v5.1.2

Release synopsis: Mostly a bugfix release with some improvements to CI, domain variables, and NetCDF groups support

What's Changed

• Should fix more but now all "Error in sys.excepthook:" by @ocefpaf in #1069
• Fix some broken links by @ocefpaf in #1070
• add NCEI downstream plugin test by @ocefpaf in #1072
• Test against numpy 2.0 by @ocefpaf in #1073
• Fix lint by @ocefpaf in #1074
• Fix filepath bug by @ocefpaf in #1075
• Use README.md as quickintro by @ocefpaf in #1077
• Dataset from zarr by @ocefpaf in #1071
• add cc-plugin-og plugin test by @ocefpaf in #1078
• Conda was clobbering the dev version of compliance-checker by @ocefpaf in #1084
• Remove assert statement by @ocefpaf in #1083
• Split command from the result... by @ocefpaf in #1087
• We no longer need this part. by @ocefpaf in #1092
• Remove duplicated function by @ocefpaf in #1095
• Merge in develop by @benjwadams in #1097
• Update the CF version in the README by @ocefpaf in #1098
• Adding inputs (i.e. options incl. value) by @sol1105 in #1091
• Merge pull request #1097 from ioos/develop by @benjwadams in #1100
• Implement checking of domain variables against cell_measures by @benjwadams in #1089
• Fix windows tests by @ocefpaf in #1104
• Remove set check for certain variable attributes due to sorting issues by @benjwadams in #1108
• Fixes micromamba v2 failures by @ocefpaf in #1111
• Add Python 3.13 to the test matrix by @ocefpaf in #1114
• Update VCR file by @ocefpaf in #1115
• Bump minimum supported Python to 3.9 by @ocefpaf in #1117
• update pre-commits by @ocefpaf in #1120
• .is_long_time_interval() is deprecated and will be removed by @ocefpaf in #1121
• is this covered by the tests? by @ocefpaf in #1119
• Remove unused argument by @ocefpaf in #1123
• Bump codecov/codecov-action from 4 to 5 by @dependabot in #1124
• Replace httpretty by @ocefpaf in #1125
• Minimum Python support 3.10 by @ocefpaf in #1122
• Reduce the development requirements by @ocefpaf in #1126
• Group search by @benjwadams in #1130
• FIX: Error in util.py when no attributes found in StandardNameTable by @unichronic in #1134
• update pre-commits by @ocefpaf in #1136
• Filter specific warnings to find hidden bugs by @ocefpaf in #1137
• WIP Domain variables cell measures coordinates by @benjwadams in #1129

New Contributors

• @sol1105 made their first contribution in #1091
• @unichronic made their first contribution in #1134

Full Changelog: v5.1.1...v5.1.2

v5.1.1

What's Changed

• minor fixes, left over from #1026 by @ocefpaf in #1028
• workaround latest urllib3 by @ocefpaf in #1031
• Pin isodate >= 0.6.1 in requirements.txt by @benjwadams in #1034
• Update micromamba GitHub Actions by @ocefpaf in #1033
• remove MemoizedDataset by @ocefpaf in #1029
• Update precommit and fix by @ocefpaf in #1037
• let's skip this one for now by @ocefpaf in #1042
• Fix pre commits by @ocefpaf in #1038
• fix typos by @ocefpaf in #1045
• v4 is beta and was probably mistakenly release as stable by @ocefpaf in #1046
• Remove pkg resources by @ocefpaf in #1039
• move to pyproject.toml by @ocefpaf in #1024
• Merge in develop changes for 5.1.1 release preparation by @benjwadams in #1061
• removed last of pkg_resources. by @ChrisBarker-NOAA in #1060
• Some pytest fixes by @jcermauwedu in #1056
• Score fix in cf 1.6 by @Karinon in #1053
• Final merge prior to 5.1.1 release by @benjwadams in #1062

New Contributors

• @ChrisBarker-NOAA made their first contribution in #1060
• @jcermauwedu made their first contribution in #1056
• @Karinon made their first contribution in #1053

Checker bug fixes

• Fixed a logic error in CF 1.6 checker with valid_range when valid_min or valid_max were present.

Full Changelog: v5.1.0...v5.1.1

v5.1.0

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

New Contributors

• @pre-commit-ci made their first contribution in #941
• @leilabbb made their first contribution in #963
• @dependabot made their first contribution in #981

Full Changelog: v5.0.2...v5.1.0

v5.0.2

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

Full Changelog: 5.0.1...v5.0.2

scale_factor/add_offset fixes

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

CF 1.8 Support

• 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

Bugfixes to geospatial representation, CI updates

• 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.

IOOS Compliance Checker 4.3.3

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

Release Candidate 4.3.3rc2

Release candidate 2 for the IOOS Metadata Profile Version 1.2 Checker

• change standard_name_uri to standard_name_url
• add syntax checks for platform_id
• add checks for flag_meanings and flag_values on QARTOD variables
• streamline messaging for ioos_ingest, gts_ingest checks
• ensure proper syntax for wmo_platform_code
• separate checks for global gts_ingest flag and checking if the variables passed the GTS ingest requirements
• improve messaging for qartod_variables:references check
• add documentation for using ERDDAP datasets with the checker

Compliance Checker 4.3.3 Release Candidate 1

Release Candidate version 1 for IOOS Compliance Checker 4.3.3.

General

• Adds a ValidationObject class in base.py for generic validation of global attributes. Current uses include email and URL validation, among others.
• Updates attr_check function to accept variables for generic variable checks, e.g. aforementioned validators, set membership from known set of strings.

IOOS 1.2

• Adds a checker for IOOS Metadata Profile Version 1.2.