Welcome to amocarray’s documentation!

amocarray is a repository to access and work with array data from Atlantic meridional overturning circulation mooring arrays.

For recommendations or bug reports, please visit https://github.com/AMOCcommunity/amocarray/issues/new

Getting started

• Installation
  • Install for contributing

Developers' guide

• Developer Guide for amocarray
  • Table of Contents
  • 1. Quickstart: First Contribution
  • 2. Project Overview
  • 3. Project Structure
    • Project Management and Configuration Files
    • Core Modules
  • 4. Setting Up Development Environment
    • Step 1: Clone the repository
    • Step 2: Set up a virtual environment
    • Step 3: Install dependencies
    • Step 4: (Optional) Install pre-commit hooks manually
    • Step 5: Build the documentation (optional)
  • 5. Development Workflow
    • Branching Model
    • Fork & Pull Requests
    • Keeping Your Fork Up To Date
  • 6. Ignoring Local Files: .gitignore vs .git/info/exclude
    • .gitignore
    • .git/info/exclude
    • Best Practice
  • 7. Commit Message Style Guide
    • Format
    • Types
    • Examples
    • Why this matters
  • 8. Logging and Debugging
    • How logging works
    • Enabling and disabling logging
    • Writing logs in modules
    • Log levels
    • Best practices
  • 9. Troubleshooting
    • Pre-commit not running?
    • VSCode virtualenv not recognised?
    • Tests failing due to missing data?
    • Pre-commit pytest hook fails but pytest passes manually?
    • My commits are blocked by pre-commit errors?
  • 10. Further Resources
• Collaborating with git: Basic workflow
  • Forking & branching someone else’s repository
    • 1. Fork the repository
    • 2. Clone to your computer
    • 3. Find the clone on your computer
    • 4. Create a feature branch or just “branch” for edits
    • 5. Make an edit in the branch
    • 6. Commit the change in your branch
    • 7. Create a pull request to upstream main
    • 8. Compare pull request on GitHub.com
    • 9. Merge the pull request
    • 10. Rinse and repeat
• Extra GitHub features: Actions & Pages
  • This project’s Actions
  • For contributors
    • Check demo.ipynb
    • Check tests
    • Build docs
  • For maintainers
    • Build distribution
    • Publishing a release
• Project Coding Conventions
  • Python Style
    • Function Definitions
    • Function Naming
    • Docstrings
    • Line Length
    • Code Formatter
    • Imports
  • Xarray Dataset Style
    • Variables, Dimensions, Coordinates
    • Attributes
    • Notes
  • Miscellaneous
    • Pre-commit Workflow
    • Logging
    • Error Handling
  • Future Considerations
• Project Housekeeping Checklist
  • Adding a New Package
  • Updating Dependencies
  • Cleaning or Recreating the Environment
  • Pre-commit and Tests
  • Documentation
  • Before Merging a Branch

Vocabularies

• Controlled Vocabularies
  • Coordinates
    • latitude
    • longitude
  • Temperature
    • sea_water_conservative_temperature (CT)
    • sea_water_temperature (TEMP)
    • sea_water_potential_temperature (POTEMP)
  • Salinity
    • sea_water_absolute_salinity (SA)
    • sea_water_practical_salinity (PSAL)
    • sea_water_salinity (SALIN)
  • Pressure
    • sea_water_pressure (PRES)
    • sea_water_pressure_at_sea_floor (BOTPRES)
    • reference_pressure (REFPRES)
  • Density
    • sea_water_sigma_theta (SIGMA)
    • sea_water_potential_density
    • sea_water_neutral_density (GAMMA_N)
    • ocean_sigma_coordinate
    • ocean_sigma_z_coordinate
  • Velocity
    • baroclinic_northward_sea_water_velocity (VVEL_REL)
    • barotropic_northward_sea_water_velocity (VVEL_BARO)
  • Transport
    • ocean_volume_transport_across_line (TRANSPORT)
    • ocean_meridional_overturning_streamfunction (MOC)
    • ocean_meridional_overturning_mass_streamfunction
  • Freshwater Transport
    • northward_ocean_freshwater_transport (FWT)
    • northward_ocean_freshwater_transport_due_to_overturning (FWT_OV)
    • northward_ocean_freshwater_transport_due_to_gyre (FWT_GYRE)
  • Heat Transport
    • northward_ocean_heat_transport (MHT)
    • northward_ocean_heat_transport_due_to_gyre (MHT_GYRE)
    • northward_ocean_heat_transport_due_to_overturning (MHT_OV)
• Units Reference: for AC1
  • Variables
    • Mass/Volume Units
    • Length Units
    • Temperature Units
    • Conductivity Units
    • Pressure Units
    • Velocity Units
    • Angle Units (Accepted Non-SI)
    • Transport Units
    • Energy and Power Units
    • Surface Heat Flux Units
  • Mapping of Custom Conversions
  • SI Unit Prefixes
• Variable Names
  • Temperature
  • Salinity
  • Pressure
  • Density
  • Velocity
  • Transport

Data format

• Array Format (Native / Original)
  • OSNAP Original Data Format
    • OSNAP_MOC_MHT_MFT_TimeSeries_201408_202006_2023.nc
    • OSNAP_Streamfunction_201408_202006_2023.nc
    • OSNAP_Gridded_201408_202006_2023.nc
  • RAPID Original Data Format
    • moc_vertical.nc
    • ts_gridded.nc
    • moc_transports.nc
    • 2d_gridded.nc
    • meridional_transports.nc
  • MOVE Original Data Format
    • OS_MOVE_TRANSPORTS.nc
  • SAMBA Original Data Format
    • Upper_Abyssal_Transport_Anomalies.txt
    • MOC_TotalAnomaly_and_constituents.asc
  • FW2015
  • MOCHA
    • Summary of MOCHA files:
    • Potential reformats:
• OceanSITES Format for AMOC Arrays
  • File naming
    • OceanSITES: Gridded and derived data
    • File naming for array data products
    • Feature Types
  • Global Metadata
    • 1. Discovery and Identification
    • 2. Geo-spatial-temporal Metadata
    • 3. Conventions
    • 4. Publication Information
    • 5. Provenance
  • Dimension and definition
  • Coordinates
  • Geophysical variables
    • Flags and QC
  • AMOC array data
  • References
• Converting to OceanSITES format
  • OSNAP conversion thoughts
    • Potential reformats:
  • RAPID conversion thoughts
    • Potential reformats:
  • MOVE conversion thoughts
    • Potential reformats:
  • SAMBA conversion thoughts
    • Potential reformats:
• AMOCarray Format AC1
  • 1. Overview
  • 2. File Format
  • 3. Variables
  • 4. Global Attributes
  • 5. Variable Attributes
  • 6. Metadata Requirements
  • 7. Validation Rules
  • 8. Examples
  • 9. Conversion Tool
  • 10. Notes
  • 11. Provenance and Attribution

Demo notebook

• AMOCarray demo
  • Load RAPID 26°N
  • Load MOVE 16°N
  • Load OSNAP
  • Load SAMBA 34.5°S
  • Load FW2015
  • LOAD MOCHA 26.5°N
  • LOAD 41°N
  • LOAD DSO
  • Monthly Anomalies Overview

Help and reference

• GitHub Repo
• amocarray API
  • readers
    • load_dataset()
    • load_sample_dataset()
    • Submodules
  • standardise
    • clean_metadata()
    • merge_metadata_aliases()
    • normalize_and_add_vocabulary()
    • reorder_metadata()
    • standardise_41n()
    • standardise_array()
    • standardise_dso()
    • standardise_fw2015()
    • standardise_mocha()
    • standardise_move()
    • standardise_osnap()
    • standardise_rapid()
    • standardise_samba()
  • plotters
    • monthly_resample()
    • plot_amoc_timeseries()
    • plot_monthly_anomalies()
    • show_attributes()
    • show_contents()
    • show_variables()
    • show_variables_by_dimension()
  • writers
    • save_dataset()
  • tools
    • convert_units_var()
    • find_best_dtype()
    • generate_reverse_conversions()
    • reformat_units_var()
    • set_best_dtype()
    • set_fill_value()
  • utilities
    • apply_defaults()
    • download_file()
    • get_default_data_dir()
    • get_project_root()
    • load_array_metadata()
    • normalize_whitespace()
    • parse_ascii_header()
    • read_ascii_file()
    • resolve_file_path()
    • safe_update_attrs()
    • validate_array_yaml()

Indices and tables

• Index

• Module Index

• Search Page