurePolicy,PhaseId,Task,TaskId,TaskKey,TaskSelector,TaskDisplayKind,TaskContext,TaskResult,ProgressSummary,TaskIdentity,TaskProgress,ActivityTask,CancellationToken, andTaskStatus. - RNG provenance:
RNG_RECORDS_METADATA_KEY,RngRecord, andRngRecordError. - Persistent storage:
CompletedRecording,CompletedStreamSummary,JsonPayloadDecoder,JsonPayloadDecoderRegistry,JsonStringDecoder,JsonVecF64Decoder,RecordingTiming,SamplingInterval,StateStreamConfig,StorageError,StoredStateSeriesReader,SystemStateWriter,SystemStateWriterBuilder, andTimeAxisMetadata. - State:
PayloadInsertError,SimulationTime,StateError,StateFieldSchema,SystemState, andSystemStateSchema. - In-memory series:
StateSeries,StateSeriesError,StateSeriesPushError, andStateSeriesView.
The sections below document the supported constructors and operations by workflow responsibility. Generated crate documentation is the exact signature reference for every item in this list.
Runtime Scheduling and Display
First-class executable tasks belong to a phase before runtime construction. Parameterized workloads are generated directly from the configuration manager, retain all fixed and selected sweep values, and receive automatic labels from the parameters that vary:
use *;
use *;
#
max_concurrent_workloads and queue_capacity bound scheduling within each
phase. They are not CPU, memory, process, or I/O limits. Each workload owns all
scientific I/O and any subprocesses; the externally configured systemd/service
scope contains the complete application. TaskContext exposes only retained
identity/configuration, progress or activity reporting, and cancellation.
The corresponding progress_workloads_from_project and
activity_workloads_from_project factory methods remain available when each
task must capture a distinct owned, possibly non-Clone resource.
Phase transitions are automatic by default. Calling
require_confirm(true) on a phase makes a successful non-final transition
prompt for the exact word yes before the next selected phase starts. Other
answers re-prompt; end-of-input or an input error stops execution with a
structured RuntimeError. The final selected phase never prompts.
Only the active phase is displayed interactively. Plain mode emits append-only
uncolored phase and task lifecycle records. Progress updates are atomic and
remain synchronized from the application's authoritative scientific state.
WorkflowRuntime::cancellation_token permits programmatic cancellation and
shares state with interactive Ctrl-C. Display messages use a bounded 256-event
channel with backpressure and are never a substitute for task-owned durable
logs; the runtime does not silently truncate them.
RNG Records
RngRecord persists application-owned RNG identity without providing
any RNG behavior. Workflow does not generate keys, derive streams, choose
algorithms or distributions, sample values, or maintain cursors.
use *;
use ;
#
Records are indexed by namespace beneath the reserved rng_records
user-metadata key. Duplicate namespaces and malformed records are rejected.
Because recording continuation already requires exact user-metadata equality,
a changed RNG method, version, or key prevents continuation. Keys are persisted
as plain text reproducibility material and must not contain secrets.
When a scientific crate resolves optional RNG settings, record the resolved
values—not the original request. For example, PiP exposes one RngConfig
input across its stochastic APIs and returns or retains its resolved form. The
mapping into Workflow remains explicit and lightweight:
use *;
use *;
use ;
let resolved = generator.rng_config;
let method = resolved.method.expect;
let parameters = resolved.parallel_streams.map;
let record = new?;
Workflow deliberately does not depend on PiP, interpret RngConfig, or expose
a second RNG configuration API. The application chooses a stable namespace and
copies the upstream generator's resolved identity into RngRecord.
Immutable Input Artifacts
Workflow owns the generic mechanics for persisting immutable bytes inside an
execution scope. Scientific crates keep ownership of their formats and domain
metadata: they serialize their document, call persist_artifact, and embed the
returned descriptor in each recording that consumed it.
use *;
#
The filename is derived from SHA-256, publication is atomic, and identical bytes in one scope are reused. Loading rejects malformed or escaping relative paths and verifies the digest before returning bytes. Workflow deliberately does not interpret JSON, matrices, lattices, or other scientific encodings.
Mandatory Chunk Integrity
Every sealed JSONL chunk is described by an exact byte count and SHA-256 digest
in metadata.json. Verification is mandatory whenever a chunk is validated or
reconstructed. The public reader has no unchecked mode, checksum opt-out,
feature switch, or performance flag: corruption produces StorageError rather
than partially trusted scientific data.
Parsing alone is not validation. Skipping a chunk because an operation does not need its contents is permitted, but that chunk is then unexamined—not verified. Any chunk actually used to reconstruct scientific state must cross the checksum boundary first. This integrity guarantee detects accidental corruption; it is not a substitute for provenance, signatures, or validation of the scientific model itself.
The public SystemStateWriter facade owns multi-stream metadata, one bounded
queue and worker, and the recording's completion or failure lifecycle.
Format version 6 writes each record's top-level values as a positional array
whose names and order come from that stream's fields in metadata.json.
Readers require an exact width and reconstruct the existing name-addressable
state API; nested payload JSON remains opaque.
Installation
Add the crate to a Rust project:
[]
= "0.3"
The crate uses Rust edition 2024 and requires Rust 1.97 or newer.
Complete Project Example
The source repository includes examples/attractor_2d, a standalone
consumer application that exercises configuration loading, Cartesian task
expansion, directly owned mutable states, tuple payload borrowing, independent
sample streams, bounded asynchronous recording, automatic chunking, and
explicit completion. Its lazy TaskConfig iterator feeds runtime phase
construction, while stable task indices keep recording paths deterministic
regardless of completion order. It then reads the complete checkpoint's latest state with typed payload
decoders and verifies the final live-to-stored round trip exactly. From the
repository root, run:
The example is intentionally outside this crate directory and therefore is
not part of the crates.io package. Its generated recordings remain under its
ignored target/recordings directory.
Project Configuration
A project with a project-owned state contract keeps four files together:
project-root/
└── config/
├── fixed.json
├── sweep.json
├── paths.json
└── state.json
fixed.json contains values shared by every task:
sweep.json supports ordered Cartesian axes:
or correlated explicit cases:
paths.json contains shared path strings resolved relative to the project root:
Load the project and consume exact JSON names through each resolved task's read-only dictionary:
use *;
task_configs() lazily emits the complete Cartesian product—or exactly the
declared correlated cases—in stable task-ordinal order. Each item is a cheap
owned handle over shared fixed, sweep, and path storage, so it can move into a
worker queue without cloning merged JSON dictionaries:
# use *;
#
#
Matching constrains only the named sweep dimension; every combination of the
remaining axes is retained. Unique selection returns an error when no task or
more than one task matches, rather than silently choosing the first. Fixed keys
and path keys cannot be used as sweep selectors. Use
unique_task_config_matching(key, value) only when that one sweep dimension is
known to identify exactly one task, as is common for an explicit case ID.
Task handles share the parsed source allocations and do not clone values or
construct merged maps. value and require_value borrow raw JSON;
decode_value explicitly constructs one requested Rust value, while
decode_values decodes a heterogeneous tuple of two through twelve values
without an application configuration struct or merged JSON map. The final
sweep axis changes fastest. Fixed and swept names must be disjoint.
ProjectConfig::write_source_config(destination) reproduces the three
parameter/path files byte for byte beneath a new destination project. It never overwrites an
existing config/ directory. TaskParameters::to_json instead serializes one
deterministic derived fixed-plus-sweep dictionary.
ScientificProject::load requires config/state.json and exposes its shared
schema through state_schema(). This is appropriate when the project itself
defines its state contract.
A fixed-model crate should instead load its one canonical schema and pass it to
ScientificProject::load_with_state_schema:
use *;
#
Such projects contain only fixed.json, sweep.json, and paths.json; the
model dependency supplies the schema. Workflow does not choose a fallback
schema or mutate the configuration directory. The lower-level ProjectConfig
remains available when an application intentionally needs only parameter and
path configuration.
State Template
A program begins with a JSON template that declares every state key and may document its payload in natural language:
Field order defines the compact runtime slot order. The template contains no
Rust type or storage codec information. The first payload inserted into a field
establishes its concrete runtime type; that contract remains after
take_payload or clear_payload and is copied into blank states derived with
SystemState::clone_structure_without_payloads.
Descriptions remain documentation only.
Basic Usage
use *;
insert_payload consumes the supplied payload, and take_payload returns that same owned
payload. Neither operation calls Clone. Calling SystemState::clone
creates a new erased box and calls Clone for every populated payload; the
semantic depth is defined by each concrete type's Clone implementation.
Coupled Payload Access
Scientific kernels can borrow several distinct fields without payload copies, temporary extraction, locks, or application-side selector structures. Supply the expected concrete types and field names in matching tuple order:
use *;
#
#
Supported tuple arities are two through eight. The complete request is
validated before any reference is returned, and repeating a field is rejected.
Use payload or payload_mut for one field. Name lookup and type validation occur once
per tuple borrow, so the returned references should normally surround the full
kernel or simulation sweep.
In-Memory Time Series
StateSeries owns complete states for analysis. Appending validates that every
state shares the series' exact specification allocation and that simulation
indices increase strictly. Index gaps are allowed.
use *;
The collection never returns &mut SystemState, because changing a stored
state's time would invalidate ordering. payload_mut_at permits one typed payload
mutation at a time. push_state, pop_state, and into_states move ownership without
cloning. Explicit StateSeries::clone deep-clones all populated payloads; use
as_view or Arc<StateSeries> for lightweight sharing.
StateSeries performs no serialization, chunking, queueing, or disk IO. Those
responsibilities belong to the separate storage layer.
Tensor Payloads
Any concrete type satisfying Serialize + Clone + Send + 'static can be
stored. For example, an application can use a dense physics_in_parallel
tensor:
use ;
use *;
let spec = load_json_template?;
let mut state = spec.create_empty_state;
let mut population = zeros;
population.set;
population.set;
population.set;
drop;
let population = state.?;
The tensor crate is not a required runtime dependency of
scientific-workflow; applications use their own concrete serializable
scientific payload types without registering codecs.
The PiP 3.2.2 integration uses versioned Serde schemas for dense and
sparse tensors, matrices, vector lists, square lattices, and heterogeneous
PhysObj values. They reconstruct through the same generic registry path:
let decoders = new
.?
.?;
Sparse PiP records contain only sorted nonzero indices and values; Scientific Workflow does not densify them during encoding or reconstruction.
Persistent State Recording
One import brings the complete supported state, analysis, storage, reader, and decoder API into scope:
use NonZeroU64;
use *;
observe_state checks each stream's typed sampling interval before accessing any
payload. Non-due streams perform no serialization or queue work. Due streams
resolve each selected key once and borrow payloads only while producing owned
encoded bytes, after which bounded blocking backpressure applies through the
recording's single queue and worker. complete_recording_with_final_state
records a non-aligned endpoint exactly once per stream before completion. Each
chunk is synchronized, described in the sole
metadata file, atomically renamed from .jsonl.tmp to .jsonl, and followed by
a stream-directory sync. flush_stream_to_storage(stream) exposes this as an
ordered durability barrier. continue_existing_recording recovers append
position without reconstructing state, while
continue_recording_from_latest_checkpoint also returns a complete typed
checkpoint through registered decoders. Workflow verifies the selected sealed
chunk's declared byte count and SHA-256 checksum before decoding its final
record or returning an append-capable writer. A descriptor-prepared temporary
chunk completes its rename during recovery; an unpublished temporary chunk is
discarded and is not scientific checkpoint state.
Custom Payload Decoders
Each decoder is registered for one exact state key and returns that key's concrete payload type. A closure is sufficient for stateless conversion; a named decoder can carry configuration or shared resources:
use *;
use ;
;
The reader performs record parsing and key lookup, passes only the matching raw JSON value to each decoder, and moves the returned payload into the reconstructed state. Custom decoders do not handle chunks, metadata, sibling fields, or state assembly.
Testing
From the package directory:
The permanent suite contains ten integration targets. Run the core workflow
targets with --nocapture to display their stable semantic reports.
Project configuration and task expansion:
Simulation-owned state:
In-memory analysis series:
Successful storage and typed reconstruction:
Storage failure and corruption handling:
Interrupted-run recovery, checkpoint reconstruction, and append:
Configuration-generated runtime scheduling and display:
Artifact, RNG-record, and Rust/Python format conformance coverage runs as part
of cargo test --all-targets --no-fail-fast --locked.
Doctests and lint gate:
The repository's test architecture documents complete method allocation, indirect private coverage, logging rules, and completion criteria.
License
Licensed under the MIT License.