v0.4.0

What's Changed

• Update to 0.4.0-alpha.1 by @xylar in #204
• Fix the bisect utility by @xylar in #206
• Remove unused bashrc functions by @altheaden in #208
• Cleanup configure_polaris_envs.py and deploy/shared.py by @altheaden in #209
• Standardize styling for all references to Omega by @altheaden in #210
• Add nvidia to chicoma-cpu by @xylar in #211
• Add link to Omega CTest in Quick Start by @altheaden in #212
• Fix deployment on unknown machines by @xylar in #214
• Fix docs typos and add link to mache docs by @altheaden in #215
• Change references from compass to polaris by @altheaden in #218
• Remove polaris clean from check polaris commands by @altheaden in #217
• Fix how yaml model config options are update by @xylar in #219
• Bootstrap cleanup by @altheaden in #216
• Add docstrings to deploy package by @altheaden in #220
• Add support for python 3.12 by @altheaden in #222
• Tweak behavior of CI workflows by @altheaden in #223
• Add Althea as additional dependabot reviewer by @altheaden in #224
• Better support for Omega in Polaris by @xylar in #221
• Add additional flags to pip install command in docs and deployment by @altheaden in #226
• Update E3SM-Project submodule by @xylar in #228
• Set default model for mpas_to_yaml to mpas-ocean by @xylar in #227
• Fixup partition file presence by @cbegeman in #225
• Update pre-commit dependencies by @xylar in #230
• Enhance spherical tracer transport test viz by @cbegeman in #233
• Fixup graph paths for cached inputs by @cbegeman in #235
• Set default time_integrator for Omega by @xylar in #232
• Clean up the docs by @xylar in #238
• Add map between MPAS-Ocean and Omega variables by @xylar in #237
• Map time integrator for convergence tests by @cbegeman in #239
• Remove git from polaris environment by @xylar in #240
• Switch setup configuration to to pyproject.toml by @altheaden in #244
• Fix small typo in ctest path by @altheaden in #245

Full Changelog: 0.3.0...0.4.0

v0.3.0

What's Changed

• Split spack software and libs by @xylar in #165
• Add jigsaw-python as a submodule by @xylar in #166
• Add metis and parmetis to spack build by @xylar in #162
• Add MOAB to the spack build by @xylar in #176
• Update Perlmutter support by @xylar in #167
• Update scorpio to v1.4.2 by @xylar in #178
• Add Frontier as a supported machine by @xylar in #168
• Update Omega submodule by @xylar in #179
• Fix slurm handling of allocatable cores by @xylar in #181
• Fix cores_per_node for Frontier by @xylar in #180
• Remove gnu with mvapich on Anvil by @xylar in #182
• Fix libnetcdf in jigsaw build by @xylar in #184
• Fix cores_per_node calculation on Compy and Anvil by @xylar in #185
• Update to 0.3.0-alpha.1 by @xylar in #177
• Fix conda install before Jigsaw build by @xylar in #186
• Add utility for building Omega and running ctests by @xylar in #170
• Bump pre-commit/action from 3.0.0 to 3.0.1 by @dependabot in #189
• Switch the mesh used for Omega CTests by @xylar in #190
• Fix visualization of edge quantities with periodic boundaries by @cbegeman in #150
• Workaround for z-star minimum number of vertical levels by @cbegeman in #152
• Fix omega ctest mesh by @xylar in #194
• Update docs link to newer URL style by @altheaden in #195
• Add c_stdlib to jigsaw build deps by @xylar in #196
• Update to v0.3.0-alpha.2 by @xylar in #197
• Set permissions for Omega CTest downloads by @xylar in #199
• Cull ISOMIP+ planar base mesh by @xylar in #201
• Don't smooth ISOMIP+ topography on base mesh by @xylar in #202
• Add support for creating mapping files with mbtempest by @xylar in #203
• Port ice_shelf_2d test cases by @cbegeman in #158
• Add gpus-per-node to job scripts and resources by @xylar in #207

Full Changelog: 0.2.0...0.3.0

v0.2.0

What's Changed

• Update to v0.2.0 by @xylar in #103
• Add a polaris logo by @xylar in #107
• Modularization and cleanup by @altheaden in #106
• Fix dependencies in inertial gravity wave convergence test by @altheaden in #105
• Add timers to steps as they run in a suite or task by @xylar in #112
• Rename TestCase --> Task by @xylar in #110
• Remove test groups by @xylar in #111
• Reorganize validation by @xylar in #113
• Add support for shared steps by @xylar in #116
• Reorganize tasks to use shared steps by @xylar in #117
• New shared steps capability design doc by @cbegeman in #109
• Update to mpas_tools v0.23.0 by @xylar in #121
• Fix detecting step already added to task by @xylar in #122
• Clean up RPE analysis step and framework by @xylar in #123
• Updates for pyremap >= 1.1.0 by @xylar in #124
• Add shared ocean framework for spherical convergence tests by @xylar in #119
• Add support for shared config options by @xylar in #125
• Raise error only at task level on baseline failure by @xylar in #128
• Shared ocean spherical convergence analysis step by @cbegeman in #126
• Use MPAS-Tools for great circle distance in cosine bell tests by @cbegeman in #127
• Use common matplotlib style sheet in all ocean plots by @xylar in #129
• Clean up and add method to spherical convergence analysis by @xylar in #130
• Only print task baseline status if basline compared by @xylar in #133
• Enhance shared convergence steps by @cbegeman in #131
• Add geostrophic convergence test (Williamson Test 2) by @xylar in #120
• Fix conversion to absolute paths in config files by @xylar in #136
• Fix steps_to_run for shared config files by @xylar in #134
• Fixes to polaris suite and geostrophic docs by @xylar in #137
• Set config.filepath after loading new config options by @xylar in #138
• Port sphere transport test group for ocean components by @cbegeman in #104
• Use Separate geostrophic thresholds for h and norm. vel. by @xylar in #139
• Drop python 3.8 by @xylar in #142
• Switch spherical viz to use uxarray and holoviews by @xylar in #140
• Clean up plot_horiz_field() by @xylar in #143
• Allow multiple tasks to be set up with -t flag by @xylar in #135
• Fix path to cached polaris data on morpheus by @xylar in #145
• Port changes to grid_1d package from Compass by @xylar in #147
• Allow patches to be reused in plot_horiz_field() by @xylar in #146
• Fix typo in planar horiz viz by @xylar in #148
• Add functions for computing and plotting transects by @xylar in #144
• Fix issues with shared config files by @xylar in #157
• Add steps for ISOMIP+ base and culled meshes by @xylar in #141
• Remove mamba command and switch to Miniforge3 by @xylar in #161
• Port ocean internal wave test by @cbegeman in #153
• Add a version check to load script by @xylar in #156
• Removing tracers in variable list that have been turned off by default by @darincomeau in #160
• Use only Polaris release version is spack env name by @xylar in #164
• Update morpheus spack build by @xylar in #169
• Add dependabot for github actions by @xylar in #171
• Fix dependabot yaml indentation by @xylar in #172
• Bump actions/checkout from 3 to 4 by @dependabot in #173
• Bump actions/cache from 3 to 4 by @dependabot in #175
• Bump actions/setup-python from 3 to 5 by @dependabot in #174
• Update Omega submodule by @xylar in #163

Full Changelog: 0.1.0...0.2.0

v0.1.0

What's Changed

• Add pre-commit checks by @xylar in #1
• Add a .gitignore by @xylar in #2
• Add pull request template by @xylar in #3
• Add basic docs by @xylar in #4
• Build polaris and docs in github action by @xylar in #5
• Fix pushing docs to gh-pages by @xylar in #6
• Fix docs by @xylar in #7
• Add a configure script and support files by @xylar in #8
• Add config files for supported machines by @xylar in #9
• Add the compass license file by @xylar in #10
• Fix copying docs by @xylar in #11
• Fix small README typo by @jhkennedy in #12
• Add versions side bar by @xylar in #13
• Port most of the compass framework by @xylar in #14
• Add more documentation by @xylar in #15
• Add MPAS-Ocean, OMEGA and MALI submodules by @xylar in #16
• Add utilities from compass by @xylar in #17
• Remove namelist and streams from cosine bell init by @xylar in #19
• Add polaris cache command by @xylar in #18
• Add ModelStep class by @xylar in #20
• Add ocean docs to the User's Guide by @xylar in #21
• Fix deprecated calls to importlib.resources by @xylar in #22
• Add support for model config described by yaml files by @xylar in #23
• Add ocean model descriptions to docs by @cbegeman in #24
• General clean-up PR by @xylar in #26
• Ocean resources from config options by @xylar in #29
• Change how dynamic model configuration is update by @xylar in #28
• Port the baroclinic channel test group from compass by @xylar in #27
• Add test suite guidance to documentation by @cbegeman in #25
• Fix name of configure_polaris_envs.py in docs by @xylar in #31
• Update to polaris 0.1.0-alpha.3 by @xylar in #32
• Add planar horizontal viz by @cbegeman in #33
• Add job script to steps by @xylar in #36
• Reorganize the framework and organization in the developer's guide by @xylar in #38
• Add dependencies to Step class by @xylar in #39
• Add mapping file step by @xylar in #40
• Add global map plots by @xylar in #34
• Adjust ny for baroclinic channel to give 500 km domain by @xylar in #37
• Fix bug in changing permissions on downloaded files by @xylar in #42
• Various pieces of clean-up to the docs by @xylar in #44
• Use shorter imports for Component, TestGroup, etc. by @xylar in #43
• Fix error when building docs on main after merge by @xylar in #47
• Clean up cosine bell test by @xylar in #46
• Clean up baroclinic channel by @xylar in #45
• Add User's Guide template for test groups by @cbegeman in #41
• Port single column test group by @cbegeman in #49
• Add a tutorial for adding a new test group by @xylar in #48
• Find netcdf/pnetcdf with env vars on Chicoma and PM by @xylar in #50
• Fix single_column test in pr suite by @xylar in #51
• Fixup quick-start and tutorial by @cbegeman in #55
• Fixup tutorial by @cbegeman in #56
• Make subdirectories for symlinks for input files by @xylar in #59
• Explicitly specify nodes in srun calls by @xylar in #54
• Add a MANIFEST.in by @xylar in #64
• Fix check for inputs in subdirectories by @xylar in #63
• Add shared single layer yaml file by @sbrus89 in #57
• Clean up outdated format strings by @altheaden in #69
• Switch MappingFileStep to be a command-line step by @xylar in #68
• Rename steps_not_to_run and --no-steps by @altheaden in #73
• Make ocean ntasks and min_tasks a multiple of 4 by @xylar in #52
• Add surface forcing and restoring to single_column test group by @cbegeman in #66
• Logger cleanup and clarification by @altheaden in #75
• Update guidance on switching between branches by @xylar in #77
• Check available parallel resources only once by @altheaden in #76
• Separate creating parallel command and running command by @altheaden in #78
• Add an ideal age tracer case to the single column test group by @katsmith133 in #60
• Change algorithm for constraining resources by @altheaden in #79
• Change cosine bell to be single layer by @lconlon in #67
• Fix log filename for steps by @xylar in #82
• Make versions of cosine bell with and without viz steps by @xylar in #65
• Make pickle file of dependency an input by @altheaden in #80
• Remove unused check_parallel_system function by @altheaden in #81
• Get Slurm options in a separate function by @altheaden in #83
• Add Inertial gravity wave test group by @sbrus89 in #62
• Pull out common setup between run procedures by @altheaden in #84
• Rename namelist implicit bottom drag namelist option by @xylar in #87
• Ignore nonexistent step_after_run.pickle file by @altheaden in #86
• Add manufactured solution test group by @cbegeman in #72
• Fix equations in baroclinic channel User's Guide by @xylar in #88
• Remove manufactured_soluiton test case from suites by @xylar in #92
• Reformat command line help descriptions by @altheaden in #90
• Update step inputs attribute with input filenames by @altheaden in #93
• Fixup cosine bell test: Allow user changes to vert_levels cfg option by @cbegeman in #94
• Add flynt package to linter for updating format strings by @altheaden in #74
• Standardize step and test case names by @cbegeman in #96
• Assume mesh variables only in mesh file by @cbegeman in #97
• A few fixes to the docs by @xylar in #98
• Add dependency in restart test case by @xylar in #95
• Add sea ice components along with single column test case by @darincomeau in #71
• Fix cosine bell viz step by @xylar in #100
• Remove steps from steps_to_run in baroclinic_channel RPE by @xylar in #102
• Get maxLevelCell from ds, not ds_mesh in viz by @xylar in #101
• Make cell count heuristic by @altheaden in #99

New Contributors

• @jhkennedy made their first contribution in #12
• @sbrus89 made their first contribution in #57
• @katsmith133 made their first contribution in #60
• @lconlon made their fi...