.gitignore
.pre-commit-config.yaml
.prettierignore
.readthedocs.yaml
LICENSE
README.md
codecov.yml
design-doc.md
environment.yml
pyproject.toml
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/PULL_REQUEST_TEMPLATE.md
.github/dependabot.yml
.github/release.yml
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/cd.yml
.github/workflows/ci.yml
docs/Makefile
docs/classroom-surf-environment.yml
docs/conf.py
docs/index.md
docs/make.bat
docs/_static/virtual_ship_logo.png
docs/_static/virtual_ship_logo_inverted.png
docs/api/index.md
docs/contributing/index.md
docs/paper/figure1.png
docs/paper/figure1.py
docs/paper/paper.bib
docs/paper/paper.md
docs/paper/paper.pdf
docs/paper/plotting_functions.py
docs/paper/sample_expedition/CoordinatesExport-sample.xlsx
docs/paper/sample_expedition/expedition_overview.png
docs/paper/sample_expedition/MY_EXPEDITION/expedition.yaml
docs/user-guide/example_log_instruments.gif
docs/user-guide/example_plan_app.gif
docs/user-guide/image-1.png
docs/user-guide/index.md
docs/user-guide/quickstart.md
docs/user-guide/_images/AnnaWeber.jpeg
docs/user-guide/_images/ILOs.jpg
docs/user-guide/_images/MFP.jpg
docs/user-guide/_images/MFPtimeline.jpg
docs/user-guide/_images/freepik_assignment.png
docs/user-guide/_images/freepik_code_of_conduct.jpg
docs/user-guide/_images/freepik_research_vessel.jpg
docs/user-guide/_images/links.ipynb
docs/user-guide/_images/marine_ss.jpg
docs/user-guide/assignments/Code_of_conduct.ipynb
docs/user-guide/assignments/Research_Proposal_only.ipynb
docs/user-guide/assignments/Research_proposal_intro.ipynb
docs/user-guide/assignments/Sail_the_ship.ipynb
docs/user-guide/assignments/Virtualship_research_proposal.ipynb
docs/user-guide/assignments/case_studies_virtualship.ipynb
docs/user-guide/assignments/index.md
docs/user-guide/assignments/notebook_utils.py
docs/user-guide/assignments/sciencecommunication_assignment.ipynb
docs/user-guide/developer-content/parcels-meeting-Nov2025/performance/performance_v03.py
docs/user-guide/developer-content/parcels-meeting-Nov2025/performance/performance_v03_fromdata.py
docs/user-guide/developer-content/parcels-meeting-Nov2025/performance/plot_performance.py
docs/user-guide/developer-content/parcels-meeting-Nov2025/performance/results/performance_results.csv
docs/user-guide/developer-content/parcels-meeting-Nov2025/performance/results/performance_results_fromdata.csv
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/Presentation.html
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/Presentation.qmd
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/Figure_copernicusonly.png
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/Figure_fromdata_hiddenlast.png
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/Figure_fromdata_nolast.png
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/Figure_fromdata_showlast.png
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/download (1).png
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/figure1.png
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/sample_3D_temperature.html
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/sample_slider_temperature.html
docs/user-guide/developer-content/parcels-meeting-Nov2025/presentation/images/snapshot2.png
docs/user-guide/documentation/copernicus_products.md
docs/user-guide/documentation/example_copernicus_download.ipynb
docs/user-guide/documentation/pre_download_data.md
docs/user-guide/teacher-content/ILOs.ipynb
docs/user-guide/teacher-content/index.md
docs/user-guide/teacher-content/letter.md
docs/user-guide/teacher-content/UU-dyoc/example_expedition.md
docs/user-guide/teacher-content/UU-dyoc/file_permissions.md
docs/user-guide/teacher-content/UU-dyoc/vsc_overview/Presentation.html
docs/user-guide/teacher-content/UU-dyoc/vsc_overview/Presentation.qmd
docs/user-guide/teacher-content/UU-dyoc/vsc_overview/images/ship_still.mp4
docs/user-guide/teacher-content/UU-ocean-of-future/CTD_transects.ipynb
docs/user-guide/teacher-content/UU-ocean-of-future/CoordinatesExport-Transect.xlsx
docs/user-guide/teacher-content/UU-ocean-of-future/Presentation.html
docs/user-guide/teacher-content/UU-ocean-of-future/Presentation.qmd
docs/user-guide/teacher-content/UU-ocean-of-future/Tutorial1.ipynb
docs/user-guide/teacher-content/UU-ocean-of-future/Tutorial2.ipynb
docs/user-guide/teacher-content/UU-ocean-of-future/_publish.yml
docs/user-guide/teacher-content/UU-ocean-of-future/plot_3D.py
docs/user-guide/teacher-content/UU-ocean-of-future/plot_slider.py
docs/user-guide/teacher-content/UU-ocean-of-future/schedule_monitor.ipynb
docs/user-guide/teacher-content/UU-ocean-of-future/timeseries.py
docs/user-guide/tutorials/ADCP_data_tutorial.ipynb
docs/user-guide/tutorials/ADCP_transects.ipynb
docs/user-guide/tutorials/Argo_data_tutorial.ipynb
docs/user-guide/tutorials/CTD_data_tutorial.ipynb
docs/user-guide/tutorials/CTD_transects.ipynb
docs/user-guide/tutorials/Drifter_data_tutorial.ipynb
docs/user-guide/tutorials/Ship_underwater_ST_plotting.ipynb
docs/user-guide/tutorials/index.md
docs/user-guide/tutorials/old_surf_research_cloud_setup.ipynb
docs/user-guide/tutorials/surf_collaborative_setup.ipynb
docs/user-guide/tutorials/surf_research_cloud_setup.ipynb
docs/user-guide/tutorials/working_with_expedition_yaml.md
docs/user-guide/tutorials/xbt_plotting.ipynb
docs/user-guide/tutorials/assets/add-storage.gif
docs/user-guide/tutorials/assets/add-workspace.gif
docs/user-guide/tutorials/assets/initial_vs_final_drifters.png
docs/user-guide/tutorials/assets/trajan_drifters.png
src/virtualship/__init__.py
src/virtualship/_version_setup.py
src/virtualship/errors.py
src/virtualship/utils.py
src/virtualship.egg-info/PKG-INFO
src/virtualship.egg-info/SOURCES.txt
src/virtualship.egg-info/dependency_links.txt
src/virtualship.egg-info/entry_points.txt
src/virtualship.egg-info/requires.txt
src/virtualship.egg-info/top_level.txt
src/virtualship/cli/__init__.py
src/virtualship/cli/_plan.py
src/virtualship/cli/_run.py
src/virtualship/cli/commands.py
src/virtualship/cli/main.py
src/virtualship/cli/validator_utils.py
src/virtualship/expedition/__init__.py
src/virtualship/expedition/simulate_schedule.py
src/virtualship/instruments/__init__.py
src/virtualship/instruments/adcp.py
src/virtualship/instruments/argo_float.py
src/virtualship/instruments/base.py
src/virtualship/instruments/ctd.py
src/virtualship/instruments/ctd_bgc.py
src/virtualship/instruments/drifter.py
src/virtualship/instruments/ship_underwater_st.py
src/virtualship/instruments/types.py
src/virtualship/instruments/xbt.py
src/virtualship/make_realistic/__init__.py
src/virtualship/make_realistic/adcp_make_realistic.py
src/virtualship/make_realistic/ctd_make_realistic.py
src/virtualship/make_realistic/problems/scenarios.py
src/virtualship/make_realistic/problems/simulator.py
src/virtualship/models/__init__.py
src/virtualship/models/checkpoint.py
src/virtualship/models/expedition.py
src/virtualship/models/location.py
src/virtualship/models/spacetime.py
src/virtualship/static/__init__.py
src/virtualship/static/expedition.yaml
tests/conftest.py
tests/test_checkpoint.py
tests/test_mfp_to_yaml.py
tests/test_utils.py
tests/cli/test_cli.py
tests/cli/test_plan.py
tests/cli/test_run.py
tests/expedition/test_expedition.py
tests/expedition/test_simulate_schedule.py
tests/expedition/expedition_dir/.gitignore
tests/expedition/expedition_dir/expedition.yaml
tests/expedition/expedition_dir/input_data/.gitignore
tests/expedition/expedition_dir/input_data/argo_float_s.nc
tests/expedition/expedition_dir/input_data/argo_float_t.nc
tests/expedition/expedition_dir/input_data/argo_float_uv.nc
tests/expedition/expedition_dir/input_data/bathymetry.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_chl.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_no3.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_nppv.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_o2.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_ph.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_phyc.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_po4.nc
tests/expedition/expedition_dir/input_data/ctd_bgc_zooc.nc
tests/expedition/expedition_dir/input_data/drifter_t.nc
tests/expedition/expedition_dir/input_data/drifter_uv.nc
tests/expedition/expedition_dir/input_data/ship_s.nc
tests/expedition/expedition_dir/input_data/ship_t.nc
tests/expedition/expedition_dir/input_data/ship_uv.nc
tests/instruments/test_adcp.py
tests/instruments/test_argo_float.py
tests/instruments/test_base.py
tests/instruments/test_ctd.py
tests/instruments/test_ctd_bgc.py
tests/instruments/test_drifter.py
tests/instruments/test_ship_underwater_st.py
tests/instruments/test_xbt.py
tests/make_realistic/.gitignore
tests/make_realistic/test_adcp_make_realistic.py
tests/make_realistic/test_ctd_make_realistic.py
tests/make_realistic/adcp.zarr/.zattrs
tests/make_realistic/adcp.zarr/.zgroup
tests/make_realistic/adcp.zarr/.zmetadata
tests/make_realistic/adcp.zarr/U/.zarray
tests/make_realistic/adcp.zarr/U/.zattrs
tests/make_realistic/adcp.zarr/U/0.0
tests/make_realistic/adcp.zarr/U/0.1
tests/make_realistic/adcp.zarr/V/.zarray
tests/make_realistic/adcp.zarr/V/.zattrs
tests/make_realistic/adcp.zarr/V/0.0
tests/make_realistic/adcp.zarr/V/0.1
tests/make_realistic/adcp.zarr/lat/.zarray
tests/make_realistic/adcp.zarr/lat/.zattrs
tests/make_realistic/adcp.zarr/lat/0.0
tests/make_realistic/adcp.zarr/lat/0.1
tests/make_realistic/adcp.zarr/lon/.zarray
tests/make_realistic/adcp.zarr/lon/.zattrs
tests/make_realistic/adcp.zarr/lon/0.0
tests/make_realistic/adcp.zarr/lon/0.1
tests/make_realistic/adcp.zarr/obs/.zarray
tests/make_realistic/adcp.zarr/obs/.zattrs
tests/make_realistic/adcp.zarr/obs/0
tests/make_realistic/adcp.zarr/obs/1
tests/make_realistic/adcp.zarr/time/.zarray
tests/make_realistic/adcp.zarr/time/.zattrs
tests/make_realistic/adcp.zarr/time/0.0
tests/make_realistic/adcp.zarr/time/0.1
tests/make_realistic/adcp.zarr/trajectory/.zarray
tests/make_realistic/adcp.zarr/trajectory/.zattrs
tests/make_realistic/adcp.zarr/trajectory/0
tests/make_realistic/adcp.zarr/z/.zarray
tests/make_realistic/adcp.zarr/z/.zattrs
tests/make_realistic/adcp.zarr/z/0.0
tests/make_realistic/adcp.zarr/z/0.1
tests/make_realistic/ctd.zarr/.zattrs
tests/make_realistic/ctd.zarr/.zgroup
tests/make_realistic/ctd.zarr/.zmetadata
tests/make_realistic/ctd.zarr/lat/.zarray
tests/make_realistic/ctd.zarr/lat/.zattrs
tests/make_realistic/ctd.zarr/lat/0.0
tests/make_realistic/ctd.zarr/lat/0.1
tests/make_realistic/ctd.zarr/lat/0.2
tests/make_realistic/ctd.zarr/lon/.zarray
tests/make_realistic/ctd.zarr/lon/.zattrs
tests/make_realistic/ctd.zarr/lon/0.0
tests/make_realistic/ctd.zarr/lon/0.1
tests/make_realistic/ctd.zarr/lon/0.2
tests/make_realistic/ctd.zarr/max_depth/.zarray
tests/make_realistic/ctd.zarr/max_depth/.zattrs
tests/make_realistic/ctd.zarr/max_depth/0.0
tests/make_realistic/ctd.zarr/max_depth/0.1
tests/make_realistic/ctd.zarr/max_depth/0.2
tests/make_realistic/ctd.zarr/min_depth/.zarray
tests/make_realistic/ctd.zarr/min_depth/.zattrs
tests/make_realistic/ctd.zarr/min_depth/0.0
tests/make_realistic/ctd.zarr/min_depth/0.1
tests/make_realistic/ctd.zarr/min_depth/0.2
tests/make_realistic/ctd.zarr/obs/.zarray
tests/make_realistic/ctd.zarr/obs/.zattrs
tests/make_realistic/ctd.zarr/obs/0
tests/make_realistic/ctd.zarr/obs/1
tests/make_realistic/ctd.zarr/obs/2
tests/make_realistic/ctd.zarr/raising/.zarray
tests/make_realistic/ctd.zarr/raising/.zattrs
tests/make_realistic/ctd.zarr/raising/0.0
tests/make_realistic/ctd.zarr/raising/0.1
tests/make_realistic/ctd.zarr/raising/0.2
tests/make_realistic/ctd.zarr/salinity/.zarray
tests/make_realistic/ctd.zarr/salinity/.zattrs
tests/make_realistic/ctd.zarr/salinity/0.0
tests/make_realistic/ctd.zarr/salinity/0.1
tests/make_realistic/ctd.zarr/salinity/0.2
tests/make_realistic/ctd.zarr/temperature/.zarray
tests/make_realistic/ctd.zarr/temperature/.zattrs
tests/make_realistic/ctd.zarr/temperature/0.0
tests/make_realistic/ctd.zarr/temperature/0.1
tests/make_realistic/ctd.zarr/temperature/0.2
tests/make_realistic/ctd.zarr/time/.zarray
tests/make_realistic/ctd.zarr/time/.zattrs
tests/make_realistic/ctd.zarr/time/0.0
tests/make_realistic/ctd.zarr/time/0.1
tests/make_realistic/ctd.zarr/time/0.2
tests/make_realistic/ctd.zarr/trajectory/.zarray
tests/make_realistic/ctd.zarr/trajectory/.zattrs
tests/make_realistic/ctd.zarr/trajectory/0
tests/make_realistic/ctd.zarr/winch_speed/.zarray
tests/make_realistic/ctd.zarr/winch_speed/.zattrs
tests/make_realistic/ctd.zarr/winch_speed/0.0
tests/make_realistic/ctd.zarr/winch_speed/0.1
tests/make_realistic/ctd.zarr/winch_speed/0.2
tests/make_realistic/ctd.zarr/z/.zarray
tests/make_realistic/ctd.zarr/z/.zattrs
tests/make_realistic/ctd.zarr/z/0.0
tests/make_realistic/ctd.zarr/z/0.1
tests/make_realistic/ctd.zarr/z/0.2
tests/make_realistic/problems/test_scenarios.py
tests/make_realistic/problems/test_simulator.py