CalCOFI integrated database release v2026.10.05

Release date: 2026-10-05 · promoted (latest.txt)

The grid is one cell per official station, and a key no longer names the same water

grid was 218 Voronoi cells of an idealized lattice (5, 10 and 20 station units in +proj=calcofi), clipped by a coarse coastline and patched by hand: 48 sites lay more than 1 km off their line, 19 cells were in several pieces, and 13 cells held two to four of the official stations, which is why the climatology moved to site_key in v2026.09 (CalCOFI/workflows#130, #86, CalCOFI/db-viz-station#19). It is now one cell per official station, beside the previous cells it keeps: 225 cells.

• 113 station cells: the Voronoi tessellation of the official station positions (https://calcofi.org/sampling-info/station-positions/, the nine SCCOOS inshore stations included), confined to the 106 previous cells it replaces, so an outer station's cell stops where the previous grid stopped it (line 95.0 in the south, 20 nautical miles beyond line 93.3). Every official station is the site of its own cell (grid.geom_ctr, on its line by construction) and no cell holds two.
• 112 kept cells: the previous cells whose label lies more than 20 nautical miles outside the official pattern, with their own boundaries, pieces and keys. No sample row whose previous cell is kept changes key (0 of 455,930), and historical line 96.7 stays in the line-100 cells.
• Both end at the OpenStreetMap coastline (islets under 1 km² dropped, pulled back 300 m, simplified to 100 m) instead of Natural Earth's. The table's columns are unchanged.

Built by calcofi4r::cc_grid_build() (calcofi4r's cc_grid), with the rules and the evidence in explore_grid_voronoi.

• Keys. The form is unchanged (st{station}-ln{line}, _hist for a kept historical cell); a station cell is named for its station, decimals as listed (st26.7-ln93.3, st27.7-ln90, st26.4-ln93.4). 29 keys are new and 22 retire. 196 of the previous 218 keys survive as names; for the 112 kept cells the name is the same water, for 84 it is an official station's cell whose polygon changed: st30-ln90 was the cell of four stations and keeps 52% of its water.
• New table grid_crosswalk (prev_grid_key, grid_key, overlap_km2, prev_frac, grid_frac; primary key the pair; grid_key → grid): every overlapping pair of a previous and a current cell, with the overlap area (EPSG:3310) and its share of each. All 218 previous keys are in it. Shares are of the whole cell and are not rescaled: 180 previous cells sum to one within 1e-6 and 38 fall short by the part of the cell that is land under the finer coastline, at most 2.2%. Each kept cell is an identity row (82 of the 112 with a share of exactly one).
• sample.grid_key / obs.grid_key. 188,384 of v2026.10.01's 1,469,239 sample rows (12.8%) have a different grid_key in this release, per dataset in the table below; without the 3,255 NULL keys DIC gains it is 12.6%. On v2026.10.01's positions alone the share was 12.7% (8.2% of rows before 1984, 17.2% from 1984), 5.4% to a cell that is not their previous cell renamed; all of them inside the official pattern: 34% of the rows in nearshore standard cells, 1% in offshore standard ones, none in a kept cell. No row that had a cell loses it, and 5 gain one (2 farallon_bird-mammal, 1 sio_pic-zooplankton, 2 swfsc_cufes).
• Assignment is deterministic. assign_grid_key() took LIMIT 1 with no order, so a position on an edge two cells share keyed to either; it is now the key that sorts first, and calcofi4r::cc_grid_key() is the same rule in R (identical on all 226,762 distinct sample positions and on every cell vertex).
• New gates. check_grid_key_assignment() recomputes the cell of every sample position and stops the release on a key that is not that cell. It is what catches an ingest staged against the previous grid: of v2026.10.01's keys, 185,761 name another cell of the new grid and 59,688 of those are surviving names that pass the foreign-key check. check_grid_crosswalk() gates the crosswalk. At the re-stage check_grid_key_assignment() passes on the staged shards of all 21 datasets: 0 of 1,479,442 sample rows carry a key that is not the cell of their position (the 409 calcofi_phytoplankton rows are unkeyed by design). It reads the grid shard the ingests write, which is cc_grid (225 of 225 cells equal at 1e-9), not a grid rebuilt from text, which puts 91 positions on a shared edge in the other cell.
• Not single-piece everywhere. 13 kept cells are in several pieces, as 10 of them already were (cells that span the Baja California peninsula): keeping them as they were is what keeps every historical key. One station cell, st53-ln60, carries 21 km² of Tomales Bay as a detached part: that water was in a replaced cell and opens to the sea only through a kept one.
• Unchanged: the climatology is keyed on site_key and no mean moves; climatology.grid_key (the station's modal cell) takes a new label on about one row in nine.

Rows whose grid_key changed, per dataset (sample, this release against v2026.10.01):

"This release" is the count of sample rows whose grid_key differs from v2026.10.01's on the same sample_key (NULL counts as a value). The middle column is v2026.10.01's own positions keyed against the new grid (explore_grid_voronoi, gate 5). The two agree row for row on 13 of the 16 datasets (calcofi_phytoplankton, which has no grid key, included). The three that differ were re-staged for another reason:

• swfsc_ichthyo: the 3,385 rows of the two 1982 cruises leave and 2,521 nets arrive, so the count falls on the rows that remain: 32,034 = 8,693 sites + 11,563 tows + 11,778 nets, none gaining or losing a key (the leaving rows held 634 of the 32,668 changes recomputed on the final grid).
• swfsc_cufes: compared on (time, position), because every sample_key is rebuilt; 9,224 of the 9,227, and the other 3 left with the 1,583 samples SWFSC removed.
• calcofi_dic: 3,255 of its 3,261 rows had no grid_key and now have one (see "DIC: every sample with a position carries a grid_key"), and 3 of the 6 that had one change with the grid: 3,258 differ, against 768 on positions alone.

Overall 188,384 against the 186,522 from positions: DIC's fill adds 2,490, and the ichthyo and CUFES rows that left take away 625 and 3 (net +1,862). Without DIC's NULL fills it is 185,129 (12.6%).

Consumers: a grid_key stored from an earlier release (a URL, a cache, a per-cell statistic) must be mapped through grid_crosswalk, not matched by name. grid.station and grid.line are no longer whole numbers for some cells, and seven lines hold a single station (81.7, 81.8, 85.4, 86.8, 88.5, 91.7, 93.4: six SCCOOS stations and the rosette station 81.8 46.9), so a section along line 93.3 no longer includes station 93.4 26.4 and code that rounds a line or matches it within 0.5 picks up 93.4 with 93.3. grid.geom_ctr (lon_ctr / lat_ctr in grid.geojson) is the station, not a centroid. grid.geojson grows from 7,474 to 31,660 vertices. grid.geom is still a mix of polygons and multipolygons. calcofi4r::cc_grid* change with it (sta_lin / sta_pos are doubles; cc_grid_v1 is the previous grid).

CTD cruise 2607: the bottle-corrected preliminary file brings corrected salinity, oxygen, chlorophyll and nitrate estimates, bottle values and per-cast products on all 72 casts

v2026.10.01 carried cruise 2026-07-3322 (2607SH) from the corrected Preliminary CTD file, with no bottle merge. This release reads the Preliminary CTD & Bottle file: all 144 of the cruise's sample rows go from data_stage = preliminary_without_bottle to preliminary_with_bottle, and the cruise goes from 69,617 to 155,693 obs rows and from 1,464,396 to 2,356,899 obs_ctd_full rows. What a user gains is the corrected series that file carries: the cruise-corrected, station-corrected and bottle series arrive (86,138 obs and 897,033 obs_ctd_full rows added, 2,823 and 44,843 changed, 62 and 4,530 est_nitrate_cruise_corr values removed), and all 72 casts carry the per-cast products (mixed-layer depth 10.1 to 55.1 m, median 16.8 m; chl_max, chl_max_depth, chl_integrated, chl_integrated_depth). The sensor values already published are unchanged: 3,724 temperature pairs matched on sample and depth differ by at most 0.0000 °C.

Against the cast's own bottles the corrections look sound: salinity agrees to a median 0.0041 (95th percentile 0.023) PSS-78 on the upcast, and station-corrected oxygen to a median 0.050 mL/L (95th percentile 0.22). Nothing published is outside a physical range.

Four gaps, recorded in the cruise's first-look checks, come with the provider's file:

• No near-surface nitrate estimate below 0 is published. No est_nitrate_* value is 0 or negative (0 of 45,063 station-corrected values in the 1 m table), so where the estimate read below 0 the profile is missing: 28 of the 60 casts with station-corrected nitrate have no value above 10 m, 24 none above 30 m. The gap is depleted water (bottles at 0–30 m read a median 0.05 µmol/L), not missing water; in a section it is a blank band over the nitracline offshore.
• Station-corrected nitrate is absent on 12 of the 72 casts, six of them consecutive on line 90 (stations 110, 100, 90, 80, 70, 60); the cruise-corrected series is absent on 5.
• Every pH value is flagged 8 (questionable) by the provider: 3,724 thinned values go from no flag in v2026.10.01 to 8, and all 56,993 in the 1 m table; the values are unchanged.
• Estimated chlorophyll has holes: 125 interior 1 m bins are missing on 5 casts, and 5 casts that reach 199 m stop short of it; no value is 0 or below. chl_integrated sums only the bins present, so chl_integrated_depth is below 199 m on 23 casts, most of them shallow nearshore casts.

Consumers: cc_qual_ok_sql() now removes every 2607 pH value (all are flagged 8), where it removed none in v2026.10.01; a nitrate or chlorophyll section of this cruise has the blank bands described above.

CTD casts: one copy per file, casts tested by their median position, two stations repaired, pigment floors (#131)

Five defects in ingest_calcofi_ctd-cast.qmd found by auditing v2026.10.01 against the provider's *_CTDBTL_* files (CalCOFI/workflows#131).

• One copy of each file (2204SH). The archive holds the bottle-merged file twice, db-csvs/ (May 2022) and csvs-plots/ (February 2025 re-export: nutrients, BTL_Temp, 559 more OxBuM, corrected Ox*uM_StaCorr; times to the minute, SPAR/PAR to three figures). Both were read and, writing the time differently, both survived dedup: 2,941,303 duplicated keys in obs + obs_ctd_full. Where a May 2022 scan fell on a whole minute the keys matched and the older copy won the tiebreak: 14 bottles lost nutrients, BTL_Temp and OxBuM, the 92 missing values. Now the re-export alone is read (CTD_COPY_PREFER; seven other archives hold byte-identical copies and keep the shortest path, as dedup did). The re-export also drops 7 shallow bottles and moves one, which leave with the old copy.
• Distance filter on the cast's median position. A cast within 10 km of its station keeps every scan; a scan more than 0.05 deg from the median (a GPS glitch) keeps its values at the median position. A cast whose median fails keeps the old per-scan test. Restores 2404SH's 626 glitch scans (11 bottles) and GPS-glitched scans on 0801JD, 0711NH, 0310NH, 1507OC and 10 other cruises.
• Stations. 2204SH casts 094/095 write line 066.3 but sit on 063.3 (CTD_STATION_OVERRIDE, questions.csv Q43); 2504SH cast 045 is a real occupation 11.0 km off 083.3 039.4, kept at its true position (CTD_OFF_STATION_KEEP).
• Pigment floors. btl_chlorophyll_a -1 and btl_phaeopigment -5, the floors calcofi_bottle declares; near-zero negative readings return, -99 still falls.
• Mis-filed upcasts (1604SH, 2105SH). Direction comes from the Cast_ID; seven upcasts filed in the downcast file stop doubling (75,310 duplicated keys).
• Ratchets. A (cast, depth) read twice stops the render outside CTD_DUP_SCAN_CRUISES; CTD_DUP_SCAN_MAX holds the cruises still open (1501NH dualTCO/ re-processing, 9510NH / 9504NH extra casts reusing cast numbers, six with 1-177 scans: 1,951,755 keys) to their count; they are tracked in CalCOFI/workflows#134.

Measured (diff_stage_vs_release() per cruise on the 2026-10-04 re-stage against v2026.10.01; obs 18,843,115 → 18,781,256 rows and obs_ctd_full 284,379,888 → 282,680,638; the diff ignores grid_key):

Duplicated keys in the two tables together go from 4,968,368 to 1,951,755. The rules were first run on the source files of the 39 affected cruises by a mini-pipeline that reproduces v2026.10.01's obs and obs_ctd_full row for row under the old rules (obs +21,587 / −169,369 / ~12,882; obs_ctd_full +273,352 / −2,863,345 / ~321,217). It excluded two things, and, cell by cell (cruise × type), every difference from the measurement is one of them:

• Cruise 2607's new file (2026-07-3322; see the section on it): obs +86,138 / −62 / ~2,823, obs_ctd_full +897,033 / −4,530 / ~44,843, and all 4,127 (obs) and 66,846 (obs_ctd_full) quality-code changes of the two tables.
• The depth-constant guard (next section): obs −153 / ~3, obs_ctd_full −1,760 / ~31, in eight cruise × series cells.

Prediction + 2607 + guard equals the measurement exactly for every added and removed count. The changed counts are 2 (obs) and 62 (obs_ctd_full) lower than that sum, all spar and par on 2022-04-3322; that residual (0.02% of the changed values) is unexplained, and no row added or removed differs. The duplicated keys fall by exactly what the mini-pipeline gave, 159,594 in obs and 2,857,019 in obs_ctd_full; the 1,951,755 that remain are the keys CTD_DUP_SCAN_MAX holds open. Bottle-grain obs rows (btl_*, salinity_btl, oxygen_btl_*) equal the prediction cruise by cruise: 2022-04 +303 / −3,409, 2024-04 +127, 2025-04 +57, 2008-01 +840, 2007-11 +346, 2016-04 −364, 2021-05 −176.

sample goes 19,330 → 19,336 (six casts arrive, four on 2022-04-3322 and two on 2025-04-3322; none leaves); 50 casts differ in position or time (21 of them on 2008-01-31JD); grid_key changes on 4,791 of the 19,330.

CTD: derived series that hold one value at every depth are withheld

A series can be in bounds, unflagged and still not a profile. A census of every ctd-cast downcast CSV (libs/census_depth_constant_ctd.R → data/qc/ctd_depth_constant_census.csv; a cast is judged with at least 6 values over at least 50 m and is constant when its range is below 1e-9) found the provider's EstNO3_CruiseCorr (est_nitrate_cruise_corr) is one value over the whole cast on 441 of 5,066 judged casts (8.7%), across 20 of 76 cruises, and on every judged cast of seven (2304SH, 2504SH, 2301RL, 2307SR, 2105SH, 2411SR, 0810NH), while EstNO3_StaCorr on the same casts varies (0 of 4,241). Mostly exact zeros, the rest a per-cast offset (Rasmus Swalethorp's transect-plotter screenshot of line 93.3 showed vertical stripes). The same shape is in Ox1uM_CruiseCorr (329 casts of 9,837, three cruises), OxAveuM_StaCorr (124 of 4,321, three cruises) and a handful of casts in EstChl_* and the other Ox*_StaCorr columns (2-8 each); Salt*_Corr, Ox*_CruiseCorr (other than Ox1uM) and EstNO3_StaCorr have none.

ingest_calcofi_ctd-cast.qmd now calls calcofi4db::check_depth_constant_series() (4.17.3) after the accepted flags and overrides and before the sensor-pair averages, and drops those (cast, series) values (dropped, not flagged); a sensor-pair average that rested on a withheld sensor is rebuilt from the other. questions.csv Q42 asks the CTD team whether EstNO3_CruiseCorr is a per-cast offset in these files and whether to withhold or recompute it.

What the render dropped (the ctd-cast render of 2026-10-04, data/qc/ctd_depth_constant_dropped.csv): eight cruise × series cells on four cruises, every withheld value an exact 0. "Values withheld" counts every depth of those casts, including values v2026.10.01 never held, so it exceeds what leaves the release.

Against v2026.10.01 that is 1,760 obs_ctd_full rows removed (115 + 173 + 111 + 184 + 229 + 294 + 229 + 425) and 153 obs rows (16 + 24 + 22 + 27 + 6 + 58); 31 obs_ctd_full and 3 obs values change, oxygen_umol_kg_ave_sta_corr on 2022-04-3322 rebuilt from the other sensor. The census above counted 441 casts of EstNO3_CruiseCorr alone, across 20 cruises; the cells in the table are the ones that first render withheld.

In total the corrected guard removes 800,651 obs_ctd_full values and 44,054 obs values and changes 7,920 and 619 (the rebuilt averages); 532 and 77 values the first render withheld return.

Why only 32, and the second test. The chunk grouped by ctd_cast_uuid, which hashes each scan's time, so a "cast" held one value except in minute-resolution files, and the 32 cells were stretches of a cast inside one minute. It now judges (cruise_key, cast_key, cast_dir), one direction of one occupation, with two tests (calcofi4db: check_depth_constant_series() with a composite cast_col, and the new check_zero_runs()):

1. whole cast constant: >= 6 values over >= 50 m, range below 1e-9, every judged series;
2. a run of exact zeros within a cast: >= 6 consecutive zeros over >= 50 m (a step of <= 5 m inside a run), the run only, on the bottle-corrected oxygen and salinity. Not on estimated nitrate or chlorophyll: their zeros are the estimate clipped at zero where the quantity vanishes (nitrate's long zero runs start at the surface, 623 of 700, beside ~0.1 µM; chlorophyll's reach the 200 m end of its range below the chlorophyll layer, 1,259 of 1,480, beside ~0.003 µg/L). Station-corrected oxygen ramps to 0 where its per-cast regression fails (2408SR cast 033: sensor 26 µmol/kg at 322 m, 0.0 from 322 to 517 m).

Measured on the re-render of 2026-10-04 (finished 21:33), as rows removed against the staging build of that afternoon, which carried the 32-cell version. The prediction made from the wrangling database matched exactly on six series and to within 82 rows on the other three (cruise 2204SH, whose runs the earlier deletions had split in that database):

The averages are rebuilt from the sensors that remain, so they follow the sensors: an average whose sensors are both withheld goes, one with a single sensor left becomes that sensor instead of its mean with 0 (178 + 42 casts change, by up to 328 µmol/kg / 7.5 mL/L). Downcasts of est_nitrate_cruise_corr: 435 against the census's 441 (the census counts 2105SH's two upcasts filed in the downcast file and the duplicate copies of 0707, 1701). Every value either test withholds outside est_nitrate_cruise_corr is an exact 0, so no real near-constant profile is caught. Of the 1,051 values the 2026-10-04 render withheld on 2204SH and 1501NH, the 752 oxygen values stay withheld (zero runs); the 299 est_chlorophyll_a_sta_corr zeros return. ctd-derived: 4 casts lose their four chl_* values (all-zero est_chlorophyll_a_sta_corr); sigma_theta_ave, spice and the mixed-layer depths rest on temperature and salinity, which neither test touches.

CTD derived products: the CTD team's mixed-layer depth and chlorophyll-maximum definitions

calcofi_ctd-derived now computes its per-cast products by the definitions Rasmus Swalethorp gave on 2026-09-23 (questions.csv Q01, Q02; adopted 2026-10-01; CalCOFI/workflows#101, #102). v2026.10.01 shipped interim choices, so the headline mixed-layer depth changes on every cast that has one, and chl_max and chl_integrated on nearly every one (8,792 of 9,008 and 8,897 of 8,921 casts); the table below has every type.

• Mixed-layer depth: a new headline key, mld_sigma_theta_002. It is the depth at which sigma-theta is 0.02 kg m⁻³ greater than at 10 m, the CalCOFI legacy definition. The interim headline mld_sigma_theta_003 (Δσθ 0.03) is retired: its registry row stays, marked RETIRED with is_canonical = FALSE, and no row carries it. The key is new rather than reused because the old name states its 0.03 threshold. A consumer that asked for mld_sigma_theta_003 by name must switch; the Explorer reads its per-cast list from the registry and needs no change. mld_sigma_theta_0125 and mld_temperature_02 are unchanged, now described as alternatives to the headline. A cast that starts below 10 m, or never crosses the threshold, still has no value.
• chl_max_depth / chl_max (same keys) are the depth and value of the highest 3 m running mean of est_chlorophyll_a_sta_corr. v2026.10.01 used a 5 m running median. chl_max is now the mean at that depth.
• chl_integrated (same key) is the sum of the 1 m bins over the top 200 m, or to the bottom on shallower casts. v2026.10.01 integrated with trapezoids, so values move slightly. chl_integrated_depth is unchanged.
• Registry fix: the nine calcofi_ctd-derived types (spiciness0, sigma_theta_ave, the MLD and chlorophyll types) listed calcofi_ctd-cast as their _source_datasets. They now name the dataset that publishes them, calcofi_ctd-derived.
• measurements.json lists the per-cast types. The mixed-layer depths, chl_max_depth, chl_max, chl_integrated and chl_integrated_depth each get an entry with grain: "sample", so calcofi.io can give them a page. counts.sample_measurement_rows counts their rows.
• Correction to v2026.10.01's notes: that section listed ctd_geostrophic as a new table, but release_database.qmd did not publish it, and it is not in this release either. It is still computed and staged, pending questions Q03/Q04 (CalCOFI/workflows#103). datasets.json no longer lists it among the dataset's tables.

Per-type change against v2026.10.01 (diff_stage_vs_release() on the 2026-10-04 re-stage; casts = casts with a value, changed = the same cast with a different value, largest change in the type's unit):

Casts gain a value (79 chl_integrated and chl_integrated_depth, 75 chl_max and chl_max_depth, 76 mld_sigma_theta_0125, 4 mld_temperature_02, 9,180 mld_sigma_theta_002); no value of those types is removed or blanked. The obs series sigma_theta_ave goes 663,106 → 668,279 rows (+5,550, −377, none changed) and spiciness0 663,077 → 668,250 (+5,550, −377, 19 changed by at most 1.7e-5).

CTD casts: two provider questions on bottle values after 2021-05

calcofi_bottle ends 2021-05-13, where the provider's bottle database ends; later bottle values reach the release only as the btl_* types on calcofi_ctd-cast, from preliminary CTD + bottle files and with no quality code (the source files carry no flag column for any bottle value). Two proposed questions go to the provider (metadata/calcofi/ctd-cast/questions.csv Q40, Q41): whether btl_* values are equivalent to the bottle database for 2021 onward, and whether a bottle database later than 2021-05 is available or scheduled. No data changes.

Ichthyoplankton: cruises 198202JD and 198212JD leave (swfsc_ichthyo_09)

SWFSC (Ed Weber, 2026-09-25) moved cruises 198202JD and 198212JD (1982-02-31JD, 1982-12-31JD) back to its staging schema: they were sorted for anchovy only, so every other taxon read as a zero catch. The 2026-09-26 source export no longer contains them, so the re-stage drops them: 1,128 site (61,104 → 59,976), 1,112 tow (75,506 → 74,394) and 1,145 net sample rows; 1,100 obs rows (all abundance: 1,055 on 1982-02, 45 on 1982-12); 1,054 stage and 1,308 body_length obs_attribute rows; and 1,145 each of std_haul_factor, prop_sorted and volume_sampled sample_measurement rows. swfsc_ichthyo obs goes 482,250 → 481,150 on these cruises alone (487,616 with the nets added in the next section). All of these counts equal the 2026-10-04 re-stage's. The ingest now asserts both cruises are absent from what it loads. Zero handling is unchanged: a tow with no row for a taxon is a true zero and stays in the denominator (the provider: "the others are true zeros and have valid positive zooplankton volumes"). Both cruises leave cruise. One consequence reaches another dataset (see "Euphausiids: 40 tows of February 1982 have no cruise_key").

Ichthyoplankton: the source is SWFSC's 2026-09-26 export; v2026.09.11 to v2026.10.01 carried the 2026-09-04 ingest

From v2026.09.11 to v2026.10.01 every release shipped the swfsc_ichthyo shard staged on 2026-09-04, and its grid from 2026-06-07. Each provider export after that changed the source's shape (first ShipLookup.ShipIces, then the 2026-09-26 export's TitleCase tables), the ingest's integrity check stopped the notebook, and the halt was silent: the render exited 0 and the pipeline recorded the ingest as built. The check now fails the render (calcofi4db, development version), and the ingest reads the 2026-09-26 export. What changes for a user, measured against v2026.10.01:

• The two 1982 staging cruises leave, exactly as in the section above (1,128 sites, 1,112 tows, 1,145 nets; 1,100 obs; 1,054 egg stage and 1,308 body_length rows).
• 2,521 nets are added to existing tows (2,470 port-side nets of bongo tows, 48 starboard, 3 unsided; on 47 cruises 1977-12 to 2013-04, 1,229 of them in 1977-12 to 1978-08), with their effort (2,521 each of volume_sampled, std_haul_factor, prop_sorted; 23 more of each plankton biomass) and their catch: 6,469 obs rows (297 egg, 5,767 larva, 405 invertebrate; 6,491 before the pairs below are summed), 765 body_length and 10 larva stage rows. No site or tow is added: the nets lie on 2,494 existing tows.
• 32 larval counts are corrected by the provider (e.g. one net's northern anchovy 178 → 225), 2 body_length and 8 larva stage counts change, and 1 larva stage row is added on an existing net.
• 629 larval stage rows leave (tally 29,498, on 69 cruises 1984-01 to 2019-04): the export replaced larvaesize + larvaestage with one LarvaeMeasured table, and these (net, species) pairs have measured larvae but none with a stage. Asked: swfsc_ichthyo_18. 974 measured rows (tally 2,320, lengths only) name no larva count row and cannot be placed: flagged, not released (swfsc_ichthyo_17).
• Egg stages 12-15 leave (swfsc_ichthyo_02; Ben Best, 2026-10-01): v2026.10.01 published 790 egg stage rows (2,029 eggs) on a scale that ends at 11; the 2026-09-26 export holds 669 (1,756 eggs), now screened out and listed in data/flagged/egg_stage_12_15_screened.csv. They are not only Dover and Rex sole: 1,238 of the eggs are northern anchovy and 400 Pacific sardine at stage 12 (asked: swfsc_ichthyo_22). Egg abundance totals are unchanged.
• Counts are summed by AphiaID (swfsc_ichthyo_04/_05/_13; "aggregate by AphiaID", Bill's taxonomy stands): 31 species codes share 13 taxon_keys (e.g. 683 Sebastes and 3023 S. crocotulus; 788 S. leptorhynchus and 792 S. californiensis, which the source gives one AphiaID). Where two of them were counted in one net their rows are now one: 25 such pairs (22 of them on the new nets), so obs has no duplicated (sample, taxon, life stage) any more (v2026.10.01 had 3). The final count is 482,250 − 1,100 + 6,491 − 25 = 487,616. Every code keeps its own dataset_taxon row and verbatim name; no taxon_key changes. ds_source_json now holds the AphiaID the source gave: 11 codes whose AphiaID WoRMS has superseded (e.g. Myctophum lychnobium 272723 → key worms:1888085 Dasyscopelus lychnobius) used to show the accepted id there.
• depth_max_m of every ichthyo tow and net is Net.NetDepth, the maximum possible depth of the net, nominal (swfsc_ichthyo_08/_19): 61,625 of 74,394 tows and 65,128 of 77,888 nets (Manta surface tows have none); obs_bio's fallback depth for ichthyo follows. Where the sea floor is shallower the net did not reach it: 210 stations; the release counts these apart from depth errors, with their own ratchet (210).
• New: fish, SWFSC's Fish table (fish grown past the larval stage): 10,796 rows, 18,789 fish on 7,179 nets, 240 species codes, keyed (sample_key, species_id) with taxon_key. Not in obs until its life stage and overlap with the larval count are known (swfsc_ichthyo_20).
• New: ship_ices on ship and cruise, beside ship_nodc (swfsc_ichthyo_14). Keys are unchanged (cruise_key stays YYYY-MM-NODC); the codes differ for one ship, FROSTI (NODC OIFS, ICES 18DN).
• swfsc_ichthyo obs goes 482,250 → 487,616; obs_attribute body_length 241,871 → 241,328, stage 128,107 → 125,766; sample 213,122 → 212,258; cruise 691 → 694 rows (the two 1982 cruises leave; 1998-03, 1998-05 and 1998-06 JD and 2017-07 and 2018-07 Lasker arrive without stations: they are CUFES-only cruises, Cufes.CruiseId names them).
• grid is the rebuilt 225-cell grid (identical to calcofi4r::cc_grid 1.25.0, see the grid section above): with it 8,693 ichthyo sites (11,563 tows, 11,778 nets) change grid_key; none gains or loses one. 2,084 sites off the grid (ETP and elsewhere, swfsc_ichthyo_07) are kept with a NULL grid_key.
• Zero catches are true zeros (swfsc_ichthyo_09): 6,302 of 74,394 tows caught nothing and stay as samples with their effort; every one with a net has a positive volume. Net effort is SWFSC's own (the standard haul factor is not recomputed) and none is missing.
• Measured at the 2026-10-04 re-stage (swfsc_ichthyo re-staged from the 2026-09-26 export; the figures a reply to SWFSC can quote). The counts above agree with the stage, except the 6,491 → 6,469 new-net obs rows, which the summed pairs explain. sample 213,122 → 212,258 (net 76,512 → 77,888: 2,521 added to 2,494 existing tows on 47 cruises 1977-12-31JD to 2013-04-3322, 1,145 leaving with the 1982 cruises; 0 sites or tows added). No taxon_key changes. body_length 241,871 → 241,328 (+765, −1,308, 2 changed); stage 128,107 → 125,766 (larva +11, −629 with a tally of 29,498, 8 changed; egg −1,723 = 1,054 on the 1982 cruises + 669 at stages 12–15, tally 1,756 eggs, none left at stage 12 or above); sample_measurement 320,110 → 324,284. 9 of the 6,302 zero-catch tows have no net record, and every net of the others has a positive volume_sampled (as do all 77,888 nets). The 2,084 off-grid sites (2,720 tows, 2,720 nets) all have a position. fish carries a taxon_key on every row. grid_key changes on 8,693 sites, 11,563 tows and 11,778 nets (32,034), none gained or lost; 1998-03, 1998-05, 1998-06 JD, 2017-07 and 2018-07 arrive in cruise (694 rows).
• Not ingested: Cufes (another change repoints ingest_swfsc_cufes.qmd at it), SpeciesItisLookup, SpeciesWormsLookup (used to check the keys, data/flagged/species_worms_lookup_check.csv), PreservativeLookup, and Station arrival/departure times, bottom depth and bucket temperature.

CUFES: the source is SWFSC's own export, and eggs per m³ are published

swfsc_cufes was read from NOAA CoastWatch ERDDAP (erdCalCOFIcufes). It now reads Cufes.csv from SWFSC's CSV export of its CalCOFI database (2026-09-26, Ed Weber), where each sample carries its CufesId and the CruiseId of its cruise. Record by record, the export holds 47,989 of ERDDAP's 49,572 samples. Where both have a sample, its times and egg counts are identical, and its positions and environment differ by no more than float rounding (≤ 1.5e-5). Both run from 1996-03-15 to 2022-04-27. Measured against v2026.10.01:

• 1,583 samples leave (9,016 abundance rows; 18,218 eggs, 15,252 of them "other fish"). 1,563 have no position at either end, and SWFSC removed them at source (swfsc_cufes_04). They include all of cruises 1998-09, 1999-08 and 2000-01 New Horizon. The other 20 have a stop position only, and v2026.10.01 placed them there (asked: swfsc_cufes_09). Every remaining sample has a position.
• A new measurement type, egg_concentration (count/m³; 275,081 rows on all 47,989 samples, one per egg count, same taxon and life_stage = egg). It is Ed Weber's standardization (swfsc_cufes_01): eggs/m³ = (count / minutes sampled) / mean pump speed, with minutes = stop − start and the pump speed in m³/min (swfsc_cufes_02). It is computed only where the minutes and both pump speeds are positive, which every sample of this export is. The raw counts still publish as abundance (count), unchanged. One sample's stop pump speed reads 40 m³/min (others 0.27–1.07), which makes its concentration about 30 times too low. It is published as shipped and asked about (swfsc_cufes_10).
• Every sample has a cruise_key, taken from the provider's CruiseId through cruise.cruise_uuid. Before, 5,053 had none, and 6,212 keys change: 5,049 are filled (on 2017-07 and 2018-07 Lasker, 1998-03/05/06 and 1997-03 Jordan, and others). 1,163 move to the cruise SWFSC designates: 743 from 1998-02-31JD to 1998-03-31JD, and 420 from 1996-04-31JD to 1996-03-31JD. The date-span rule (resolve_cruise_key(), span then the source's Cruise) gives the same key on all 47,989.
• sample_key is built from CufesId (swfsc_cufes:underway:<CufesId>, previously the ERDDAP row number), and CufesId is released as sample.source_uuid, as ichthyo's UUIDs are. Every CUFES sample_key changes.
• grid_key: 9,224 samples change cell. All of them come from the rebuilt 225-cell grid (section above), none from the new source. 754 samples (9,048 obs rows) lie outside the grid, against 2,319 in v2026.10.01, most of which had no position at all.
• swfsc_cufes sample goes 49,572 → 47,989. obs goes 284,097 → 550,162 (abundance 275,081 + egg_concentration 275,081). Taxa are unchanged: the six keys, now checked against SWFSC's Species.csv AphiaIDs. The underway temperature, salinity, wind and pump speed are still not published, as before.

Measured at the 2026-10-04 re-stage, comparing on datetime and position because every sample_key changes (136 datetimes repeat, the position separates them): all 47,989 samples pair one to one with v2026.10.01's on the same datetime and a position within 1e-4 degree, and none is added. The 275,081 abundance rows that remain equal their v2026.10.01 values (0 changed); 206,893 of the 275,081 egg_concentration rows are 0, from zero counts, and the largest is 870.5 eggs m⁻³. Of the 9,224 samples that change cell, 2 had none before.

Three cetacean datasets: sightings, sonobuoy and eDNA (licence pending; provider asked)

sio_cetacean-sightings, sio_cetacean-sonobuoy and sio_cetacean-edna ship for the first time, staged from CalCOFI/marmam-app at commit 7bc0e18 (CalCOFI/workflows#117). They ship without a settled licence or citation: nothing is invented, the gap is recorded and the provider is asked (questions.csv Q01/Q02 of each; sightings carries the EDI knb-lter-cce.262.2 terms and citation as custom, sonobuoy and eDNA say license: unknown with an empty citation). funding is blank on all three: the ONR award marmam-app names (N00014-22-1-2719, FY22) cannot have funded 2004-2012 data, and the provider is asked what did.

• sio_cetacean-sightings: visual line-transect sightings and effort, quarterly cruises 2004-2022 (effort through 2021, so 2022 sightings have no effort to normalise against, Q07). Staged shard: 8,087 sample (1,980 transect effort segments + 6,107 sighting), 6,097 obs (group_size, one per counted sighting; the 10 sightings with a Best of 0 or blank keep their sample and publish no obs), 1,980 sample_measurement (transect_length) and 19,086 obs_attribute rows (effort status, group size min/max, calf count). Behaviour is held back: the codes are bare numbers with no codebook, in the same behavior type that farallon_bird-mammal fills with words, so the 10,108 behaviour rows the staged shard carried are not published until the lab supplies the codebook (Q03). 67 cruises, all with a cruise_key. It leaves the catalog's holdings and enters as a released dataset.
• sio_cetacean-sonobuoy: hourly presence of blue, fin and humpback whale calls in sonobuoy recordings, 2004-2012. Staged shard: 4,206 sample (962 deployment + 3,244 scan, one analysed hour), 9,270 obs (acoustic_presence, 1,978 of them 1) and 2,229 obs_attribute (call_type); 35 cruises, every hour with a cruise_key. The hydrophone depth is not recorded, so depth is NULL on every sample and obs, not 0 m. The 154 hours scanned only "adhoc" keep their sample and publish no presence value.
• sio_cetacean-edna: NCOG seawater eDNA screened for seven cetaceans, 2014-2016. Staged shard: 133 sample (water, one per sample, each timed by its CalCOFI bottle cast) and 497 obs (edna_presence, 71 sequenced samples x 7 species, 15 detections). The 62 samples listed as "not sequenced, PCR negative" did not amplify: they stay as samples with no edna_presence rows, not zeros, until the provider says what a PCR negative means (Q04). parent_sample_key is NULL (every sample is a root).

What else changes for consumers:

• sample_type gains sighting, deployment, scan (and water, filter with the eDNA datasets).
• measurement_type gains acoustic_presence, calf_count, call_type, edna_presence, effort_status, group_size, group_size_max, group_size_min and transect_length. behavior's _source_datasets names only farallon_bird-mammal: sio_cetacean-sightings publishes no behaviour row until its codebook arrives (Q03). edna_presence is emitted differently by the two eDNA datasets (see the calcofi_2022-edna section).
• Counts pool across observer teams: sio_cetacean-sightings and farallon_bird-mammal count cetaceans on the same cruises with independent observers, so summing the two counts some animals twice (both descriptions say so).
• check_taxon_registries() skips taxon_override.csv rows only for datasets held out of a release (exclude = ds_excluded, calcofi4db 4.17.2); these datasets are no longer among them.

Measured at the 2026-10-04 re-stage: sio_cetacean-sightings 8,087 sample (6,107 sighting, 1,980 transect), 6,097 obs, 19,086 obs_attribute (calf_count 3,159, effort_status 5,755, group_size_max 5,091, group_size_min 5,081; no behavior) and 1,980 sample_measurement; sio_cetacean-sonobuoy 4,206 sample (962 deployment, 3,244 scan), 9,270 obs (1,978 present), 2,229 obs_attribute, with depth NULL on every sample and obs; sio_cetacean-edna 133 sample and 497 obs (15 detections).

A new dataset: calcofi_2022-edna, vertebrate eDNA from the October 2022 cruise (detections only)

ingest_calcofi_2022-edna.qmd ingests the GBIF/OBIS Darwin Core Archive "CalCOFI October 2022 Vertebrate eDNA" (Patin and O'Donnell, version 1.2, doi:10.15468/n52j6r, CC BY 4.0; linked to Patin et al. 2026): 47 water filters (sample_type = 'filter', one per parentEventID) from CalCOFI/GEMCAP stations on cruise 2022-10-33UD, 2022-10-13 to 2022-10-18, each run through a mitochondrial D-loop assay (cetaceans) and/or a 12S rRNA MiFish assay (fish). Staged shard: 47 sample, 148 obs (74 edna_presence, 51 edna_reads_dloop, 23 edna_reads_12s; 19 taxa) and 482 sample_measurement (co-collected nutrients, chlorophyll fluorescence, oxygen in mg/L, DNA concentration, and the per-assay raw and filtered read totals).

Detections only. The source archive holds positive detections only, so the dataset publishes edna_presence = 1 and the read counts, and the absence of a row is not a non-detection here (unlike sio_cetacean-edna, where 0 means not detected in a sequenced sample). Whether filters or assay runs with no detection were omitted is asked of the provider (Q08, high, no longer a blocker). Reads are a semi-quantitative signal of PCR-amplified DNA, not abundance, and are not comparable between assays. Not yet linked: site_key and parent_sample_key are NULL on every filter (CalCOFI/workflows#125). The shared measurement_type registry gains edna_reads_dloop, edna_reads_12s, edna_reads_raw_*, edna_reads_filtered_*, oxygen_mg_l and dna_concentration. chl_fluor, which calcofi_mets shares, gets a floor of its own (see the section on it below).

Measured at the 2026-10-04 re-stage: 47 sample (grid_key and cruise_key on all 47, site_key on none), 148 obs (74 edna_presence, all 1; 51 edna_reads_dloop; 23 edna_reads_12s) and 482 sample_measurement over 12 types.

A new dataset: cce-lter_iron, dissolved iron on CalCOFI cruises, 2002–2004

ingest_cce-lter_iron.qmd ingests the CCE-LTER EDI package knb-lter-cce.21.3 (Barbeau, doi:10.6073/pasta/63c4e57f87861db3acaf80d1dec103e1), fetched and md5-pinned by libs/download_iron.R (CalCOFI/workflows#82). With no cast or bottle number in the source, it mints its own sample arm (170 surface pole samples, Nov 2002 – Jul 2004, keyed cce-lter_iron:bottle:{study_name}-{index_number} from the source's own unique pair, not row position) and publishes 170 obs rows in the env realm of one new measurement type, dissolved_iron (nmol/L; the file header says "nM/L", confirmation pending, Q04).

Held out, on purpose. chl_response_to_fe (the iron-addition bioassay response) is not released until the provider answers Q01 (is it a unitless treatment:control ratio, a concentration or a code? its EML scale is nominal); Q01 stays open with priority blocker. total_iron is not registered because the revision has no real value (170 of 170 rows are the -999 sentinel). Neither has a row in measurement_type, so neither appears in the measurements catalog.

The source's undocumented -999 sentinel becomes NULL (Q06), and Datetime PST is read as a fixed UTC−8 offset pending the provider's answer to Q02. The license is the package's own free-text rights statement (custom), not a CC grant. Open provider questions: Q01, Q04 (units, detection limit, whether the 0.05 nmol/L floor is one), Q07 (operational definition of "dissolved", contamination control).

Re-staged 2026-10-04 from the restored source file: 170 sample and 170 obs (dissolved_iron, 0.05 to 8.2 nmol/L), all keyed to a cell of the new grid.

DIC: every sample with a position carries a grid_key

In v2026.10.01 sample.grid_key was NULL on 3,255 of 3,261 calcofi_dic rows. The sample arm took grid_key only from the matched calcofi_bottle cast, and 3,255 DIC samples match no cast, though every one carries a latitude, longitude and datetime. The ingest now assigns grid_key from each sample's own position (assign_grid_key() against the swfsc_ichthyo grid) and keeps a matched cast's key where there is one: 3,262 of 3,262 resolve (0 outside the grid). Measured at the 2026-10-04 re-stage: sample.grid_key NULL 3,255 → 0; of the 6 samples that already had a key, 3 change with the rebuilt grid and 3 do not; check_grid_key_assignment() finds 0 wrong. 3 obs rows of a cast-matched sample carry the cast's key and differ from their sample's. calcofi_phytoplankton stays NULL by design: it is region-pooled. The obs and cruise_key changes that go with this are in the next section.

DIC: the values on samples that match no bottle cast are published (Ben, 2026-10-04)

Until v2026.10.01 the DIC obs arm joined casts, so a DIC sample that matches no bottle cast published a sample row and no observation: 3,255 of the 3,261 minted DIC samples, about 12,700 of the 16,391 non-missing DIC / total alkalinity / CTD temperature / salinity source values. They are now published, wherever the source gives the sample a depth, on the sample's own calcofi_dic:bottle:<md5> key with the source's own depth, the grid_key of its position, and a cruise_key where the SWFSC reference resolves one (below). These values are not linked to a bottle cast: the source names no cast (calcofi_dic_01, open), so parent_sample_key is NULL and the sample is its own root. The 3,708 values of a matched cast are all still published (937 / 835 / 1,028 / 908), with one change of key: 61 of them, on six Niskins, move from their calcofi_bottle:bottle: key to a minted DIC key (555915 at 13 m: 13 values; 588517, 654186, 655848 and 657308 at 10 m: 11 each; 891715 at 51 m: 4; and one more DIC sample is minted, 3,262 in all: 7 on a matched cast, 3,255 matching none). DIC rows at station 106.7 100.0, 1984-01-19 match two casts (22605 and 22606) that tie on date; match_by_site_datetime() has no tie-break, and the re-staged bottle shard resolved the tie to cast 22605, which holds no bottle within 1 m of the DIC depth, where v2026.10.01 had 22606 (bottle 555915 at 13 m, and the five other Niskins above). The matching count (1,086 rows) is unchanged. Tie-break: calcofi4db issue to file.

obs (calcofi_dic) against v2026.10.01 at the 2026-10-04 re-stage, net of the 61 values that change key (the totals do not depend on how the matching resolves):

3,647 values keep their key and value, the 61 leave a cast's key and arrive on minted keys, and 12,681 are new; compared without the sample key, 0 values are removed and 12,681 added. No value, depth or quality code changes.

The 12,681 sit on 3,254 samples. One unmatched sample has no source depth (Depth = -999: expocode 33RL20210116, station 080.0 090.0, 2021-01-20) and stays a sample row with no observations (its DIC 2007.2 and TA 2208.4 umol/kg are the 2 source values left out). Values the provider flags WOCE 3 / 4 / 9 are published with their flag as for the cast-matched ones (141 of the 12,681: alkalinity 65, dic 71, salinity 5); qual_ok / cc_qual_ok_sql() exclude them. All 12,681 are within the declared bounds (dic 0..5000, alkalinity 0..5000, ctdtemp_its90 -2..40, salinity_pss78 0..45); depths span 0..3,542 m (check_depth_bounds() clean).

cruise_key on the 3,255 samples that match no cast: 2,920 resolved (NULL → key), 335 left NULL, from the sample's ship (EXPOCODE NODC prefix, else Ship_Name) and date by resolve_cruise_key(); the EXPOCODE start month is not used as the designation (calcofi_dic_07, open). The 335 are 8 EXPOCODEs for which the reference holds no cruise of that ship and month (NOAA Ship Sally Ride 240 samples, McArthur 51, Oceanus 41, David Starr Jordan 3), the same on the 2026-09-26 ichthyo export as before it. site_key is the source's own station on all of them.

Limitations. 3,218 of the 3,254 published samples carry a date on the 1st (1,926) or the 20th (1,292) of a month, an apparent month-precision stand-in: use their year and month, not their day. The values are not deduplicated against calcofi_bottle's own dic_rep1 / alkalinity_rep1 (separate measurement types, calcofi_dic_08 / _09); some may be the same Niskins (not verified).

Bottle: salinity quality codes above 9 become blank (calcofi_bottle_01)

The provider (Rasmus Swalethorp, 2026-09-18) answered that a quality code above 9 is impossible (codes were dragged down a spreadsheet by accident) and to turn every such code into a blank. In the source 194903-202105_Bottle.csv that is 880 rows, all salinity, all cruise 2021-05-3322 (880 distinct bottles; codes 10 to 344: 52 in 10–17, 593 in 18–253 and 235 in 254–344); no other quality column holds a code above 9. In obs_env those 880 measurement_qual values go from the code to NULL; the salinity values and the row count are unchanged. A blank is not a verdict on the value: calcofi_bottle_13 (that cruise reads 24.2–27.1 PSU where its neighbours read 32.8–34.5) is still open, and cc_qual_ok_sql() excludes only codes 8 and 9, so a filtered query returns the same 880 rows before and after. Measured at the 2026-10-04 re-stage: the 880 salinity measurement_qual values go from the code to NULL, and nothing else changes: obs is 11,135,581 rows on both sides (11,134,701 unchanged, 880 with only the code changed) across 26 types, sample_measurement (268,876 rows across 15 types) is identical, and the stage holds no code above 9.

Phytoplankton: repeated rows dropped (workflows#124)

Two sets of source rows carried the same species code twice in one sample, so a summed abundance (a total, a mean) doubled while a presence count did not. The ingest now drops the second row where the two hold the same value: 4,251 phytoplankton_abundance rows leave obs / obs_bio (159,804 → 155,553; the 409 region_pool samples are unchanged).

• Cruises 0704, 1202, 1203: 1,496 codes x 4 regions each are duplicated (4,488 pairs); 4,198 pairs are identical and 4,198 rows go. 1202 and 1203 sit in both the 1996–2012 and the 2012–2018 workbook, and the 2007 sheet has two columns both labelled "CalCOFI 0704".
• Code 178: the same row twice in 53 samples (1902–2211); 53 rows go.
• 290 pairs stay. Their two rows hold different values (288 on 0704, one each on 1202 SE and 1203 Alley) and we cannot tell which is right until the provider answers calcofi_phytoplankton_06 (Q06). They are listed, with both values and their source sheets, in metadata/calcofi/phytoplankton/duplicate_pairs_differing.csv; the ingest asserts that (phyto_sample_id, species_code) is unique outside that list. A consumer summing abundance still double-counts those 290 (code, sample) cells.

Measured at the 2026-10-04 re-stage: phytoplankton_abundance 159,804 → 155,553 rows (−4,251). Compared as a multiset of (sample, value), the stage lacks exactly 4,251 release rows and adds none; 65 of the 409 region_pool samples lose rows, and the 409 samples are unchanged in every column.

Phytoplankton: named codes stop falling into "not identified further"; one rule for unknown species

53 codes with real names keyed only their functional-group class. The ingest's WoRMS cache (metadata/calcofi/phytoplankton/taxon_worms.csv) had no AphiaID for 75 of the source's 384 defined species codes. Those fell through to the six ds_common_name rows in metadata/taxon_override.csv and keyed their class (Bacillariophyceae, Dinophyceae, Coccolithophyceae, Dictyochophyceae). That is right for the source's own unidentified classes ("indistinguished pennate diatoms", "pennate sp. 6"). For 53 real names it was a failed lookup, so "Diatoms, not identified further" and its siblings silently absorbed named taxa. Among them were both Pseudo-nitzschia size classes (codes 94 and 400: cells counted in 405 and 234 source samples, 1996–2022), Calcidiscus leptoporus (223) and Ditylum brightwellii (43). The lookups failed for four reasons:

• Source spelling slips: Rhisosolenia, brightwelli, obtusidiens, Lithodesmum, octanarius, …
• Qualifiers the name cleaner turned into an empty query: "slim" / "robust Pseudo-nitzschia spp.".
• Open nomenclature queried verbatim: "Hemiaulus 1".
• Accepted species the WoRMS name services never return: Calcidiscus leptoporus (worms:235923) and Rhabdosphaera clavigera (worms:235972).

One rule for what the source names. species stays verbatim (it is the name a consumer displays); name_query is what is looked up:

• Clear spelling slips are fixed in the query only. The species keys its accepted WoRMS record (16 codes).
• An unknown species of a named genus keys that genus. This covers "sp. 1" / "sp. a", "spp.", size classes, spores, "complex", "cf." determinations, a species WoRMS does not hold (Prorocentrum cinctum), and species of one genus counted together ("Ceratium kofoidii + C. boehmii"). A known species with a "var." / "spore" / "minute form" suffix keeps its species key.
• The genus keyed is the accepted one. Where WoRMS files the source's species under another accepted genus, the genus codes key that genus, so a hierarchy rollup agrees with the species items: the six "Ceratium spp." codes key Tripos (worms:494057), as the 19 Ceratium species already did. species still reads "Ceratium spp.".
• Older rows are brought into line too. The rule also applies to the older "cf." and combined rows, which keyed a species ("Chaetoceros cf. subtilis" keyed C. subtilis; "Actinoptychus adriaticus + A. vulgaris" keyed A. adriaticus). Those species items now fold into their genus.
• Species of two genera counted together key their lowest common ancestor in WoRMS's classification, not the class: "Dactyliosolen phuketensis + Guinardia striata" keys Rhizosoleniaceae (worms:149068), "indistinguished Gyrosigma spp. + Pleurosigma spp." keys Pleurosigmataceae (worms:149032), and "Mastogloia woodiana + pennate a" keys Bacillariophyceae (worms:148899), the common ancestor of a named Mastogloia and an unidentified pennate. questions.csv Q09 asks the provider.
• Same spelling, wrong author. Five cached rows keyed a later, unaccepted name spelled like the source's, not the accepted species. They now key the accepted record:
  • Chaetoceros debilis (codes 367 and 521): Leegaard 1920 (worms:961758) → Cleve 1894 (worms:149219).
  • Chaetoceros peruvianus (34): Gran 1908 (worms:961865) → Brightwell 1856 (worms:178185).
  • Coscinodiscus perforatus (501): Cleve & Möller 1878 (worms:962307) → Ehrenberg 1844 (worms:149272).
  • "Rhizosolenia hebetata f. hebetata" (390) had keyed R. hebetata (Hensen) Margalef, a synonym of R. semispina, so it merged with f. semispina (code 62). It now keys its own form (worms:163347).
• A dinoflagellate keyed to a diatom. "Prorocentrum compressum" (code 102) keyed worms:978142, a diatom variety (Pyxidicula compressa var. compressa), because WoRMS files that name as a synonym of a diatom. It now keys Prorocentrum (worms:109566), like the other "Prorocentrum sp." codes. Four cached ranks that said "Species" for varieties and a form were corrected.

Result. By the resolution order applied to the committed registries:

• 118 codes change taxon_key: 54 leave their class (53 for a genus or species, 1 for a family), 56 move from a species to its genus, 1 from a species to a family, 1 from a species to the class, 1 from the source's genus to the accepted genus (Ceratium → Tripos), and 5 move to the accepted record of the same name. No other code moves.
• 17 codes stay at class level: 16 unidentified classes and the one two-genus entry whose common ancestor is the class. The ingest allowlists them one code at a time and stops if any other code reaches only a class.
• Distinct worms taxon_keys in dataset_taxon go from 299 to 296 (plus 10 dataset-local keys, unchanged); 295 of them have observations, because code 258 (Peridiniella catenata, worms:110156) is defined in the source and has no row.
• obs has one row per source measurement: 155,553 after the repeated rows above (159,804 before). Only taxon_key moves, on 48,633 rows (the 118 codes; 5,925 of them with cells counted); the stage is consistent with that, though the moved rows cannot be separated by value from the 4,251 dropped.
• Consumers must sum. Several codes now share one taxon_key within the same sample (30 keys do: Oxytoxum 10 codes, Bacillariophyceae 9, Dinophysis 8, Nitzschia 8, Prorocentrum 8, Chaetoceros 7, Protoperidinium 6, Tripos 6). A consumer that counts rows per taxon rather than summing value per sample double-counts. obs.obs_id stays unique, so no gate fails.
• The release's dataset_taxon.ds_scientific_name still holds the WoRMS name, not the source's own spelling; the verbatim name is in the ingest's taxon_worms.csv (species).

Two phytoplankton common names. WoRMS, GBIF, ITIS and NCBI Taxonomy were checked for every phytoplankton taxon. Beyond the classes, only two species have an English name, and both are WoRMS's single English vernacular: Noctiluca scintillans "sea sparkle" (worms:109921) and Pyrocystis fusiformis "ocean night light" (worms:110328). They are added to metadata/taxon_common.csv.

Euphausiids: 40 tows of February 1982 have no cruise_key, because the ichthyoplankton reference no longer holds cruise 198202JD

cce-lter_euphausiids resolves its cruise keys against the cruise reference that swfsc_ichthyo supplies. SWFSC moved cruise 198202JD (1982-02-31JD) back to its staging schema (see "Ichthyoplankton: cruises 198202JD and 198212JD leave"), the 2026-09-26 export holds no row for it, and 40 cce-lter_euphausiids tow samples of February 1982 that carried 1982-02-31JD now have no cruise_key (NULL cruise_key on the dataset 420 → 460). The cruise took place: the tows' values, positions and dates are unchanged, and the dataset's 100,505 obs rows are identical to v2026.10.01's. Apart from grid_key (1,954 rows, see the grid section), these 40 keys are the only change to the dataset's sample. The release ratchet on NULL cruise_key for this dataset is raised by those 40 in release_database.qmd and returns to 420 when SWFSC restores the cruise row (swfsc_ichthyo Q23, which asks whether the Cruise table can keep a row for a cruise whose ichthyoplankton data are staged).

Consumers: a join of cce-lter_euphausiids to cruise on cruise_key loses these 40 tows.

chl_fluor floors at −1 µg/L, so the 102 near-zero readings of calcofi_mets stay published

chl_fluor is shared with calcofi_mets, so a bound declared for it applies there too. It now declares valid_min = -1 µg/L, the floor calcofi_bottle declares for chlorophyll-a. A floor of 0 would have removed 102 calibrated-fluorescence values from calcofi_mets (minimum −0.112, median −0.03 µg/L): they are real near-zero readings, not sentinels. Measured at the 2026-10-04 re-stage: with the floor at −1 the 102 negative chl_fluor readings (−0.112 to −0.00025) are published, and calcofi_mets obs (511,395 rows) and obs_mets_full (19,926,523 rows) are identical to v2026.10.01's.

sample and sample_root carry hex7, so a per-sample value can be drawn in hexagons

A value held per sampling event in sample_measurement (a cast's mixed-layer depth, a net's volume filtered) had no H3 cell: the cell lived only on observations (obs_bio.hex7, obs_env.hex7), and a per-sample value has no observation row to borrow one from. The Explorer's Hexagons lens could not draw the seven per-cast calcofi_ctd-derived types for that reason.

• sample.hex7 and sample_root.hex7 (new column, UBIGINT, last on each table). The H3 cell at resolution 7 of the event's own position, NULL where the position is missing or not finite. sample_root.hex7 is its root's sample.hex7, copied. The change touches no other column: on a dry run over v2026.10.01 every other value of both tables is unchanged, row for row.
• One definition with the observations. hex7 is the resolution-7 parent of the resolution-10 cell of the position, built from the same SQL as obs.hex_id and obs_bio.hex7 / obs_env.hex7. It is not the resolution-7 cell the position falls in: H3 cells do not nest exactly, and the two differ for 101,770 of 1,463,329 positioned samples (7.0 %).
• By how much (dry run on v2026.10.01): 1,463,329 of 1,469,239 sample rows and 415,628 of 421,538 sample_root rows get a cell. The rest have no place: 5,761 samples with no position (calcofi_mets 4,039, swfsc_cufes 1,563, cce-lter_zoodb 155, cdfw_dungeness-crab 4) and 149 calcofi_mets samples holding one coordinate without the other. Of the 652,879 sample_measurement values, 652,871 now reach a hexagon through sample; through sample_root alone 332,152 do, because 320,719 values sit on non-root samples (ichthyoplankton nets, crab subsamples). sample grows 25.9 → 27.7 MB (+6.7 %), sample_root 10.5 → 11.5 MB (+9.0 %).
• A sample's cell is not always its observations' cell, and that is correct. sample holds one position per event; a CTD observation holds its own scan's position, and a DIC draw its own. Where the ship drifts across a cell edge during a cast, some scans are in the neighbouring hexagon: 1,012,956 of 33,139,449 observations (3.1 %), on 925 of 9,674 calcofi_ctd-cast casts, 893 of the 9,275 casts with calcofi_ctd-derived profiles and 235 of 789 calcofi_dic samples. None of the other 13 datasets differs, and no observation that sits at exactly its sample's position (17,341,531 of them) is in another cell.
• Gate. check_sample_hex7() (release_database.qmd, chunk browser_objects) fails the release unless a cell is present exactly where the position is finite, is at resolution 7, is equal on sample and sample_root for every root, and equals the cell of every observation at the same position. Observations in another cell than their sample are reported. Four test_release.qmd contract rows assert the same on the published objects.

Consumers: additive, nothing to change. To place a per-sample value, join sample_measurement to sample on sample_key and read hex7 (sample_root reaches root samples only). Coarser hexagons are calcofi4db::h3_parent_sql(hex7, res), plain bit arithmetic that needs no extension. Join an observation to its sample on sample_key, never on the cell.

Correction: the obs objects still ship; #92 tracks their removal

The v2026.09.10 notes below say its cut was the last to ship the obs table's objects and that "the next release drops the obs objects and the twin". That did not happen: v2026.10.01 still exported the 16 obs partition objects and obs.parquet, and this release does too. They go only when every reader has moved to obs_bio + obs_env or the obs catalog view (issue #92, open; seven readers break with no change). Until the release that drops them says so here, read obs_bio / obs_env or the view, not the table's objects.

calcofi.io measurement pages: face, why and method rows for the keys that had none

The landing site draws each /measurements/ page from measurements.json, which carries the five face registries (metadata/measurement_{face,why,method,chem,scale}.csv). In v2026.10.01 three published keys had no face (oxygen_ml_l_ave_cruise_corr, sigma_theta_ave, spiciness0), four no why (those and uws_flow) and three no method. They now have rows, so their pages publish all three sections: oxygen_ml_l_ave_cruise_corr reuses the dissolved-oxygen rows (face, chemistry, why), sigma_theta_ave stands in for sigma_theta, and spiciness0 and uws_flow get their own why rows. Rows are also written for the per-cast mixed-layer-depth and chlorophyll types of calcofi_ctd-derived (mld_sigma_theta_002, mld_sigma_theta_0125, mld_temperature_02, chl_max, chl_max_depth, chl_integrated, chl_integrated_depth; the headline mixed-layer depth states the provider's 0.02 kg m⁻³ from 10 m criterion, and the retired mld_sigma_theta_003 has none). Because the catalog now lists per-cast types (the CTD derived products section above), these keys get a /measurements/ page that says each is one value per cast. Rows for the eDNA types (edna_presence, edna_reads_*) and group_size / acoustic_presence are written too, but those are obs_bio keys, which the catalog does not list, so they render nowhere yet. No data changes.

Contents (generated)

25 tables, 373,474,855 rows, 2.73 GB.

Datasets (22): calcofi_2022-edna, calcofi_bottle, calcofi_ctd-cast, calcofi_ctd-derived, calcofi_dic, calcofi_mets, calcofi_phyllosoma, calcofi_phytoplankton, cce-lter_euphausiids, cce-lter_iron, cce-lter_picoplankton-bacteria, cce-lter_zoodb, cce-lter_zooscan, cdfw_dungeness-crab, farallon_bird-mammal, sio_cetacean-edna, sio_cetacean-sightings, sio_cetacean-sonobuoy, sio_mesopelagic-fish, sio_pic-zooplankton, swfsc_cufes, swfsc_ichthyo

Validation: 92 pass / 0 fail / 4 skip (consumer-contract suite, 2026-10-05T18:58:44Z).

Software: calcofi4db 4.21.0, calcofi4r 1.25.0.

How to cite

CalCOFI (2026). CalCOFI Integrated Database, release v2026.10.05 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://doi.org/10.5281/zenodo.23170248

Cite the source datasets you use alongside the release:

• calcofi_2022-edna — Patin N, ODonnell G (2026). CalCOFI October 2022 Vertebrate eDNA. Version 1.2. Occurrence dataset. https://doi.org/10.15468/n52j6r · CC-BY-4.0
• calcofi_bottle — CalCOFI. (2023). CalCOFI Bottle Database 194903-202105. CalCOFI.org. · license pending
• calcofi_ctd-cast — CalCOFI. (2023). CalCOFI CTD Cast Files. CalCOFI.org. · license pending
• calcofi_ctd-derived — CalCOFI. (2026). CalCOFI CTD Derived Hydrographic Products (from the CalCOFI CTD Cast Files). CalCOFI.io. https://calcofi.io/workflows/ingest_calcofi_ctd-derived.html · license pending
• calcofi_dic — Keeling, C.D.; Lueker, T.J.; Emanuele, G.; Dickson, A.G.; Martz, T.R.; Wolfe, W.H.; Mau, A. (2025). Discrete profile dissolved inorganic carbon, total alkalinity, water temperature and salinity measurements for CalCOFI (NCEI Accession 0301029). NOAA NCEI. https://doi.org/10.25921/3w9f-jd72 · CC-BY-4.0
• calcofi_mets — CalCOFI. Underway (METS) TSG/Meteorology Data. CalCOFI.org. · license pending
• calcofi_phyllosoma — CalCOFI - Scripps Institution of Oceanography and T. Koslow. 2017. Data pertaining to lobster phyllosoma, Panulirus interruptus, collection methods, locations, identification and staging (1951-2008, months of July and August) ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/9e38121ebb26f1b59b7b39b2eff844fa · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.188.4)
• calcofi_phytoplankton — CalCOFI - Scripps Institution of Oceanography, California Current Ecosystem LTER, and E. Venrick. 2023. Temporal and spatial changes of the abundance and species composition of phytoplankton in the California Current from samples collected aboard CalCOFI cruises from summer 1996 through 2022. ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/60edabfbfd85c623fce05822befaa071 · CC0-1.0 (https://creativecommons.org/publicdomain/zero/1.0/)
• cce-lter_euphausiids — Ohman, M.D. 2022. California Current Ecosystem Euphausiid data, Brinton and Townsend Euphausiid Database (BTEDB) ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/4a92a0044bcd1523a4f994ece874a57d · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.313.1)
• cce-lter_iron — California Current Ecosystem LTER, CalCOFI - Scripps Institution of Oceanography, and K. Barbeau. 2017. Measurements of dissolved inorganic concentrations of nutrient iron and of iron limitation at selected stations and depths from CalCOFI cruises in the California Current System, Nov. 2002 - July 2004 (completed) ver 3. Environmental Data Initiative. https://doi.org/10.6073/pasta/63c4e57f87861db3acaf80d1dec103e1. · custom (https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.21.3)
• cce-lter_picoplankton-bacteria — Landry, M. (2004-2023). Picoplankton and Bacteria Abundance (CalCOFI Cruise). CCE LTER. · license pending
• cce-lter_zoodb — citation pending · custom (https://oceaninformatics.ucsd.edu/zoodb/)
• cce-lter_zooscan — citation pending · custom (https://oceaninformatics.ucsd.edu/zooscandb/)
• cdfw_dungeness-crab — Rogers-Bennett, L.; Jones, E.; Klemmedson, A. (2026). CDFW Dungeness Crab Megalopae from archived CalCOFI plankton samples (1949-2014). California Department of Fish and Wildlife, published through CalCOFI / Scripps Institution of Oceanography. · CC-BY-4.0
• farallon_bird-mammal — citation pending · custom (https://oceanview.pfeg.noaa.gov/CalCOFI/app/resources/docs/Data_Sharing_Agreement_FarallonInstitute.pdf)
• sio_cetacean-edna — citation pending · unknown
• sio_cetacean-sightings — CalCOFI - Scripps Institution of Oceanography and J. Hildebrand. 2017. Index of visual monitoring, location, species behavior, and identification of cetaceans from CalCOFI cruises in the California Current System, 2005-2015 (ongoing). ver 2. Environmental Data Initiative. https://doi.org/10.6073/pasta/9ee6ca9b4a316708ca3d17ddc92debfb · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.262.2)
• sio_cetacean-sonobuoy — citation pending · unknown
• sio_mesopelagic-fish — Koslow, J. Anthony (2016). CalCOFI Trawl Data. In California Cooperative Oceanic Fisheries Investigations (CalCOFI): Acoustic and Trawl Data. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0BZ64DH · CC-BY-4.0
• sio_pic-zooplankton — citation pending · license pending
• swfsc_cufes — citation pending · custom (https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIcufes.das)
• swfsc_ichthyo — NOAA Fisheries SWFSC. CalCOFI Ichthyoplankton Database. · license pending

Access

con <- calcofi4r::cc_get_db(version = "v2026.10.05")

con = calcofi4py.cc_get_db("v2026.10.05")

Parquet: https://storage.googleapis.com/calcofi-db/ducklake/releases/v2026.10.05/parquet/{table}.parquet; full history: RELEASES.md.