v0.1.5b

Final beta

Version update addressing a number of changes since v0.1.4b with issues planned and logged in milestone 1.

This is the final version of CTDCAL prior to a major refactor, with this version emphasizing future support, bug fixes, and legacy code.

General & Github integration

• Transition to Python 3.11 and remove numerous depreciation errors
• Repair CodeCOV actions
• Fix a number of unit tests
  • Pytest actions
  • Changes for updated modules
  • Implement RINKO unit tests

Documentation

• Update missing entries in CTDCAL API
• Fixes for Readthedocs documentation generation
• Assessed and itemized a number of TODO markers

Code

Flagging

• Implement new flags file to consolidate multiple sensor types

Configuration and directories

• Start consolidation of user settings into a .YML config file
• Retire the scratch_folder from the old data folder setup

Methods

• Add support for new soak detection method
• Add support for turbidity and CDOM fluorometer sensors
• Fixes to oxygen fitting from recent cruise experiences

Tools

• Improvements to QC tool
  • Plotting residuals
  • Support for visualizing oxygen and temperature
  • Minor bugfixes
• Implement a number of ODF discrete file warnings for analyst's reference
  • SBE35 refT, ODF autosal, ODF Winkler oxygen
• Support to merge multiple final bottle products for different CTDs

Plotting

• Add param-vs-param plots

v0.1.4b

The UX Release

Modules

ctdcal.io

• two new functions for reading Exchange data files from local filesystem or URL, load_exchange_btl and load_exchange_ctd (see CCHDO File Formats)

Miscellaneous

• Logging messages of all levels are now logged to ctdcal.log file
• ctdcal CLI now has a --debug flag to display all logging levels (instead of WARNING and above)
• Tutorial notebooks on how to use ctdcal can be found in the docs
• ctdcal quick-convert CLI command to create Exchange ct1 files from Sea-Bird .cnv files, without performing any calibration
• ctdcal qc CLI command to launch interactive data flagging tool
• Data flagging tool now has an exit button to halt the local server process
• Added Wetlabs Fluorometer to convert.py
• Start testing process_bottle and oxy_fitting modules
• By default, only logging levels WARNING and above will be displayed in terminal (see --debug addition above)
• Fixed bug when loading single station ssscc.csv files into fit_ctd

v0.1.3b

What's Changed

Modules

Outdated code from merge_codes has been removed. Relevant code has already been implemented in flagging and new io module.
report_ctd merged into new ctdcal.io module

io

• Created new ctdcal.io module for all non-ODF-specific reading/writing functions (#39)
• Refactor and test odf_io (#37)

ctd_plots

• Refactor and test ctd_plots (#35)
• ctd_plots functions now return axis handle if filename is not given
• cmocean is no longer a module dependency
• Hardcoded cruise report plot code removed from ctd_plots in favor of ctdcal/scripts/cruise_report.py script
• _intermediate_residual_plot() is now wrapped around residual_vs_pressure() instead of being a duplicate function

equations_sbe

• Tests for equations_sbe (#36)
• Conversion functions will now return a list of missing coefficients (instead of first missing in equation)
• Zero-values in input frequency arrays are now NaN'd out by default (applies to sbe3, sbe4, and sbe9 conversions)

Miscellaneous

• Outdated code in top-level old folder has been removed in favor of SBEReader class and equations_sbe module
• cmocean is no longer a package dependency
• Renamed master branch to main
• Fix sphinx/RTD version bug by importing ctdcal._version instead of importlib.metadata.version("ctdcal")
• Fix GitHub Action run-tests bug which triggered twice when pushing tagged commits
• Set up Codecov

Initialize testing

• Create tests using pytest for fit_ctd and flagging modules.
• Ensure tests pass on multiple OS and python versions using GH Actions and status badges

Fix config loader bug

Include user_settings.yaml in ctdcal package (as intended), which fixes failing calls to ctdcal.get_ctdcal_config()

PyPI release

This is the first release which should result in a published version on PyPI.

Initial release

Primarily for setting up PyPI