Compliance-checker

Overview
- Adds partial support for CF 1.9
- Extensive improvements to CF conformance
- Many CI/quality of life improvements for the codebase

What's Changed
* Fix GHA for PyPI uploads by ocefpaf in https://github.com/ioos/compliance-checker/pull/933
* mark ERDDAP test with vcr by ocefpaf in https://github.com/ioos/compliance-checker/pull/931
* Excludes _Encoding attribute from being checked by CF var naming conv… by benjwadams in https://github.com/ioos/compliance-checker/pull/939
* Fixes errors when running --Describe-checks / -D option by benjwadams in https://github.com/ioos/compliance-checker/pull/938
* Add additional implementation, unit tests for CF Conformance section … by benjwadams in https://github.com/ioos/compliance-checker/pull/937
* Remove extraneous attribute checks on coordinate variables by benjwadams in https://github.com/ioos/compliance-checker/pull/940
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/941
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/942
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/943
* Removes deprecated NumPy types by benjwadams in https://github.com/ioos/compliance-checker/pull/944
* Only allow fixed length string variables to be one or two-dimensional by benjwadams in https://github.com/ioos/compliance-checker/pull/961
* Leilabbb cf1 9 2 5 1check missing data valid and actual range of data by leilabbb in https://github.com/ioos/compliance-checker/pull/963
* Ocean sigma z coordinate appendix d by leilabbb in https://github.com/ioos/compliance-checker/pull/964
* Calendar fixes conformance by benjwadams in https://github.com/ioos/compliance-checker/pull/962
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/968
* 7.1 cell boundaries by leilabbb in https://github.com/ioos/compliance-checker/pull/967
* updated check_cell_measures by leilabbb in https://github.com/ioos/compliance-checker/pull/966
* Updated check_compression_gathering by leilabbb in https://github.com/ioos/compliance-checker/pull/965
* Fix handling of skip_checks option by mhidas in https://github.com/ioos/compliance-checker/pull/975
* Fix units check for status_flag variables by mhidas in https://github.com/ioos/compliance-checker/pull/978
* add dependabot to keep the GHA updated by ocefpaf in https://github.com/ioos/compliance-checker/pull/979
* Use micromamba v2 by ocefpaf in https://github.com/ioos/compliance-checker/pull/980
* Bump codecov/codecov-action from 2 to 3 by dependabot in https://github.com/ioos/compliance-checker/pull/981
* Bump pypa/gh-action-pypi-publish from 1.5.0 to 1.6.4 by dependabot in https://github.com/ioos/compliance-checker/pull/982
* Bump actions/checkout from 2 to 3 by dependabot in https://github.com/ioos/compliance-checker/pull/984
* Bump actions/setup-python from 2 to 4 by dependabot in https://github.com/ioos/compliance-checker/pull/983
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/974
* Revert "Only allow fixed length string variables to be one or two-dimensional" by benjwadams in https://github.com/ioos/compliance-checker/pull/988
* Make calendar check case insensitive by benjwadams in https://github.com/ioos/compliance-checker/pull/987
* Fix calendar crossing 1582 issue on some builds by benjwadams in https://github.com/ioos/compliance-checker/pull/990
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/991
* Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.7.1 by dependabot in https://github.com/ioos/compliance-checker/pull/993
* Bump pypa/gh-action-pypi-publish from 1.7.1 to 1.8.0 by dependabot in https://github.com/ioos/compliance-checker/pull/994
* Bump pypa/gh-action-pypi-publish from 1.8.0 to 1.8.1 by dependabot in https://github.com/ioos/compliance-checker/pull/995
* Bump pypa/gh-action-pypi-publish from 1.8.1 to 1.8.3 by dependabot in https://github.com/ioos/compliance-checker/pull/998
* update standard names URL by dnowacki-usgs in https://github.com/ioos/compliance-checker/pull/997
* Update check_cell_measures() function in cf_1_6.y by leilabbb in https://github.com/ioos/compliance-checker/pull/992
* Merge in development branch for CF 1.9 by benjwadams in https://github.com/ioos/compliance-checker/pull/999
* Bump pypa/gh-action-pypi-publish from 1.8.3 to 1.8.4 by dependabot in https://github.com/ioos/compliance-checker/pull/1000
* Bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 by dependabot in https://github.com/ioos/compliance-checker/pull/1002
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ioos/compliance-checker/pull/1001
* Exclude miscellaneous files from being checked by codespell by benjwadams in https://github.com/ioos/compliance-checker/pull/1004
* Fixes dead ERDDAP link in integration tests by benjwadams in https://github.com/ioos/compliance-checker/pull/1005
* Fix numpy deprecations that are errors in 1.24.2 by ocefpaf in https://github.com/ioos/compliance-checker/pull/1009
* Remove unused helper functions for axes by benjwadams in https://github.com/ioos/compliance-checker/pull/1016
* fix minor inconsistencies in GHA by ocefpaf in https://github.com/ioos/compliance-checker/pull/1013
* [CF 1.9] Ensure time coordinate variables have a calendar attribute s… by benjwadams in https://github.com/ioos/compliance-checker/pull/1003
* Implement majority of conformance for CF section 4.4 by benjwadams in https://github.com/ioos/compliance-checker/pull/1014
* Check strict monotonicity of coordinate variables by benjwadams in https://github.com/ioos/compliance-checker/pull/1017
* Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 by dependabot in https://github.com/ioos/compliance-checker/pull/1018
* WIP check root group attr names, not running tests by benjwadams in https://github.com/ioos/compliance-checker/pull/921
* Refactor cell_measures, properly handling quantity squared/cubed by benjwadams in https://github.com/ioos/compliance-checker/pull/1019
* Formula terms revamp by benjwadams in https://github.com/ioos/compliance-checker/pull/1021
* Ruff take 2 by ocefpaf in https://github.com/ioos/compliance-checker/pull/1020
* Build api docs v2 by ocefpaf in https://github.com/ioos/compliance-checker/pull/1008
* Bump rossjrw/pr-preview-action from 1.3.1 to 1.4.2 by dependabot in https://github.com/ioos/compliance-checker/pull/1022
* Add unsigned int variables to valid CF 1.9 variable types. by benjwadams in https://github.com/ioos/compliance-checker/pull/1023
* Fix a broken link and drop a removed one. by ocefpaf in https://github.com/ioos/compliance-checker/pull/1027
* Enable bugbear... by ocefpaf in https://github.com/ioos/compliance-checker/pull/1026
* Merge in develop branch in preparation for Compliance Checker v5.1.0 by benjwadams in https://github.com/ioos/compliance-checker/pull/1025

New Contributors
* pre-commit-ci made their first contribution in https://github.com/ioos/compliance-checker/pull/941
* leilabbb made their first contribution in https://github.com/ioos/compliance-checker/pull/963
* dependabot made their first contribution in https://github.com/ioos/compliance-checker/pull/981

**Full Changelog**: https://github.com/ioos/compliance-checker/compare/v5.0.2...v5.1.0

- Numerous fixes to CF 1.6 conformance
- Fixes handling of standard name modifiers
- Fixes to calendar handling
- Fixes to flag related attributes when only one flag is specified
- Adds possible corrections when an invalid CF standard name is provided
- Code cleanup, pre-commit and CI fixes, narrower exception handling

PRs list
* Taxa names by benjwadams in https://github.com/ioos/compliance-checker/pull/889
* fix typo by ocefpaf in https://github.com/ioos/compliance-checker/pull/895
* test on py310 by ocefpaf in https://github.com/ioos/compliance-checker/pull/894
* Re enable flake8 by ocefpaf in https://github.com/ioos/compliance-checker/pull/901
* Add code coverage to GitHub Actions by benjwadams in https://github.com/ioos/compliance-checker/pull/900
* Fix undefined variables/tests, linter fixes by benjwadams in https://github.com/ioos/compliance-checker/pull/903
* use pathlib by ocefpaf in https://github.com/ioos/compliance-checker/pull/908
* Standard name units and modifiers by benjwadams in https://github.com/ioos/compliance-checker/pull/909
* Fix none cases and bail out in failure cases for units checks by benjwadams in https://github.com/ioos/compliance-checker/pull/910
* Fix protocol tests that had broken URLs by benjwadams in https://github.com/ioos/compliance-checker/pull/912
* Handle scalar flag attributes by benjwadams in https://github.com/ioos/compliance-checker/pull/915
* Adds checks for .nc filename extensions by benjwadams in https://github.com/ioos/compliance-checker/pull/916
* Fix integration tests rebase by benjwadams in https://github.com/ioos/compliance-checker/pull/913
* Improve conformance by benjwadams in https://github.com/ioos/compliance-checker/pull/917
* Handle nonstandard calendar and leap time in time variables by benjwadams in https://github.com/ioos/compliance-checker/pull/918
* Add checks/tests for external variables by benjwadams in https://github.com/ioos/compliance-checker/pull/920
* Test for CF 1.6 conformance section 3 by benjwadams in https://github.com/ioos/compliance-checker/pull/923
* Flag fixes by benjwadams in https://github.com/ioos/compliance-checker/pull/924
* Standard name recommendations by benjwadams in https://github.com/ioos/compliance-checker/pull/925
* Fixes spelling issues reported by `codespell` by benjwadams in https://github.com/ioos/compliance-checker/pull/926
* Pre commit fixup/code cleanup by benjwadams in https://github.com/ioos/compliance-checker/pull/927
* add pre-commit-ci-config by ocefpaf in https://github.com/ioos/compliance-checker/pull/928
* Merge in CI changes from develop branch by benjwadams in https://github.com/ioos/compliance-checker/pull/929
* Precommit additional fixes by benjwadams in https://github.com/ioos/compliance-checker/pull/930


**Full Changelog**: https://github.com/ioos/compliance-checker/compare/5.0.1...v5.0.2

Fixes a number of long-standing issues with `scale_factor` and `odd_offset` type comparison when comparing non-equivalent types.

- Adds support for CF 1.8
- Support to only run a subset of checks with `-i`/`--include-checks` option
- Code coverage support added in GitHub Actions continuous integration
- Fixed various issues in code base including unused variables and dead code paths

- Numerous updates to `featureType` representation to better fit the CF Conventions specifications

- Updates for building via GitHub Actions, including pushing to PyPI.

- Fixes handling of `scale_factor` and `add_offset` attributes.

Release for the IOOS Metadata Profile Version 1.2 Checker.

General
- Enables fetching from remote, non-OPeNDAP NetCDF files which use a `Content-Type` header of `application/x-netcdf`
- Enables fetching of datasets from ERDDAP TableDAP endpoints
- Skips iterating Python setup requirements twice
- Escape variable output in HTML format
- Allow in-memory loading of remote NetCDF datasets

CI/Build
- Adds pre-commit hooks in GitHub

IOOS Checker
- Update GTS ingest logic
- Correct platform detection
- Add z variable logic
- Various fixes/improvements to error messages