[FEAT] Add report generation

[eleanorfrajka]

This is an edit on the other PR, which maybe isn't how I should've added it.

Generates reports as *.rst including information about the variable mapping and basic plots. I haven't tested it yet for mooring data--so the example (also included in the docs) is for a profile with plot.

[Copilot]

Pull request overview

This PR adds a comprehensive pipeline-based processing system to SeaSenseLib along with report generation capabilities. The changes introduce a modular, configurable architecture for Level-1 oceanographic data processing with 7 pipeline stages: mapping, unit handling, derivation, metadata extraction, metadata enrichment, validation, and finalization.

Changes:

• New pipeline system with 7 configurable processing stages
• Report generation functionality (mentioned in title but writer implementation not visible in diff)
• JSON-based knowledge base for parameters, mappings, and conventions
• Updated CF Convention version from 1.8 to 1.13
• Added conservative temperature derivation
• Extensive test coverage for new pipeline components
• CLI enhancements with logging support and pipeline controls

Reviewed changes

Copilot reviewed 151 out of 162 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
tests/*	Comprehensive test suite for pipeline stages, handlers, and utilities
seasenselib/pipeline/*	Complete pipeline system implementation with stages and handlers
seasenselib/knowledge/*	JSON knowledge base for parameters, mappings, units, and conventions
seasenselib/readers/*	Updated readers to support pipeline system and add format_mappings()
seasenselib/writers/*	Added logging to writers
seasenselib/plotters/*	Lazy matplotlib import optimization
seasenselib/parameters.py	Added conservative_temperature and knowledge base loader
seasenselib/core/io_manager.py	Added return_metadata support
seasenselib/cli/*	Enhanced CLI with logging configuration and lightweight parser mode
pyproject.toml	Version bump to 0.5.0, added pint dependency
requirements*.txt	Added pint dependency
notebooks/demo.ipynb	Added pipeline examples and report generation demo
docs/source/index.rst	Added reports section

Comments suppressed due to low confidence (2)

seasenselib/readers/base.py:204

• This import of module logging is redundant, as it was previously imported on line 17.
  seasenselib/writers/base.py:226
• Overridden method signature does not match call, where it is passed too many arguments. Overriding method method ReportWriter.write matches the call.
  Overridden method signature does not match call, where it is passed an argument named 'title'. Overriding method method ReportWriter.write matches the call.
  Overridden method signature does not match call, where it is passed an argument named 'include_plot'. Overriding method method ReportWriter.write matches the call.
  Overridden method signature does not match call, where it is passed an argument named 'plot_output_dir'. Overriding method method ReportWriter.write matches the call.
  Overridden method signature does not match call, where it is passed an argument named 'processing_metadata'. Overriding method method ReportWriter.write matches the call.

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