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Gallery: update COP maps example #3934

Merged
merged 5 commits into from
Feb 10, 2021
Merged

Gallery: update COP maps example #3934

merged 5 commits into from
Feb 10, 2021

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rcomer
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@rcomer rcomer commented Dec 7, 2020 •
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🚀 Pull Request

Description

Some bits of this example weren't doing what its comments said it was doing. Other bits just didn't make sense to me:

  • The callback function was supposed to get the "experiment" from the directory name, but the files are all in the top level sample_data directory, so this added coordinate was the same regardless of file. Part of the reason this hasn't been noticed before was probably because the "experiment" coordinate never got used after it was added. I've updated the callback to get the experiment out of the filename. Also loaded the two files together, then extracted the cubes in a loop. This is a little contrived, but gives us an excuse to use the coordinate we went to the trouble of adding with the callback. It's also the first time I've used CubeList.extract_cube (new at Iris v3!)

  • Looping through slices of the cubes doesn't make sense to me as there is only one latitude-longitude slice. I have instead looped through the experiments as this reduces repeated code.

  • The suptitle comment claimed it was using the date in the format "MonthName Year", when it was actually just "Year" 🤷‍♀️

  • For the colour array, I've used np.stack instead of np.array and .T because, well, I just like np.stack.

Consult Iris pull request check list

@rcomer rcomer changed the title Gallery: update COP maps Gallery: update COP maps example Dec 7, 2020
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rcomer commented Dec 23, 2020

Alternatively, the callback function could just be removed. The plot will obviously work fine without it. For a user who is actively looking for advice on writing callback functions, I'm not sure that the gallery would be the obvious place to look, as it's really about plotting.

@trexfeathers trexfeathers added the Peloton 🚴‍♂️ Target a breakaway issue to be caught and closed by the peloton label Jan 6, 2021
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rcomer commented Jan 27, 2021

Rebased 💃

@bjlittle bjlittle assigned jamesp and unassigned pp-mo Feb 3, 2021
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jamesp commented Feb 8, 2021

Hi @rcomer, I'm going to take a look at this PR for you. The docs have had a bit of a re-org over the last week, would you mind rebasing this PR on the latest main? thanks!

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rcomer commented Feb 8, 2021

Thanks @jamesp, I have now rebased and think everything is in order.

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jamesp approved these changes Feb 10, 2021
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Looks good to me @rcomer, thanks for the contribution! 👍

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jamesp commented Feb 10, 2021

Alternatively, the callback function could just be removed. The plot will obviously work fine without it. For a user who is actively looking for advice on writing callback functions, I'm not sure that the gallery would be the obvious place to look, as it's really about plotting.

As a new user getting to know iris, I found the callback use helpful. Up until then I didn't realise it was possible so I wouldn't have even known what to search for! It's a good addition to the examples.

@jamesp jamesp merged commit 9317133 into SciTools:master Feb 10, 2021
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rcomer commented Feb 10, 2021

Thanks @jamesp, great to have a fresh pair of eyes on this 👀

@rcomer rcomer deleted the gallery-cop-maps branch February 11, 2021 10:53
trexfeathers pushed a commit that referenced this pull request Feb 15, 2021
@bjlittle @pp-mo
@stephenworsley @tkknight @jamesp @rcomer
Update mesh-data-model branch (#4009)
7e541ec 
* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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>
trexfeathers pushed a commit that referenced this pull request Feb 15, 2021
@bjlittle @pp-mo
@stephenworsley @tkknight @jamesp @rcomer
Update mesh-data-model branch (#4009) (#4011)
04ec3b2 
* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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>
trexfeathers pushed a commit that referenced this pull request Feb 22, 2021
@bjlittle @pp-mo
@stephenworsley @tkknight @jamesp @rcomer @akuhnregnier
Master to mesh data model (#4022)
59fa3f1 
* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#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 <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>
trexfeathers pushed a commit that referenced this pull request Feb 22, 2021
@bjlittle @pp-mo
@stephenworsley @tkknight @jamesp @rcomer @akuhnregnier
Mesh data model to ng vat mesh api (#4023)
eb7dfc3 
* Update mesh-data-model branch (#4009)

* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#4022)

* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#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 <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>
bjlittle added a commit that referenced this pull request Feb 23, 2021
@trexfeathers @bjlittle
@pp-mo @stephenworsley @tkknight @jamesp @rcomer @akuhnregnier
Mesh API Merge-Back (#4027)
520d135 
* 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 <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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. (#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 <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#4022)

* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#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 <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 (#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 <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>
bjlittle added a commit that referenced this pull request Feb 25, 2021
@trexfeathers @bjlittle
@pp-mo @stephenworsley @tkknight @jamesp @rcomer @akuhnregnier
Mesh tests (#4034)
48028e9 
* 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 <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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. (#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 <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#4022)

* Add abstract cube summary (#3987)

Co-authored-by: stephen.worsley <stephen.worsley@metoffice.gov.uk>

* 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 <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 (#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 <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 (#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 <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 (#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 <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>
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@rcomer @jamesp @pp-mo @trexfeathers