Changelog

Source: NEWS.md

oceancube 0.3.0

Release

• Freezes a 49-export API after hardening its scientific contracts, property tests, offline real-data fixtures, dependency boundary, and provenance.

• Adds read-only deferred access to one local NetCDF file with bounded reads; this is not remote access, multi-file processing, or a lazy computation graph.

• Preserves and validates a bounded CF metadata, time/calendar, climatological time, and positive-down metric vertical subset without silent conversion.

• Adds certified vertical reduction, integration, depth sampling, gradients, transition-layer and oxygen diagnostics, mixed-layer depth, an optional TEOS-10 bridge, and signed stratification diagnostics.

• Establishes renderer-neutral visualization data and six static ggplot views, including Hovmoller diagrams and certified core 2-D map styles. Specialized D3 visualization is not implemented.

• Deprecates 13 historical temporal, provider, and spatial compatibility exports while preserving their signatures for this release.

• Certifies the C1-C10 vertical-ocean engine as globally coherent within its bounded supported subsets. DEC-040 freezes canonical positive-down metric depth, distinct value and diagnostic semantics, explicit gap/missingness behavior, the C9-to-C10 TEOS-10 chain, signed N-squared, immutable source CF, Provenance V1, and the repository-only hardening-evidence policy. Phase C is complete and certified.

• Adds stratification() and extends mixed_layer_depth() plus transition_layer() with the certified C10 density-MLD, pycnocline-candidate, and signed TEOS-10 N-squared paths over C9 state. Temperature and density MLD, pycnocline and maximum N-squared remain separate scientific quantities.

• Adds thermodynamic_state() as the certified C9 TEOS-10 bridge from exact CF Practical/Absolute Salinity and in-situ/potential/Conservative Temperature to SA, CT, sea pressure, in-situ density, and reference-pressure potential density. The compiled gsw dependency is optional via Suggests; complete source states must pass its 75-term funnel, while cell means, generic salinity identities, fallbacks, density MLD, pycnocline, and N2 remain rejected unless covered by the separately certified C10 contract.

• Adds mixed_layer_depth() for the first locally supported absolute temperature departure from a configurable near-surface reference. C8 is restricted to direct CF point-temperature profiles; gaps, missing paths, inversions, open bottoms, provenance, and QA remain explicit. Density-based, gradient, and hybrid MLD definitions are deferred to a separately certified TEOS-10 thermodynamic engine; the density method is now certified separately through C9/C10 state.

• Adds oxygen_boundary() and extends transition_layer() with branch-aware upper_oxycline and lower_oxycline candidates. Oxygen identity is gated by preserved CF standard_name and same-family units; the core, gaps, cell-mean brackets, explicit user threshold, provenance, and QA remain visible. No universal OMZ/ODZ threshold is introduced.

• Adds transition_layer() as the bounded variable-aware interpretation layer above depth_gradient() and depth_feature(). Preserved source CF standard_name and compatible units authorize unthresholded thermocline (negative temperature-gradient) and halocline (absolute salinity-gradient) candidates; gaps, ties, incompleteness, sign, basis, provenance, and QA remain explicit.

• Adds depth_feature() for conservative strongest-gradient candidate detection on certified depth_gradient() outputs. Absolute, positive, and negative polarity are explicit; local support excludes gapped secants, ties remain ambiguous, and incomplete profiles cannot claim a guaranteed global maximum.

• Adds depth_gradient() for signed adjacent-level vertical secants with respect to canonical positive-down depth in metres. Point and certified cell-mean semantics remain distinct; midpoint outputs have no layer bounds, and explicit support gaps are recorded rather than filled.

• Adds depth_sample() for certified metric-depth reconstruction: exact source-cell sampling for CF cell means and local linear interpolation for CF point values. It rejects explicit gaps, ambiguous interior boundaries and extrapolation, and sampled outputs never inherit physical layer bounds.

• Adds layer_integral() for certified metric integration of CF vertical cell means over explicit depth bounds. It uses canonical metre overlaps, strict missingness, symbolic derived units, indexed deferred reads, and never substitutes the unrelated CF depth: sum cell method.

• Adds exact elapsed UDUNITS month/year decoding and a bounded generic CF climatological-time descriptor under current CF metadata. Climatological cubes are guarded from ordinary temporal analytics; inconsistent provider coverage is rejected without provider-specific repair.

oceancube 0.2.0

Validation, inspection, and visualization

• Adds cube_validate() for non-destructive contract diagnostics and cube_inspect() for compact dimension, coordinate, storage, missingness, and provenance summaries.
• Adds viz.map(), viz.section(), viz.profile(), viz.transect(), and viz.timeseries(). They return static ggplot objects from explicit cube selections without interpolation, smoothing, imputation, or animation.

Selection and extraction

• Stabilizes the backward-compatible cube_transect() contract. CRS-bearing paths can no longer be silently ignored, matching diagnostics retain requested-to-cell distance, and ambiguous axes or selectors are rejected.

Time and calendar foundation

• Adds cube_aggregate_time() for day, ISO-week, calendar-month, meteorological-season, and calendar-year aggregation with finite-value and min_n policies. Date stays Date and POSIXct stays UTC POSIXct.
• Adds cube_climatology() for recurrent daily, monthly, and seasonal cycles. Period-year replicates receive equal weight; explicit leap-day policies, reference-period clipping, sample SD, and optional coverage diagnostics are retained with the recurring pseudo-time cycle.
• Adds cube_anomaly() for difference and standardized anomalies. Coordinates, variables, units, calendars, and Date/POSIXct source classes must align exactly. Non-finite values are masked; zero or non-finite SD produces a missing standardized anomaly, while negative finite SD is invalid.
• Adds cube_trend() for descriptive per-cell linear slopes against actual elapsed historical time. Date and irregular/subdaily UTC POSIXct sampling are supported, with output units per year, day, hour, or second. The method performs no significance inference, Sen/Theil–Sen slope, Mann–Kendall test, breakpoint, change-point, or regime analysis. Recurring climatology pseudo-time is rejected.
• Preserves POSIXct instants and fractional-second precision, normalizes stored timestamps to UTC without changing instants, supports the approved Gregorian-family calendars, and rejects duplicate, unsorted, or unsupported time axes instead of silently repairing them.

Compatibility and corrected behavior

• to_month(), clim_day(), and clim_month() delegate supported workflows to the canonical aggregation and climatology engines. Climatology min_n counts valid period-year replicates, and leap = "feb28" no longer double-weights leap years.
• anom_diff() and anom_z() adapt compatible legacy climatologies and delegate to cube_anomaly(). This corrects legacy acceptance of equal-sized but coordinate-, variable-, unit-, calendar-, or time-class-misaligned data.
• signal_noise() retains its historical name for compatibility but documents its quantity precisely as the standardized climatological anomaly magnitude, abs(z), by default. signed = TRUE returns signed z; it is not a generic signal-to-noise ratio estimator.

Backends and package boundary

• Temporal engines and visualization selections use bounded reads from lazy local NetCDF sources rather than materializing the full source. Analytical cube outputs are materialized in memory where their contracts require it.
• oceancube owns descriptive cube transformations. Spatial indicators, inference, uncertainty, and structural/regime analysis remain downstream responsibilities such as spatind.

Known limitations

• NetCDF access is read-only and local. Writing, OPeNDAP, THREDDS, Zarr, cloud stores, and unstructured or curvilinear-grid analytics are not implemented.

oceancube 0.1.0

Core architecture

• Defines a validated five-dimensional ocean_cube contract ordered as longitude, latitude, depth, time, and variable.
• Keeps physical storage behind a shared backend interface while preserving public results and legacy workflows.

Backends

• Supports in-memory arrays and serializable descriptors for read-only local NetCDF files.
• Adds controlled block reads, non-contiguous selections, materialization with cube_collect(), and explicit file-change diagnostics.

Selection, masks, and geometry

• Adds discrete slices, closed-range crops, point/profile/series extraction, ordered transects, polygon cell-centre masks, horizontal cell area, layer thickness, cell volume, and sparse polygon weights for rectilinear grids.

Climatology and anomalies

• Preserves monthly and daily climatologies, absolute and standardized anomalies, vertical summaries, and event linkage through the backend interface.

Known limitations

• NetCDF access is read-only and local. Grids must be rectilinear. Geometry features require the optional sf package; spatial indicators and inference belong to the separate spatind package.