v1.2.0

What's Changed

• Update to v1.2.0-alpha.1 by @xylar in #420
• Fix symlinks to latest compass load scripts by @xylar in #421
• Give log path for failed tests only in suite by @xylar in #423
• Fix namelist errors in internal_wave by @altheaden in #424
• Update E3SM-Project submodule to current master by @xylar in #426
• Add monthly output test and update daily output test to match by @xylar in #411
• Fix prefix for compass env script in tutorials by @xylar in #427
• Add function for logging function calls by @xylar in #425
• Add jigsaw spherical mesh steps by @xylar in #422
• Switch Step attributes from cores to ntasks and cpus_per_task by @xylar in #413
• Move run operations from testcase to run/serial by @altheaden in #428
• Switch global_ocean and hurricane to framework base and culled mesh by @xylar in #429
• Add comparison to default baroclinic channel by @mark-petersen in #431
• Remove dThreshMLD validation from mixedLayerDepth AM by @xylar in #433
• Port legacy dam break test case by @cbegeman in #417
• New Mesh: Add ARRM10to60E2r1 mesh by @xylar in #414
• Remove --exclusive flag from slurm steps by @xylar in #436
• Add a step for making mapping files for e3sm_to_cmip by @xylar in #437
• Copy MPAS model executable to work directory by @xylar in #360
• Add scripts for using git bisect by @xylar in #354
• Drop compass_ prefix from job script names by @xylar in #438
• Fix job script name in matrix utility by @xylar in #439
• Switch from 2- to 4-digit year in global ocean by @xylar in #443
• spelling typo by @cwsmith in #445
• Add wetdry suite by @sbrus89 in #441
• Add more projection grids to diagnostics_files by @xylar in #447
• Add a sigma vertical coordinate to ocean framework by @xylar in #442
• Add python 3.11 and drop python <3.8 by @xylar in #450
• Switch to mambaforge and add mamba init by @xylar in #453
• Remove all references to badger by @xylar in #455
• Add support for perlmutter CPU nodes by @xylar in #446
• Add thin film cases to ISOMIP+ Ocean0 by @cbegeman in #449
• Add error message for namelist replacements by @cbegeman in #457
• Update ocean test case namelists by @cbegeman in #459
• Port merry-go-round test group from legacy by @cbegeman in #452
• Add ismip6 forcing testgroup by @hollyhan in #410
• Add a utility for testing updates to E3SM submodule by @xylar in #466
• Add a recipe for OSU tidal prediction software by @xylar in #464
• Switch Chrysalis Intel to use OpenMPI by default by @xylar in #468
• Clean up ISOMIP+ by @xylar in #467
• Update to 1.2.0-alpha.3 with mache 1.9.0 by @xylar in #473
• Add a template for PRs with a checklist by @xylar in #472
• Add SO12to60E2r5 (without ice-shelf cavities) by @xylar in #460
• Fix typo in hurrincane init plotting by @sbrus89 in #475
• Constrain shapely by @xylar in #476
• Update hdf5 in pnetcdf and scorpio packages to match conda-forge by @xylar in #477
• Update E3SM-Project submodule by @xylar in #461
• Bugfix for dam break tests by @cbegeman in #451
• Add tides test case by @sbrus89 in #456
• Fix provenance when E3SM submodule not needed by @xylar in #478
• Add database_component parameter for input files by @xylar in #479
• Update E3SM-Project submodule by @xylar in #480
• Remove critical passages stream for tides init by @sbrus89 in #484
• Override constrain_resources() in individual steps by @xylar in #481
• Rename master --> main by @xylar in #485
• Remove xtime variable from ocean climatology by @hollyhan in #486
• Add an option to process 4-km resolution forcing files by @hollyhan in #465
• Disable otps on OSX by @xylar in #487
• Reorganize ISOMIP+ steps by @xylar in #469
• Update shapely, geometric_features and mpas_tools by @xylar in #490
• Fix landIceFraction in ISOMIP+ by @xylar in #470
• Fix docs for matrix utility by @xylar in #491
• Replace deprecated importlib.resources.path() call by @xylar in #493
• Update MALI-Dev submodule by @matthewhoffman in #492
• Fix base env update in Azure tests by @xylar in #504
• Update to compass v1.2.0-alpha.4 and mache v1.10.0 by @xylar in #496
• Fix ISOMIP+ docs by @xylar in #505
• Fix handling of ntasks = 1 for single node by @xylar in #508
• Update conda pnetcdf and scorpio versions by @xylar in #509
• Fix deployment using python 2 by @xylar in #511
• Add chicoma-cpu support by @xylar in #494
• Fix code for not adding mamba to .bashrc by @xylar in #514
• Add pep8 guidance to docs by @cbegeman in #518
• Use Wedge elements for all MALI tests by @mperego in #510
• Add nonhydrostatic test group by @scalandr in #374
• Fix nonhydro documentation by @xylar in #526
• Port overflow test group by @cbegeman in #501
• Cleanup ocean RPE tests by @cbegeman in #516
• Elaborate note on not mixing envs for different branches by @matthewhoffman in #529
• Find netcdf and pnetcdf with env vars on Chicoma and PM by @xylar in #531
• Add GitHub Actions and remove Azure Pipelines by @xylar in #534
• Increase timeout for docs GitHub Action by @xylar in #535
• Fix docs version in GitHub Actions by @xylar in #536
• Remove Azure badge by @xylar in #537
• Add sea-ice graph partitioning to files_for_e3sm test case by @xylar in #489
• Port cosine bell initial state by @cbegeman in #519
• Remove init mode namelist, stream from cosine bell case by @cbegeman in #540
• Add Kuroshio8to60E2r4 and Kuroshio12to60E2r4 meshes by @ytakano3 in #525
• Update albany_input.yaml with new basal pressure setting by @trhille in #542
• Add config_flowParamA_calculation = 'PB1982' to namelists by @trhille in #543
• Add bed topo to cell spacing by @trhille in #448
• Add Thwaites UQ study framework by @matthewhoffman in #488
• Fix deployment with latest conda (23.1.0) by @xylar in #545
• Allow test cases to run on login nodes by @xylar in #538
• Enable easier mache testing by @xylar in #523
• Add instructions for deploying spack by @xylar in #527
• Fix isomip_plus streamfunction computation by @xylar in #548
• Add support for spherical meshes in ISOMIP+ by @xylar in #471
• Add --verbose flag to deployment script by @xylar in #553
• Fix print for petsc in verbose mode by @xylar in #554
• Fix ISOMIP+ test names in suites by @xylar in #556
• Update docs for e3sm_update utility by @xylar in #557
• Update E3SM-Project submodule by @xylar in #558
• Make mapping file for sea-ice partitioning in compass by @xylar in #559
• Add metadata in files_for_e3sm for existing meshes by @xylar in #560
• Use verbose 20xx creation date for e3sm_to_cmip maps by @xylar in #561
• Update algorithm for core counts for MPAS partition files by @xylar in #563
• Fix compass cache by @xylar in #572
• Add missing land-ice mask file to cull mesh output by @xylar in #577
• Add files_for_e3sm steps for ocean and sea-ice meshes by @xylar in #570
• Simplify adding test cases to global_ocean by @xylar in #578
• Add WCwISC14 and ARRMwISC12to60 meshes by @xylar in #575
• Remove Ifpack and ML preconditioners from landice test inputs by @mcarlson801 in #583
• Remove extra newline by @xylar in #584
• Update E3SM-Project submodule by @xylar in #585
• Switch to 64 vertical levels for 3 meshes by @xylar in #581
• Add information on enabling hyperthreading to docs by @xylar in #579
• Change algorithm for constraining resources by @xylar in #573
• Update guidance on switching between branches by @matthewhoffman in #574
• Add bathymetry remapping by @xylar in #566
• Add region masks for MALI Antarctic mesh by @hollyhan in #406
• Update to v1.2.0-alpha.5 by @xylar in #555
• Don't allow version of scikit-image with bad dependencies by @xylar in #591
• Add ismip6 run testgroup by @hollyhan in #397
• Update cached EC mesh and init files by @xylar in #594
• Only cull topography for cull_mesh steps that have it by @xylar in #596
• Skip cached steps when computing suite resources by @xylar in #597
• Update geometric_features to v1.2.0 by @xylar in #592
• Reduce no. of processes for QU240 cull_mesh step by @xylar in #599
• Add VLR test to internal wave case by @cbegeman in #564
• Change np.bool to bool by @mark-petersen in #600
• Lint ice shelf tests by @xylar in #601
• Enable submeso. parameterization in global_ocean by @xylar in #533
• Add job script to steps by @xylar in #603
• New floating land ice variables by @cbegeman in #512
• Update E3SM-Project submodule by @xylar in #606
• Adjust #cells in baroclinic channel to define 160x500km domain by @dengwirda in #605
• Refactor land-ice mesh generation test cases by @trhille in #590
• Fix bug in changing permissions on downloaded files by @xylar in #609
• Bump all the meshes to E3SM v3, revision 1 by @xylar in #611
• Add a test case for extrapolating WOA 2023 data by @xylar in #604
• Fix wISC in mesh prefix by @xylar in #613
• Add WOA23 initial condition by @xylar in #610
• Generalize MALI ensemble framework by @matthewhoffman in #552
• Add land-ice floating variables to ocean_mesh step by @xylar in #617
• Fix substitution of levels at runtime in global_ocean by @xylar in #615
• Fixup namelists for single layer RK4 ocean tests by @cbegeman in #619
• Update explicit top drag coefficient namelist option by @cbegeman in #622
• Update global ocean init cache files by @xylar in #621
• Cleanup ocean bottom drag namelist options by @cbegeman in #551
• Update e3sm project by @xylar in #624
• Add double quotes to flag by @mark-petersen in #626
• Remove unused namelist option by @xylar in #633
• Explicitly specify nodes in srun calls by @xylar in #630
• Get global ocean resources and time steps based on mesh size by @xylar in #631
• Add general QU and Icos meshes by @xylar in #632
• Add more graph partition sizes by @xylar in #628
• Add a tutorial on creating RRM meshes by @xylar in #635
• Add ocean wetting-and-drying ramp tests by @cbegeman in #620
• Remove unused BGC configuration from global ocean by @xylar in #638
• Always remap topogrpahy, even for low res meshes by @xylar in #639
• Renormalize topography after remapping in global_ocean by @xylar in #640
• Update cached QU240 and QUwISC240 mesh and init files by @xylar in #642
• Bound graph partition sizes by @xylar in #643
• For smaller meshes, create partitions for a single task by @xylar in #644
• Add partition files for 52-core nodes by @xylar in #645
• Add lock exchange test group by @scalandr in #637
• Update E3SM-Project submodule by @xylar in #648
• Add a global ocean test case for computing and running with data (prescribed) melt rates by @xylar in #580
• Update E3SM-Project submodule by @xylar in #649
• Update E3SM-Project submodule by @xylar in #651
• Fix use of depricated np.float in hurricane analysis step by @sbrus89 in #653
• Increase the max Haney number to 20 by @xylar in #655
• Added hurricane test case with local time-stepping by @gcapodag in #618
• Switch to python masking for culling landice meshes by @xylar in #658
• Some cleanup related to spherical meshes by @xylar in #659
• Update to 1.2.0-alpha.6 by @xylar in #641
• Update tolerance on circ shelf decomp test by @matthewhoffman in #660
• Don't run remap_ice_shelf_melt without ice-shelf cavities by @xylar in #661
• Update to MPAS-Tools v0.22.0 by @xylar in #662
• Sort mesh indices before saving culled global ocean meshes by @xylar in #657
• Clean up global ocean test group for large meshes by @xylar in #663
• Update conda packages for unsupported machines by @xylar in #665
• Add RRS6to18 and RRSwISC6to18 meshes by @xylar in #576
• LandIce: Added tests using the FO depth integrated model by @mperego in #634
• Minor changes to lts forward nmlist and streams by @gcapodag in #673
• Fix nEdges float --> int in graph files by @xylar in #674
• Update to mpas_tools 0.23.0 by @xylar in #675
• Add test cases for subglacial hydrology using Humboldt mesh by @matthewhoffman in #440
• Add a step for remapping sea surface salinity restoring by @xylar in #676
• Two fixes to data ice shelf melt fluxes by @xylar in #678
• Add nonhydro overflow by @scalandr in #647
• Break up data_ice_shelf_melt test by @xylar in #679
• Add a test for log-law ocean bottom drag by @cbegeman in #646
• Add missing data ice-shelf melt cache files by @xylar in #681
• Add a step for remapping iceberg climatologies by @xylar in #677
• Remove data_ice_shelf_melt tests from suites by @xylar in #683
• Simplify global ocean dynamic adjustment test cases by @xylar in #682
• Update tests to support start year of 0001 by @matthewhoffman in #684
• Update to geometric_features 1.3.0 by @xylar in #687
• Update to GEBCO 2023 topography by @xylar in #688
• Update E3SM-Project submodule by @xylar in #692
• Add parabolic bowl test case by @sbrus89 in #670
• Add additional ice_shelf_2d test cases by @cbegeman in #685
• Allow culled mesh to be converted to CDF-5 format by @xylar in #697
• New Mesh: ECwISC30to60E3r2 by @xylar in #689
• New Mesh: IcoswISC30E3r2 by @xylar in #691
• New Mesh: SOwISC12to60E3r1 by @xylar in #669
• Add a few isomip_plus configurations for wetting and drying by @cbegeman in #696
• Update to pyremap 1.1.0 by @xylar in #698
• Use pyremap 1.0.1 by @xylar in #702
• Fix ISOMIP+ plotting by @xylar in #705
• Fix dynamic adjustment time parsing for OSX by @xylar in #709
• Update E3SM-Project submodule by @xylar in #708
• Update variables checked in DISMF performance test by @xylar in #694
• Update to pyremap v1.1.0 (again) by @xylar in #713
• Temporary fix to reinstall mamba=1.5.1 by @xylar in #714
• Update to mpas_tools 0.26.0 by @xylar in #718
• Add decomp test case to the drying slope test group by @cbegeman in #695
• Fix conversion to absolute paths in config files by @xylar in #719
• Remove temporary fix for mamba 1.5.1 by @xylar in #720
• Fix variable name in iceberg climatologies by @xylar in #721
• Add step for reconstruction coeffs by @xylar in #717
• Add drying_slope convergence tests by @cbegeman in #703
• add the variable 'zbnds' for ocean depth by @hollyhan in #541
• Increase remap tasks by @xylar in #727
• Fixed issue with convert_culled_mesh_to_cdf5 for hurricane test case by @gcapodag in #726
• Fix landice/antarctica/mesh_gen by @trhille in #730
• Update conda parallelio to 2.6.2 by @xylar in #731
• Fix a bug in how landIceMask is computed by @xylar in #732
• Add a version check to load script by @xylar in #739
• Replace init mode in drying slope test cases by @cbegeman in #716
• Update to 1.2.0-alpha.7 by @xylar in #704
• Update to mpas_tools 0.29.0 by @xylar in #742
• Use only compass release version is spack env name by @xylar in #743
• Update E3SM-Project submodule by @xylar in #744
• New Mesh: IcoswISC30E3r5 by @xylar in #735
• Remove mamba commands and switch to Miniforge by @xylar in #751
• Update namelist options for recent changes to Redi and Adams-Bashforth 2 by @xylar in #745
• Add info about viewing compiled docs via www at NERSC by @matthewhoffman in #740
• Add jigsaw-python as a submodule by @xylar in #755
• Several fixes to deployment by @xylar in #757
• Add optional support for alphaBetaLab package by @xylar in #758
• Fix jigsaw build by @xylar in #760
• Add dependabot for github actions by @xylar in #761
• Bump actions/setup-python from 3 to 5 by @dependabot in #762
• Bump actions/cache from 3 to 4 by @dependabot in #764
• Bump actions/checkout from 3 to 4 by @dependabot in #763
• Add LTS option to dam_break and parabolic_bowl test cases by @gcapodag in #738
• Update file names on LCRC server by @trhille in #767
• Fix land-locked cells at calving fronts by @xylar in #752
• Add Crane Glacier mesh generation by @trhille in #756
• Add isunnguata sermia mesh generation test case by @trhille in #602
• Bump pre-commit/action from 3.0.0 to 3.0.1 by @dependabot in #773
• Make sure ny is even in ISOMIP+ test cases by @xylar in #772
• Add FRIS meshes by @irenavankova in #774
• Fix incorrect creation dates for e3sm_to_cmip maps by @xylar in #776
• Update e3sm_to_cmip_maps step to create E3SMv3 maps by @xylar in #779
• Add files_for_e3sm step for remapping rms tidal velocity by @xylar in #770
• Allow decimal time steps in isomip_plus by @xylar in #775
• Reroute missing fluxes in data ice-shelf melt fluxes (DISMF) by @xylar in #777
• Switch DISMF to Paolo et al. (2023) dataset by @xylar in #778
• Fix the sign of the heat flux for DISMF by @xylar in #781
• Fix typo culeed --> culled by @xylar in #784
• Port the MISMIP+ spinup testcase from the old version of compass by @andrewdnolan in #737
• Create test for extracting a MALI subdomain from a larger domain by @matthewhoffman in #562
• Create ensemble of branch runs for projections by @matthewhoffman in #616
• Updated data interpolation for Antarctica mesh generation case by @matthewhoffman in #750
• Add edge masks to default arguments of make_region_masks landice framework function by @andrewdnolan in #786
• Fixes to landlocked cells when culling global meshes by @xylar in #790
• Switch pr and nightly suites to use Icos meshes by @xylar in #791
• Fix DISMF dataset name in global ocean forward runs by @xylar in #789
• Update E3SM-Project submodule by @xylar in #795
• Only make tidal mixing files for meshes with cavities by @xylar in #798
• Update MALI-Dev submodule to latest develop by @xylar in #796

New Contributors

• @cwsmith made their first contribution in #445
• @mperego made their first contribution in #510
• @ytakano3 made their first contribution in #525
• @mcarlson801 made their first contribution in #583
• @dengwirda made their first contribution in #605
• @gcapodag made their first contribution in #618
• @dependabot made their first contribution in #762
• @irenavankova made their first contribution in #774

Full Changelog: 1.1.0...1.2.0