v3.3.0: Merge pull request #672 from British-Oceanographic-Data-Centre/develop

Summary

New features

• Add .zarr handling. Include as a notebook example
• Add notebook example for visualisation over poles. Specific plotting contours and quivers in Arctic on ORCA tripolar grid)

Behind the scenes

• Update for python=3.10
• Tidying of example scripts
• Improved unit test coverage

What's Changed

• micro edit by @jpolton in #621
• update read_bodc dimension to include id_dim by @jpolton in #623
• Allow CRPS to accept nD arrays - flatten first by @jpolton in #618
• Updated directory name for notebooks by @roje-bodc in #630
• create pylint action by @soutobias in #633
• Tidy up example scripts directory by @roje-bodc in #634
• add by @soutobias in #641
• add by @soutobias in #642
• run notebooks on coast repo by @thogar-computer in #631
• Feature/python3.10 update by @roje-bodc in #643
• Change matplotlib backend for unit tests by @roje-bodc in #645
• remove deprec warning by @soutobias in #649
• Bug/#628 cartopy quivers by @b-barton in #647
• update github actions versions by @soutobias in #652
• Feature/585 gsw version by @jpolton in #586
• 0624/polar quivers notebook by @b-barton in #650
• Standardized tide gauge objects by @soutobias in #651
• 0653/merge plot polar contour by @b-barton in #654
• Feature/zarr files by @soutobias in #655
• create changes for the new release by @soutobias in #656
• create changes for the new release by @soutobias in #657
• correct notebook for polar plotting and remove files by @soutobias in #659
• correct notebook by @soutobias in #660
• Create a new release (3.2.2) by @soutobias in #658
• Soutobias patch 1 by @soutobias in #661
• Correct python version on yml file by @soutobias in #662
• comment notebook by @soutobias in #665
• Correct github workflow for the markdown general by @soutobias in #667
• Update polar_plotting and zarr notebooks - bug on notebook general workflow by @soutobias in #668
• correct zarr installation on workflows by @soutobias in #669
• correct release by @soutobias in #671
• Correct release by @soutobias in #672

New Contributors

• @soutobias made their first contribution in #633
• @b-barton made their first contribution in #647

Full Changelog: v3.2.1...v3.3.0

v3.2.1

Summary

• Profile.process_en4(). Added keyword option (remove_flagged_neighbours=bool), a new EN flag to remove close points.
• Profile.process_en4(). Remove bug to correctly reject salinity points. (Salinity was being rejected at bad temperature points)
• Profile.mask_means() —> Profile.mask_stats(), which includes standard deviation and means over regions
• MaskMaker edits - new FSC region in NW European shelf. Harmonise naming convention for NW shelf regions.
• coast.Gridded() can take indices to perform subsetting prior to generating the Gridded object (which isn’t scaling well is subsets are called in other ways.)
• new CurrentsOnT() subclass of Gridded(), with methods for mapping velocities to t-points for analysis (self-complete but not fully implemented)

What's Changed

• bug fixes in process_en4() by @jpolton in #609
• fix depreciated syntax. cannot define gridded.landmask = None by @jpolton in #614
• 606 circulation and fluxes in global model data jp by @jpolton in #616
• 606 circulation and fluxes in global model data by @jasontempestholt in #607
• update: 3.2.1 by @jpolton in #619

Full Changelog: v3.2.0...v3.2.1

Nov22

What's Changed

• Fixed dangling file openings by @ledm in #582
• dask and xarray >= 2022.3.0 by @jpolton in #592
• Add MaskMaker.make_region() by @jpolton in #595
• Feature/593 obs_operator fix by @jpolton in #596
• Add MaskMasker.quick_plot() by @jpolton in #599

Tutorials

• mask_maker_tutorial
• tidegauge validation update (more figures)

Tests for new features

New Contributors

• @ledm made their first contribution in #582

Full Changelog: v3.1.2...v3.2.0

tutorial updates

Major updates to tutorials:

• tidegauge_tutorial.ipynb
• 0._profile_introduction.ipynb

Minor updates:

• update cartopy=0.21.0
• minor bug fixes e.g in Tidegauge()

NOWMAPS-sep22

Bug fix in dependency conflicts.
For now specify:
- numpy==1.22.3
- dask==2022.3.0
- dask[complete]==2022.3.0
- xarray==2022.3.0
- netCDF4==1.5.8

---

v3.1.0 release notes
MAJOR CHANGES AND NEW FEATURES:

• netcdf domain variables renamed/ mapped according to json config.
• SE-NEMO branch merged.
• code refactor.

BUGS:

• deprecated xr.ufunc removed
• git actions improved

DOCS:

• Notebooks are now EXECUTED in action, converted to markdown and included in documentation site with images included.
• Github actions flowchart github-actions-flowchart.md updated.
• Several Jupyter Notebooks Added

NOWMAPS-sep22

MAJOR CHANGES AND NEW FEATURES:

• netcdf domain variables renamed/ mapped according to json config.
• SE-NEMO branch merged.
• code refactor.

BUGS:

• deprecated xr.ufunc removed
• git actions improved

DOCS:

• Notebooks are now EXECUTED in action, converted to markdown and included in documentation site with images included.
• Github actions flowchart github-actions-flowchart.md updated.

Several Jupyter Notebooks Added

IMMERSE-jun22

MAJOR CHANGES AND NEW FEATURES:

• Package restructure, contents of directory 'coast' moved into directories 'coast/data', 'coast/diagnostics' and 'coast/_utils'.
• Added support for streaming Copernicus Marine Service (and other) datasets via OPeNDAP.
• Variable names made mandatory for subset_indices() in gridded.py.

BUGS:

• Package 'utide' upgraded to 0.3.0 fixing failing references.
• Additional data files made available to further support unit tests.

DOCS:

• All docstrings are now extracted, converted to markdown and included in documentation site.
• Notebooks are now converted to markdown and included in documentation site.
• Github actions flowchart github-actions-flowchart.md added.

Jupyter Notebooks Added:

• seasonal_decomp_example.ipynb.
• altimetry_tutorial.ipynb.
• amm15_example_plot.ipynb.
• anchor_plots_of_nsea_wvel.ipynb.
• tideguage_validation_tutorial.ipynb.
• tidetable_tutorial.ipynb.

CONGA

MAJOR CHANGES AND NEW FEATURES:

• Updated unit_testing to be more flexible and more distributed across separate files.
• Added a coverage metric to assess the amount of code that is tested in unit_testing.
• Tidegauge now has two dimensions Tidegauge(id_dim, time), instead of just time. Breaking change
• New Profile.average_into_grid_boxes() routine, for transforming a profile into a Gridded object
• New json configuration files for NEMO-ERSEM output and NEMO data from CMEMS
• Added World Ocean Database reading method into Profile()
• Updated functionality for contour methods on Gridded objects: Return length diagnostic; add new ContourT() class for fluxes of tracer along t-points.
• Seasonal decomposition utility using a Dask wrapper
• Add xesmf wrapper that takes in a pair of Gridded datasets and prepares them for use with xesmf

UPDATES:

• Interpolate_vertical now handles empty profiles, returning an empty profile on the new depths
• Profile has also been reorganised into core Profile and ProfileAnalysis() classes
• Tidegauge and Tidegauge_multiple have been reorganised into Tidegauge() and TidegaugeAnalysis() classes
• Indexed classes no longer read default file types on initialisation but can be handed a dataset using the dataset = arg

BUGS:

• Bug fixes in Tidegauge()/TidegaugeAnalysis()
• Bug fixes in Profile()/ProfileAnalysis()

DOCS:

• General website updates to reflect the changes in this version
• Rewritten Github workflow webpage
• Rewritten Unit_test webpage

IMMERSE-restructure

Summary

• update matplotlib>=3.4.3 dependency
• update cartopy>=0.20.1 references (not included in pip build as not straight forward)
• update documentations for package versions
• update documentation for configuration files

What's Changed

• update numpy version by @jpolton in #346
• Update setup.py by @jpolton in #347
• Test by @davbyr in #348
• Develop by @jpolton in #349
• version bump by @jpolton in #350
• small bugfix by @davbyr in #354
• DEBUG -> CRITICAL by @davbyr in #356
• Develop by @jpolton in #357
• update matplotlib. Add cartopy as core dependency by @jpolton in #359
• Develop by @jpolton in #361

Full Changelog: v1.2.0-alpha...v1.2.7

IMMERSE-restructure

The core data handling has been restructured to permit tidier expansion for more model and observational data types.
A new Gridded class is introduced as a generalisation of the defunct NEMO class.
A new Indexed class is introduced as a parent to:

• Profile (which can store and manipulate profile data)
• Timeseries --> Tidegauge, TidegaugeMultiple
• Track --> Altimetry

In addition some new classes are added to Indexed() for subsequent development

• Argos
• Glider
• Lagrangian

Other changes

• Apply Black formatting (line length = 120) to all Python modules.
• Add automatic formatting via Black as a GitHub action
• Temporal aggregation functionality with user defined seasons
• xarray version update. (0.15 --> 0.19.0)
• add utide package

Full Changelog: v0.5.0...v1.2.0-alpha