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mergeback from main #5023

Merged
merged 107 commits into from
Oct 12, 2022
Merged

mergeback from main #5023

merged 107 commits into from
Oct 12, 2022

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pp-mo
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@pp-mo pp-mo commented Oct 12, 2022

Updating this F-B prior to restarting the work.
This will probably invalidate #4835, but that's OK I am about to put up a slightly more rational version

bjlittle and others added 30 commits June 28, 2022 10:32
@bjlittle
Python 3.9 CI & Combine CI workflows (#4832)
a908a27 
* combine ci workflows

* remove badge

* ci unpin python
@bjlittle
post #4759 review actions (#4833)
92f5840
@bjlittle
pytest less verbose (#4837)
b21edd0
@rcomer
Remove redundant testing assert methods (#4838)
ded2a4d 
* remove assertWarnsRegexp

* remove assertStringEqual

* post rebase tidyings

* whatsnew
@trexfeathers
NetCDF Generation Adjustments (#4836)
32b515b
@bjlittle
remove pillow pin from setup.cfg (#4839)
07b223a
@bjlittle
Support python 3.10 (#4840)
44fae03 
* extend ci support for py310

* fix Cell.__hash__ py310 nan behaviour

* review actions
@bjlittle
update github app docs (#4844)
40e9a9e
@rcomer @web-flow
Lockfile update and Gregorian to Standard calendar change (#4847)
158b015 
* sed gregorian

* sed CALENDAR_GREGORIAN

* rename cml files

* revert whatsnew 2.1 and test_cf.py

* revert spelling_allow

* post rebase sed 'gregorian'

* Updated environment lockfiles

* cf-units minimum pin

* review actions

Co-authored-by: Lockfile bot <[email protected]>
@scitools-ci @web-flow
Updated environment lockfiles (#4850)
7187b0e 
Co-authored-by: Lockfile bot <[email protected]>
@bjlittle
avoid setuptools deprecation (#4848)
c0c86c2
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#4851)
28da785 
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](pre-commit/pre-commit-hooks@v4.2.0...v4.3.0)
- [github.com/psf/black: 22.3.0 → 22.6.0](psf/black@22.3.0...22.6.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@bjlittle
Alternative Cell.__hash__ implementation for NaN support (#4852)
7992fb5 
* Alternative Cell.__hash__ implementation for NaN support

* add whatsnew entry
@bjlittle
whatsnew update (#4853)
d9318f5
@bjlittle
adopt setuptools-scm for auto versioning (#4841)
036c90c 
* adopt setuptools-scm for auto versioning

* update py310.yml requirements

* update locks

* simplify docs version

* update dev release docs

* update .gitignore for vscode

* update locks

* add exclude _version.py to MANIFEST.in

* review actions

* update lock files

* update pyproject.toml

* what a whatsnew entry
@bjlittle
fix rtd version (#4855)
573780b
@scitools-ci @web-flow
Updated environment lockfiles (#4858)
2cbaec7 
Co-authored-by: Lockfile bot <[email protected]>
@rcomer
pytest verbosity (#4861)
2e63cdc
@scitools-ci @web-flow
Updated environment lockfiles (#4867)
7b12120 
Co-authored-by: Lockfile bot <[email protected]>
@rcomer
Recommend pytest in developer guide (#4866)
7800907 
* recommend pytest

* pros and cons

* tweaks
@rcomer
add missing skips (#4865)
56a97d6
@scitools-ci @web-flow
Updated environment lockfiles (#4873)
09fac5b 
Co-authored-by: Lockfile bot <[email protected]>
@rcomer
Replace testing helper function (#4878)
1f7a4a7 
* replace unmasked_data_as_1d_array

* whatsnew
@rcomer @pre-commit-ci
Cube arithmetic array type handling (#3790)
2b3329f 
* add new tests; fix existing tests

* force lhs lazy if rhs lazy

* black

* add in-place tests

* add handling for unmasked, masked real array combo

* add tests for false skeleton

* rearrange _math_op_common if-loops

* revert maths.py to upstream/master

* simpler solution

* reduce masking arithmetic tests

* expand and improve tests

* add whatsnew

* fix rebase snafu

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update following numpy#21977

* Revert "update following numpy#21977"

This reverts commit 7d62ad6.

* update comment

* a before b

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@bjlittle @trexfeathers
automate sdist and wheel build and publish (#4849)
f3a7234 
* automate sdist and wheel build and publish

* update names

* tidy package manifest and discovery

* add note to dev docs

* update MANIFEST.in

* Update .github/workflows/ci-wheels.yml

Co-authored-by: Martin Yeo <[email protected]>

* add unshallow comment to rtd

* reinstate docs release

* add pypa build comment

* test wheel

* added whatnew + tweak nox wheel emsgs

* Update docs/src/developers_guide/release.rst

Co-authored-by: Martin Yeo <[email protected]>
@trexfeathers
Warn users of increased recombine_submeshes memory demand. (#4881)
22854da 
* Warn users of increased recombine_submeshes memory demand.

* Clearer what's new entry.
@bjlittle
Sphinx reset modules (#4885)
597be8a 
* fix sphinx-gallery

* change gallery index reference
@scitools-ci @web-flow
Updated environment lockfiles (#4884)
caad256 
Co-authored-by: Lockfile bot <[email protected]>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#4886)
b6b54cf 
updates:
- [github.com/PyCQA/flake8: 4.0.1 → 5.0.2](PyCQA/flake8@4.0.1...5.0.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@rcomer
fix percentile docstring (#4888)
08fe9c1
scitools-ci bot and others added 29 commits September 20, 2022 09:51
@scitools-ci @web-flow
Updated environment lockfiles (#4971)
0dea897 
Co-authored-by: Lockfile bot <[email protected]>
@dependabot
Bump peter-evans/create-pull-request from 4.1.1 to 4.1.2 (#4974)
46755fa 
Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.1.1 to 4.1.2.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@18f9043...171dd55)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot
Bump actions/stale from 5 to 6 (#4977)
d18b84c 
Bumps [actions/stale](https://github.com/actions/stale) from 5 to 6.
- [Release notes](https://github.com/actions/stale/releases)
- [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md)
- [Commits](actions/stale@v5...v6)

---
updated-dependencies:
- dependency-name: actions/stale
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@stephenworsley
Update release guide (#4963)
a131d86 
* update release guide

* adress review comments
@lbdreyer
Add short entry to release guide about what to do with the whats new …
831816e 
…for point releases. (#4980)
@pp-mo @lbdreyer
Reinstate CubeList._repr_html_() (#4976)
1d6d979 
* Test the calls implementing Cube and Cubelist printing, and repr_html().

* Reinstate CubeList._repr_html_() method.

* Review changes.

* Add whatsnew.

* Typo in whatsnew.

* Update docs/src/whatsnew/3.3.rst

Co-authored-by: lbdreyer <[email protected]>

Co-authored-by: lbdreyer <[email protected]>
@scitools-ci @web-flow
Updated environment lockfiles (#4991)
04e5920 
Co-authored-by: Lockfile bot <[email protected]>
@pp-mo
Fix name loader problem (#4933)
d38c504 
* Fix name loader problem; enforce expected type of all cube cell_methods.

* Review change: fix import order.

* Update imagerepo.json for skipped changes from test-iris-imagehash v0.16.
@trexfeathers @web-flow
Port dependency fixes to v3.3.x. (#4992)
2a41be2 
* Lockfile updates (#4968)

* Updated environment lockfiles

* Adjustments for Cartopy v0.21.0 (SciTools/cartopy@fcb784d).

* Cartopy >=0.21 pin.

* What's New entry.

* WIP try netCDF4 pin.

* Try pip installing netcdf4==1.6.1 as requested by @ocefpaf.

* Revert "Try pip installing netcdf4==1.6.1 as requested by @ocefpaf."

This reverts commit ce9f890.

* netcdf4!=1.6.1

* Align Conda YAML formatting.

Co-authored-by: Lockfile bot <[email protected]>

* New lockfiles.

* What's New entry.

* What's New correction.

Co-authored-by: Lockfile bot <[email protected]>
@dependabot
Bump peter-evans/create-pull-request from 4.1.2 to 4.1.3 (#4995)
e96a053 
Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.1.2 to 4.1.3.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@171dd55...671dc9c)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@pp-mo
Netcdf separate loadsave (#4803)
d8f8dac 
* Split iris.fileformats.netcdf into separate load+save submodules.

* Fix mutable default.

* Fixes.

* Fix iris.fileformats.netdf.__all__.

* Fix tests.

* Fix license header.

* Move unit tests for sub-module APIs.

* Review changes.

* Add whatsnew; slightly improved module docstrings.
@ESadek-MO
Added a glossary for Iris docs. (#4902)
96c00b6
@trexfeathers
Adaptions for Matplotlib 3.6 (#4998)
04e757f 
* Change deprecated MPL colormap registration - matplotlib/matplotlib#23668.

* Adapt benchmark for importing palette to cope with MPL 3.6.

* What's New entry.

* What's New typo.

* Reformat import_iris imports.
@stephenworsley
Update whatsnew for 3.3.1 release (#5002)
6829e61 
* set whatsnew release date

* fix whatsnew
@trexfeathers
Fix benchmarks netcdf import (#5001)
da03d73 
* Enable manual GHA benchmark run with custom first_commit.

* Modified benchmark netcdf import - #4803.
@stephenworsley
Merge branch 'v3.3.x' into mergeback_v3.3.1
c4781ec 
* v3.3.x:
  Update whatsnew for 3.3.1 release (#5002)
  Port dependency fixes to `v3.3.x`. (#4992)
  Fix name loader problem (#4933)
  Reinstate CubeList._repr_html_() (#4976)

# Conflicts:
#	.github/workflows/ci-tests.yml
#	requirements/ci/nox.lock/py310-linux-64.lock
#	requirements/ci/nox.lock/py38-linux-64.lock
#	requirements/ci/nox.lock/py39-linux-64.lock
#	requirements/ci/py310.yml
#	requirements/ci/py38.yml
#	requirements/ci/py39.yml
#	setup.cfg
@trexfeathers
Merge pull request #5004 from stephenworsley/mergeback_v3.3.1
f69b93f 
Mergeback v3.3.1
@bouweandela @trexfeathers
Speed up operations that use the Coord.cells method for time coordi…
2742211 
…nates (#4969)

* Convert all time points at once before generating cells

* Small simplification

* Add a whatnew entry

* Fix link

Co-authored-by: Martin Yeo <[email protected]>

Co-authored-by: Martin Yeo <[email protected]>
@trexfeathers
Correct wrong type of equality check in benchmark GHA. (#5005)
24ff3bd
@rcomer
remove outline workaround (#4999)
04122c0
@scitools-ci @web-flow
Updated environment lockfiles (#5008)
7ba620e 
Co-authored-by: Lockfile bot <[email protected]>
@ESadek-MO
Updated "glossary" entry to link to iris glossary (#5012)
536ff51 
Instead of Python-Glossary
@rcomer @pp-mo
DOC: add show option to Makefiles (#5000)
b5245f6 
* DOC: add show option to Makefiles

* fix typo

Co-authored-by: Patrick Peglar <[email protected]>

Co-authored-by: Patrick Peglar <[email protected]>
@pp-mo
Sample code to convert ORCA data into a meshcube. (#5013)
959b590 
* Sample code to convert ORCA data into a meshcube.

* Better illustrative image.

* Added whatsnew.
@trexfeathers
New LBFC-CF mappings (#4859)
bae9953 
* New LBFC-CF mappings based on info from Julian Heming.

* Further mappings.

* What's New entry.
@rcomer
Cell comparison: remove ancient netcdftime/cftime workarounds (#4729)
d1f3e45 
* remove ancient workarounds

* whatsnew
@scitools-ci @web-flow
Updated environment lockfiles (#5018)
379c098 
Co-authored-by: Lockfile bot <[email protected]>
@bouweandela
Speed up Cube.subset/Coord.intersect (#4955)
6117f60 
* Speed up Cube.subset/Coord.intersect

* Add a whatsnew entry
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#5021)
ea67311 
updates:
- [github.com/psf/black: 22.8.0 → 22.10.0](psf/black@22.8.0...22.10.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pp-mo pp-mo merged commit d93ad62 into FEATURE_xarray_readwrite Oct 12, 2022
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10 participants
@pp-mo @bjlittle @rcomer @trexfeathers @krikru @lbdreyer @stephenworsley @ESadek-MO @schlunma @bouweandela