v26.1

What's Changed

Major changes in this release are:

• Upgrade to Python 3.14
• Migrate to Pixi for dependencies and environments management
• Disable Baynes Sound AGRIF runs

Security

• Add envvar for debug log token to skookum deployment docs by @douglatornell in #374

Features

• Remove VHFR FVCOM model runs from automation and repository by @douglatornell in #347
• Handle missing "WWATCH3 run" item in the checklist by @douglatornell in #349
• Refactor make_runoff_file workers by @douglatornell in #351
• Refactor make_201702_runoff_file checklist by @douglatornell in #352
• Add backfill support to download_weather worker by @douglatornell in #359
• Improve wave plots by @douglatornell in #370
• Disable forcing links for orcinus-nowcast-agrif by @douglatornell in #420
• Delete ECCC GRIB files after crop_gribs processing by @douglatornell in #421
• Remove outdated make_201702_runoff_file worker and references by @douglatornell in #445
• Change to use Pixi for package & environment management by @douglatornell in #477

Bug Fixes

• Handle 400 HTTP error in get_onc_ferry worker by @douglatornell in #348
• Fix run_date scope in after_update_forecast_datasets() by @douglatornell in #353
• Update collect_river_data checklist structure re: issue #170 by @douglatornell in #354
• Handle missing "WWATCH3 run" item in the checklist by @douglatornell in #355
• Fix wave height and period obs processing by @douglatornell in #360
• Correct make_plots wwatch3 run type selection logic by @douglatornell in #364
• Fix test_run_NEMO_hindcast tests by @douglatornell in #365
• Fix bugs in GHA pytest workflow by @douglatornell in #396
• Fix flaky tests in test_run_NEMO_hindcast by @douglatornell in #397
• Use np.trapezoid instead of np.trapz by @douglatornell in #410
• Set "water depth units" col dtype in turbidity CSV by @douglatornell in #449
• Handle missing TheodosiaDiversion obs in make_runoff_file by @douglatornell in #456

Documentation

• Update ReadTheDocs badge URL & Arbutus Cloud links in docs by @douglatornell in #375
• Avoid sphinx-linkcheck GHA workflow timeouts by @douglatornell in #398
• Add sphinx-copybutton and improve code block formatting by @douglatornell in #476

Maintenance

• Refactor test fixtures to add type annotations by @douglatornell in #350
• Switch test logging from mock logger to caplog. by @douglatornell in #346
• Update ERDDAP weather dataset ID in config & tests by @douglatornell in #369
• Update LiveOcean file URL templates in config & tests by @douglatornell in #373
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #376
• Update Neah Bay ssh CSV file template by @douglatornell in #381
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #385
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #389
• Unpin xarray version thanks to cfgrib update by @douglatornell in #388
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #392
• Add erddapy package to all environment files by @douglatornell in #395
• Add unique suffix to downloads cache key by @douglatornell in #400
• Updates to work on new orcinus HPC cluster configuration by @douglatornell in #386
• Update host name from robot.graham to robot.nibi by @douglatornell in #403
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #405
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #416
• Update supervisor to >=4.3.0 in all env files by @douglatornell in #419
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #431
• Update test log assertions and dependencies by @douglatornell in #433
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #436
• Use regex for CSV delimiter in make_runoff_file by @douglatornell in #460
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #463
• Update nibi forcing file paths to use rrg-allen by @douglatornell in #467
• Improve GitHub Actions workflows based on zizmor static analysis by @douglatornell in #473

Dependency Updates

• Bump codecov/codecov-action from 5.4.0 to 5.4.2 by @dependabot[bot] in #356
• Bump h11 from 0.14.0 to 0.16.0 in /envs by @dependabot[bot] in #358
• Bump codecov/codecov-action from 5.4.2 to 5.4.3 by @dependabot[bot] in #361
• Bump setuptools from 70.0.0 to 78.1.1 in /envs by @dependabot[bot] in #362
• Bump tornado from 6.4.2 to 6.5.1 in /envs by @dependabot[bot] in #363
• Bump mamba-org/setup-micromamba from 2.0.4 to 2.0.5 by @dependabot[bot] in #367
• Bump requests from 2.32.3 to 2.32.4 in /envs by @dependabot[bot] in #368
• Bump urllib3 from 2.3.0 to 2.5.0 in /envs by @dependabot[bot] in #371
• Bump pillow from 11.2.1 to 11.3.0 in /envs by @dependabot[bot] in #372
• Bump pypdf from 5.6.0 to 6.0.0 in /envs by @dependabot[bot] in #377
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #378
• Bump codecov/codecov-action from 5.4.3 to 5.5.0 by @dependabot[bot] in #379
• Bump h2 from 4.2.0 to 4.3.0 in /envs by @dependabot[bot] in #380
• Bump mamba-org/setup-micromamba from 2.0.5 to 2.0.6 by @dependabot[bot] in #382
• Bump codecov/codecov-action from 5.5.0 to 5.5.1 by @dependabot[bot] in #383
• Bump mamba-org/setup-micromamba from 2.0.6 to 2.0.7 by @dependabot[bot] in #384
• Bump pip from 23.3 to 25.2 in /envs by @dependabot[bot] in #387
• Bump pypdf from 6.1.1 to 6.1.3 in /envs by @dependabot[bot] in #391
• Bump brotli from 1.1.0 to 1.2.0 in /envs by @dependabot[bot] in #393
• Bump pip from 25.2 to 25.3 in /envs by @dependabot[bot] in #394
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in #399
• Bump pypdf from 6.2.0 to 6.4.0 in /envs by @dependabot[bot] in #401
• Bump fonttools from 4.60.1 to 4.61.0 in /envs by @dependabot[bot] in #402
• Bump urllib3 from 2.5.0 to 2.6.0 in /envs by @dependabot[bot] in #404
• Bump codecov/codecov-action from 5.5.1 to 5.5.2 by @dependabot[bot] in #406
• Bump filelock from 3.20.0 to 3.20.1 in /envs by @dependabot[bot] in #407
• Bump bokeh from 3.8.1 to 3.8.2 in /envs by @dependabot[bot] in #408
• Bump pynacl from 1.5.0 to 1.6.2 in /envs by @dependabot[bot] in #409
• Bump urllib3 from 2.6.0 to 2.6.3 in /envs by @dependabot[bot] in #411
• Bump pypdf from 6.4.0 to 6.6.0 in /envs by @dependabot[bot] in #412
• Bump virtualenv from 20.35.4 to 20.36.1 in /envs by @dependabot[bot] in #413
• Bump filelock from 3.20.1 to 3.20.3 in /envs by @dependabot[bot] in #414
• Bump distributed from 2025.11.0 to 2026.1.1 in /envs by @dependabot[bot] in #415
• Bump wheel from 0.38.4 to 0.46.2 in /envs by @dependabot[bot] in #417
• Bump pypdf from 6.6.0 to 6.6.2 in /envs by @dependabot[bot] in #418
• Bump pip from 25.3 to 26.0 in /envs by @dependabot[bot] in #422
• Bump cryptography from 44.0.1 to 46.0.5 in /envs by @dependabot[bot] in #424
• Bump pillow from 12.0.0 to 12.1.1 in /envs by @dependabot[bot] in #425
• Bump pypdf from 6.6.2 to 6.7.1 in /envs by @dependabot[bot] in #426
• Bump pypdf from 6.7.1 to 6.7.2 in /envs by @dependabot[bot] in #427
• Bump pypdf from 6.7.2 to 6.7.4 in /envs by @dependabot[bot] in #429
• Bump pypdf from 6.7.4 to 6.7.5 in /envs by @dependabot[bot] in #430
• Bump pypdf from 6.7.5 to 6.8.0 in /envs by @dependabot[bot] in #432
• Bump tornado from 6.5.4 to 6.5.5 in /envs by @dependabot[bot] in #434
• Bump black from 26.3.0 to 26.3.1 in /envs by @dependabot[bot] in #435
• Bump pypdf from 6.8.0 to 6.9.1 in /envs by @dependabot[bot] in #437
• Bump codecov/codecov-action from 5.5.2 to 5.5.3 by @dependabot[bot] in #438
• Bump pypdf from 6.9.1 to 6.9.2 in /envs by @dependabot[bot] in #439
• Bump requests from 2.32.5 to 2.33.0 in /envs by @dependabot[bot] in #440
• Bump cryptography from 46.0.5 to 46.0.6 in /envs by @dependabot[bot] in #441
• Bump codecov/codecov-action from 5.5.3 to 6.0.0 by @dependabot[bot] in #442
• Bump mamba-org/setup-micromamba from 2.0.7 to 3.0.0 by @dependabot[bot] in #443
• Bump pygments from 2.19.2 to 2.20.0 in /envs by @dependabot[bot] in #444
• Bump cryptography from 46.0.5 to 46.0.6 in /envs by @dependabot[bot] in #446
• Bump cryptography from 46.0.6 to 46.0.7 in /envs by @dependabot[bot] in #447
• Bump pypdf from 6.9.2 to 6.10.0 in /envs by @dependabot[bot] in #448
• Bump pytest from 9.0.2 to 9.0.3 in /envs by @dependabot[bot] in #450
• Bump pypdf from 6.10.0 to 6.10.2 in /envs by @dependabot[bot] in #452
• Bump mako from 1.3.10 to 1.3.11 in /envs by @dependabot[bot] in #453
• Bump lxml from 6.0.2 to 6.1.0 in /envs by @dependabot[bot] in #454
• Bump gitpython from 3.1.46 to 3.1.47 in /envs by @dependabot[bot] in #455
• Bump pip from 26.0 to 26.1 in /envs by @dependabot[bot] in #457
• Bump gitpython from 3.1.47 to 3.1.49 in /envs by @dependabot[bot] in #458
• Bump mako from 1.3.11 to 1.3.12 in /envs by @dependabot[bot] in #459
• Bump gitpython from 3.1.49 to 3.1.50 in /envs by @dependabot[bot] in #461
• Bump urllib3 from 2.6.3 to 2.7.0 in /envs by @dependabot[bot] in #462
• Bump idna from 3.11 to 3.15 in /envs by @dependabot[bot] in #464
• Bump codecov/codecov-action from 6.0.0 to 6.0.1 by @dependabot[bot] in #465
• Bump codecov/codecov-action from 6.0.1 to 7.0.0 by @dependabot[bot] in #466
• Bump tornado from 6.5.5 to 6.5.6 in /envs by @dependabot[bot] in #469
• Bump pypdf from 6.10.2 to 6.12.0 in /envs by @dependabot[bot] in #468
• Bump tornado from 6.5.6 to 6.5.7 in /envs by @dependabot[bot] in #470
• Bump pypdf from 6.12.0 to 6.13.3 in /envs by @dependabot[bot] in #471
• Bump cryptography from 46.0.7 to 48.0.1 in /envs by @dependabot[bot] in #472
• Bump msgpack from 1.1.2 to 1.2.1 in /envs by @dependabot[bot] in #474
• Bump actions/checkout from 6 to 7 by @dependabot[bot] in #475
• Bump pillow from 12.2.0 to 12.3.0 by @dependabot[bot] in #483
• Bump gitpython from 3.1.50 to 3.1.54 by @dependabot[bot] in #484
• Bump setuptools from 82.0.1 to 83.0.0 by @dependabot[bot] in #485

Full Changelog: v25.1...v26.1