MeshMetadata class. #4002
Merged
MeshMetadata class. #4002
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
@bjlittle can you clarify: do we definitely not want to include |
|
@trexfeathers From our discussion, what I recall is that |
It should be the same behaviour for either, since we do not plan to allow for |
|
Ready for your review again @bjlittle. I've added the extra members for the dimension names. |
trexfeathers
force-pushed
the
mesh-metadata
branch
from
f764c9a
to
bc620a4
Compare
bjlittle
approved these changes
Feb 15, 2021
bjlittle
added a commit
that referenced
this pull request
Feb 23, 2021
* add ugrid mesh-api stubs (#4001) * add additional mesh stubs (#4005) * Update mesh-data-model branch (#4009) (#4011) * Add abstract cube summary (#3987) Co-authored-by: stephen.worsley <[email protected]> * add nox session conda list (#3990) * Added text to state the Python version used to build the docs. (#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 (#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 <[email protected]> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <[email protected]> * normalise version to implicit development release number (#3991) * Gallery: update COP maps example (#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (#3941) * Cubesummary tidy (#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 (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (#4006) * update setuptools description (#4008) Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> * MeshMetadata class. (#4002) * MeshMetadata class. * MeshMetadata extra members for dim names. * Comment for BaseMetadata refactoring. * add meshmetadata services (#4012) * Mesh api coord manager (#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 (#4023) * Update mesh-data-model branch (#4009) * Add abstract cube summary (#3987) Co-authored-by: stephen.worsley <[email protected]> * add nox session conda list (#3990) * Added text to state the Python version used to build the docs. (#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 (#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 <[email protected]> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <[email protected]> * normalise version to implicit development release number (#3991) * Gallery: update COP maps example (#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (#3941) * Cubesummary tidy (#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 (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (#4006) * update setuptools description (#4008) Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> * Master to mesh data model (#4022) * Add abstract cube summary (#3987) Co-authored-by: stephen.worsley <[email protected]> * add nox session conda list (#3990) * Added text to state the Python version used to build the docs. (#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 (#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 <[email protected]> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <[email protected]> * normalise version to implicit development release number (#3991) * Gallery: update COP maps example (#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (#3941) * Cubesummary tidy (#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 (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (#4006) * update setuptools description (#4008) * cirrus-ci compute credits (#4007) * update release process (#4010) * Stop using deprecated aliases of builtin types (#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 <[email protected]> * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <[email protected]> * Updated whatsnew. Co-authored-by: Bill Little <[email protected]> * celebrate first time iris contributors (#4013) * Docs unreleased banner (#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 (#4018) * cirrus-ci conditional tasks (#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 (#4020) Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Alexander Kuhn-Regnier <[email protected]> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Alexander Kuhn-Regnier <[email protected]> * Connectivity manager (#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 (#4025) * minor fixes * wip * add mesh pickle support (#4026) Co-authored-by: Bill Little <[email protected]> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Alexander Kuhn-Regnier <[email protected]>
bjlittle
added a commit
that referenced
this pull request
Feb 25, 2021
* add ugrid mesh-api stubs (#4001) * add additional mesh stubs (#4005) * Update mesh-data-model branch (#4009) (#4011) * Add abstract cube summary (#3987) Co-authored-by: stephen.worsley <[email protected]> * add nox session conda list (#3990) * Added text to state the Python version used to build the docs. (#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 (#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 <[email protected]> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <[email protected]> * normalise version to implicit development release number (#3991) * Gallery: update COP maps example (#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (#3941) * Cubesummary tidy (#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 (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (#4006) * update setuptools description (#4008) Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> * MeshMetadata class. (#4002) * MeshMetadata class. * MeshMetadata extra members for dim names. * Comment for BaseMetadata refactoring. * add meshmetadata services (#4012) * Mesh api coord manager (#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 (#4023) * Update mesh-data-model branch (#4009) * Add abstract cube summary (#3987) Co-authored-by: stephen.worsley <[email protected]> * add nox session conda list (#3990) * Added text to state the Python version used to build the docs. (#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 (#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 <[email protected]> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <[email protected]> * normalise version to implicit development release number (#3991) * Gallery: update COP maps example (#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (#3941) * Cubesummary tidy (#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 (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (#4006) * update setuptools description (#4008) Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> * Master to mesh data model (#4022) * Add abstract cube summary (#3987) Co-authored-by: stephen.worsley <[email protected]> * add nox session conda list (#3990) * Added text to state the Python version used to build the docs. (#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 (#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 <[email protected]> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <[email protected]> * normalise version to implicit development release number (#3991) * Gallery: update COP maps example (#3934) * update cop maps example * comment tweaks * minor comment tweak + whatsnew * reinstate whatsnew addition * remove duplicate whatsnew * don't support mpl v1.2 (#3941) * Cubesummary tidy (#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 (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * update readme badges (#4004) * update readme badges * pimp twitter badge * update readme logo img src and href (#4006) * update setuptools description (#4008) * cirrus-ci compute credits (#4007) * update release process (#4010) * Stop using deprecated aliases of builtin types (#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 <[email protected]> * Update lib/iris/tests/test_cell.py Co-authored-by: Bill Little <[email protected]> * Updated whatsnew. Co-authored-by: Bill Little <[email protected]> * celebrate first time iris contributors (#4013) * Docs unreleased banner (#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 (#4018) * cirrus-ci conditional tasks (#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 (#4020) Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Alexander Kuhn-Regnier <[email protected]> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Alexander Kuhn-Regnier <[email protected]> * Connectivity manager (#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 (#4025) * minor fixes * wip * add mesh pickle support (#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 <[email protected]> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: James Penn <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: Alexander Kuhn-Regnier <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
🚀 Pull Request
Description
Implemented the
MeshMetadataclass and tests, in readiness to support theMeshclass.Consult Iris pull request check list