Skip to content

Update coasts package to version 4.20.0: updated documentation to re… #528

Update coasts package to version 4.20.0: updated documentation to re…

Update coasts package to version 4.20.0: updated documentation to re… #528

Triggered via push October 4, 2026 15:35
Status Success
Total duration 58m 13s
Artifacts 1
Build R container
2m 55s
Build R container
Ingest static assets
1m 35s
Ingest static assets
Ingest GPS trips
4m 52s
Ingest GPS trips
Match GPS and survey data
1m 31s
Match GPS and survey data
Enrich taxa with FishBase data
2m 25s
Enrich taxa with FishBase data
Ingest GPS tracks
3m 43s
Ingest GPS tracks
Preprocess GPS tracks data
21m 13s
Preprocess GPS tracks data
Predict fishing tracks and aggregate to H3 grid
15m 46s
Predict fishing tracks and aggregate to H3 grid
Export WIO data
3m 22s
Export WIO data
Export fishers stats
1m 56s
Export fishers stats
Run spatial CPUE model
5m 34s
Run spatial CPUE model
Export spatial outputs as JSON/GeoJSON for web
3m 40s
Export spatial outputs as JSON/GeoJSON for web
Fit to window
Zoom out
Zoom in

Annotations

6 warnings and 120 notices
WARN
89 of 946 taxa names matched no FishBase/SeaLifeBase species and were dropped: Abalistes stellaris, Scaridae, Brachyura, Carangoides armatus, Actinopterygii, Solea bleekeri, Parupeneus macronema, Charybdis feriatus, Chromis multilineata, Sorsogona prionota, Liza alata, Selachimorpha (Pleurotremata), Leiognathus equulus, Octopus cyaneus, NA, Haemulidae (=Pomadasyidae), Ulua mentalis, Carangoides fulvoguttatus, Pristotis jerdoni, Sepiidae, Sepiolidae, Synagrops microlepis, Valamugil cunnesius, Pomadasys multimaculatum, Carangoides ferdau, Valamugil spp, Sepia prashadi, Sepia latimanus, Stegastes apicalis, Carangoides coeruleopinnatus, Caesionidae, Algae, Epinephelus chabaudi, Secutor insidiator, Labridae (ex Scaridae), Synodontis zambesiensis, Histioteuthis dofleini, Etrumeus teres, Rhamphochromis brevis, Stegastes dorsopunicans, Carangoides gymnostethus, Herklotsichthys quadrimaculat., Liza vaigiensis, Sepia pharaonis, Parupeneus heptacanthus, Leiognathus leuciscus, Chromis intercrusma, Auxis thazard, A. rochei, Synagrops adeni, Carangoides oblongus, Stolephorus commersonii, Chelon macrolepis, Thryssa baelama, Premnas biaculeatus, Upeneus arge, Alectis indica, Pomacentrus agassizi, Thunnini, Octopus aegina, Loligo duvauceli, Carangoides orthogrammus, Plectorhinchus orientalis, Carangoides equula, Carangoides malabaricus, Parapenaeopsis sculptilis, Chromis margaritifer, Thryssa vitrirostris, Carangoides chrysophrys, Liza dumerili, Paracaesio xanthura, Loliginidae, Ommastrephidae, Carangoides dinema, Stegastes fasciolatus, Reptantia, Strongylura leiura, Zebrasoma veliferum, Ambassis productus, Himantura granulatus, Crenimugil crenilabis, Valamugil seheli, Secutor ruconius, E. fuscoguttatus x E. lanceolatus, Abudefduf luridus, Ambassis commersoni, Sepia trygonina, Chromis dimidiata, Cociella crocodila, Carangoides plagiotaenia, Leiognathus dussumieri, Pomadasys opercularis
WARN
Failed to create 2dsphere index: Index build failed: 7fb076c7-7985-4934-9301-cfe9ff6758b2: Collection portal.wio_gaul2 ( 81c75ec6-9281-466c-9abe-660d48fd3cae ) :: caused by :: collection scan stopped. totalRecords: 18; durationMillis: 161ms; phase: collection scan; collectionScanPosition: RecordId(18); readSource: kMajorityCommitted :: caused by :: Can't extract geo keys: *** _id: ObjectId('6ac27a81b3a34f7553098f14'), iso3_code: "TZA", gaul1_name: "Kaskazini Pemba", gaul2_name: "Micheweni", geometry: *** type: "MultiPolygon", coordina
WARN
Failed to create 2dsphere index: Index build failed: aa7bc972-925c-4538-9425-58ff71ef1575: Collection portal.wio_gaul1 ( 2ecfa951-6ae6-4f78-ac90-0f457e2caa4b ) :: caused by :: collection scan stopped. totalRecords: 5; durationMillis: 158ms; phase: collection scan; collectionScanPosition: RecordId(5); readSource: kMajorityCommitted :: caused by :: Can't extract geo keys: *** _id: ObjectId('6ac27a7db3a34f7553098ee7'), iso3_code: "TZA", gaul1_name: "Tanga", geometry: *** type: "MultiPolygon", coordinates: [ [ [ [ 39.0352, -5.3714 ], [ 39
WARN
77 trip(s) revised by PDS are too long to predict; their files stay as they are and will be queued again next run
WARN
Skipping 198 trip(s) spanning > 5 days (IDs: 10579226, 10667906, 10797328, 11764837, 11781714, 11781722, 11781728, 11781947, 11785296, 11798762, 11798812, 11800140, 11801183, 11801206, 11819908, 11824638, 12047334, 13538978, 13889043, 13897835, 14020005, 14026248, 14133813, 14159300, 14248868, 14248869, 14251332, 14256294, 14300374, 14410128, 14410129, 14410132, 14410141, 14410142, 14410143, 14410145, 14410146, 14410147, 14410148, 14410154, 14410157, 14410160, 14410169, 14410170, 14419581, 14426872, 14435867, 14437813, 14452384, 14454042, 14455928, 14478602, 14478852, 14479232, 14484759, 14484948, 14486032, 14490643, 14499230, 14499292, 14505638, 14517256, 14517421, 14530361, 14541455, 14576754, 14578065, 14578438, 14578791, 14596027, 14640775, 14641243, 14657319, 14671211, 14672093, 14692374, 14754754, 14773203, 14847024, 14880620, 14907966, 14917078, 14927555, 14951120, 14951492, 14951780, 14952607, 14954865, 14965855, 14969765, 14980949, 14981319, 15005613, 15005747, 15006983, 15019233, 15038361, 15040373, 15040491, 15040651, 15040664, 15048463, 15050619, 15051707, 15055352, 15056600, 15059190, 15069591, 15074704, 15083360, 15086066, 15110498, 15111803, 15116206, 15118268, 15118393, 15131805, 15143641, 15156437, 15157630, 15211281, 15216883, 15216902, 15220930, 15225522, 15247602, 15256975, 15257586, 15262108, 15265117, 15271764, 15282083, 15287034, 15287035, 15287036, 15287037, 15287041, 15297669, 15311711, 15318293, 15319384, 15320346, 15334836, 15342909, 15345308, 15351019, 15351064, 15351150, 15352515, 15359797, 15360417, 15362089, 15382632, 15408671, 15421878, 15445740, 15448144, 2335178, 2359445, 2361328, 2365619, 2373334, 2404095, 2412993, 2437365, 2445535, 2446863, 2713356, 2721594, 2809967, 2814249, 2815140, 3088569, 3251255, 3295739, 3453864, 4474333, 4781534, 4781603, 4782486, 4782831, 4782896, 4814203, 4997708, 5152619, 5168468, 5851840, 7355604, 7520544, 8636700, 8655459, 8657128, 8663566, 8915080, 9342968, 9556078, 9697060, 9776875)
WARN
4 trips failed to fetch or were empty
Build R container
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Using bucket: peskas-api-prod
INFO
Retrieving wf-surveys-merged__20261002171551_e507498__.parquet
INFO
Using bucket: zanzibar-prod
INFO
Retrieving wf-adnap-surveys-merged__20261003040556_7027eef__.parquet
INFO
Using bucket: mozambique-prod
INFO
Retrieving kenya-surveys-matched-trips__20261004152157_9f57c51__.parquet
INFO
Using bucket: kenya-prod
INFO
Downloading merged trip data from regional buckets...
INFO
Using configutation: production
INFO
Loading configuration file...
Match GPS and survey data
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Using configutation: production
INFO
Loading configuration file...
Ingest static assets
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Uploading taxa-fishbase-enriched__20261004154253_81ee894__.parquet to cloud storage
INFO
Uploading enriched taxa data (5356 rows, 3931 species, FishBase / SeaLifeBase latest) to cloud storage
INFO
Joining and deduplicating biological data
INFO
Fetching biological data from FishBase / SeaLifeBase
INFO
Filtering to FAO area(s) 51, 57
INFO
Expanding 949 taxa against FishBase / SeaLifeBase latest
INFO
Downloading taxa metadata from cloud storage
INFO
Using configutation: production
INFO
Loading configuration file...
Enrich taxa with FishBase data
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Uploading pds-trips__20261004154336_81ee894__.parquet to cloud storage
INFO
Kept 124980 of 139129 trips from devices currently under: WorldFish - Mozambique, Totalenergies Mozambique TEPMA1 (formerly Syberintel), Kenya, Kenya AABS, WorldFish - Kenya, WorldFish - Tanzania AP, WorldFish - Zanzibar, MAF / WorldFish
INFO
Using configutation: production
INFO
Loading configuration file...
Ingest GPS trips
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Processing complete. Successfully processed 2 tracks.
INFO
Processing 2 new tracks in parallel...
INFO
Setting up parallel processing with 3 workers...
INFO
Checking existing tracks in cloud storage...
INFO
Reading trip IDs...
INFO
Downloading pds-trips__20261004154336_81ee894__.parquet
INFO
Getting trips file from cloud storage...
INFO
Using configutation: production
INFO
Loading configuration file...
Ingest GPS tracks
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Uploading grid summaries...
SUCCESS
Track preprocessing complete
INFO
Uploading preprocessed tracks...
INFO
Processing 9383 tracks in parallel...
INFO
Setting up parallel processing with 3 workers...
INFO
Listing raw tracks...
INFO
Checking existing preprocessed tracks...
INFO
Using configutation: production
INFO
Loading configuration file...
Preprocess GPS tracks data
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Pushing performance_metrics MongoDB...
INFO
Pushing fisher statistics to MongoDB...
INFO
Merging datasets datasets...
INFO
Using configutation: production
INFO
Loading configuration file...
Export fishers stats
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Uploading metrics_gaul1 data to MongoDB
INFO
Pushing regional time series metrics to MongoDB...
INFO
Index may need to be created manually via MongoDB shell
INFO
Uploading wio_gaul2 data to MongoDB
INFO
Index may need to be created manually via MongoDB shell
INFO
Uploading wio_gaul1 data to MongoDB
INFO
Pushing combined geospatial data to MongoDB...
INFO
Loading geospatial data from cloud storage...
INFO
Using configutation: production
INFO
Loading configuration file...
Export WIO data
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Downloading 116 predicted track files with 3 workers...
INFO
116 new files to aggregate (skipping 124739 already done)
INFO
120 aggregated file(s) deleted or replaced upstream: withdrawing 93 trip(s) from the effort store
INFO
Loaded per-trip effort store: 639092 rows, 103101 trips
INFO
Listing predicted track files...
INFO
Retrieving pds-trips__20261004154336_81ee894__.parquet
INFO
Building trip -> gear/country lookup...
INFO
Model version: 0.1.0
INFO
Using configutation: production
INFO
Loading configuration file...
INFO
Skipping 124662 trips at v0.1.0, 318 to process (191 of them refreshed after a PDS revision)
INFO
Re-predicting 191 trips revised by PDS since they were fetched
INFO
Deleting 6 file(s): their trip is no longer listed by PDS
INFO
Total trips to consider: 124980
INFO
Fetching trips from PDS API (from 2018-01-01)...
INFO
Loading device registry...
INFO
Model version: 0.1.0
INFO
Using Python: /opt/ssfaitk/bin/python3
INFO
Using configutation: production
INFO
Loading configuration file...
Predict fishing tracks and aggregate to H3 grid
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Trip effort: 2424 rows | 488 trips | 1452 H3 cells
INFO
Downloaded 100,977 fishing points across 488 trips
INFO
Downloading 552 matched track files (out of 124855 total predicted)
INFO
Downloading matched predicted tracks for CPUE model ...
INFO
Matched trips: 969 catch records | 552 unique PDS trips | 3 countries | 2025-03-03 -> 2026-09-26
INFO
Retrieving trips-matched__20261004154022_81ee894__.parquet
INFO
Downloading trips-matched (all countries) ...
INFO
=== CPUE pipeline | H3 res = 9 | method = weighted ===
INFO
Using configutation: production
INFO
Loading configuration file...
Run spatial CPUE model
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"
INFO
Uploaded: timor_leste_effort_gear_h3res9__20261004163357_81ee894__.zip
INFO
Uploaded: mozambique_effort_gear_h3res9__20261004163351_81ee894__.zip
INFO
Uploaded: tanzania_effort_gear_h3res9__20261004163348_81ee894__.zip
INFO
Uploaded: zanzibar_effort_gear_h3res9__20261004163346_81ee894__.zip
INFO
Uploaded: kenya_effort_gear_h3res9__20261004163342_81ee894__.zip
INFO
Exporting gear shapefiles for: Kenya, Zanzibar, Tanzania, Mozambique, Timor-Leste
INFO
Retrieving predicted-pds-h3_grid_r9__20261004162432_81ee894__.parquet
INFO
Loading effort grid (predicted-pds-h3_grid_r9) ...
INFO
Using configutation: production
INFO
Loading configuration file...
INFO
Uploaded: pds-h3-effort-gear-r9__20261004163204_81ee894__.json
INFO
Uploaded: pds-h3-effort-r9__20261004163200_81ee894__.json
INFO
Study period inferred: 2018-02-07 to 2026-10-03 (3161 days)
INFO
Collapsing effort grid over gear/country ...
INFO
Effort grid: 111402 rows | 60165 cells
INFO
Retrieving predicted-pds-h3_grid_r9__20261004162432_81ee894__.parquet
INFO
Loading effort grid (predicted-pds-h3_grid_r9) ...
INFO
=== Web spatial export | H3 res = 9 ===
INFO
Using configutation: production
INFO
Loading configuration file...
Export spatial outputs as JSON/GeoJSON for web
"The ubuntu-latest label will migrate to Ubuntu 26 beginning October 19, 2026. For more information, see https://github.com/actions/runner-images/issues/14748"

Artifacts

Produced during runtime
Name Size Digest
WorldFishCenter~peskas.coasts~ZM97TB.dockerbuild
84.6 KB
sha256:e40dab25e86c7e2fda2199efc9f4301f8dada3b84fbaa43132712af5d6ed8602