mesh-data-model update#4296
Merged
stephenworsley merged 37 commits intoSciTools:mesh-data-model_updatedfrom Aug 31, 2021
Merged
mesh-data-model update#4296stephenworsley merged 37 commits intoSciTools:mesh-data-model_updatedfrom
mesh-data-model update#4296stephenworsley merged 37 commits intoSciTools:mesh-data-model_updatedfrom
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* TopologyMetadata class. * Connectivity class first pass. * Enhanced Connectivity intelligence for masked elements. * ConnectivityMetadata tests. * Connectivity correct xml behaviour and better _values setting. * Connectivity better shape validation message. * Connectivity: corrected element size validation message. * Connectivity unit tests. * Connectivity additional unit tests. * Connectivity in other unit tests. * Connectivity __init__ docstring. * Connectivity complete docstrings. * Alphabetise ConnectivityMetadata usages. * Connectivity clearer handling of locations and dims. * Connectivity handle standard_name and units if provided. * Connectivity align start_index docstring with UGRID conventions. * Connectivity UGRID_CF_ROLES class attribute. * Connectivity improved validate_arg_vs_list(). * Make Connectivity's extra attributes truly read-only. * Connectivity stop overriding str and repr. * Connectivity improved src_lengths and lazy operations. * Connectivity indices typo. * Connectivity resource-light indices validation. * Connectivity enable transposed equivalence. * Connectivity defaults stated in docstrings. * Docstring corrections. * test_class_connectivitymetadata updated to use src_dim. * Connectivity transpose creates a new class from scratch instead of copying. * Connectivity final review improvements.
* move connectivity to experimental * drop pyugrid from py38.yml * Update lib/iris/coords.py Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> * Update lib/iris/common/metadata.py Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> * Update lib/iris/experimental/ugrid.py Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> * review actions - drop logger Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>
* Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk>
* Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) * cirrus-ci compute credits (SciTools#4007) * update release process (SciTools#4010) * Stop using deprecated aliases of builtin types (SciTools#3997) * Stopped using deprecated aliases of builtin types. This is required to avoid warnings starting with NumPy 1.20.0. * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * Updated whatsnew. Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * celebrate first time iris contributors (SciTools#4013) * Docs unreleased banner (SciTools#3999) * baseline * removed debug comments * reverted * remove line * Testing * testing extensions * testing rtd_version * fixed if * removed line * tidy up * tidy comments * debug of pre-existing rtd variables * added reminder * testing * testing still * updated comments * added whatsnew * expanded the if conditiion * review actions * Update layout.html Remove alternative banner that used the RestructuredText notation. * review actions * drop __unicode__ method usage (SciTools#4018) * cirrus-ci conditional tasks (SciTools#4019) * cirrus-ci conditional tasks * use bc for bash arithmetic * revert back to sed * use expr * reword * minor documentation changes * review actions * make iris.common.metadata._hexdigest public (SciTools#4020) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com>
* add ugrid mesh-api stubs (SciTools#4001) * add additional mesh stubs (SciTools#4005) * Update mesh-data-model branch (SciTools#4009) (SciTools#4011) * Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> * MeshMetadata class. (SciTools#4002) * MeshMetadata class. * MeshMetadata extra members for dim names. * Comment for BaseMetadata refactoring. * add meshmetadata services (SciTools#4012) * Mesh api coord manager (SciTools#4015) * add mesh coordinate manager * wip * make shape methods private + reorganise method order * review actions * partial mesh * wip * Mesh data model to ng vat mesh api (SciTools#4023) * Update mesh-data-model branch (SciTools#4009) * Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> * Master to mesh data model (SciTools#4022) * Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) * cirrus-ci compute credits (SciTools#4007) * update release process (SciTools#4010) * Stop using deprecated aliases of builtin types (SciTools#3997) * Stopped using deprecated aliases of builtin types. This is required to avoid warnings starting with NumPy 1.20.0. * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * Updated whatsnew. Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * celebrate first time iris contributors (SciTools#4013) * Docs unreleased banner (SciTools#3999) * baseline * removed debug comments * reverted * remove line * Testing * testing extensions * testing rtd_version * fixed if * removed line * tidy up * tidy comments * debug of pre-existing rtd variables * added reminder * testing * testing still * updated comments * added whatsnew * expanded the if conditiion * review actions * Update layout.html Remove alternative banner that used the RestructuredText notation. * review actions * drop __unicode__ method usage (SciTools#4018) * cirrus-ci conditional tasks (SciTools#4019) * cirrus-ci conditional tasks * use bc for bash arithmetic * revert back to sed * use expr * reword * minor documentation changes * review actions * make iris.common.metadata._hexdigest public (SciTools#4020) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com> * Connectivity manager (SciTools#4017) * ConnectivityManager first pass. * ConnectivityManager align with proposed CoordManager. * Connectivity Manager review actions. * Connectivity Manager more review changes. * Use metadata_manager for Mesh location dimension. * Mesh dimension name abstraction. * Align Cooord and Connectivity Managers filters methods. * Completed Mesh class. * filter_cf improvements. * Moved filter_cf. * Mesh connectivity manager namedtuples comment. * Mesh removed trailing underscores. * Mesh _set_dimension_names improvements. * Mesh import rationalisation. * Mesh connectivity manager remove NDIM. * Connectivity manager use lazy indices_by_src(). * Connectivity manager clearer removal syntax. * Connectivity manager don't override __init__. * Connectivity manager correct base class syntax. * Metadata filter hexdigest reference fix. * test_MeshMetadata fix. * Rename filter to metadata_filter. * minor fixes (SciTools#4025) * minor fixes * wip * add mesh pickle support (SciTools#4026) Co-authored-by: Bill Little <bill.james.little@gmail.com> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com>
* Fix some problems with existing tests. * Add MeshCoordMetadata, and tests. * Add tests. * Tidy import code + cleaner package namespace. * Fix duplicated comment. * Rationalise which non-member metadata item in testing. * Remove 'mesh' from MeshCoordMetadata. * Common code to add metadata methods into lenient service collections.
* add ugrid mesh-api stubs (SciTools#4001) * add additional mesh stubs (SciTools#4005) * Update mesh-data-model branch (SciTools#4009) (SciTools#4011) * Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> * MeshMetadata class. (SciTools#4002) * MeshMetadata class. * MeshMetadata extra members for dim names. * Comment for BaseMetadata refactoring. * add meshmetadata services (SciTools#4012) * Mesh api coord manager (SciTools#4015) * add mesh coordinate manager * wip * make shape methods private + reorganise method order * review actions * partial mesh * wip * Mesh data model to ng vat mesh api (SciTools#4023) * Update mesh-data-model branch (SciTools#4009) * Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> * Master to mesh data model (SciTools#4022) * Add abstract cube summary (SciTools#3987) Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> * add nox session conda list (SciTools#3990) * Added text to state the Python version used to build the docs. (SciTools#3989) * Added text to state the Python version used to build the docs. * Added footer template that includes the Python version used to build. * added new line * Review actions * added whatsnew * Iris py38 (SciTools#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * normalise version to implicit development release number (SciTools#3991) * Gallery: update COP maps example (SciTools#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (SciTools#3941) * Cubesummary tidy (SciTools#3988) * Extra tests; fix for array attributes. * Docstring for CubeSummary, and remove some unused parts. * Fix section name capitalisation, in line with existing cube summary. * Handle array differences; quote strings in extras and if 'awkward'-printing. * Ensure scalar string coord 'content' prints on one line. * update intersphinx mapping and matplotlib urls (SciTools#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (SciTools#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (SciTools#4006) * update setuptools description (SciTools#4008) * cirrus-ci compute credits (SciTools#4007) * update release process (SciTools#4010) * Stop using deprecated aliases of builtin types (SciTools#3997) * Stopped using deprecated aliases of builtin types. This is required to avoid warnings starting with NumPy 1.20.0. * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * Updated whatsnew. Co-authored-by: Bill Little <bill.little@metoffice.gov.uk> * celebrate first time iris contributors (SciTools#4013) * Docs unreleased banner (SciTools#3999) * baseline * removed debug comments * reverted * remove line * Testing * testing extensions * testing rtd_version * fixed if * removed line * tidy up * tidy comments * debug of pre-existing rtd variables * added reminder * testing * testing still * updated comments * added whatsnew * expanded the if conditiion * review actions * Update layout.html Remove alternative banner that used the RestructuredText notation. * review actions * drop __unicode__ method usage (SciTools#4018) * cirrus-ci conditional tasks (SciTools#4019) * cirrus-ci conditional tasks * use bc for bash arithmetic * revert back to sed * use expr * reword * minor documentation changes * review actions * make iris.common.metadata._hexdigest public (SciTools#4020) Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com> * Connectivity manager (SciTools#4017) * ConnectivityManager first pass. * ConnectivityManager align with proposed CoordManager. * Connectivity Manager review actions. * Connectivity Manager more review changes. * Use metadata_manager for Mesh location dimension. * Mesh dimension name abstraction. * Align Cooord and Connectivity Managers filters methods. * Completed Mesh class. * filter_cf improvements. * Moved filter_cf. * Mesh connectivity manager namedtuples comment. * Mesh removed trailing underscores. * Mesh _set_dimension_names improvements. * Mesh import rationalisation. * Mesh connectivity manager remove NDIM. * Connectivity manager use lazy indices_by_src(). * Connectivity manager clearer removal syntax. * Connectivity manager don't override __init__. * Connectivity manager correct base class syntax. * Metadata filter hexdigest reference fix. * test_MeshMetadata fix. * Rename filter to metadata_filter. * minor fixes (SciTools#4025) * minor fixes * wip * add mesh pickle support (SciTools#4026) * Test Mesh WIP. * Mesh face_dimension not set for topology_dimension=1. * Mesh testing WIP. * Mesh tests WIP. * Mesh tests WIP. * Mesh tests complete. * Mesh repr tests. * experimental.ugrid restore class ordering. * Mesh tests - move global and class variables into setUpClass methods, to play nicely with unittest. * Delete commented code. * Mesh clearer distinction between coords and connectivities filters. * Mesh tests slight readability improvement. Co-authored-by: Bill Little <bill.james.little@gmail.com> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Alexander Kuhn-Regnier <ahf.kuhnregnier@gmail.com>
* add mesh public doc-strings * review actions * review actions * review actions
* Add MeshCoord with basic tests. * Revised __init__; fixed copy mechanisms. Still WIP. * Apply suggestions from code review Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> * Review changes. * Rethink getitem and copy; test points and bounds results. * Fix for changed API on rebase. * Review changes. * Review changes. * Adjust equality behaviour, and test it. * Tiny fix. Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>
…590] (SciTools#4053) * Better calculations for MeshCoord lazy/real points and bounds. * Allow for possibly tranposed connectivity indices. * Handle connectivity src_dim and start_index: Tests that, and edge location. * Tidy following rebase. * Extra review change. * Simplify basic calc; test handling of invalid index values. * Review changes.
* MeshCoord str/repr support. * Left-over old review change. * Remove some unused legacy code.
* MeshCoord changes : add shape in printout; support __hash__ for use in sets/dicts. * Add mesh_coords key to Cube.coord/coords. With tests.
* Add cube mesh+location access methods. * Add tests for Cube.__eq__ with MeshCoords. * WIP: enforce compatibility of a cube's MeshCoords. * Add Cube.mesh_dim(); ensure all mesh-coords have the same cube dims. * Docstring fixes and improvements. * Factor out test-mesh-cube creation into iris.tests.stock. * Make cube.mesh and cube.location properties.
…VD-1681, AVD-1683) (SciTools#4074)
…ata-model Merge master to mesh data model
* initial support for unstructured plotting using pyvista * extend slider support for projections * add comments * review actions + slider event auto-updates picked cell stats * restructure with ugrid module * add notebook support * add rcParams + various fixes * cirrus-ci skip conda update * include add_title rcParams * review actions * review actions * fix slider label to support non-time * slider and picking units handling * review actions * add cell picking nan count * pin conda * pin mpl to 3.3.4 * update broken link * review actions * support ipyvtk notebook backend * undo cirrus-ci task skippers * skip autodocs building ugrid.plot
* Deduce correct topology-dimension from connectivities, and be tolerant on loading. * Added simple integration tests. * Review changes. * Review changes: use 'logging' module in place of 'warnings'. * Replace deprecated assertion method; check logged message levels. * Simplify logging tests; tidy synthetic file creation.
…dated Update the `mesh-data-model` feature branch wrt `main`
* add whatsnew for UGRID support * add description of UGRID work * fix links * add highlight * address review comments * address review comments * address review comments
trexfeathers
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Feature: UGRID
Type: Feature Branch
stephenworsley
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Aug 27, 2021
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Looks good to me.
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This should be merged into
mesh-data-model_updatedvia a merge commitLatest updates for the
mesh-data-modelfeature branch.mesh-data-model_updatedwill replace the currentmesh-data-model, but only after:I finish some offline benchmarking experiments