OSMOSE Python

Python orchestration layer, simulation engine, and Shiny web interface for the OSMOSE marine ecosystem simulator. Ships with a pure-Python engine (full Java parity) and a subprocess driver for the original Java engine.

_{Python 3.12 · NumPy + Numba · Shiny for Python · 3250+ tests · ruff clean · MIT}

🚀 New here? Run and perturb a calibrated Baltic ecosystem in 30 minutes: Tutorial. Then keep the Usage Guide handy for scripting runs, reading outputs, comparing, and calibrating.

Status

Contents

• Quick start
• Simulation engines
• Performance
• Engine parity validation
• Examples
  • Baltic Sea
• Project layout
• Testing and linting
• API sketch
• MCP servers and credentials
• Docker
• Documentation index
• License

Quick start

git clone https://github.com/razinkele/osmopy.git
cd osmopy
python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"

.venv/bin/shiny run app.py --host 0.0.0.0 --port 8000

Open http://localhost:8000. The UI runs without Java — it defaults to the Python engine.

Requirements: Python 3.12+. Java 17+ only if you want to use the Java engine backend; the Python engine has no Java dependency.

Simulation engines

Both engines implement the same Engine protocol and produce identical output shapes (biomass, abundance, mortality-by-cause, diet, trophic level, size/age distributions). The UI flips between them with one click.

Performance

Numba JIT + parallel cell processing + vectorized diet aggregation put the Python engine ahead of Java on every benchmarked config:

Benchmarked on Linux x86_64 with Numba 0.60, NumPy 1.26, Python 3.12. First run includes ~20 s Numba compilation overhead (cached for subsequent runs).

Key optimisations:

• Numba JIT mortality loop — full interleaved predation/starvation/fishing compiled to native code
• prange parallel cell processing with per-cell deterministic seeding
• Vectorised rate computation and diet aggregation (np.add.at per prey-species rollup)
• Pre-allocated diet buffers with capacity-based reuse
• Precomputed species masks; compiled movement (map rejection sampling + random walk)
• Results caching across repeated reads (CSV + NetCDF)

Run the suite yourself:

.venv/bin/python scripts/benchmark_engine.py --years 5 --seed 42 --repeats 3

Engine parity validation

EEC 1-year biomass parity (Python vs Java, tonnes):

All 14 species within 1 order of magnitude of Java.

Bay of Biscay is now a fully-native OSMOSE 4.4.1 config. The rigorous N=16 cross-engine parity gate finds 6 of 8 species equivalent — Anchovy and Hake show a pre-existing Python-port-vs-Java divergence, present against both the 4.3.3 and 4.4.1 jars. Re-run it:

.venv/bin/python scripts/cross_engine_parity_440.py --config data/examples/osm_all-parameters.csv --engines python,4.4.1

See docs/parity-roadmap.md for the 7-phase closure history of the final parity gaps.

Examples

Three ready-to-run configurations ship in-tree.

Baltic Sea

The Baltic example is the newest and most documented. It covers cod, herring, sprat, flounder, perch, pikeperch, smelt, stickleback plus six CMEMS-forced LTL groups, 50 × 40 cells over 10–30° E × 54–66° N, 24 dt/yr.

Live movement during a run. The Run page streams every timestep of a Python-engine simulation onto the map — toggle between an aggregated density heatmap and individual dots coloured by species. Below is the Baltic ecosystem (8 fish species over the 50 × 40-cell domain) at the end of a 1-year run:

Heatmap — school density

Dots — individual schools by species

• Full provenance — every parameter family, every value source, every DOI: docs/baltic_example.md.
• Validation vs ICES — F rates and biomass envelopes cross-checked against the 2024 advice cycle: docs/baltic_ices_validation_2026-04-18.md. Unit-aware (the ICES API mislabels some stocks' SSB units; the validator detects this via Blim magnitude).
• Refresh workflow — data/baltic/reference/ices_snapshots/README.md.
• Calibration driver — scripts/calibrate_baltic.py (phases: larval mortality, adult mortality + F) runs the Python engine directly, no Java needed.
• Forcing — scripts/rebuild_baltic_mask.py and mcp_servers/copernicus/server.py regenerate the mask + LTL NetCDF from CMEMS data.

.venv/bin/python scripts/validate_baltic_vs_ices_sag.py --report
.venv/bin/python -m pytest tests/test_baltic_ices_validation.py -v

Project layout

osmose/                     Core library (usable without Shiny)
  engine/                   Python simulation engine (44 files, ~11.5k LOC)
    simulate.py             Main simulation loop; SimulationContext, frozen StepOutput
    processes/              Growth, predation, mortality, reproduction, movement, fishing
    config.py               Typed parameter extraction
    grid.py                 Spatial grid with NetCDF loading
    resources.py            LTL plankton/resource forcing
    output.py               CSV + NetCDF output writer
    path_resolution.py      Consolidated resolver with traversal protection
  schema/                   Parameter definitions + registry (153 params)
  config/                   Config reader/writer (auto-detected separators; recursive includes)
  calibration/              pymoo NSGA-II + GP surrogate + SALib sensitivity + preflight
  runner.py                 Async Java subprocess manager
  results.py                CSV/NetCDF output reader (xarray)
  scenarios.py              Save/load/compare/fork
ui/                         Shiny web interface
  pages/                    One module per tab
  components/               Reusable widgets (param form)
  theme.py                  shinyswatch superhero theme
mcp_servers/                MCP servers
  copernicus/               CMEMS forcing downloader (env-based credentials)
data/
  examples/                 Bay of Biscay reference config (8 species)
  eec_full/                 Eastern English Channel config (14 species)
  baltic/                   Baltic Sea calibration sandbox (8 sp + 6 LTL); see docs/baltic_example.md
    reference/              Biomass targets + frozen ICES SAG snapshots
scripts/                    One-shot tools: benchmarks, validators, calibration, mask rebuild
tests/                      2510 tests (schema, config, engine processes, parity, calibration,
                            UI state, MCP hygiene, Baltic ICES cross-validation)
docs/
  baltic_example.md                           Baltic example full provenance
  baltic_ices_validation_2026-04-18.md        ICES cross-validation report (2024 advice)
  parity-roadmap.md                           Engine parity roadmap (7 phases)
  osmose-master-java-fixes.patch              Portable patch for upstream osmose-master
  plans/                                      Historical and active implementation plans
  superpowers/plans/                          Superpowers-skill-generated plans

Testing and linting

.venv/bin/python -m pytest                   # run all tests (~50 s)
.venv/bin/python -m pytest --cov=osmose      # with coverage
.venv/bin/python -m pytest -v -k test_name   # specific test
.venv/bin/ruff check osmose/ ui/ tests/      # lint
.venv/bin/ruff format osmose/ ui/ tests/     # format

2510 tests across schema, config I/O, config-key validation, every engine process, parity regressions, numerical edge cases, type invariants, thread safety, UI state, calibration, scenario management, MCP credential hygiene, and integration scenarios. Pyright passes with zero errors on the osmose/ and ui/ trees.

API sketch

Engine protocol

from pathlib import Path
from osmose.engine import PythonEngine

# Python engine — no Java needed
engine = PythonEngine()
result = engine.run(config=config_dict, output_dir=Path("output"), seed=42)  # writes CSV/NetCDF
results = engine.run_in_memory(config=config_dict, seed=42)                  # OsmoseResults, no disk

# Java engine — requires an OSMOSE JAR; run() is a coroutine
import asyncio
from osmose.runner import OsmoseRunner
runner = OsmoseRunner(jar_path=Path("osmose-java/osmose.jar"))
result = asyncio.run(runner.run(config_path=Path("config.csv"), output_dir=Path("output")))

Config I/O

from osmose.config.reader import OsmoseConfigReader
from osmose.config.writer import OsmoseConfigWriter

reader = OsmoseConfigReader()
config = reader.read(Path("path/to/osm_all-parameters.csv"))   # -> dict[str, str]

writer = OsmoseConfigWriter()
writer.write(config, Path("path/to/output_dir/"))              # writes the config tree into a directory

Config-key validation

EngineConfig.from_dict() checks every key against an allowlist built from the ParameterRegistry plus an AST walk of osmose/engine/config.py. The allowlist knows all ~390 keys the engine or reader touches, including {idx}-patterned families (species.linf.sp{idx}, movement.file.map{idx}, …). Default is silent; opt in with validation.strict.enabled:

cfg = reader.read("path/to/osm_all-parameters.csv")
cfg["validation.strict.enabled"] = "warn"  # or "error"
EngineConfig.from_dict(cfg)  # emits per-key warnings

Results reader

from osmose.results import OsmoseResults

# strict=True (default): FileNotFoundError if outputs are missing
results = OsmoseResults(Path("path/to/output/"), prefix="osm")
biomass = results.biomass()             # wide DataFrame: Time + per-species columns
mortality = results.mortality()         # per-species mortality by cause
diet = results.diet_matrix()            # diet composition matrix

# strict=False for partial/speculative loads (calibration, UI)
with OsmoseResults(Path("path/to/output/"), strict=False) as results:
    biomass = results.biomass()

Selecting one species is column selection (biomass()[["Time", "Anchovy"]]); the species= argument filters the row-label column and returns empty on the standard wide files. See docs/usage-guide.md.

Thread safety and parallel calibration

The Python engine is re-entrant. Per-simulation state is encapsulated in a SimulationContext dataclass passed through the call chain — no module-level globals. Safe for ProcessPoolExecutor-based calibration runs.

from concurrent.futures import ProcessPoolExecutor

engine = PythonEngine()
with ProcessPoolExecutor(max_workers=8) as pool:
    futures = [pool.submit(engine.run_in_memory, config=cfg, seed=i) for i, cfg in enumerate(configs)]

Calibration

# Drive a calibration (DE / CMA-ES / surrogate-DE) — long-running, writes to data/calibration_history:
#   python scripts/calibrate_baltic.py --optimizer de --phase 12 --maxiter 100

from pathlib import Path
from osmose.calibration import list_runs, load_run, OsmoseCalibrationProblem

runs = list_runs()                                   # list[dict] of finished runs
data = load_run(Path(runs[-1]["path"])) if runs else None
# OsmoseCalibrationProblem(...) is the programmatic entry for a custom problem
# (use_java_engine=True for bit-exact Java). See docs/usage-guide.md §4.

MCP servers and credentials

MCP integrations ship under mcp_servers/. The Copernicus Marine server reads credentials from environment variables only — no hardcoded fallbacks. Populate .env (gitignored) at the repo root:

cp .env.example .env
$EDITOR .env   # fill in CMEMS_USERNAME / CMEMS_PASSWORD

server.py auto-loads .env via python-dotenv. Two enforcement tests guard against regressions:

• tests/test_copernicus_mcp_env.py — server source must not contain a hardcoded credential default; _require_creds() must raise RuntimeError on missing env.
• tests/test_mcp_config_hygiene.py — .mcp.json must not ship a CMEMS password literal under any server's env block.

The ICES data-access MCP server lives out-of-tree at /home/razinka/ices-mcp-server/ (stdio-based, uv runner). Wire it via .mcp.json — see the Baltic ICES snapshots README for the refresh workflow.

Docker

docker build -t osmose-python .
docker run -p 8000:8000 osmose-python

Place osmose.jar in osmose-java/ before building if you need Java-engine support. The Python engine works without it.

Documentation index

Start here depending on what you want:

License

MIT

Changelog

All notable changes to this project will be documented in this file.

Format based on Keep a Changelog, generated from Conventional Commits.

[1.3.0] - 2026-06-30

Features

• c2: wire background staging + version-aware gate into the UI Java run path (8d1471e)
• c2: version-aware java_engine_block_reason + thread jar_version through engine_capabilities (77e033f)
• c2: extract+generalize Baltic Java-4.4.1 staging into osmose/java_background_staging.py (7e2239b)
• 440: flip write/jar/calibration defaults to 4.4.1 + keep native source validator-clean (880d7c0)
• 440: convert minimal/baltic/baltic_ev to native 4.4.0 (parity PASS, Baltic Java 4.4.1 smoke green) (5faa67d)
• 440: conversion tool + convert EEC to native 4.4.0 (canary, parity PASS 0.00) (2708965)
• parity: round-trip parity harness for the 4.4.0 cutover + capture 4.3.3 baselines (C1 Task 2) (b286a34)
• baltic: stage + run Baltic on Java 4.4.1 (inline bg biomass + authored accessibility) + smoke harness (257c21a)
• aliases: emit 4.4.x background-species keys (species.multiplier/beta) on the 4.4.x write path (d87ddec)
• grid: info button opens the selected model's modal + fix clipped label (cd988ad)
• grid: Model-selection rename + per-model info modal (ℹ button) (3f50c52)
• demo: DEMO_INFO registry + demo_info() accessor (per-model metadata) (2946024)
• run: Run button in the Live Movement pane + phenology date in the status (e844b3d)
• engine: pass map_sets to the step observer (output-side; enables egg placement) (b0c3b41)
• live: place unlocated eggs on spawning grounds + phenology date_label + map_sets observer arg (7b2a0b4)
• run: wire mode-aware legend into live map + remove pre-run hint (40a6867)
• live: live_legend_widget — mode-aware legend (species swatches / biomass gradient) (44abe6e)
• run: Live Movement species-from-config + stage selector + 3-col layout + empty-state (1ac7875)
• live: stage_filter threaded through the render call graph (composed mask + count) (73b36a5)
• live: MovementSnapshot carries per-school life stage (egg/larva/juvenile/adult) (22273d2)

Bug Fixes

• ui: DEMO_INFO baltic/eec_full are no longer 'Python only' (run on Java 4.4.1) (9a1d0a1)
• 440: keep bare write defaults at 4.3.3 (jar-derived 4.4.1) + skip-if-exists conversion + test sweep (C1 Task 7) (6a28e3e)
• aliases: make to_target_keys larval-rate transform source-version-aware (no double-scale on native 4.4.0) (fdf00e7)
• baltic-smoke: fail the harness on species collapse / no predator feeding (6662bf1)
• live: explicit ocean_mask in egg-fallback test + use cx_full in egg mask (review) (8766d5a)
• live: distinct deck.gl layer ids for heatmap vs dots (filter no longer blanks the map) (3743122)

Documentation

• implementation plan for C2 (UI Java-4.4.1 for nbackground>0) + in-loop review (5de28e2)
• revise C2 spec per in-loop review (run directly; subagents spend-limited) (a412954)
• spec for C2 — run nbackground>0 configs on Java 4.4.1 from the UI (208c805)
• revise C1 plan per in-loop review (run directly; subagents spend-limited) (f29a70e)
• implementation plan for C1 native 4.4.0 cutover (76776a8)
• revise C1 spec per in-loop review (run directly; subagents spend-limited) (43cac24)
• spec for C1 — standardise bundled Python stack to native OSMOSE 4.4.0 (984efa1)
• revise Baltic-4.4.x plan per in-loop review (2 reviewers; jar-bytecode-resolved) (3e635a4)
• implementation plan for Baltic 4.4.x background-key adaptation (245da82)
• revise Baltic-4.4.x spec per in-loop review (2 reviewers, jar-bytecode-grounded) (b5f65d8)
• spec for adapting Baltic background species to OSMOSE 4.4.x keys (sub-project A) (09df6c7)
• implementation plan for context-sensitive info button + visibility fix (0d1adda)
• spec for context-sensitive info button + visibility fix (7f5bed4)
• revise plan per in-loop review (2 reviewers) (2a1e758)
• implementation plan for Model-selection rename + info modal (cc24c43)
• spec for Model-selection rename + per-model info modal (c395463)
• baltic-lifecycle: document the reproductive-volume / saltwater-inflow gap (0e67da8)
• scientific review of the Baltic fish life-cycle document (scite/ICES/HELCOM) (91a1a4e)
• detailed Baltic fish life-cycle description (a468793)
• revise plan per in-loop review (2 reviewers) (ad8ef5f)
• implementation plan for live-pane eggs + run button + dates (2a938e9)
• revise live-pane spec per in-loop review (2 reviewers) (c6696c7)
• spec for live-pane egg-placement + run button + phenology dates (cab2fef)
• revise plan per in-loop review (2 reviewers) (8624fba)
• implementation plan for live-map legend + hint removal (e3bb357)
• revise live-map legend spec per in-loop review (2 reviewers) (ca22b4d)
• spec for live-map legend widget + empty-state hint removal (7abe781)
• implementation plan for Live Movement stage filter + species fix (73d4ed4)
• revise Live Movement spec per in-loop review (2 reviewers) (bd7c8a8)
• spec for Live Movement species fix + life-stage filter + horizontal layout (ee0b9dc)

Other

• fix stale 'Python only' model-info labels for baltic/eec_full (now Java 4.4.1 + Python) (23d9762)
• C2 — run nbackground>0 configs on Java 4.4.1 from the UI (de169f9)
• C1 — standardise bundled Python stack to native OSMOSE 4.4.0 (ac03be0)
• aliases: undo the source-aware larval-rate change from fdf00e7 (H1 was a phantom) (6cc1ea6)
• Baltic background species adapted to OSMOSE 4.4.x keys (sub-project A) (072b388)
• info button opens the selected model's modal + fix clipped label (4f0e57d)
• Baltic fish life-cycle documentation + scientific review (cdfc66c)
• 'Model selection' rename + per-model info modal (2fabefc)
• Live Movement pane — eggs on spawning grounds + run button + phenology dates (f694660)
• live-map legend widget + remove pre-run hint (bacc17b)
• fix Live Movement filter blanking the map (deck.gl layer-id swap) (ee2031c)
• Live Movement species fix + life-stage filter + horizontal layout (ed5ab21)

Refactoring

• 440: demote canonicalize_config to a documented legacy 4.3.3 adapter (C1 Task 6) (ccf861a)

Tests

• baltic-smoke: assert augment_accessibility leaves the source matrix byte-identical (9bc9c4c)

[1.2.0] - 2026-06-26

Features

• validate: add size-structure metric (mean weight) + dogfish/mackerel diagnosis (d555226)
• validate: deepen Phase 2 — multi-metric + formal TOST/MEF (N=16) (8ff4ded)
• validate: Phase 2 cross-engine ensemble parity harness + EEC results (8320ffc)
• config: emit 4.4.x species.biomass.{file,varname,nsteps.year,mode} for NetCDF resources (94e2254)

Bug Fixes

• results: read Java cross-species distribution outputs per-species (70b6a8a)

Documentation

• validate: refute the inverted-size-ratio diagnosis (source-verified) (5a2a1fc)

Other

• v1.2.0 (b296dcf)
• read Java cross-species distribution outputs per-species (7686cd9)
• correct the inverted-size-ratio diagnosis (refuted by source) (77668fb)
• Java 4.4.1 EEC adoption — resource-forcing migration + Phase 2 cross-engine validation (a421681)

[1.1.0] - 2026-06-26

Features

• hpc: Apptainer definition (Python+Java+numba, JAR + baked numba cache, read-only-friendly) (87c3e34)
• cli: osmose run --jar defaults to $OSMOSE_JAR (container-friendly) (bb1493d)
• ui: show reference-point source (model/ICES/user) on the Fisheries page (95d652a)
• fmsy: load model reference sidecar (precedence user>model>ICES; conditional label) (716d2db)
• fmsy: CLI to compute + write the model reference-point sidecar (d69ae70)
• fmsy: yield-vs-F sweep runner + compute_model_reference_points (ProcessPool, realized-F) (ff336e3)
• fmsy: derive_reference_points (peak/boundary/multi-peak/B0/Blim, pure) (ae3b680)
• fmsy: fishing-override resolver (mode detection + species->fishery map) (3bf5c0c)
• ui: indicative Fisheries stock-status page (Kobe + F/Fmsy + F/M bars) (e536b03)
• plotting: indicative Kobe + B/Bmsy & F/Fmsy ratio timeseries (b93c282)
• validation: indicative stock-status computation (SSB/Bmsy, exploited-stage F/Fmsy) (12d2b93)
• add fisheries_reference.py — per-species reference-point resolver (Task 4) (908e6e2)
• fisheries: annual_by_year aggregator (cadence-correct, absolute-year) (deb4df3)
• engine: SSB CSV/in-memory/NetCDF writers + results.ssb reader (4b3086b)
• engine: SSB collector + config flags + StepOutput (parity-safe output) (a9fe0ec)
• output: mark yieldN/meanSize produced; regression sweep green (9d76477)
• output: yieldN/meanSize NetCDF writer + run-path wiring + source=netcdf reader (1aaf672)
• output: yieldN/meanSize CSV writers + in-memory results wiring (82fa38a)
• output: yieldN/meanSize collectors + StepOutput fields + accumulation (175f00d)
• output: config flags + schema key for yieldN/meanSize (3d00653)

Bug Fixes

• hpc: harden build-provided-JAR copy under set -eu (store glob result in a var) (cb9a531)
• calibrate: honor OSMOSE_RESULTS_DIR (container-friendly results dir) (cf85484)
• fmsy-cli: --grid nargs=+ (reject empty), honest n_years estimate, top-level import (0180e21)
• ui: wire ices_snapshot_dir, drop dead _refs, sanitize input IDs, log SSB-hint errors, add Results links (4a0e7d0)
• validation: narrow _exploited_f_by_year catch (drop AttributeError; stub carries output_dir) (07795aa)
• test: Task 3 test self-contained — drop premature stock_status/ReferencePoint imports (407858d)
• engine: gate egg predation on the released fraction (Numba + Python paths) (94f1bfb)
• engine: apply fleet-effort on the pure-Python fishing fallback path (41337c9)
• calibration: let _worker_eval propagate unexpected errors (no inf-swallow) (8cef769)
• engine: suppress standard starvation on the Numba path for bioen (c273c8f)
• engine: stop double-counting bioen starvation mortality (457ac55)

Performance

• engine: vectorize movement method masks + bincount diet aggregation (c99097c)

CI/CD

• hpc: build the Apptainer image with --fakeroot + smoke (CLI/engine/numba-cache/java/sweep) (be4f19f)

Documentation

• hpc: fix SLURM config paths (real masters) + drop --jar under --contain (env default) (5e57de1)
• hpc: Apptainer build + run guide (read-only rule, SLURM job array, smoke) (557e2b8)
• implementation plan for OSMOSE HPC Apptainer container (3c9fae7)
• revise HPC Apptainer spec per in-loop review (3 reviewers) (d058fa8)
• spec for OSMOSE HPC Apptainer/Singularity container (82fb7b7)
• fmsy: clarify _FORCE_OUTPUTS — only output.ssb.enabled gates in-memory; yield flag inert (6564063)
• fix model-refpoints plan per apply-and-run workflow review (21 findings) (a1d6cf1)
• implementation plan for model-internal fishery reference points (188a3b3)
• revise model-refpoints spec per in-loop workflow review (19 findings, 5 critical) (e367ba7)
• spec for model-internal fishery reference points (Fmsy/Bmsy/Blim sweep) (3488090)
• fix fisheries plan per in-loop workflow review (9 findings) (8788990)
• implementation plan for fisheries stock-status diagnostics (e5dc3f6)
• revise fisheries spec per round-3 multi-angle review (22 findings) (b923bae)
• reframe fisheries spec per deep literature review (indicative; B=user Bmsy; ICES Fmsy only) (d728c31)
• revise fisheries stock-status spec per in-loop workflow review (77afc6e)
• spec for fisheries stock-status diagnostics (Kobe / B-ref / F-Fmsy) (07b8f79)
• split semicolon-joined test statements (ruff E702) in yieldN/meanSize plan (1cad736)
• fix yieldN/meanSize plan per multi-angle workflow review (4b07d1e)
• implementation plan for Python-engine yieldN + meanSize (CSV + NetCDF) (799c71a)
• revise yieldN/meanSize spec per in-loop review (b56b0f5)
• spec for Python-engine yieldN + meanSize outputs (CSV + NetCDF) (5d0bb80)
• perf: fix RNG-spike plan per in-loop workflow review (e6f2bd8)
• perf: implementation plan for Stage-0 RNG-reproduction spike (d2c7191)
• perf: spec for Stage-0 RNG-reproduction feasibility spike (0270755)
• spike: task-6 post-review fixes note (run_all defaults + boundary_probe hoist) (d65ef8c)
• spike: update task-6 report with run_all results (1dba643)
• spike: task-6 boundary-free bench report (cfd867b)
• spike: task-4 C kernel build report (7812235)
• perf: round-2 plan clarifications (non-blocking) (5f55b78)
• perf: fix kernel-spike plan per in-loop review round 1 (6c7aeab)
• perf: implementation plan for native-predation-kernel spike (7b93119)
• perf: revise kernel-spike spec per in-loop review (2766c05)
• perf: spec for native predation-kernel feasibility spike (83d65e6)
• round-2 plan review (execution-ready) + fix egg-test size-ratio keys (7bcbe76)
• rework remediation plan per 5-angle plan-review workflow (24 defects) (e44dfb6)
• implementation plan for high-findings remediation (08f16b7)
• resolve high-findings spec open questions (EEC/Java parity, keep Fix 2, fallback now) (6007478)
• rework high-findings spec against the production (Numba) dispatch path (b76aa89)
• design spec for deep-review high-findings remediation (f06190b)
• readme: fix dots screenshot (was a heatmap) + clearer caption (b163fa6)
• readme: add live-movement screenshots (heatmap + dots) from Baltic (90c2807)

Other

• v1.1.0 (1b96984)
• OSMOSE HPC Apptainer/Singularity container (ddc0d2c)
• model-internal fishery reference points (Fmsy/Bmsy/Blim sweep) (c78c15d)
• indicative fisheries stock-status diagnostics (ede0a77)
• Python-engine yieldN + meanSize outputs (CSV + NetCDF) (af19fa0)
• Merge Stage-0 RNG-reproduction feasibility spike (dbca0e1)
• rng: orchestrator + RNG-reproduction feasibility artifact + verdict (a552a31)
• rng: C-vs-Numba per-cell RNG-gen speed probe (3f42aff)
• rng: bit-exact parity gate (C vs njit oracle across n x seed grid) (57081bf)
• rng: C NumPy-legacy MT19937 (seed+permutation+shuffle) + cffi build (a9e9ae7)
• rng: scaffold + njit cell-RNG oracle (mirrors mortality.py:1479-1497) (4b2c925)
• Merge engine perf: vectorize movement masks + bincount diet aggregation (c415c19)
• Merge native-predation-kernel feasibility spike (610f517)
• perf: gitignore build artifacts + untrack SDD scratch (4a9dbb8)
• perf: orchestrator + native-predation-kernel spike artifact + verdict (b1a8d90)
• perf: boundary-free throughput bench + boundary-cost probes (4fb9d0d)
• perf: C-vs-Numba parity gate (<=1e-12 op-order rounding) (a75b830)
• perf: C leaf transcription + cffi build (portable & native) (eed83a6)
• perf: leaf-arg reconstruction + p10/p50/p95 cell selection (7a374c5)
• perf: capture cell-loop pre-state via monkeypatched parallel kernel (79c31c6)
• perf: native-predation harness scaffold + provenance guards (67dfdff)
• Merge fix/high-findings-remediation: deep-review high findings (668021f)

Tests

• engine: recalibrate the two Baltic bands shifted by the egg-retention fix (f2e1834)
• tutorial: xfail biomass-pyramid band shifted by the Java-validated egg-retention fix (a4a2a00)
• engine: Java cross-check + EEC/BoB parity baselines for egg-retention fix (02b14b0)
• engine: xfail type-III FR invariant flipped by the egg-retention equilibrium shift (9b0d9ba)

[1.0.0] - 2026-06-22

Features

• scenarios: compare in a modal with shared diff table + edge states (95fef3b)
• config-diff: shared classify + render component (88138d7)
• run: live card collapse = stream gate; heatmap fallback; 0.5s throttle; drop switch/auto-enable (d4027c6)
• run: compact busy indicator (corner pill, not full overlay) (ab69f7f)
• run: default the UI engine to Python (Java still selectable) (a36f170)
• run: choose_live_layer (dots->heatmap fallback) + dot_cap 5000->2000 (acbe0e2)
• run: auto-enable live movement for spatial (regular-grid) configs (d363ee1)
• run: wire py_threads -> numba.set_num_threads (0=auto), drop dead py_verbosity (54ac7f6)
• run: Python progress bar + in-place console line (reuses step_observer) (c7b4bb6)
• run: pure run-observer + spatial predicate + progress label (af9617d)
• forcing: convert-only CLI (bring-your-own downloaded file) (a2f1a00)
• forcing: NetCDF writers + package public API (fee1ec7)
• forcing: phy_to_physics temperature/salinity conversion (5787f18)
• forcing: bgc_to_ltl 6-group conversion (Mode A/B), grid-general (00c1feb)
• forcing: grid-parameterized regrid/resample/mask helpers (a8605c9)
• run: capability panel render from describe_engine (65ed363)
• run: active-engine indicator slot (ab6e08d)
• capabilities: describe_engine for the Java engine + total fallback (26623d5)
• capabilities: describe_engine for the Python engine (c1e0e36)
• capabilities: EngineCapability dataclass + truthiness helper (3e3814a)
• ui: Scenario Wizard — guided New-Scenario flow on the Scenarios page (#82) (a8f3b80)
• maps: Map Builder page — author spatial grid maps on the config grid (#81) (2fd868d)
• config: canonicalize at validators + allowlist 4.4.0 keys (717934d)
• engine: canonicalize config at from_dict + unified-ingestion/new-key reads (1c93a4a)
• config: to_target_keys inverse (leaf-scoped, merge non-invertible) + drift guard (882f70f)
• config: canonicalize_config wrapper + malformed-version hardening (bc9f1cf)
• config: add 4.4.0 migration chain entry + skip-if-target-exists applier (e98b064)
• config: lock OSMOSE 4.4.0 rename set (ported from Releases.java $15) (cefad37)
• engine: enable meanTL in Baltic config + e2e community-output integration test (cb8d6b8)
• engine: write community biomass/abundanceDistribBySize CSVs (1839706)
• engine: write 1D meanTL CSV from captured per-species mean TL (915fd89)
• engine: capture biomass-weighted per-species meanTL into StepOutput (337179b)
• engine: add output.meanTL.enabled config flag (output_meantl) (77914a3)
• results: wire Sheldon spectrum, ABC chart + community-metrics panel into Diagnostics (ad43ab3)
• plotting: Sheldon NBSS + ABC dominance-curve charts (00ae25e)
• community-metrics: community_report orchestrator + markdown formatter (f11c4ba)
• community-metrics: Warwick ABC W-statistic + dominance curves (ed3f4e1)
• community-metrics: Mean Trophic Level + Marine Trophic Index (1cff03b)
• community-metrics: Sheldon NBSS mass spectrum + size diversity + totals (37102a4)
• community-metrics: shared helpers (window-mean, species cols, L-W coeffs) (966b884)
• fishbase-ui: surface inline bootstrap panel on the species setup page (683fe08)
• fishbase-ui: review/apply helpers + inline bootstrap panel server (4568075)
• fishbase: TRAIT_MAP + fetch_traits (median/range, Speccode quirk, a/b check) (6420e7f)
• fishbase: resolve_species (scientific/common, FB→SLB fallback) (6c0c03e)
• fishbase: client skeleton — _load_table with disk cache + typed errors (d1c26a9)
• run: make the three Run-page cards body-collapsible (22abf2d)
• calibration: select process backend at NSGA-II sites + benchmark switch (7a87c86)
• calibration: ProcessPoolExecutor backend for NSGA-II (forkserver, broken-pool recovery) (681bd7f)
• calibration: picklable BiomassRMSE/DietDistance objective functors (6cde163)
• feedback: header modal + token-gated read API route (insert before catch-all) (602cc3b)
• ui: feedback modal + submit handler (appends, no HTTP POST) (6d435ff)
• feedback: osmose/feedback store + token check (pure core) (ace5320)
• ui: wire startup changelog modal (shiny:connected, once per version) (1fb2a3b)
• ui: About modal renders README/Changelog + startup changelog modal (f802f42)
• docs: osmose/docs_content loader + changelog parser (9370244)
• ui: Parameter Sensitivity Explorer page + app registration (9d4690b)
• calibration: persist live sensitivity result via sobol_io (148c874)
• ui: make_sobol_tornado horizontal Sobol chart builder (22898ee)
• calibration: sobol_io artifact store + pure view helpers (b43baa2)
• scenario-diff: render config-diff panel + wire accordion (4685459)
• scenario-diff: add _classify_config_diffs classifier (50ff30c)
• ui: live movement view on the Run page (map + queue + poll + render) (46be06a)
• engine: optional step_observer hook in the Python simulate loop (6aeadb8)
• live-movement: add deck.gl heatmap + dots layer builders (b088c0e)
• live-movement: add MovementSnapshot + build_snapshot + queue observer (aa171a2)
• ui: embed Scenario Diff tab + sub-server in Results page (26ab806)
• ui: add scenario_diff tab module (nav panel + server) (782e1de)
• add biomass_long normalizer + make_biomass_overlay chart (fb4c536)
• ui: add make_diff_map + shared NaN→None serializer (a6b685a)
• spatial: add spatial_diff_2d + grid_latlon for scenario diff (78bb307)
• calibration: Pareto solution picker + config export (0ade369)
• ui: per-cell time-series panel on Spatial Results (14f0093)
• spatial: cell_timeseries backend for per-cell NetCDF extraction (14491a3)
• ui: live config validation panel on the Setup page (2a331b6)
• config: add summarize_config_validation helper (single source of truth) (dc198d8)
• ui: Results Trophic Network sub-tab (pyvis iframe, cached layout, index slider) (3c843ad)
• trophic: species_layout fixed positions + make_trophic_network_html pyvis builder (82e338d)
• trophic: diet_network_at per-timestep species aggregation (prey-sum, dead-stage-excluded predator mean) (e13ffac)
• trophic: pyvis dep + dietMatrix wildcard reader + label/time/universe helpers (7a3adc6)
• config: check_config.py CLI for parse diagnostics (2ed40a4)
• config: recursive-ref diagnostics + shipped-config regression (2b59546)
• config: line-numbered unparseable/empty_key/duplicate_key diagnostics (7261f73)
• config: ConfigDiagnostic dataclass + format/has-errors helpers (eaf0f7f)
• size-spectrum: compute_size_spectrum.py CLI (945978a)
• plotting: make_size_indicator_timeseries trend chart (873269f)
• size-spectrum: per-timestep indicator series + markdown report (70ec335)
• size-spectrum: compute_size_spectrum + LFI/slope/mean-size indicators (07ed094)
• size-spectrum: community by-size reader + reshape/window helpers (09d6dd5)
• history: RUN_HISTORY_DIR constant + default_run_history() helper (ba9cc28)
• ui: Compare Runs output-delta chart + table (run_delta wired) (908fc2a)
• ui: _delta_for_selected helper for Compare Runs output delta (320bd4b)
• delta: compare_runs CLI (5c17d7d)
• delta: diverging-bar run-delta chart (0e757e0)
• delta: markdown delta report (dac5f7e)
• delta: SpeciesDelta + run_delta (union, abs/pct, from-zero, ranked) (2a7927f)
• delta: per-species windowed-mean normalizer (wide + long output shapes) (bc160fe)
• fisheries: fix mortalityRate reader + compute_mortality_balance CLI (b55b15e)
• fisheries: F/M bar chart (d046c55)
• fisheries: F/M markdown report (7d32137)
• fisheries: MortalityBalance + compute_mortality_balance (F/M) (d00dedf)
• fisheries: annual_rate aggregation (per-step → annual, windowed) (b48beae)
• fisheries: mortalityRate CSV reader (2-row header + trailing comma) (23bd3b7)
• fr: shepherd-fr eval mode + FR-on/off process diagnostic (4c1f111)
• fr: phase-14 calibration scaffolding + reconstructed phase-13 base (a5846c1)
• fr: functional-response branch in numba kernel + njit arg threading (92efe26)
• fr: functional-response branch in Python predation kernel + kernel-vs-oracle value test (e909dee)
• fr: EngineConfig fr_shape/fr_halfsat 4-layer wiring + fixture fix (ddf84a9)
• fr: parse functional-response keys on background-predator path (8eb65f3)
• fr: parse functional-response keys with strict validation (focal path) (861610e)
• fr: add predator functional-response schema fields (d9465df)
• tutorial: pivot substrate to data/baltic/ subset (5 synthetic-3sp T4 attempts BLOCKED) (6a193ea)
• tutorial: stub _tutorial_config helper module (f69b435)
• calibration-ui: N-other-live-runs disclosure badge with [switch] stub (6523583)
• calibration-ui: current best parameters block with bound-distance hints (cb987ee)
• calibration-ui: convergence chart shows best-ever reference line from history (44de081)
• calibration-ui: per-species ICES proxy table with magnitude factor (3d5432b)
• calibration-ui: run header + liveness_state + pure-helper tests (e4dc2f7)
• calibration-ui: module-level RESULTS_DIR + scan helpers + LiveSnapshot reactive (3affb6e)
• calibration: NSGA-II callback writes checkpoint + save_run; chart-update regression-pinned (98d5596)
• calibration: surrogate-DE writes CalibrationCheckpoint per real-eval round (fe97352)
• calibration: CMA-ES writes CalibrationCheckpoint each generation (e518c3c)
• calibration: DE wires save_run on completion with tempfile 0o600 fallback (167e6f3)
• calibration: DE writes CalibrationCheckpoint with main-thread residual re-eval (4d0603c)
• calibration: make_banded_objective returns (callable, residuals_accessor) (d8f6631)
• calibration: _ObjectiveWrapper captures per-species residuals + sim_biomass (51b5723)
• calibration: LiveSnapshot for atomic per-tick scan results (ab9ed59)
• calibration: is_live + probe_writable + liveness_state classifier with boundary tests (1cd64b5)
• calibration: read_checkpoint with 4-kind discriminator, size guard, invariant-error catch (07c004b)
• calibration: write_checkpoint with atomic tmp+rename and numpy coercion (636623e)
• calibration: CheckpointReadResult discriminated union with two-sided invariants (e70ca55)
• calibration: CalibrationCheckpoint dataclass with 14 post_init invariants (3cabd6c)
• calibration: scaffold checkpoint module with default_results_dir (b950754)
• economics: DSVM bioeconomic demo + spatial-output bugfix (#47) (cd590c1)
• validation: ICES output validation harness (#46) (969351f)

Bug Fixes

• config-diff: use plain-dict impl per spec, drop unused typing imports (97b757e)
• run: session.on_ended cancels the run + _session_alive guards (no DestroyedReactiveError cascade) (b00f674)
• forcing: narrow phyc/zooc to non-None for pyright in Mode A (7d3abe2)
• complete the incomplete remediation edges (PR-C) (#93) (c0728e7)
• scenarios: harden scenario-store deserialization + validation (PR-B) (#92) (701d026)
• maps: Map Builder correctness (polygon mask-edit, lonlat edge, blank shape) (#91) (f3846ac)
• packaging: working Docker image + runtime CI gate + demo data resolution (#89) (dc65979)
• config: config/schema hardening (validate_value coercion + 4.4.0 migration gates) (#88) (286d375)
• calibration: one failure policy — a bad candidate scores inf on all backends (#87) (643aac9)
• engine: warn loudly on parsed-but-unapplied mortality features (#86) (f5b0fcf)
• PR-4 IO robustness (cancelled-run status + empty-CSV reader) (#85) (922dd59)
• scenarios: backup path appends '.bak' instead of replacing the suffix (#84) (ac5bdea)
• plotting: apply theme template + title dict to new charts (house style) (19f9f44)
• community-metrics: cast pd.to_numeric for pyright (08dd7df)
• trophic: parse the Python-engine diet matrix (_) — fixes KeyError 'Prey' (888a482)
• results: isolate _get_result_data memo cache to stop diet_chart recalc desync (578879d)
• fishbase: ruff format + rename e2e to test_e2e_fishbase.py (CI collect-ignore glob) (d184810)
• fishbase: pyright-clean reductions (numpy float array + casts for pandas stubs) (cb0071e)
• fishbase: defensive column guards in _match_in_db (review finding) (6747143)
• deploy: poll the HTTP health check instead of a single early probe (9ed8a7f)
• deploy: run prod from a git clone + guard Shiny OTel source extraction (1dcac33)
• run: block the Java engine for background-species configs (Baltic is Python-only) (9f45cff)
• ui: render diet heatmap from the engine's _ matrix (9d1359f)
• calibration: OSMOSE_RESULTS_DIR override + StateDirectory so prod checkpoints are writable (8b48545)
• types: suppress reportPrivateImportUsage for layer_legend_widget under shiny_deckgl v1.9.2 (6182b4b)
• ci: declare httpx in [dev] for the feedback-endpoint TestClient tests (003336c)
• tests: skip copernicus mcp-env tests when fastmcp/copernicusmarine absent (6fa0769)
• ui: fire-and-forget Python run so the live view streams mid-run (476071b)
• scenario-diff: resolve pyright errors, show real time in map titles, add changelog (eb7dcc0)
• ui: render species-dimmed spatial output in Map/Flat views (81d6609)
• types: cast pandas reductions to silence real groupby unions; drop mis-diagnosed pyright pin (93e2413)
• ci: pin shiny<1.6 and pyright<1.1.410 to stop unpinned CI drift (6a56528)
• types: resolve pyright errors in trophic_network/size_spectrum/fisheries (2ab217a)
• ui: keep validation panel full-width above the split layout (aebfb6b)
• trophic: don't double-apply threshold (sub-5% slider was silently clamped) (5197f15)
• ui: populate Compare Runs selector from run history on Results-tab entry (7215809)
• ui: drop vestigial output_dir guards from Compare Runs readers (2958eee)
• ui: Run tab + Compare Runs use canonical run-history dir (default_run_history) (b0b96cc)
• fisheries: F/M on exploited life stage(s), excluding unfished-stage natural mortality (fec2172)
• fisheries: sum F and M across life stages (fishing is on Pre-recruits, not Recruits) (ccbcebb)
• fr: diagnostic preserves per-predator calibrated K + seeds=1 warning (b4fa377)
• fr: phase-14 raises (not warns) when frozen phase-13 base is missing (fcff417)
• scope bit-exact parity to Python 3.12 and omit JIT modules from coverage (2e9fcc9)
• pyright: silence 57 errors only visible against the CI-mirror venv (eda4273)
• resolve pyright errors (28 -> 0) — incl. one real runtime bug (2bc6305)
• docker: install git so pip can resolve shiny_deckgl git+https dep (d437597)
• deps: correct shiny_deckgl git URL and pin tag that exists (599dd1d)
• ui: Results tab now displays after a Run (df48294)
• tutorial: preserve Beat 6 edits across re-runs (conditional copytree) + enforce strict-key validation in regression test (75c2a32)
• calibration: reject duplicate param_keys + banded_loss-without-targets (8dbe54e)

Performance

• engine: replace np.add.at with np.bincount in _collect_spatial_outputs (P2) (#41) (c59ae85)
• engine: hoist predation scratch buffers per-cell (K1/P1) (#40) (255f060)

CI/CD

• add numba-disabled leg exercising pure-Python engine fallbacks (98d3e53)
• visual: target the visual test file so collection skips [dev]-only-dep modules (c1b1c16)
• visual: drop ini addopts in workflow (xdist's --dist not in [viztest]) (b2d0721)
• visual: runbook + opt-in digest-pinned gate with per-page baseline updates (a342100)
• actions: bump checkout/setup-python/upload-artifact to Node 24 majors (4d22db9)
• type-check: type-check the 3.13 path via pyright --pythonversion matrix (032a87e)
• install numba in dev deps so tests don't run the slow fallback path (f854978)

Chores

• gitignore e2e screenshot + calibration-history artifacts (f623fc6)
• run: ruff format fixups for run-feedback UI changes (9ef440a)
• config: PR1 final gate fixes (001c530)
• deploy: silence benign pip noise (root-user warning + leftover ~dist dirs) (c608a06)
• live-movement: widen dot-jitter period, drop dead test branch, fix stale comment (dc97ad0)

Documentation

• amend scenario-diff plan per 3-angle in-loop review (19b48fb)
• implementation plan for scenario-diff polish (19d8e1e)
• round-2 clarity fixes to scenario-diff spec (90e95d0)
• amend scenario-diff spec per 3-angle in-loop review (ce4768d)
• design spec for scenario-diff polish (shared component + modal) (4ba0f51)
• amend hardening plan per in-loop plan review (blocker + 2 major + minor) (380228d)
• implementation plan for deep-review latent-item hardening (dc15a7d)
• amend hardening spec per in-loop review (2 major + minors) (115b562)
• design spec for deep-review latent-item hardening (a1edda0)
• Sphinx + GitHub Pages API reference site (#94) (1f3a37e)
• harden Run-page-rework plan per workflow review (dot_cap override, layer key, stale tests, CancelledError, e2e race) (910e1ab)
• implementation plan for Run-page rework (547d112)
• spec for Run-page rework (python default, compact UI, live-stream crash fix) (be4c323)
• jar-swap: retarget resume plan to v4.4.1 (v4.4.0 resource-forcing bug fixed upstream) (d1aee23)
• run-feedback plan 2nd-pass review fixes (drain placement, e2e budget, comments, docstring) (73fa6c3)
• harden run-feedback plan per multi-angle workflow review (025b296)
• implementation plan for Python run-progress feedback (f50cf91)
• spec round-3 fixes (year off-by-one via 1-based done + pure label helper, py_threads min=0) (7bb1816)
• spec round-2 fix (e2e_baltic.py:57 also clicks the live toggle) (809da1d)
• spec round-1 review fixes (progress lifecycle, ndtperyear key, e2e toggle, threads idempotency) (5380229)
• spec for Python run-progress feedback (788c978)
• forcing: add osmose/forcing to CLAUDE.md architecture tree (ef6438b)
• harden CMEMS-forcing plan per multi-angle workflow review (984651f)
• plan round-1 review fixes (parity mask, package init, lint scope) (7a40c22)
• implementation plan for CMEMS forcing conversion core (sub-project A) (30b1d4f)
• spec for CMEMS forcing conversion core (sub-project A) (c3c7654)
• plan round-3 fix (update stale e2e comment, don't delete) (de825df)
• plan round-2 polish (stale-ref grep, files header, e2e id note) (416d766)
• plan round-1 review fixes (panel_conditional, e2e, citations) (156dcce)
• implementation plan for Run-page engine-capability transparency (bb15f0c)
• spec for Run-page engine-capability transparency (f227a49)
• deep-review remediation plan (2026-06-20) (#83) (271e2c7)
• OSMOSE 4.4.0 jar-swap resume plan (cross-engine + ICES validation) (#80) (64ba5ec)
• plan: PR1 2nd in-loop review fixes (CI/pitfalls/DRY angles) (eab16dd)
• plan: PR1 in-loop review fixes (3 angles, all verified) (ed86058)
• plan: PR1 (core config migration to 4.4.0) — 8 TDD tasks (9be003e)
• spec: config-migration v3 — ground in Releases.java, fix merge direction (1f28b6d)
• spec: config-key migration v2 after in-loop review (2 rounds) (a52bdfa)
• spec: config-key migration to OSMOSE 4.4.0 (canonical=new, read-aliases) (57a465d)
• in-loop review fixes for community-outputs spec+plan (8be75f7)
• plan: Python-engine community outputs (DistribBySize + meanTL) (c47bb31)
• spec: Python-engine community outputs (DistribBySize + meanTL) (396ac22)
• changelog: community size-spectrum extension (Sheldon NBSS + MTL/MTI/ABC) (b172c43)
• in-loop review fixes for community size-spectrum spec+plan (e3a4cae)
• plan: community size-spectrum extension implementation plan (e32bd24)
• spec: community size-spectrum extension (Sheldon NBSS + community metrics) (0644eb0)
• plan: full Baltic e2e test implementation plan (inline, 3 phases) (98e5fd3)
• spec: full Baltic e2e (run + live movement + Results outputs) design (8a3432a)
• changelog: add FishBase/SeaLifeBase trait bootstrap to Unreleased (33e00a1)
• plan: round-3 review fixes — SLB per-table degrade, cache evict, sentinel filter, multi-candidate picker, inline panel (drop render-in-modal) (2c700bd)
• plan: round-2 nit — correct Task 7 e2e header (modal-open smoke, no network) (4eccb08)
• plan: round-1 review fixes — pyarrow dep, field.description, Shiny-safe ids, modal reset, busy indicator (b4f6858)
• plan: FishBase trait bootstrap implementation plan (8 tasks, TDD) (810db98)
• spec: correct FishBase access to Source Cooperative parquet snapshots (4081c8a)
• spec: FishBase/SeaLifeBase species-trait bootstrap design (c53dc2f)
• fix visual plan/spec per live-run findings (#main_nav clip, gate-tolerance self-consistency) (369b936)
• revise visual-regression spec+plan per efficacy/maintenance/cost/operability review (b8a9553)
• revise visual-regression plan per in-loop review (upload-artifact@v6, branches/permissions, max_ratio doc) (c5a1241)
• implementation plan for UI visual regression tests (5cc4291)
• revise visual-regression spec per 3-round in-loop review (eb7e125)
• design spec for UI visual regression tests (1c8d73d)
• record shiny 1.6.x as the supported runtime (DEPLOY.md, CHANGELOG) (1e91671)
• implementation plan for the shiny 1.6.3 port (6996297)
• round-2 spec fixes (Bootstrap-match rationale, deploy.sh version-aware, cma np.Inf, floor-vs-lock) (2d71206)
• revise shiny-1.6 spec per round-1 review (6de1284)
• design spec for porting to shiny 1.6.3 everywhere (9d79645)
• DEPLOY.md — restart osmose-shiny.service after every pull (96b43d1)
• round-2 plan review of NSGA-II (blocker + major, verified by running) (729a60e)
• address plan review of NSGA-II speedup (blocker + majors) (ec21408)
• implementation plan for NSGA-II ProcessPoolExecutor speedup (b056407)
• round-4 review of NSGA-II spec (1 major guardrail + nit) (8df47d0)
• round-3 review of NSGA-II spec (1 major + nit) (9579e41)
• round-2 review of NSGA-II spec (blocker + 2 majors) (7e55f5d)
• address round-1 review of NSGA-II process-pool spec (3 majors) (2e13f64)
• spec for NSGA-II ProcessPoolExecutor speedup (8db6640)
• round-2 plan-review fix — read_feedback docstring <=100 cols (b78b7b1)
• plan-review nits for feedback system (all 3 angles converged) (81b169f)
• implementation plan for feedback system (sub-project 2) (436f9c3)
• address round-1 review of feedback-system spec (blocker + 2 majors) (b0c3375)
• spec for feedback system (sub-project 2) (826ac0e)
• freshen README + cut CHANGELOG v0.13.0; bump version (86adb6b)
• plan-review nits for docs-in-app (all 3 angles converged) (e5e8969)
• implementation plan for docs-in-app (sub-project 1) (4acac33)
• round-2 review fix for docs-in-app spec (converged) (5db432b)
• address round-1 review of docs-in-app spec (ab06a22)
• spec for Docs-in-app (sub-project 1) (15b7bf9)
• plan-review fix — structure test asserts unique nav value (d40cf59)
• implementation plan for Parameter Sensitivity Explorer (c6ca9a4)
• round-4 review fixes for sensitivity-explorer spec (converged) (5155f83)
• address round-3 review of sensitivity-explorer spec (917f685)
• address round-2 review of sensitivity-explorer spec (4 majors) (736d985)
• address round-1 review of sensitivity-explorer spec (78b9c45)
• spec for Parameter Sensitivity Explorer page (f92a86e)
• plan-review nits (badge cell format-clean; spec table font-size) (1ca2790)
• implementation plan for config-diff panel (e67b7bf)
• round-2 review fixes for config-diff spec (converged) (42da847)
• address in-loop review of config-diff spec (e5b5149)
• spec for Scenario Diff config-diff panel (1929afd)
• live-movement: add CHANGELOG entry; clarify MovementSnapshot.status (3cb20a1)
• live-movement: add converged spec + implementation plan (d8644e5)
• scenario-diff: add converged spec + implementation plan (a1289a1)
• usage: add task-oriented usage guide + docs index; fix stale README API sketch (a1fc860)
• plans: add backlog infra+viewers plan (CI matrix, narrative docs, viewers) (b85de20)
• changelog: note live config validation panel (51869ab)
• implementation plan for real-time config validation (e1c1b43)
• fold round-2 in-loop spec review (fresh angles, executed vs real code) (79acb47)
• fold in-loop spec review (2 reviewers, executed vs real code) (d1fac36)
• real-time config validation in the form — design (5a06504)
• changelog: property-based tests via Hypothesis (e61407d)
• fold in-loop plan review (executed the plan's code) (18df305)
• property-based tests (Hypothesis) implementation plan — 7 tasks (2e81fea)
• fold round-3 in-loop review (empirical mutation + post-edit consistency) (26cd978)
• fold round-2 in-loop review (teeth + operational angles) (728f4b1)
• fold in-loop spec review (2 executing reviewers, prototyped vs real code) (f59a87d)
• property-based tests (Hypothesis) design — focused 4 targets (1cbc91f)
• changelog: trophic-network animation (pyvis) (42827db)
• trophic-network animation (pyvis) implementation plan (738a16a)
• round-2 clean — fix debounce primitive (throttle/debounce, not reactive.event) (4144166)
• fold pyvis in-loop review (2 BLOCKERs) into trophic-network spec (3eedc61)
• revise trophic-network spec to pyvis node-link (Sankey killed by review) (bdc5bde)
• changelog: config parser diagnostics (d335964)
• in-loop review fixes for config-parser-diagnostics plan (395cdd8)
• config parser diagnostics implementation plan (b13cbd2)
• round-2 clean — classify empty-key on the post-rstrip value (f892ef8)
• in-loop review fixes for config-parser-diagnostics spec (b115f95)
• CMEMS temperature forcing design spec (engine NetCDF-temp loader + baltic_ev) (7dc9627)
• changelog: community size-spectrum diagnostics (d7003de)
• in-loop review fixes for size-spectrum plan (2c4a6ac)
• size-spectrum diagnostics implementation plan (356c782)
• round-2 clean — note the private _read_output_csv coupling (bf62283)
• revise size-spectrum spec per round-1 in-loop review (b0945c3)
• community size-spectrum diagnostics design spec (1d38809)
• changelog: Compare Runs works without a loaded output dir (32347e4)
• in-loop review fixes for compare-runs decouple plan (c3401ac)
• compare-runs decouple-from-output-dir implementation plan (d62e850)
• in-loop review fixes for compare-runs decouple spec (4a4ba3a)
• compare-runs decouple-from-output-dir design spec (3ec348c)
• in-loop review fixes for run-history plan (126aaae)
• run-history canonical-dir implementation plan (e679f05)
• run-history canonical-dir reconciliation design spec (49ebd70)
• ui: document Compare Runs output-delta section (110b011)
• ui: in-loop review polish (broaden render guards, prompt clarity, structure note) (8a64263)
• ui: Compare Runs output-delta implementation plan (3d990f8)
• ui: Compare Runs output-delta section design spec (7070a0e)
• delta: document compare_runs CLI + deferred follow-ons (dfcb422)
• delta: round-2 deep-review fixes (fixture preamble + window guard) (8760cd9)
• delta: fix plan after deep 4-angle in-loop review (eb7dd6e)
• delta: implementation plan + spec wide-format correction (9773993)
• delta: result delta-tracking design spec (5de6746)
• fisheries: document F/M diagnostics CLI + deferred Kobe follow-up (6d8b2f5)
• fisheries: rescope to F/M diagnostics after 4-angle in-loop review (0c2c9f6)
• fisheries: fisheries-diagnostics implementation plan (535ea90)
• fisheries: fisheries stock-status diagnostics design spec (78f64cc)
• percid overshoot diagnostic — proven cause, fix deferred (9dad350)
• fr: phase-14 Baltic FR verdict + diagnostic per-predator K reporting (f04b2c2)
• fr: clarify PR-B review nits (predator-set sync note, override comment) (0370697)
• fr: config keys + cross-feature caveats + prey-predation-reduction consequence test (e1f4173)
• fr: final clean-pass polish (prey-survival test robustness) (89d274b)
• fr: round-7 confirmation-review fixes (a7054a0)
• fr: round-6 plan rewrite after 4-angle in-loop review (7bb68bc)
• fr: round-5 spec re-review fix + implementation plan (705525d)
• rewrite FR spec after round-4 review (2 CRITICALs) (93e88b8)
• fold round-3 diagnostic refinements into FR spec (44cb1e9)
• revise FR spec after round-1+2 in-loop review (e58c942)
• add predator functional response (aggregate, opt-in) design spec (7d18047)
• plan: refine density-dependent recruitment plan per review (441ac54)
• plan: density-dependent recruitment implementation plan (c01684c)
• plan: density-dependent recruitment design (hockey-stick + Shepherd) (5198ed9)
• revise PR #48 plan after second deep review (3b33118)
• implementation plan for PR #48 rebase + Task 11 (3dcd2cc)
• revise PR #48 design after deep multi-angle review (6fde858)
• design for PR #48 rebase + Task 11 resolution (c2122b9)
• plan: Ev-OSMOSE FIE-on-cod spec + r2 plan with review fixes (03941da)
• tutorial: polish — log_y axis + honest narrative about Baltic transient dynamics (c2ba915)
• tutorial: top-of-page README callout + doc-index row + tutorials index (735f350)
• tutorial: Beats 2-6 + closing + troubleshooting (Baltic substrate) (aa3631c)
• tutorial: preamble + Beat 1 paste-and-run script (Baltic substrate) (694bc99)
• plan: r3 of 30-min tutorial plan — fix duplicated suffix, wire numba_warmup, add Predator-extinct branch (3c582ba)
• plan: r2 of 30-min tutorial plan — apply round-1 review (TDD discipline, parameter pre-tuning, stopping criterion, conditional commits) (4b1654e)
• plan: 30-min 3-species tutorial implementation plan (12 tasks) (f9c3ee3)
• spec: r6 of 30-min tutorial — fix stale 0.8/0.99 reference in Task 9 (5502bf2)
• spec: r5 of 30-min tutorial — apply round-5 polish (CONFIG/build_config cleanup, accessibility 0.99, BASELINE_PERTURBATION used, ruff-clean skeleton, task ordering) (1585599)
• spec: r4 of 30-min tutorial — apply round-4 review (CONFIG/build_config naming, row count, relativefecundity, accessibility scaling, headless fallback) (2349b62)
• spec: r3 of 30-min tutorial — apply rounds 1-3 in-loop review (8bd86c9)
• spec: 30-minute 3-species tutorial design (e35625a)
• calibration: design spec + implementation plan for progress dashboard (95039b2)
• perf: 2026-05-08 perf arc overview (#45) (09bdb8a)
• perf: P4b not-shipping — post_init bypass below 2% gate (#44) (45a0556)
• perf: P4 not-shipping — state.replace cache below noise floor (#43) (9b8ed62)
• perf: P3/A4 not-shipping — compute_feeding_stages already below gate (#42) (8a2f9da)
• plan: post-v0.12.0 perf plan — K1 + np.add.at + state.replace (r3) (#39) (d5e71d5)

Other

• v1.0.0 (2849b96)
• Merge feat/scenario-diff-polish: shared config-diff component + compare modal (3624c11)
• record real run duration_sec across both engine paths (f77528d)
• sweep osmose_wizard_/osmose_maps_/osmose_val_ temp dirs (e4b411c)
• warn on unsupported fishing selectivity types 2/3 (silently knife-edged) (8f40eea)
• Merge feat/run-page-rework: Python default, compact Run UI, live-stream crash fix (70c9499)
• Merge feat/python-run-feedback: Python-engine run-progress feedback (f1682ae)
• Merge feat/cmems-forcing-core: CMEMS->OSMOSE forcing conversion core (sub-project A) (9d39da0)
• Merge feat/run-engine-capability: Run-page engine-capability transparency (8560cc6)
• redact leaked credential from tracked docs + scan whole tree (#90) (de6537d)
• OSMOSE 4.4.0 jar swap — PR-A: config value-migration layer (#79) (c9454d9)
• Config-key migration to OSMOSE 4.4.0 — PR2 (UI/writer/calibration wiring) (#78) (dc2d701)
• declare pyarrow runtime dep for fishbase parquet reads (6094c84)
• version-aware dependency upgrade (cma/shinyswatch/shinywidgets/deckgl) with floor check (d8eadad)
• promote shiny to 1.6.x; pin shinyswatch>=0.11, shinywidgets>=0.7, cma>=4.0, shiny_deckgl@v1.9.2 (1e71007)
• Apply ruff formatting to app.py (fix: code-quality) (c82d27c)
• trophic: fold in-loop plan-review fixes (5d46d25)
• temperature-forcing: close the line — no engine bug, blocked behind calibration (34c558b)
• helcom: freeze HOLAS-3 fish snapshot; no validator (rescoped after in-loop review) (c890e12)
• test(history)+docs: lock writer==reader run-history dir invariant (77c1324)
• run-history: round-3 clean — sync File Structure header with Step-1b files (818a059)
• run-history: fold round-2 findings — writer-test CWD-pollution fix + grep-count correction (77e8f5f)
• Density-dependent recruitment: Shepherd stock-recruitment (+ hockey-stick) (#50) (0b1fc27)
• Ev-OSMOSE FIE-on-cod: genetics plumbing + engine fixes + baltic_ev fixture (#48) (29b5206)
• Merge pull request #49 from razinkele/fix/shiny-deckgl-pin (3e58091)

Refactoring

• scenario-diff: delegate config table to shared component (e2c8ba1)
• run: assert choose_live_layer (drop dead layer-builder re-exports + noqa) (e2c3ae7)
• mcp: delegate generate_osmose_* to osmose.forcing core (55b47fb)
• run: engine tabs -> client-side conditional settings (no input race) (4ef6746)
• config: route Run gate and CLI through summarize_config_validation (DRY) (a394bb1)
• ui: extract _compare_run_choices helper (0fdf6c0)

Styling

• e2e: ruff format test_e2e_baltic.py (lint = check + format) (584979a)
• fishbase: apply ruff format (the format changes that the prior bad git-add aborted) (2603697)
• apply ruff format to 91 drifted files (6a7e941)
• test: drop unused pytest import in test_ices_proxy (2cfb168)
• test: hoist E402 imports (7e13ed0)

Tests

• e2e: compare-scenarios modal renders a diff (e483786)
• assert a fresh session config_dir survives a normal-age cleanup sweep (c3d5bff)
• e2e: expand live card (new stream gate) instead of the removed switch (a0de6b8)
• e2e: drop manual live-toggle clicks (auto-on); assert plain-run progress (df47e80)
• capabilities: cover unknown-engine fallback, list isolation, truthiness edges (f9d34ce)
• config: bioen ingestion-unification parity gate (base-wins, intended change) (b6babf8)
• engine: parity note + final gates for community outputs (a9a3017)
• community-metrics: real-data eec smoke + final gate pass (9d176d3)
• e2e: assert Baltic spatial output renders (pill enables + map) + screenshot (ac92437)
• e2e: assert Baltic biomass chart + diet heatmap render (regression guard) (dc9daf3)
• e2e: Baltic full-run skeleton — load + Python run + live movement (1912dec)
• visual: refresh setup baseline for the FishBase bootstrap panel (3afae99)
• fishbase: e2e smoke — bootstrap panel renders on setup page (aa3a40e)
• fishbase: record cod + green-crab parquet fixtures (634b637)
• otel-guard: defer app import into test bodies to fix CI collection (b141bfa)
• visual: suppress Shiny toast to fix movement-page snapshot flake (b9179af)
• visual: authoritative container baselines (5 pages, inspected) (82428a2)
• visual: retry-until-stable capture (fixes Setup non-determinism in CI container) (46612f5)
• visual: use top-level import re instead of import (final-review nit) (19f3d78)
• visual: Fishing, Movement, Advanced page snapshots (b55d81f)
• visual: Playwright harness + nav-chrome and Setup snapshots (4b50b32)
• visual: pure compare_images core (ratio + pixel-floor + mean-delta) with unit tests (d769c55)
• visual: add viztest extra, visual marker, collection guard, gitattributes (eb942f9)
• e2e: dismiss the startup changelog modal before nav clicks (4e740cb)
• feedback: e2e submit→store + CHANGELOG entry (ab6e6ed)
• docs: restore hardened e2e modal dismissal (focus-independent + localStorage poll) (044db54)
• docs: restore plan-verbatim e2e modal dismissal (fix: spec-compliance) (e5439bb)
• docs: e2e startup modal + About tabs; CHANGELOG entry (06e6541)
• sensitivity: e2e explorer page + CHANGELOG (3eb4873)
• scenario-diff: e2e config-diff panel + CHANGELOG (0624769)
• e2e: live movement view streams during a Python run + cancel path (da7a430)
• e2e: scenario diff tab renders overlay + spatial maps (cfaf086)
• harden csv-overlay perf guard against xdist contention (02c43d3)
• parallelize suite with pytest-xdist (~3.5x faster) (30efbca)
• skip eec/baltic data-dependent tests when gitignored artifacts absent (7d07de7)
• hypothesis: make window property two-sided (final-review teeth fix) (e7268bb)
• hypothesis: size-spectrum helper properties (convexity, LFI boundary, bin-width, window) (1c09159)
• hypothesis: diet_network_at properties (bounds, monotonicity, prey-sum, dead-stage) (512559b)
• hypothesis: preamble-detection properties (detect-k, no-raise, cache-invalidation) (2baea1b)
• hypothesis: config writer->reader round-trip properties (aa6d5a0)
• hypothesis: shared property-test strategies (f9c15bb)
• hypothesis: add hypothesis dev dep + deterministic ci profile (34f73a6)
• fr: background-inclusive diet aggregator + width-16 diagnostic test (4aefd36)
• fr: bit-exact parity-off gate + type1==absent + background-on + inert-prey-only (8356f54)
• fr: wire numba=False to the Python predation fallback via _HAS_NUMBA patch (57fa1ba)
• fr: shared run harness + FR config-injection helpers (cb8211e)
• tutorial: share Baltic sim across tutorial tests via module-scoped fixtures (06163ca)
• conftest: ignore e2e modules at collection when playwright missing (9e523d8)
• tutorial: encode measured equilibrium bounds (Baltic, seed=42) (3db8d5f)
• tutorial: replace numba_warmup stub with real session-scoped warmup (8e261f7)
• tutorial: regression test in final form (RED until Tasks 4-9) (3a23a3c)
• add tmp_results_dir + synthetic species fixtures for calibration tests (c3f573f)

[0.12.0] - 2026-05-08

Features

• schema: choice_labels for fisheries.selectivity.type ENUM (Phase 2 finisher) (#27) (f436be5)

Bug Fixes

• validation: close broad schema-engine parity TODO from C1 (#28) (8b5908d)
• engine: average distribution dicts across recording window (M1) (#22) (f8dfd42)
• ui+engine: cooperative cancellation through simulate() (C4 Phase B) (#18) (f7d8e28)
• ui: render multi-value config entries as read-only text inputs (H12) (#17) (3958b41)
• app: defer cleanup_old_temp_dirs() until first session start (H11) (#15) (e0ead58)
• engine: Phase 3 — M4 Gompertz bounds, M5 accessibility/n_dead clamps, RNG docs (#11) (f16a057)
• engine: reproduction parameter bounds (H10) (#10) (8ff56a7)
• schema: field-quality fixes from Phase 2 plan (#9) (dc95f55)
• validation: close schema-coverage gaps on examples + minimal (H1, H4, H2) (#8) (dd55620)
• schema: movement keys (C1) — engine reads movement.{property}.map{N} (#5) (06b432e)
• ui: invalidate state.output_dir on failed/cancelled run (C4 Phase A) (#7) (65b0d7e)
• ui: path-traversal hardening in results page (C3) (#6) (de9bfa0)
• schema: output.bioen.sizeInf -> sizeinf; engine never read camelCase (C2) (#4) (b62ff8e)
• validation: allowlist baltic background-species keys (C5) (#3) (d7b9a6d)

Performance

• engine: vectorise _precompute_map_indices per-species (A2) (#36) (1f717fe)
• engine: vectorise accessibility school-index lookup (A1) (#35) (70cc1da)
• mortality: drop redundant n_dead zeros allocation (H6 partial) (#31) (e0e1d94)
• bench: --config flag + per-fixture grid resolution + name-list guard (#30) (38dc8f3)
• engine: vectorise biomass_by_cell DSVM accumulator (H7) (#29) (8c6621e)

Documentation

• perf: A3 not-shipping post-mortem (#37) (3c0b66c)
• plan: vectorise the non-JIT'd Python-side perf hot paths (#34) (ceb59f5)
• plan: kernel-surgery plan for remaining Phase 4 perf items (r2, post-review) (#32) (39725cf)
• plan: add deep-review remediation plan (9-iter loop-converged) (3851b9e)

Other

• v0.12.0 — Python-side perf wins + deep-review remediation + B-H (#38) (31a2386)
• K4 — eec_full 5yr profile + go/no-go decisions for K1/K2/K3 (#33) (1839a1c)
• Merge origin/master into local master (ebe8343)
• bounded-runtime DE — patience + wall-clock cap (post-incident) (cf5cb8e)
• DE intermediate checkpointing — interrupt-safe long runs (a6c596b)
• optimizer benchmark on synthetic problems (fe0c04c)
• --optimizer flag wires CMA-ES + surrogate-DE into calibrate_baltic (135aa8f)
• surrogate-de: nfev accounting, GP fit recovery, warm-start warn (8edffa4)
• cmaes: correctness fixes for success flag, bounds, NaN handling (54b61d1)
• harden D4 sensitivity script against silent data loss (b7a5708)
• add GP surrogate-assisted DE runner (Tier C1 speedup) (8649e55)
• add CMA-ES runner (Tier C2 speedup) (6a90cf6)
• add Sobol sensitivity script for phase 12 param pruning (D4) (15e610f)
• launch wrapper for Tier A+B fast phase 12 calibration (f775df3)
• warm-start, tunable tol, and Tier A speedup knobs (1ae7630)
• phase12: enable Beverton-Holt density-dependent recruitment (816d5c1)
• background: set length on background schools (bg-predation fix) (92088c9)
• v0.10.0 — calibration on PythonEngine in-memory (d4eebe1)

Refactoring

• schema: Phase 2 field-quality bundle — predation, bioen, ltl, fishing (#26) (936769c)
• ui: consolidate state.loading into state.busy (M10) (#19) (27fe142)
• ui: extract input_id_for_field/key helpers (M13) (#16) (6dda518)
• ui: make _inject_random_movement_ncell pure (H3) (#14) (7133fa3)

Tests

• engine: NaN propagation through fishing_mortality (H8 — final) (#25) (c654f7d)
• engine: JIT determinism across thread counts (H9 — verified) (#24) (399339c)
• engine: NaN propagation extensions for reproduction/accessibility/starvation (H8) (#23) (30b04f6)
• engine: pin size-bin Java parity (M3 — verified, no code change) (#21) (6aa5cc4)
• engine: NaN/Inf propagation audit through mortality processes (H8) (#20) (9c85a8b)
• Phase 5a — L brittleness fix, M7 lifespan boundary, M8 runner failure modes (#13) (64a623a)
• engine: pin feeding-stage Java parity (M2 — verified, no code change) (#12) (a0574e4)

[0.11.0] - 2026-04-28

Bug Fixes

• engine: slice per-species arrays to focal-only in reproduction (37bc1d1)

Documentation

• plan: Beverton-Holt + Ricker stock-recruitment implementation plan (c6b1b2f)
• spec: add .docx version of non-rectangular grids study (2daf029)
• spec: non-rectangular grid feasibility study (a5481b1)
• plan: round-3 cleanups — commit-message pattern + _expected_errors note (15673e7)
• plan: tighten init signature decision (round-2) (d1202f3)
• plan: calibration plan round-1 review fixes (836625b)
• plan: calibration-python-engine implementation plan (dc5faae)
• spec: round-3 final-pass fixes (cb94146)
• spec: pin cache-key authoritative source (round-2 cleanup) (080fd78)
• spec: calibration spec round-1 review fixes (ea185fa)
• spec: calibration throughput — port NSGA-II to PythonEngine in-memory (d7fa894)

Other

• bump 0.10.0 -> 0.11.0 (origin already has v0.10.0 tag at d4eebe1) (a24090d)
• docs+version: Beverton-Holt SR documented as post-parity divergence (e74326d)
• reproduction: apply stock-recruitment to per-step eggs (1c9cb28)
• reproduction: cleanup — NDArray annotations, diagnostic mismatch error, sharper zero-SSB test (57ad8b4)
• reproduction: add apply_stock_recruitment helper (B-H + Ricker) (db9338e)
• config: cleanup — docstring, schema desc trim, top-level pytest import, n_bkg consistency (bdaa398)
• config: parse stock.recruitment.{type,ssbhalf} per species (33c216f)
• add stock.recruitment.{type,ssbhalf} fields per species (05eed2f)
• compare two phase-12 calibration runs (d8df5db)
• activate grey seal + cormorant background species (f54bb26)
• widen mortality bounds instead of background species (edcea8b)
• handle --phase 12 (joint optimization) (a9b43d4)
• add joint phase 1+2 option (--phase 12, 24 params) (ef802c2)
• cap DE workers at 8 (from -1) to avoid RAM exhaustion (8b42497)
• enable DE process-pool parallelism (da7956d)
• widen flounder + pikeperch fishing upper bounds (8c8a349)
• Revert "baltic: add grey seal + cormorant as background species" (6541e9f)
• add grey seal + cormorant as background species (4d5e7fb)
• 2026-04-21/22/23/24 session work — map fixes, calibration, plan (0d1cdf3)

Tests

• reproduction: multi-step integration smoke for B-H + Ricker (9e74dd8)
• reproduction: derive season from cfg.n_dt_per_year, isolate rng per call (c58f702)
• reproduction: pin linear-formula regression for type=none across SSB sweep (52653ab)
• reproduction: fix misleading SSB comment, isolate RNG per call (62c715c)

[0.10.0] - 2026-04-21

Documentation

• parity roadmap STATUS-COMPLETE audit — mark Phases 2/3/4 shipped (9f8af75)

Other

• v0.10.0 — calibration on PythonEngine in-memory (d4eebe1)

[0.9.3] - 2026-04-19

Features

• predation: public predation_for_cell API (Phase 7.1 commit 1) (72f80a3)

Documentation

• CHANGELOG entry for Phase 7.1 predation reconciliation (0b82e68)
• tests: fix stale predation() docstring in rng_consumers (20649e0)
• parity-roadmap §7.1 STATUS-COMPLETE (Phase 7.1) (7f9a3e7)
• plan: round-2 clarify cell_x/cell_y irrelevance for dispatch (af256ff)
• plan: Phase 7.1 plan round-1 review fixes (f4914d1)
• plan: Phase 7.1 predation-reconciliation implementation plan (e8d10cc)
• spec: Phase 7.1 round-4 review — bug-hunting pass (4fec5c8)
• spec: Phase 7.1 review-driven revisions (6c3aced)
• spec: Phase 7.1 predation-reconciliation design (0f16837)

Other

• v0.9.3 (ea31ac8)

Refactoring

• predation: update stale comments in predation_for_cell (Phase 7.1 task 3 follow-up) (009c781)
• predation: delete batch predation() orchestrator (Phase 7.1 commit 3) (37ceeb1)
• tests: expand single-school resource test to 2 schools (Phase 7.1 task 2 follow-up) (ed62a76)
• tests: migrate test_engine_rng_consumers to predation_for_cell (Phase 7.1 commit 2f) (2aa6018)
• tests: migrate test_engine_feeding_stages to predation_for_cell (Phase 7.1 commit 2e) (12c8255)
• tests: migrate test_engine_background to predation_for_cell (Phase 7.1 commit 2d) (5ca231a)
• tests: migrate test_engine_predation to predation_for_cell (Phase 7.1 commit 2c) (ec3edd3)
• tests: migrate test_engine_diet to predation_for_cell (Phase 7.1 commit 2b) (9461419)
• tests: migrate test_engine_predation_helpers to predation_for_cell (Phase 7.1 commit 2a) (0ca3c60)

[0.9.2] - 2026-04-19

Features

• config: unknown-key validation at EngineConfig.from_dict (Phase 7.3) (327a20c)

Bug Fixes

• config: spec-review polish — restore UnknownKey export + strip empty-key artefact (66b3dcd)

Documentation

• update README + CLAUDE.md for Phase 7.3 config validation (3af9f9a)
• CHANGELOG entry for Phase 7.3 config validation (f29c91d)
• plan: iter-4/5/6 review fixes — warn-mode integration, glob helper, arithmetic cleanup (008a8bb)
• plan: iter-3 Step 7 hint fixes (744ae1b)
• plan: iter-2 fixes — drop unused functools import + rewrite stale path prose (5761a72)
• plan: iter-1 review patches to config-validation plan (bad68cb)
• plan: config-validation implementation plan (Phase 7.3) (33b0478)
• spec: remove stale +13/d124de6 baseline paragraph (iter-2 fix) (557ee1b)
• spec: iteration-1 review patches to config-validation design (1a0c996)
• spec: self-review fixes to config-validation design (e8294ee)
• spec: config validation design (Phase 7.3) (4d273e6)
• parity-roadmap: Phase 7 honesty pass — 7.2 shipped, 7.1+7.3 scoped accurately (d124de6)
• parity-roadmap: Phase 6 STATUS-COMPLETE (bioenergetic module) (ede19d3)

Other

• v0.9.2 (0e59258)
• config: align logging + canary loader with project conventions (d7181ca)

[0.9.1] - 2026-04-19

Features

• economics: wire write_economic_outputs into simulate end-of-run + STATUS-COMPLETE Front 6 (1dcffd7)

Chores

• replace deprecated update_navs + gitignore ephemeral paths (b1e9328)

Other

• v0.9.1 — Front 6 wire-up + post-release cleanups (7c68e7a)

Tests

• e2e: sync Playwright assertions to current tab labels (259d3d1)

[0.9.0] - 2026-04-18

Features

• output: spatial outputs — biomass / abundance / yield-biomass NetCDF (901b3be)
• output: NetCDF per-species distributions + mortality-by-cause (d5947f0)
• output: diet CSV Java-parity — one file, one row per recording period (5e96916)
• calibration-ui: Pareto/Weighted toggle for surrogate optimum (84e5ab7)
• calibration-ui: n_workers numeric input for preflight (95e858d)
• calibration-ui: red-banner modal for PreflightEvalError (c8b2e32)
• calibration: ICES SAG validator for Baltic F rates and biomass envelopes (2be016f)
• calibration: problem.py robustness (timeout/stderr/cleanup) (8358725)

Bug Fixes

• baltic: post-rename cleanup + Java-compat regression tests (89734a0)
• calibration: unit-aware F weighting + defensive snapshot pull + coverage tests (590240e)
• calibration: surrogate multi-obj returns Pareto or weighted-sum (6d75310)
• calibration: loud failures + abort threshold in preflight eval (4de10ae)

Performance

• calibration: parallelize preflight eval with ThreadPoolExecutor (a454758)

Chores

• gitignore .bak + calibration_results; archive sensitivity plan (355e7f4)

Documentation

• post-session roadmap STATUS-COMPLETE for fronts 1-4 (7482b6f)
• SP-4 changelog + Phase 5 STATUS-COMPLETE (445f354)
• plans: fix stale test-count arithmetic in SP-4 plan self-review (e03a69c)
• spec,plans: iteration-2 spec + plan patches for SP-4 (47349a8)
• spec: SP-4 spec iteration-1 patches (internal consistency + Java parity) (fc7b4cc)
• plans: iteration-2 patches to SP-4 plan (542bcf9)
• plans: rewrite SP-4 plan after 4-reviewer ground-truth audit (0c74795)
• plan: SP-4 output system implementation plan (e036338)
• spec: scrub two residual output.spatialized.* config-key references (8ad2103)
• spec: SP-4 review-round-1 corrections (553ece4)
• spec: SP-4 output system design (Front 4) (b77e85d)
• changelog for calibration UI Phase 3 (62f628b)
• plan,spec: plan review-round-1 corrections (a476a0e)
• plan: calibration UI Phase 3 implementation plan (aef168f)
• spec: fix SilentException import path to shiny.types (was shiny.reactive) (0bbfdfb)
• spec: calibration UI Phase 3 review-round 1 corrections (38676a1)
• spec: calibration UI Phase 3 design (Front 3) (1cafed5)
• modernize README (TOC, Baltic example section, doc index) + changelog for review fixes and provenance doc (034f614)
• baltic: full provenance doc for the Baltic example (sources, scripts, per-parameter refs) (4031138)
• changelog for Baltic ICES cross-validation (9797e2f)
• baltic: document ICES snapshot refresh workflow (722f21f)
• baltic: summarize ICES cross-validation findings and known limits (2926436)
• baltic: scaffold ICES SAG snapshot directory + manifest (028beb7)
• roadmap for closing remaining fronts (ICES MCP → Java fishery reformat → UI Phase 3 → SP-4) (2fa0737)
• plans: STATUS-COMPLETE banners on three more shipped plans (fb08acc)
• plans: STATUS-COMPLETE banners on five already-shipped plans (934b46b)
• plans: loop-review patches to ICES SAG validation plan (518de4b)
• plans: mark UI Phase 2 complete; fix ICES plan MCP-shape drift (a313866)
• plan for ICES SAG cross-validation of Baltic calibration (d923ad0)
• changelog for calibration/sensitivity fixes (b8a58b4)

Other

• v0.9.0 — full Phase 5 output-system parity + calibration UI Phase 3 + Baltic ICES validation (37bdafb)
• baltic: strip underscores from fishery names for Java-engine compatibility (98f478e)
• baltic: freeze ICES SAG snapshots for eight Baltic stocks (2024 advice, cod.27.22-24 on 2022) (a7d65a5)
• load-example picker on grid page + calibrate_baltic popsize_mult (fc5f271)
• baltic: grid-mask rebuild + ICES validation + whitefish→smelt swap (d61ea1c)

Refactoring

• scripts: return-type hint + itertools counter in calibrate_baltic (7ace2f3)
• calibration: split detect_issues into per-category helpers (95db190)
• calibration: split run_preflight into Morris/Sobol stages (13f9474)

Tests

• make_minimal_engine_config helper for SP-4 tests (0779581)
• calibration: regression fence for F-rate and biomass-envelope drift vs ICES (0435fde)

[0.8.1] - 2026-04-17

Features

• auto-load .env in copernicus MCP server (9b8d197)
• data: add Baltic NetCDF grid and fix LTL trophic level key (f1bcd8f)
• engine: wire XorshiftRNG into simulation via java_compat_rng flag (9bf9d11)
• engine: add Java-compatible Xorshift RNG for bit-exact parity (70425ee)
• add dynamic accessibility, Python engine UI, Baltic example, and renderer badge (396e496)
• engine: wire bioen starvation into mortality loop with bioen_enabled switch (24e8296)
• engine: add foraging mortality function with constant and genetic modes (60dc41f)
• engine: add by-dt-by-class additional mortality variant (eb6f977)
• engine: add fishing scenario auto-detection from config keys (0579da2)
• engine: wire Gaussian/log-normal selectivity into fishing mortality (3e8c509)
• engine: add catch-based proportional allocation fishing variants (f713b7a)
• engine: add rate-by-dt-by-class fishing mortality variant (cdeb063)
• engine: add Gaussian and log-normal fishing selectivity types (496dbce)
• engine: add SingleTimeSeries and GenericTimeSeries with CSV loading (f976c7b)
• ui: add preflight screening checkbox, modal, and handler wiring (4f7b565)
• calibration: export preflight API from init (47d0fc0)
• calibration: add run_preflight() two-stage orchestrator (fe6229a)
• calibration: add preflight issue detection logic (4ad9231)
• calibration: add Morris screening with multi-objective aggregation (36db8b4)
• calibration: add preflight data model — enums and dataclasses (165d1ba)
• calibration: export history module from init.py (a1a63d8)
• calibration: add banded loss, validation, history, and 2D sensitivity handlers (6a9bb06)
• calibration: restructure tabs, add banded loss/validation/history/correlation UI (1da6bdf)
• calibration: add history persistence module (2b42a0b)
• calibration: add correlation chart, upgrade sensitivity for multi-objective (aa242e7)
• calibration: export new public API from init.py (953405a)
• calibration: add evaluation cache and schema validation to problem (ec2b148)
• calibration: add surrogate cross-validation and fit_score_ (00c724d)
• calibration: extend sensitivity analysis for multi-objective (d1dd600)
• calibration: add multi-seed validation and candidate ranking (c1a27e2)
• calibration: add composable banded loss objectives (855b594)
• calibration: add BiomassTarget data model and CSV loader (9af1cd7)

Bug Fixes

• engine: keep Numba enabled with java_compat_rng flag (3270bc1)
• engine: distinguish null-map migrations from placement failures in warning (679b70f)
• tests: update tests for new fishing config fields and sigmoid API (64c5676)
• apply test coverage + dependency ordering review to plan (653149d)
• apply code correctness + spec alignment review to plan (7027c98)
• deploy: add --root-path /osmose for reverse proxy WebSocket routing (b28db08)
• calibration: single-obj Pareto crash, NSGA-II convergence persistence, absolute HISTORY_DIR (6716e99)
• calibration: track duration_seconds, fix surrogate convergence format, add post_validation API (6861b26)
• docs: Phase 2 plan — fix except placeholder, thread-safe history save, dead code (d6a043e)
• docs: Phase 2 spec — add objective_names to history JSON, derive species_names (b5d1e27)
• docs: correct Phase 2 spec — navset names, tmpl params, run_id conflicts (74a07ee)
• calibration: guard worst_species_penalty against empty list, document first-objective-only metrics (87baf55)
• engine: align egg detection to first_feeding_age_dt (F4E) (6d7502c)
• ui: accessibility, UX safety, and consistency improvements (cb35aef)
• config: validation, writer routing, scenario persistence fixes (3b5601c)
• engine: safety and correctness fixes across engine processes (39ad713)

Performance

• calibration: gate history buttons on tab selection + reactive trigger (d6d3f29)

Chores

• gitignore operational dirs (.remember, logs, cmems_cache) (9b427ec)
• clean up ruff F401/F841 in non-CI-scoped scripts (d1ee962)
• register ICES MCP server in .mcp.json (ab3fd88)

Documentation

• ship osmose-master java test/build-discipline patch (34707a4)
• add 2026-04-17 deep-review fixes plan (4525c92)
• apply 4-task review to SP-5 bioen activation plan (01b6fad)
• add SP-5 bioen activation implementation plan (123bdd1)
• apply 3-task review to SP-2 additional mortality plan (bb32dd7)
• add SP-2 additional mortality variants implementation plan (cc72bdb)
• apply 5-task review to SP-1 fishing plan (bec15e8)
• add SP-1 fishing system completion implementation plan (8011c4d)
• apply 5-task review to SP-3 timeseries plan (4bac915)
• add SP-3 time-series framework implementation plan (104b784)
• apply 5-iteration Java source review to parity spec (4f3863a)
• apply review fixes to Java parity spec (9 issues) (cb8ae1d)
• add full Java OSMOSE 4.3.3 parity design spec (3bcdd3e)
• apply 10-task review to preflight implementation plan (540c96f)
• add pre-flight sensitivity analysis implementation plan (c9e202a)
• apply 6-iteration review to pre-flight sensitivity spec (9c24e33)
• add pre-flight sensitivity analysis design spec (dcad6a7)
• add ICES data access implementation plan (b4cf65e)
• apply 4-iteration review to ICES data access spec (a6e1558)
• add ICES data access MCP server + skill spec (b1a78ef)
• add calibration UI Phase 2 implementation plan (9ab6b31)
• add calibration UI Phase 2 design spec (0b8cc86)
• add calibration library gaps Phase 1 implementation plan (b2b110d)
• fix 10 issues in calibration library gaps spec (f8c6f03)
• add calibration library gaps Phase 1 design spec (7dbb43b)

Other

• v0.8.1 — deep-review fixes (credentials, types, docs) (e2bedc2)
• 2026-04-17 deep-review fixes (credentials, types, docs) (2c45323)
• encode calibration preflight invariant via _require_preflight helper (5a50a36)
• widen param_names annotation for pandas DataFrame columns (0caf824)
• annotate reactive.value generics for cal_X/cal_F (b036a1f)
• broaden load_timeseries return, align ByYearTimeSeries param name (f23e733)
• narrow stage_accessibility and access_matrix for prey-scale path (b5e47c2)
• cast bioen eta to float to match bioen_starvation signature (4653d81)
• hoist fishing_catches to narrowed local in catch allocator (dde6d78)
• declare SchoolState.imax_trait and guard None in fields() iterators (59ccca1)
• remove committed CMEMS credentials from .mcp.json, document env setup (6e71a2e)
• require CMEMS credentials from env, remove hardcoded fallback (ddb742b)
• add reference_point_type and metadata to Baltic targets CSV (a8a56ef)

Refactoring

• extract _require_creds helper, add behavioral guard test (3973069)
• deploy: switch from shiny-server to standalone Uvicorn service (2eb860a)

Styling

• format calibration UI Phase 2 files (597b592)
• format calibration library gap files (b9c5881)

Tests

• detect literal CMEMS credentials under any mcpServers env block (3b618e4)

[0.8.0] - 2026-04-13

Features

• engine: add movement.map.strict.coverage config key (M-7) (9911cc7)
• engine: add uncovered-slot fixture + strict parameter to MovementMapSet (M-7) (e3c218a)
• ui: extract parse_nspecies to shared _helpers.py (M-9) (2c5ba61)
• engine: MPAZone validates grid shape and binary values (I-8) (195b873)
• engine: validate bioen_* field coupling at EngineConfig construction (I-2) (ed009b3)
• engine: add SchoolState.validate() for biological invariants (I-1) (936eb33)
• add Java/Python tabbed layout to Run page (f6bc5c9)
• wire new pages with engine-gated nav items (578a2ac)
• add Ev-OSMOSE genetics stub page module (14d2332)
• add Python engine diagnostics page module (3d02fac)
• add economic module stub page module (2febf66)
• add Java/Python engine selector toggle in header (9991f74)
• add engine_mode reactive field to AppState (d20862d)
• register Map Viewer tab in app navigation (0d1b778)
• add Map Viewer page with file list and deck.gl preview (842594a)
• move model info into header bar, remove second row (e8a2f42)
• deep review fixes, CSV separator fix, automation setup, map display tests (634498e)
• add species distribution and fishing maps to grid overlay selector (b141fcd)
• wire Spatial Results page into nav with disabled pill state (b4f7cf6)
• implement spatial_results_server with data loading and map rendering (74ca06d)
• add spatial_results page skeleton with UI layout (6a32e18)
• genetics: seeding phase + config fields for transmission_year and neutral loci (579bf66)
• genetics: add neutral loci to GeneticState and inheritance (d6b6295)
• genetics: wire trait_overrides into _bioen_step and _bioen_reproduction (1b3384a)
• economics: add economic CSV output files (261d2fb)
• economics: add annual reset and catch memory update in simulation loop (c659736)
• economics: add full cost model, stock catchability, and catch memory (136a5b0)
• economics: add travel cost and stock-dependent revenue calculations (5b5afaf)
• economics: integrate effort map into fishing mortality scaling (b7c7ae1)
• simulate: wire genetics and economics into simulation loop (884cb21)
• config: add genetics_enabled and economics_enabled flags to EngineConfig (a564167)
• economics: add DSVM logit choice model and effort aggregation (b138f17)
• economics: add FleetConfig, FleetState, and config parsing (9612e98)
• genetics: add gametic inheritance with fecundity-weighted parent selection (8157bf4)
• genetics: add trait expression and phenotype override mechanism (3274519)
• genetics: add GeneticState with compact/append sync and initial genotype creation (3d5bc5e)
• genetics: add Trait dataclass and TraitRegistry with config parsing (7381795)

Bug Fixes

• ui: log exc_info in _close_spatial_ds instead of bare pass (M-8) (04b5824)
• engine: apply _require_file to 4 adjacent silent-failure sites (26cf198)
• raise KeyError on NetCDF variable name mismatch for background species (C-8) (3d2d134)
• raise on missing config files instead of silent fallback (C-3..C-7) (fa0c5f9)
• pad fishing_seasonality/discard_rate for background species (C-1, C-2) (f177926)
• tests: register osmose plotly template in conftest to fix isolation failures (3bf4bf2)
• gracefully skip invalid scenario names in import_all (M6) (7c5af1a)
• reject oversized ZIP entries in scenario import_all (M10) (de264ed)
• reset key_case_map between read() calls on same reader (M7) (1cdb77a)
• normalize partial-year spawning tail with warning (M2 followup) (4d80db1)
• normalize spawning season per-year chunk instead of total (M2) (55349dd)
• sanitize exception messages in UI notifications (H14) (3f981c0)
• add path traversal guard to comparison_chart and config_diff_table (H12, H13) (adcbb38)
• register atexit cleanup for export and demo temp dirs (H10, H11) (6179e8d)
• move state.dirty.set inside reactive.isolate in forcing sync (H8) (616efeb)
• raise ValueError on asymmetric species column in RMSE merge (H7 followup) (4c8c622)
• include species in RMSE merge to prevent cross-product (H7) (f7e9319)
• filter internal _-prefixed keys from config writer output (H6) (0b4407f)
• aggregate movement map coverage warning instead of per-slot flooding (H5) (d6d42ec)
• use integer sampling instead of round() to avoid boundary cell bias (H4) (c4cce5a)
• preserve distribution dicts in _average_step_outputs (H3) (2dda4c4)
• use live abundance*weight in Python fallback predation (H1) (f05c2fb)
• explicit NotImplementedError in JavaEngine.run_ensemble (C7) (96925fd)
• tests: add W=c*L^b value pin and tighten bounds in weight-length test (C6 followup) (0f6f12a)
• replace tautological weight-length test with meaningful assertions (C6) (083ae5f)
• consume reactive.poll result so calibration UI updates (C5) (b9ce68e)
• CSV map orientation, colormap, layer toggle, multi-value config guard (247a232)
• restore hasattr fallback in make_legend for server compatibility (92ec20a)
• address round 3 review findings (9b004bd)
• add type annotations for reactive values, fix f-string lint warning (e8db4a7)
• handle all-NaN data in spatial scale info display (5c91e27)
• guard shiny:connected handler against duplicate registration (44473be)
• address review findings across spatial results implementation (c76ba79)
• remove unused math and _sdgl imports from grid.py (c2eb8ff)

Performance

• calibration: reuse problem instance and add cleanup (a57f681)
• ui: add config value accessor and cache grid NetCDF loads (ea82aa8)
• io: add CSV/preamble caching and fix double stat() (83f5ea3)
• engine: vectorize hot-path loops and reduce allocations (7006418)
• vectorize temperature lookups in _bioen_step via get_grid (M13) (ea8e5c3)
• vectorize load_csv_overlay cell loop with NumPy (44e1e54)

Chores

• delete unused JavaEngine stub + Engine Protocol + redundant Path import (I-10, M-2) (3f707ea)
• gitignore superpowers workspace + skill review HTML (41c8f29)
• fix remaining ruff errors (FleetState forward ref, ambiguous l) (d31fdcd)
• tests: ruff auto-fix unused imports and drop duplicate classes (d980e89)

Documentation

• update README, CHANGELOG and bump version to 0.8.0 (cb2f447)
• engine: document population.seeding.year.max is global-only per Java parity (M-5) (48bb1c8)
• remove duplicate focal_starvation_rate_max in plan 1 task 3 (review loop 2) (9930818)
• fix 8 blockers in v3 deferred plans after thorough review loop (feb98ec)
• add implementation plans for 3 v3 deferred items (I-3, M-7, D-1+M-5+M-9) (be2e62f)
• add design specs for 3 v3 deferred item plans (I-3, M-7, D-1+M-5+M-9) (f914e51)
• engine: clarify cell_id expression when resources is None (M-6) (51e1c19)
• make output.py TODOs actionable / link to roadmap (M-4) (1eee064)
• revise v3 remediation plan after 5 review loops (e9bad01)
• add deep review v3 remediation plan (28 tasks, 7 phases) (e387de7)
• add fresh deep review v3 findings document (34 items) (441b378)
• engine: pin phi_t Arrhenius fallback behavior for e_d==e_m (C3) (e9dd7c0)
• add deep review v2 Phase 3-5 implementation plan (a7b59e6)
• enable bypass permissions and mark UI tightening plan complete (4cd9edd)
• add UI tightening + engine selector spec and plan (b0edf1b)
• add implementation plan for Grid / Spatial Results split (521d7e9)
• add spec for splitting Grid & Maps into Grid + Spatial Results (bab5d72)
• add Ev-OSMOSE + DSVM fleet dynamics design specification (0a33fe9)

Other

• Merge branch 'refactor/from-dict-split-2026-04-12' — I-3 from_dict monolith split (e4100f3)
• docs+test: pin SimulationContext diet field two-way coupling (M-14) (592d0c6)
• docs+test: pin StepOutput age/size distribution pairing invariant (M-13) (9c3531b)
• Merge feat/ev-osmose-economic-mvp: Ev-OSMOSE genetics + DSVM fleet dynamics Phase 1 MVP (5b0e0aa)

Refactoring

• engine: extract _parse_output_flags from from_dict (I-3 step 5/5) (05d1d03)
• engine: extract _merge_focal_background from from_dict (I-3 step 4/5) (3dd4551)
• engine: extract _parse_predation_params from from_dict (I-3 step 3/5) (52c65a4)
• engine: extract _parse_reproduction_params from from_dict (I-3 step 2/5) (a21c8c7)
• engine: extract _parse_growth_params from from_dict (I-3 step 1/5) (de71cde)
• ui: wire parse_nspecies into forcing.py (M-9) (034a1cc)
• ui: extract format_timing_pairs from diagnostics.py (M-9) (4fd32a4)
• ui: extract collect_resolved_keys from fishing.py (M-9) (ab2f327)
• ui: extract count_map_entries + wire parse_nspecies in movement.py (M-9) (4658092)
• engine: extract _accessibility_path_or_none helper (M-3) (b251f0d)
• engine: consolidate per-species timeseries CSV loaders into one helper (I-9) (b586642)
• extract _DEFAULT_VIEW_STATE in map_viewer.py (07fba24)
• consolidate FakeInput into shared test helpers (24dd1e4)
• replace string sentinels with named constants in grid.py (d8eaa48)
• extract _compute_half_extents to deduplicate finite-difference logic (e3fe543)
• extract _find_config_file helper to deduplicate file search (cf62ac0)
• extract _overlay_label and discover_spatial_files into grid_helpers (81a3394)
• remove Spatial Distribution tab from Results page (4c11a2b)
• rename Grid & Maps tab to Grid (f9c5ff1)
• move make_legend and make_spatial_map to grid_helpers for sharing (53af11a)

Styling

• tighten nav pills, card headers, and content gap spacing (ede6e39)
• tighten header bar spacing and reduce element sizes (546b7e1)
• compact header padding, nav pill spacing, and section labels (b500011)
• add osm-disabled class for greyed-out nav pills (242cc17)
• ruff format remaining genetics and economics files (f185d95)
• fix ruff lint warnings in genetics and economics tests (dcc040b)

Tests

• update tests for performance optimizations (8195aa2)
• ui: pin reactive.isolate write-propagation semantics (D-1) (23397ef)
• ui: add pure-helper unit tests for spatial_results._nc_label (M-9 partial) (4b5bfab)
• strengthen construction-only assertions in config validation tests (M-12) (bab8013)
• deduplicate test_parse_label (M-11) (42821ed)
• strengthen test_zero_rate_no_mortality with non-zero control school (M-10) (19d3129)
• pin additional_mortality_by_dt override step-rotation (I-7b) (ea827e9)
• pin out_mortality rate application when is_out=True (I-7a) (948078f)
• cover reproduction 'n_eggs < n_new' collapse branch (I-6) (6b50c83)
• pin _average_step_outputs multi-element branch contract (I-5) (8869743)
• add direct behavioral test for _predation_on_resources (I-4) (166d917)
• add coverage for output.step0.include and partial flush (H18) (00ff908)
• assert movement map warning fires once per species (H5 followup) (53b5690)
• add _map_move_school uniform placement regression test (H4 followup) (2d3596a)
• add E2E Playwright tests for Map Viewer page (6f9c070)
• add e2e tests for Spatial Results disabled pill and Grid rename (97278a1)
• genetics: 5 statistics tests for trait expression and neutral loci (78b9258)
• economics: add multi-fleet non-interference tests (4cced56)
• economics: add days-at-sea tracking and forced port tests (786431c)
• add integration tests for genetics and economics modules (b60f0c0)

[0.7.0] - 2026-04-05

Features

• add post_init validation to MPAZone, ResourceSpeciesInfo, BackgroundSpeciesInfo, CalibrationPhase (H10) (a3465fa)
• add context manager protocol to OsmoseResults (H4) (4d58ee0)
• add post_init validation to OsmoseField, Grid, and SchoolState (H3a-c) (ef96bbf)
• add EngineConfig post_init validation for array lengths and biological constraints (dd56db5)
• FreeParameter uses Transform enum + bounds validation (81385dd)
• emit ImportWarning when Numba is unavailable in engine processes (079ad59)
• add strict mode to OsmoseResults to raise on missing data (399d485)

Bug Fixes

• remove stale Phase 1 docstring and align output prefix to 'osm' (C6, H13) (9d59d9e)
• default strict=True for OsmoseResults, fix version fallback, narrow UI catches (C4, H7, H8) (72c1b5b)
• close OsmoseResults in calibration and handle malformed CSVs (C3, C5, M17) (d9e8216)
• add epsilon guards to f_o2 and phi_t to prevent NaN on edge cases (C2) (c3fab38)
• abort calibration when >50% of candidates fail (H6) (033de9a)
• use age_dt < first_feeding_age_dt for larvae check instead of is_egg (C2) (87e8ce9)
• wrap xr.open_dataset in context managers to prevent file handle leaks (H2) (0e0fa73)
• add logging for empty DataFrame returns and ncell injection skip (H5, SF3) (92786ab)
• use hasattr guard instead of broad except AttributeError in sync_inputs (C8) (5f7f231)
• validate CSV grid dimensions in movement map loader (C7) (f18370a)
• guard against division by zero when size_ratio_min is 0 (C1) (f63adf0)
• update bioen test to use lowercase sizeinf config key (C5 follow-up) (deddf6b)
• add missing calibration objective exports to all (H8) (7778964)
• use _log.warning instead of warnings.warn for Numba fallback (H7) (979a4ac)
• replace assert with if/raise for bioenergetics validation (C3) (0f92a81)
• use mortality.additional key pattern in calibration auto-detect (C6) (286a4f4)
• lowercase config key lookups for ndtperyear and bioen sizeinf (C4, C5) (b746f37)
• add path traversal guard to _resolve_file (68cc9ba)
• address all remaining review findings (minor+medium) (a458236)
• add global_map_idx bounds check + clamp inf in nan_to_num (1462d6c)
• address review findings — guards, NaN clamping, tests (f833582)

Performance

• vectorize fishing spatial map and MPA lookups (H12) (0d8e020)
• precompute species masks once in _bioen_step instead of 6 times (M1) (24770b1)

Chores

• add .worktrees to .gitignore (deef65f)

Documentation

• bump v0.7.0 — update CHANGELOG, README, and version for deep review #2 remediation (e167049)
• fix misleading comments across 7 files (M19-M25) (1add9fb)
• fix misleading comments across 7 files (M19-M25) (7768b82)
• fix comment quality issues from deep review (d1438a9)
• fix stale comments, schema descriptions, and docstrings (H9, M10-M14) (016a2d3)
• update README with latest benchmarks and EEC biomass parity table (16bd43d)

Other

• Merge branch 'deep-review-2-remediation' (58b9740)

Refactoring

• extract shared Numba mortality cause-dispatch, eliminating 3x duplication (H2) (d8dc189)
• split _collect_outputs into focused sub-functions with shared species-mean helper (H5) (ac3ca6c)
• make SchoolState and StepOutput frozen to enforce immutable-replacement pattern (H9) (367b777)
• consolidate 4 duplicated path resolvers into shared module (H6) (9729e8c)
• replace module-level mutable globals with SimulationContext (C1) (341e930)
• BFS deque, Scenario validation, batch append, mask UI warning, reader skip count (M4-M9) (1a34715)
• move _last_key_case_map from module global to AppState (H1 partial) (7d27ab3)
• add type annotations to config validator public API (M15) (5102268)

Styling

• apply ruff format across codebase (9431c75)

Tests

• add UI state and ensemble edge case tests (T7, T8) (bd286f2)
• add numerical edge case and ENUM validation tests, fix validate_field ENUM gap (T3, T6) (5544cd1)
• add config reader error path tests for circular refs, path escape, file size (T2) (cd83324)
• add _bioen_step orchestration tests for temperature branches and edge cases (T1) (302e1d4)
• add coverage for out_mortality formula, config errors, writer semicolon, resource depletion (T1,T4,T5,T7) (d955e1c)

[0.6.0] - 2026-03-22

Features

• wire Numba movement batch into movement() and simulate() (cd3224f)
• add _map_move_batch_numba for compiled movement (001355e)
• add _precompute_map_indices for movement Numba path (fd4fc46)
• add _flatten_all_map_sets for Numba movement data (1d13a44)
• wire batch cell loop into mortality() orchestration (Phase A) (c255eeb)
• add _mortality_all_cells_numba batch function (513720f)
• add _pre_generate_cell_rng for batch RNG pre-generation (0b6c81c)
• add --statistical mode to save_parity_baseline.py (b9edab6)

Bug Fixes

• sp_ids[k] → sp_ids[idx] bug in movement Numba function (bfd02a0)

Performance

• vectorize _precompute_effective_rates with NumPy (0b57e70)
• add prange parallel cell processing (Phase B) (8cce908)
• move RNG generation into Numba batch function (Phase A) (a549090)

Documentation

• fix 3 review issues in scaling parity spec (round 3→4) (abf5447)
• add scaling parity spec (movement Numba + vectorized rates) (efb936d)
• add sync comments for duplicated Numba inner loops (5534d72)
• add parity tests to performance spec, fix review round 3 (2cbc34b)
• add Python engine performance optimization design spec (15cf94f)

Other

• v0.6.0 — Python engine faster than Java (8509845)
• final baselines after scaling parity — Python 1.5x faster than Java on EEC 5yr (fcc8fd1)
• save EEC 5yr pre-scaling baseline (17.9s) (44b8d04)
• generate 10-seed statistical baseline for BoB 1yr (dab7e47)
• save 5yr pre-Phase-A timing baseline (69e30a7)

Tests

• add TestStatisticalParity for cross-version RNG tolerance (6fed9fc)

[0.5.0] - 2026-03-22

Features

• ui: add ambient ocean atmosphere, sonar spinner, polished notifications (d117776)

Bug Fixes

• preserve original key case when writing config back to Java (b9ce724)
• remove overly aggressive overlay failure notifications (9dc62a2)
• migrate from deck_legend_control to layer_legend_widget for shiny_deckgl 1.9 (c5229b1)
• ui: address code review findings across 11 UI files (854a7da)
• engine: apply larva mortality as full per-cohort rate, fix output headers (b6045bf)
• engine: larva mortality rate is per-timestep, not annual (c96ceaf)
• enable both biomass+abundance flags in distribution tests (4138a1e)
• warn on malformed fishing seasonality, narrow movement map exception (0aa569a)
• use utf-8 encoding with replace fallback, warn on unparseable lines (2aea6f1)
• narrow except Exception blocks to specific exceptions in UI sync code (279f470)
• register temp dir cleanup for scenario export downloads (85522d6)
• map None returncode to -1 instead of masking as success (4ddbe9b)
• remove duplicate growth_class parsing block (b74e902)
• remove double 1e-6 conversion on fishing yield (eacc5f9)
• remove duplicate age/size distribution block that overwrote correct results (8a7eaa4)
• engine: config-dir-aware file resolution + v4 fisheries seasonality (97ac300)

Other

• v0.5.0 — full EEC parity (14/14) via unified predation architecture (c8de5fb)
• restore larva mortality /n_dt_per_year division (2531801)

Tests

• add test_engine_accessibility.py for predation accessibility matrix (772b655)

[0.4.0] - 2026-03-20

Features

• engine: complete all 5 bioen output CSVs (ingestion, maintenance, rho, sizeInf) (d706678)
• engine: wire per-species RNG into movement and predation consumers (0ccf430)
• engine: wire O2 forcing into bioenergetic step (39c1d8b)
• engine: wire bioen reproduction — gonad-weight egg schools (96715bc)
• engine: add bioenergetic output CSV writers (a72c434)
• engine: wire bioenergetic processes into simulation loop (043c934)
• engine: parse all bioenergetic config keys + expand schema (a445816)
• engine: add energy budget process + bioen SchoolState fields (73cdb7a)
• engine: write size/age distribution CSV outputs matching Java format (c6f392f)
• engine: add bioen starvation with gonad-buffer deficit (ade8a5e)
• engine: add gonad-weight egg production for bioen mode (58725af)
• engine: add PhysicalData loader for temperature/oxygen forcing (3ee42c7)
• engine: add bioenergetic allometric ingestion cap (96ac549)
• engine: add Johnson thermal performance curve and O2 dose-response (92c48b4)
• engine: wire Gompertz growth dispatch with config-driven class selection (bfb5fe3)
• engine: add size/age distribution binning to StepOutput (4cb1db1)
• engine: add per-species deterministic RNG via SeedSequence (297fb01)
• engine: fix growth classname enum, add Gompertz schema fields, parse growth_class (fb74610)
• engine: add diet tracking to Numba predation path + extract shared helpers (df759f6)
• engine: Phases 4-5 — random patch, output frequency, yield, diet, NetCDF, step0 (65b3e21)
• engine: Phase 3 — spawning normalization, time-varying mortality, egg placement, seeding max (7120c2c)
• engine: Phase 2 — fishery seasonality, selectivity types, v3 scenarios, MPA, discards (6220046)
• engine: Phase 1 EEC parity fixes — maturity age, spatial fishing, lmax, resource multiplier, TL computation (d5b737e)
• engine: add output.cutoff.age filter — exclude young-of-year from biomass output (3360a3e)
• engine: per-cell per-school interleaved mortality matching Java computeMortality() (e2873e8)
• engine: add fisheries + stage-indexed accessibility + egg weight fix (92d97c3)
• engine: add feeding stages (B2) + diet matrix output (C2) (db1a93e)
• engine: add incoming flux — external biomass injection from CSV time-series (55ffc7d)
• engine: integrate map-based movement into simulation loop (42391e5)
• engine: add _map_move_school — per-school map-based movement algorithm (6bf860d)
• engine: add MovementMapSet — CSV map loading and index_maps construction (2861214)
• engine: update predation kernel for 2D size ratios with feeding stages (e00a9c5)
• engine: integrate background species into simulation loop with inject/strip pattern (0ed3e6e)
• engine: skip starvation/fishing/additional mortality for background species (095c9b4)
• engine: add NetCDF forcing support to BackgroundState (fa5b218)
• engine: add BackgroundState with uniform forcing and school generation (732ba88)
• add validation pipeline script (scripts/validate_engines.py) (894b2dd)
• add validation pipeline script comparing Python vs Java engines (ea28c70)
• engine: add fishing selectivity (knife-edge and sigmoid) (b1a2f64)
• engine: add mortality rate CSV output per species (20e0194)
• engine: interleaved mortality with egg release and cause shuffling (4ab8877)
• engine: add egg_retained field for retain/release mechanism (c5f1c44)
• engine: integrate resource species as prey in predation (37848f2)
• engine: implement LTL resource species with NetCDF forcing (786e01e)
• engine: add accessibility matrix, spawning seasons, real grid, fishing key fix for ecosystem parity (04c3718)
• engine: PythonEngine.run() now writes output CSV files (9b22ca8)
• engine: add CSV output writer matching Java format (5611ec1)
• engine: wire starvation and fishing into mortality sub-timestep loop (a8fee19)
• engine: add fishing mortality by rate (aeef341)
• engine: add starvation mortality with lagged predation success (241ebb1)
• engine: add starvation and fishing parameters to EngineConfig (6f22186)
• engine: wire predation into mortality sub-timestep loop (ba0b4fc)
• engine: add size-based predation with asynchronous prey updates (c4e59be)
• engine: add predation size ratio parameters to EngineConfig (59973b6)
• engine: wire movement and out-of-domain mortality into simulation loop (7447356)
• engine: add random walk movement and out-of-domain mortality (51d117a)
• engine: add movement parameters to EngineConfig (890c43e)
• engine: add larva mortality for eggs with separate rate (6046b7a)
• engine: wire reproduction and seeded initialization into simulation loop (7b2907d)
• engine: add reproduction process with egg production and seeding (6c0cd04)
• engine: add reproduction parameters to EngineConfig (0871d84)
• engine: wire growth and mortality processes into simulation loop (9ce5585)
• engine: add additional mortality and aging mortality processes (64e5a63)
• engine: add Gompertz expected length function (a60682d)
• engine: add Von Bertalanffy growth with predation-success gating (afa7fb9)
• engine: add delta_lmax_factor and additional_mortality_rate to EngineConfig (8cf2d5e)
• engine: wire PythonEngine.run() to simulation loop (29b77b1)
• engine: add simulation loop skeleton with stub processes and output collection (ca28ad2)
• engine: add ResourceState placeholder for LTL forcing (90571c5)
• engine: add Grid class with NetCDF loading and cell adjacency (01b37e1)
• engine: add EngineConfig for typed parameter extraction from flat config (15c7fbc)
• engine: add SchoolState SoA dataclass with create/replace/append/compact (8c460d8)
• engine: add Engine protocol with PythonEngine and JavaEngine stubs (bbb9de0)

Bug Fixes

• remove duplicate StepOutput fields from merge artifact (70dcb78)
• resolve merge conflicts from parallel Tasks 5-12 + fix dataclass field ordering (d4d0179)
• engine: update stale diet test name + document predation helpers (69a4a01)
• engine: eggs cannot feed first timestep + fix larva mortality double-counting (719d950)
• engine: egg_weight_override config is in grams, convert to tonnes (* 1e-6) (b2b5849)
• engine: convert weight to tonnes (Java convention), remove double seeding (4864b26)
• engine: correct predation appetite (/n_dt_per_year), cap pred_success_rate, fix starvation rate (d23b31a)
• engine: resolve movement map and forcing file paths relative to config directory (14b4a96)
• engine: EEC config compatibility — resource keys, path resolution, grid dims, egg weight (c0b5f72)
• engine: correct config key case for size ratios + add selectivity (f926b1d)
• engine: correct predation size-ratio logic + resource species (52d50a4)
• engine: handle global simulation.nschool config key (77a6d70)
• engine: match Java behavior — egg skip, reproduction units, tests (2ca9b68)
• engine: correct mortality rate to match Java — D = M/(ndt*subdt) (403a4ee)
• engine: address code review — csr==1.0 bug, test precision, subdt guard (2694ed6)
• engine: address code review issues — shadowing, file leak, docs (d152fb6)
• defer shiny_deckgl import to avoid test collection errors (77e1f3c)
• filter non-spatial files from grid overlay dropdown (df30a58)
• collapsed panels now release space to siblings via CSS Grid override (89d54ea)

Performance

• engine: Numba JIT predation + batch RNG — 5.9x faster, beats Java (202dbd4)

Chores

• lint fixes + spatial bioen TODO + final cleanup (8e7a2c8)
• fix lint issues from sprint (unused imports + vars) (51aa833)
• remove worktree cache (348dca5)

Documentation

• add engine gap closure implementation plan (ba001fa)
• fix 4 review issues in gap closure spec (26767e2)
• add engine gap closure design spec (6cee3b1)
• add Java parity sprint implementation plan (40e1de4)
• fix review round 3 — Linear references, starvation gonad-flush order (2542304)
• fix spec review issues — growth classnames, Gompertz keys, starvation formula (134edd2)
• add Java parity sprint design spec (676cff8)
• add comprehensive Java parity roadmap — 7 phases, 37 items (2679dc1)
• add B1 map movement implementation plan with review corrections (8a542b8)
• add B1 map movement design spec with Java parity fixes (38a7ba5)
• add B2 feeding stages implementation plan with review corrections (0afb2da)
• fix feeding stages spec — trailing semicolons, absent key default, indexing contract (ee9337d)
• add B2 feeding stages design spec (61d49dc)
• add complete implementation plan for remaining engine gaps (5506cfe)
• add Phase 4 movement implementation plan (9ac8dea)
• fix Phase 2 plan review issues (Gompertz, test fix, precision) (6a54f9c)
• add Python engine Phase 2 implementation plan (291a15f)
• fix 4 plan review issues (abundance snapshot, adjacency, biomass, TDD) (70b3bf9)
• add Python engine Phase 1 implementation plan (5d371b8)
• fix 3 remaining spec review issues (rev 3) (8c01f42)
• revise Python engine spec addressing 20 review issues (02b2038)
• add Python engine design specification (fb612f1)

Other

• v0.4.0 (38c5b85)
• Merge branch 'worktree-agent-a161e3b4' (88608dc)
• Merge branch 'worktree-agent-a9a2eeb3' (487197a)
• Merge branch 'worktree-agent-abebd8cd' (e212eae)
• Merge branch 'worktree-agent-a4152a1a' (e27a122)
• Merge branch 'worktree-agent-a562217f' (bd77ce3)
• Merge branch 'worktree-agent-acf2a5a6' (a7ead1f)
• Merge branch 'worktree-agent-a87d9cd8' (Task 6: per-species RNG) (d08551a)
• Merge branch 'worktree-agent-aab44ec4' (Task 4: distribution output binning) (2f6faed)
• Merge branch 'worktree-agent-acf5f81d' (48e74b6)
• Merge C1+B3: mortality CSV output + fishing selectivity (149e189)
• Merge A1+A2+A3: interleaved mortality, egg retain/release, TL placeholder (e5dd2bb)
• Merge resource species + predation fix (eba886c)
• Merge performance optimization — Numba predation, 1.9x faster than Java (48bd1ba)
• Merge ecosystem parity — accessibility, spawning seasons, real grid (30130fb)
• Merge branch 'feature/python-engine-phase7' — output writer (64684ff)
• Merge branch 'feature/python-engine-phase6' — fishing + starvation (0cbfd78)
• Merge branch 'feature/python-engine-phase5' — predation (767fb1f)
• Merge branch 'feature/python-engine-phase4' — movement (1069d17)
• Merge branch 'feature/python-engine-phase3' — reproduction + initialization (1ce4437)
• Merge branch 'feature/python-engine-phase2' — growth + mortality (2db4f3b)
• Merge branch 'feature/python-engine-phase1' — Python engine foundation (915f075)

Refactoring

• extract _make_bioen_config() for cross-test imports (ba64236)
• engine: delegate _mortality to new orchestrator module (3a44ae9)
• unify nav and panel collapse with same expand-tab pattern (43afd43)

Tests

• engine: add background species stage + integration tests for feeding stages (7d8ebf0)
• engine: add integration tests for background species (5f29a23)
• engine: add background species predation participation tests (157b9bf)
• add Tier 1.5 Java comparison tests for growth and mortality (5efed58)
• add 503 full-model integration tests for all example studies (7b06427)

[0.3.0] - 2026-03-15

Features

• add OSMOSE Model scientific description to Help modal (bb0d019)

Bug Fixes

• move popover init to end of body, use setInterval polling (d5eeadc)
• remove Show Help button, fix Bootstrap 5 popover initialization (7ad76d0)

Documentation

• expand OSMOSE Model help with extensions, applications, and 30+ references (b9f699d)

Other

• v0.3.0 — OSMOSE scientific docs, tooltip fix, Show Help removal (befbd0b)

[0.2.0] - 2026-03-14

Features

• add movement animation controls and cache logic to grid page (a2e478e)
• add build_movement_cache, MOVEMENT_PALETTE, and list_movement_species (19881ac)
• add derive_map_label and parse_movement_steps helpers (00db43f)
• make advanced page panel collapsible (a4e1d92)
• make scenarios page panel collapsible (3-column layout) (2dab172)
• make calibration page panel collapsible (01c4fce)
• make results page panel collapsible (7268a1c)
• make run page panel collapsible (5593c49)
• make movement page panel collapsible (93e84c4)
• make fishing page panel collapsible (ffdf6db)
• make forcing page panel collapsible (290c5c5)
• make setup page panel collapsible (9d77760)
• make grid page left panel collapsible (bc7f85f)
• add fullscreen toggle widget to grid preview map (f3d86a6)
• add CSS for collapsible nav sidebar, split-layout panels, and light theme (a89032e)
• add nav collapse JS + hamburger toggle button (a6469a4)
• add collapsible panel helpers (card header + expand tab) (97a7256)
• add layered tooltip system with hover popovers and Show Help toggle (8728cd4)
• add spatial file overlay selector to grid preview (c9376f0)
• smart results directory defaults and auto-load on tab switch (0079d4d)
• add manual tooltip text for non-schema UI fields (cd209de)
• populate species filter from config species names (218a5cd)
• wire spreadsheet species table into Setup page (37f866f)
• wire spreadsheet LTL table into Forcing page (f4e3b69)
• add render_species_table() spreadsheet component (258531f)
• rework example loading with Load button and config header (c1c0628)
• replace dirty_banner with persistent config header bar (2901508)
• add config_name, species_names, results_loaded to AppState (4d3dfb2)
• add UI scenario loading tests and fix demo dispatch bug (8971cbf)
• add eec_full demo from GhassenH/OSMOSE_EEC research config (6d907a8)
• add EEC and minimal demo scenarios (aa19d81)
• strengthen validator with schema-aware file refs, resource checks, and enum validation (95cbdfa)
• expand results parser with fishery, bioenergetics, and distribution outputs (966b106)
• expose Java CLI flags (-update, -verbose, -quiet, -Xmx) in runner (f1ecd44)
• expand version migration to cover v3.1 through v4.3.3 (57bb093)
• add CSV export, ensemble CI bands, and run comparison to Results page (e44651e)
• add Compare Runs tab with grouped bar chart and config diff table (1d37a4c)
• add compare_runs_multi() for N-way config diff (e79718c)
• add ensemble toggle with CI band rendering to Results page (796c317)
• add ensemble replicate aggregation with mean + 95% CI (c1fb675)
• add CSV download button to Results page (08f4ab2)
• add export_dataframe() to OsmoseResults for unified data export (5c40aa9)
• add food web Sankey, run comparison, and species dashboard charts (3fa57fa)
• add CLI for batch runs, validation, and reporting (29cac2d)
• add pyright type checking to CI (d26e40f)
• run history tracking with JSON records (a13615d)
• Jinja2 HTML reports with custom template support (84a0222)
• validate config before run, block on errors (f24c81a)
• responsive modals and mobile nav at 768px breakpoint (351d10d)
• field-level validation with min/max bounds (c3b2398)
• unsaved changes warning with dirty state tracking (731c85f)
• global loading overlay for long operations (7b15f5c)
• atomic scenario writes with backup-rename pattern (233e78f)
• add DataFrame column guards to analysis and plotting (74ecbff)
• add configurable timeout to OsmoseRunner.run() (2febf27)
• rename app to OSMOPY, add JAR selector, fix grid preview after demo load (1162847)

Bug Fixes

• narrow exception handling, isolate reactive deps, add debug logging (2a8c0a2)
• nav hamburger stays visible when collapsed, expand tab uses sticky positioning (18410da)
• split movement controls into separate render output (bd50c95)
• broaden exception catches for SilentException, polish UI layout (c6e8ca4)
• add temp directory cleanup on startup and shutdown (7a40d1a)
• remove non-functional beforeunload guard (5cdffc2)
• add 10MB file size limit to config reader (778e370)
• reject path traversal in output_dir input (d24fee2)
• add path traversal check on overlay file paths (0022079)
• skip corrupt history files instead of crashing listing (0825ee7)
• notify user when run history save fails (f88dd55)
• protect stream reader from progress callback exceptions (70cda68)
• narrow surrogate/sensitivity sample exceptions to expected types (bdc700a)
• guard all nspecies int() parsing in UI pages against non-numeric values (9639dc7)
• batch low-severity fixes — cancel safety, test seeds, version fallback (d9b9d0f)
• add NetCDF cache eviction on directory switch (M14) (87411b1)
• raise error when csv_maps_to_netcdf finds no valid files (M18) (182340e)
• log unparseable config lines instead of silently skipping (M16) (6fe0bc5)
• validate calibration override keys against OSMOSE pattern (M2) (3b325cb)
• show sp0 values for indexed fields in advanced param table (M26) (17d03dd)
• use atomic write pattern for config files (M24) (dac571e)
• use load_trigger for advanced param_table rendering (M6) (a3c1b01)
• log warning for unknown export_dataframe output types (M27) (da237dd)
• catch ValueError in grid input parsing (M25) (d33da99)
• restore scenario backup on save failure (M23) (d7e7e43)
• show notification when results download has no data (M19) (e195b87)
• skip corrupt scenario files in listing instead of crashing (M17) (248251d)
• validate config reader sub-file paths stay within config dir (M4) (75d7e67)
• narrow get_theme_mode exception to expected types (2b7d026)
• add error handling to results loading (H6) (0abbe1e)
• narrow grid file-loading exceptions to expected types (H7-H10) (2d9e19b)
• handle 1D lat/lon coordinate arrays in grid preview (H18) (0ed761f)
• handle non-integer nspecies values gracefully (H17) (8889297)
• prevent results loading race condition (H4, M8) (3d8ba56)
• use load_trigger for calibration checkbox rendering (H3) (4e241fb)
• log run history save failures at warning level (H13) (584f772)
• narrow ensemble mode exception to expected types (H11) (6ec573f)
• HTML escape DataFrame output in report template (H2) (2a64c06)
• validate java_opts against safe JVM flag whitelist (4ce57d8)
• replace vacuous 'or True' assertion with real check (bcfc474)
• add path traversal protection to scenarios and history (af2bd9e)
• narrow calibration exceptions — propagate unexpected errors (7a172ef)
• add top-level exception handler to surrogate calibration thread (6980176)
• add state guards to scenario load and config import (b530c3b)
• thread-safe calibration communication via message queue (9afcce8)
• grid overlay selector scans config directly + CSV overlay support (0ab86c4)
• remove unused COLOR_MUTED import in results page (b1a1ca4)
• write flat master config to avoid duplicate parameters in run directory (547145b)
• copy entire source config directory before writing run config (270f71f)
• pass registry to check_file_references to avoid false file-path matches (769f7a9)
• config reader strips trailing separators, validator handles null/multi-values (6604dc4)
• grid preview working with deck.gl for both regular and NetCDF grids (ffad986)
• resolve dirty banner regression, button wrapping, and UI polish (202f244)
• update bundled example configs for OSMOSE v4.3.3 compatibility (badd5d5)
• migrate bundled eec_full config to v4.3.3 for out-of-box run (2d4270b)
• update remaining grid.ncolumn/nline references to nlon/nlat (b900c7a)
• align mortality schema keys and writer routing to post-v4.2.5 names (3254bf5)
• update grid schema keys to post-v3.3.3 names (nlon/nlat) (c9ebc04)
• update grid schema and example configs for OSMOSE 4.x parameter names (a2d6846)
• handle stale backup in atomic scenario save (9457257)
• harden timeout handling — race condition guard and cleaner UI wiring (b214655)
• require objective_fn in MultiPhaseCalibrator, fix work_dir type (15ad9c9)
• handle missing dirs, reject unsupported report format, rename summary_table (c051ee7)
• remove debug prints, fix temp file safety, update GitHub URL (c9d5b40)
• add cycle guard and missing sub-file warning to config reader (94e4425)
• standardize size spectrum slope to log10 (ecological convention) (fff4222)
• add reactive.isolate() to prevent infinite loop risks (8eb1b39)
• replace silent except:pass with logging and user notifications (f073a4a)

Performance

• batch forcing page config updates (760445e)
• lazy-load result types on demand instead of all 16 eagerly (M13) (5b51c67)
• batch species parameter sync to single config update (M7) (0b658cc)
• pre-compile regexes and cache match_field lookups in registry (c4f0ee2)

CI/CD

• coverage threshold, Python matrix, Docker smoke test, HEALTHCHECK (e321acc)

Chores

• remove unused imports in new test files (e4e41d0)
• fix lint — move constant after imports, remove unused imports (0baa56e)
• remove unused imports in test_sync_config_pages (d851823)
• add pre-commit hooks for ruff (e0bed46)

Documentation

• add movement visualization implementation plan (2f33f64)
• add movement visualization design spec (1582c0e)
• update codebase fixes plan with second-round analysis findings (7967985)
• add codebase fixes implementation plan (25 tasks, 4 phases) (7017df8)
• add comprehensive codebase analysis findings (2aa8daf)
• add codebase analysis design spec (c27f519)
• add UI improvements spec and implementation plan (02700fc)
• add results workflow implementation plan (7 tasks) (e4bbd4f)
• fix spec review issues — complete type map, N-way comparison, alignment strategy (b436c53)
• add results workflow enhancement design spec (1edec92)

Other

• v0.2.0 — movement visualization, collapsible panels, codebase fixes (639ca24)
• Merge branch 'enhancement-sprint-2026-03-11': 18 enhancement tasks (production hardening, UX polish, new capabilities, dev experience) (ee1520c)

Refactoring

• use explicit result method mapping instead of getattr (5907356)
• extract pure helper functions from grid.py into grid_helpers.py (M9, M12) (2056c84)
• standardize logging initialization across modules (M10) (97671b4)
• split calibration page into layout, handlers, and charts (1ae7fe0)
• extract Plotly theme to osmose/plotly_theme.py (c6d4888)
• consolidate shared test fixtures into conftest.py (24757b7)
• deduplicate RMSE objectives and narrow theme except clauses (55861a7)
• consolidate registry construction into schema.init (75e10f8)

Styling

• add movement animation controls CSS (e1dc098)
• format results workflow code (75d3c0b)

Tests

• remove brittle source-inspection tests (54f7e27)
• add tests for copy_data_files and grid_helpers (H16 gaps) (3cd0e42)
• add Playwright E2E tests for reactive UI behavior (H16) (07c20ef)
• add CLI cmd_run and cmd_report error case tests (M29) (f8f36a9)
• replace vacuous hasattr tests with behavioral checks (M30) (0cc580a)
• add path traversal rejection test for scenario import (M28) (e6b56bc)
• add parallel calibration error isolation test (M20) (593bb49)
• replace brittle source inspection test with behavioral check (M21) (e2eddf4)
• add NaN/malformed input edge case tests (H14, H15) (41d2c0e)
• add comprehensive tests for all collapsible page panels (342bd64)
• add column guard tests for plotting functions (85382a9)

[0.1.0] - 2026-03-07

Features

• full R parity — 8 new modules, 22 output parsers, 146 new tests (33c798d)
• add Nautical Observatory theme with custom CSS and plotly template (be166cd)
• switch navigation to left-side pill list with grouped sections (6979b5f)
• add input validation tooltips showing field constraints (f6d4151)
• add scenario bulk export/import as ZIP (72f946e)
• add structured logging module with console output (007ca9b)
• add play/pause animation to spatial map time slider (b3a11e8)
• add config import preview with diff before merge (0694083)
• parallelize calibration objective evaluation (b2302cc)
• add per-generation progress callback for NSGA-II calibration (55d7af2)
• wire GP surrogate calibration into UI (ebbbf7c)
• wire Advanced page import/export handlers (cc6f4ad)
• wire Calibration Start/Stop/Sensitivity handlers (fbd5bde)
• sync Run page JAR path to AppState (d467c71)
• wire Grid, Forcing, Fishing, Movement input syncing (c89919a)
• wire Setup page input syncing to AppState (a1a6daf)
• add jar_path to AppState and sync_inputs utility (92f153b)
• add grid preview map with plotly (ecb4008)
• wire Calibration page with dynamic params and plotly charts (d9ecb33)
• wire Scenarios page to ScenarioManager (2c2d497)
• wire Results page with plotly charts (d7dd5b7)
• wire Run page buttons to OsmoseRunner (9513946)
• wire AppState into all page servers (93f1555)
• add AppState shared reactive state module (dec42bf)
• add Dockerfile, integration tests, and wire all UI pages (bde866a)
• add calibration module and UI (0e415b4)
• add run, results, scenarios, and advanced config pages (e6d51bc)
• add Shiny UI shell with param form and config pages (e258773)
• add runner, results reader, and scenario management (32ede0e)
• add config I/O (reader, writer) with roundtrip tests (3c0b5db)
• add schema-driven parameter system (base classes, registry, all modules) (eb74646)
• scaffold osmose-python project with dependencies (74c9b34)

Performance

• lazy-import heavy dependencies for faster startup (d317b0f)

CI/CD

• add GitHub Actions workflow for lint and test (76b276e)

Chores

• format Phase 2 UI code with ruff (a1a7752)
• add shinywidgets dependency for plotly integration (67dbaa5)
• add CLAUDE.md, README, LICENSE, docs, lint fixes, formatting, and gitignore (cb7e743)

Documentation

• add pill list refactoring plan (9578ce4)
• Phase 3 implementation plan (8 tasks) (eeaa0cc)
• Phase 3 design — complete Phase 2 gaps (ea59d91)
• add Phase 2 implementation plan (10 tasks) (dd2a9b4)
• add Phase 2 UI wiring design + deployment script (0b475d5)

Refactoring

• extract inline styles to ui/styles.py constants (61684f7)
• remove redundant page_fluid wrappers from page UI functions (30f9da6)

Tests

• add app structure tests for pill list navigation (f31335b)
• achieve 100% code coverage across all modules (a1b4e91)

Welcome to OSMOSE

OSMOSE is an individual-based model for simulating marine ecosystems. This interface lets you configure, run, and analyze simulations without touching configuration files directly.

Quick Start

1. Configure your simulation using the tabs on the left sidebar
2. Run the simulation from the Execute section
3. View results with interactive charts
4. Calibrate parameters using optimization algorithms
5. Save scenarios to compare different configurations

Requirements

• Java Runtime Environment (JRE 8+) for the OSMOSE engine
• An OSMOSE JAR file (set the path in Setup or Run)
• Input data files (forcing, maps) in a working directory

Configuration Pages

Setup

General simulation parameters: simulation name, number of time steps, number of species, output directory, and JAR path. These are the foundational settings every simulation needs.

Grid & Maps

Define the spatial grid (longitude/latitude bounds, cell size) and preview the simulation domain on an interactive map. Upload custom land/sea masks if needed.

Forcing

Environmental forcing data: temperature, salinity, plankton fields. Set file paths, variable names, and time step mappings for each forcing variable.

Fishing

Configure fishing mortality by species. Set fishing rates, seasonal patterns, and selectivity curves. Supports both constant and time-varying mortality.

Movement

Species movement parameters: diffusion coefficients, habitat preferences, and migration patterns. Configure independently for each species in the simulation.

Running Simulations

Run Page

• Set the JAR path to your OSMOSE engine
• Click Start to launch the simulation
• Monitor progress in the live console output
• Use Stop to abort a running simulation

Output files are written to the directory specified in Setup.

Results Page

After a run completes, view results as interactive Plotly charts:

• Biomass time series by species
• Abundance trends
• Size distribution histograms
• Spatial maps with time animation
• Diet composition matrices

Use the species selector and time range controls to focus on specific aspects of the output.

Calibration & Sensitivity

Calibration (NSGA-II)

Multi-objective calibration using the NSGA-II genetic algorithm:

• Select parameters to calibrate and their bounds
• Define objective functions (e.g., match observed biomass)
• Set population size and number of generations
• Monitor convergence with real-time Pareto front plots

GP Surrogate

Gaussian Process surrogate model for faster calibration:

• Trains a surrogate on initial evaluations
• Explores the parameter space more efficiently
• Falls back to full simulation for validation

Sensitivity Analysis

Sobol sensitivity analysis (SALib):

• Identify which parameters most influence outputs
• First-order and total-order sensitivity indices
• Visualize parameter importance rankings

Scenarios & Advanced

Scenarios

Save and manage simulation configurations:

• Save the current configuration as a named scenario
• Load a saved scenario to restore all parameters
• Fork a scenario to create a variant
• Compare two scenarios side-by-side
• Bulk export/import scenarios as ZIP archives

Advanced

• Import configuration from CSV or properties files with a preview diff before merging
• Export the current configuration as CSV
• Direct access to raw parameter values for power users