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Loading Benchmarks #4477

Merged
merged 24 commits into from
Feb 14, 2022
Merged

Loading Benchmarks #4477

merged 24 commits into from
Feb 14, 2022

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trexfeathers
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@trexfeathers trexfeathers commented Jan 5, 2022 •
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🚀 Pull Request

Description

  • Adds our tried and tested (offline and in iris-esmf-regrid) framework for stable generation of test data for benchmarks.
  • Introduces a method (create_um_files()) for generating synthetic FF/PP/NetCDF files for benchmarking, using Mule.
    • This avoids reliance on [potentially enormous] real files.
    • We can size the files appropriately for benchmarking purposes.
    • A useful tool when following up on performance regressions that need more info.
  • Ports our existing loading benchmarks from the offline benchmark suite.
    With some adaptations to use the new synthetic data generation.

I believe synthetic FF file generation removes the last major blocker to fully migrating our remaining offline benchmarks onto GitHub 🤞

Consult Iris pull request check list

@trexfeathers
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Have decided against caching the generated benchmark data in the GHA job - GHA relies on working out whether or not to cache at the start of the job, it is not possible to check for changes during/after. This therefore forces us to always cache, which adds time/resource when 95% of the time it would be unnecessary.

Given benchmarks run during CI will necessarily be quick - i.e. small synthetic data - it is quicker and simpler to generate data files fresh at the start of the GHA job. The benchmarks at least have the intelligence to re-use the files once they are there.

@jamesp
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jamesp commented Jan 6, 2022

I don't know how complicated your data gen scripts are, but it might be the case that regen is actually faster than restoring from cache if CPU gen speed > network IO speed.

@trexfeathers
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I don't know how complicated your data gen scripts are, but it might be the case that regen is actually faster than restoring from cache if CPU gen speed > network IO speed.

Exactly. My thoughts, but more succinct!

@wjbenfold
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Does it make sense to use real data in some of these benchmarks as well as synthetic (as a sanity check perhaps?). I believe that the benchmarks already have access to the test data

@trexfeathers
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Does it make sense to use real data in some of these benchmarks as well as synthetic (as a sanity check perhaps?). I believe that the benchmarks already have access to the test data

We've seen a few issues where a pp file with lots of layers is significantly less performant than one with a few - could we try another shape (if I understand what's here correctly) that's not very wide but quite deep?

@wjbenfold even if I make no more changes to this PR, I'm already worried about:

  1. The CI runtime
  2. The size of the changes in this PR

Better coverage is always good in principle, but benchmarks take a long time to run. So to solve Point 1 I have some future plans for splitting benchmarks into categories: CI / semi-regular / on-demand, but the complexity of that runs up against Point 2. So I'd like to lay that groundwork in a future PR, not this one, after which the whole team will hopefully find it much easier to expand benchmark coverage without my help/interference.

pre-commit-ci bot and others added 4 commits February 1, 2022 10:54
@pre-commit-ci @lbdreyer
[pre-commit.ci] pre-commit autoupdate (SciTools#4560)
d503ce6 
* v3.2.0rc0 whats new and version string (SciTools#4557)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 21.12b0 → 22.1.0](psf/black@21.12b0...22.1.0)
- [github.com/asottile/blacken-docs: v1.12.0 → v1.12.1](adamchainz/blacken-docs@v1.12.0...v1.12.1)

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

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

Co-authored-by: lbdreyer <lbdreyer@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@trexfeathers
Merge remote-tracking branch 'upstream/main' into all_benchmarks
81c4bcf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
ca169af 
for more information, see https://pre-commit.ci
@trexfeathers
Kick Cirrus.
73b8d84
@trexfeathers trexfeathers mentioned this pull request Feb 2, 2022
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pp-mo
pp-mo requested changes Feb 11, 2022
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Thanks @trexfeathers looking rather good.

Unfortunately, I'm not done with this yet, but I thought I should complete this review now so you can see my initial comments + get started on that.
Sorry for the delay, I'll get some more done this afternoon.

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Just a few points, most of them cosmetic.
Feel free to resolve whatever you may consider + reject.
Overall looking good ! 💐

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All good now except remaining question on #4477 (comment)
We can discuss that + either change it or not.
Will then merge !

@pp-mo pp-mo merged commit 15bd351 into SciTools:main Feb 14, 2022
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Thanks @pp-mo!

tkknight added a commit to tkknight/iris that referenced this pull request Mar 2, 2022
@tkknight
Merge branch 'main' into votable_issues
ea2064a 
* main: (69 commits)
  Revert plotting-vs-y (SciTools#4601)
  Bump peter-evans/create-pull-request from 3.13.0 to 3.14.0 (SciTools#4608)
  Support false-easting and false-northing when loading Mercator-projected data (SciTools#4524)
  Bump peter-evans/create-pull-request from 3.12.1 to 3.13.0 (SciTools#4607)
  Stop using nc_time_axis.CalendarDateTime (SciTools#4584)
  Utility class in netcdf loader should not be public. (SciTools#4592)
  Overnight benchmarks (SciTools#4583)
  Yaml fixes + clarifications. (SciTools#4594)
  Bump actions/script from 5.1.0 to 6 (SciTools#4586)
  Add missing commit to v3.2.x and update version number (SciTools#4593)
  docs linkcheck skip (SciTools#4590)
  Finalise whatsnew and version string update (SciTools#4588)
  [pre-commit.ci] pre-commit autoupdate (SciTools#4587)
  fix test (SciTools#4585)
  Loading Benchmarks (SciTools#4477)
  Fix load_http bug, extend testing, and note to docs (SciTools#4580)
  New tool-agnostic ASV environment management (SciTools#4571)
  Fix refresh lockfile worrkflow pull request title (SciTools#4579)
  gha: lockfiles labels and auto-pr details (SciTools#4578)
  Bump actions/script from 4 to 5.1.0 (SciTools#4576)
  ...
tkknight added a commit to tkknight/iris that referenced this pull request Mar 16, 2022
@tkknight
Merge branch 'main' into theme_play
98c5d9b 
* main: (64 commits)
  [pre-commit.ci] pre-commit autoupdate (SciTools#4587)
  fix test (SciTools#4585)
  Loading Benchmarks (SciTools#4477)
  Fix refresh lockfile worrkflow pull request title (SciTools#4579)
  gha: lockfiles labels and auto-pr details (SciTools#4578)
  Bump actions/script from 4 to 5.1.0 (SciTools#4576)
  Bump actions/stale from 4.0.0 to 4.1.0 (SciTools#4575)
  Bump peter-evans/create-pull-request from 3.8.2 to 3.12.1 (SciTools#4577)
  adopt dependabot GHA (SciTools#4568)
  New tool-agnostic ASV environment management (SciTools#4571)
  Updated environment lockfiles (SciTools#4567)
  Update version to 3.3.dev0 (SciTools#4565)
  Reset whats new (SciTools#4563)
  docs: move whatsnew (SciTools#4540)
  Deprecate regrids (SciTools#4548)
  Update latest.rst (SciTools#4556)
  Updated environment lockfiles (SciTools#4555)
  Added whatsnew for SciTools#4551. (SciTools#4553)
  Update SciTools#4505 doctests for SciTools#4528. (SciTools#4554)
  minor optimisations (SciTools#4549)
  ...
@trexfeathers trexfeathers deleted the all_benchmarks branch March 31, 2022 13:45
lbdreyer added a commit to lbdreyer/iris that referenced this pull request Sep 14, 2022
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Qa issue (#9)
edd6c33 
* 3.2 version and whats new (#4559)

* Reset whats new (#4563)

* reset whats new

* Specify minor in whats new

* update trove classifiers (#4564)

* Update version to 3.3.dev0 (#4565)

* Updated environment lockfiles (#4567)

Co-authored-by: Lockfile bot <noreply@github.com>

* New tool-agnostic ASV environment management (#4571)

* New tool-agnostic ASV env management.

* Benchmarking only build the latest Python.

* Increase benchmark accuracy by increasing rounds.

* Fix ASV rounds mistake.

* ASV clearer use of _interpolate_commands.

* adopt dependabot GHA (#4568)

* Bump peter-evans/create-pull-request from 3.8.2 to 3.12.1 (#4577)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3.8.2 to 3.12.1.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/052fc72b4198ba9fbc81b818c6e1859f747d49a8...f22a7da129c901513876a2380e2dae9f8e145330)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/stale from 4.0.0 to 4.1.0 (#4575)

Bumps [actions/stale](https://github.com/actions/stale) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/actions/stale/releases)
- [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/stale/compare/v4.0.0...v4.1.0)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/script from 4 to 5.1.0 (#4576)

* gha: lockfiles labels and auto-pr details (#4578)

* Fix refresh lockfile worrkflow pull request title (#4579)

* New tool-agnostic ASV environment management (#4571)

* New tool-agnostic ASV env management.

* Benchmarking only build the latest Python.

* Increase benchmark accuracy by increasing rounds.

* Fix ASV rounds mistake.

* ASV clearer use of _interpolate_commands.

* Fix load_http bug, extend testing, and note to docs (#4580)

* Fix opendap bug, add docs and extra testing

* Add whats new entry

* Update docs/src/whatsnew/3.2.rst

Co-authored-by: Bill Little <bill.little@metoffice.gov.uk>

* Add warning box

Co-authored-by: Bill Little <bill.little@metoffice.gov.uk>

* Loading Benchmarks (#4477)

* Synthetic FF PP NetCDF and loading benchmarks.

* fix test (#4585)

* [pre-commit.ci] pre-commit autoupdate (#4587)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 21.12b0 → 22.1.0](https://github.com/psf/black/compare/21.12b0...22.1.0)
- [github.com/asottile/blacken-docs: v1.12.0 → v1.12.1](https://github.com/asottile/blacken-docs/compare/v1.12.0...v1.12.1)
- [github.com/aio-libs/sort-all: v1.1.0 → v1.2.0](https://github.com/aio-libs/sort-all/compare/v1.1.0...v1.2.0)

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

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Finalise whatsnew and version string update (#4588)

* docs linkcheck skip (#4590)

* Add missing commit to v3.2.x and update version number (#4593)

* fix trove classifier (#4324)

* update version to 3.2. post release

Co-authored-by: Bill Little <bill.james.little@gmail.com>

* Bump actions/script from 5.1.0 to 6 (#4586)

Bumps [actions/script](https://github.com/actions/script) from 5.1.0 to 6.
- [Release notes](https://github.com/actions/script/releases)
- [Commits](https://github.com/actions/script/compare/v5.1.0...v6)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Yaml fixes + clarifications. (#4594)

* Yaml fixes + clarifications.

* Update .github/workflows/stale.yml

Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com>

Co-authored-by: Bill Little <bill.little@metoffice.gov.uk>
Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com>

* Overnight benchmarks (#4583)

* Utility class in netcdf loader should not be public. (#4592)

* Utility class in netcdf loader should not be public.

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

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

* Rename container for better clarity.

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Stop using nc_time_axis.CalendarDateTime (#4584)

* stop using CalendarDateTime

* update dependencies

* stronger tests for _fixup_dates

* add whatsnew

* Update 3.2.rst whats new with section for bug fixes (#4604)

* Bump peter-evans/create-pull-request from 3.12.1 to 3.13.0 (#4607)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3.12.1 to 3.13.0.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/f22a7da129c901513876a2380e2dae9f8e145330...89265e8d24a5dea438a2577fdc409a11e9f855ca)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Support false-easting and false-northing when loading Mercator-projected data (#4524)

* Add extra pieces to get false easting and northing

* tests

* Add extra test file ref and cml

* lib/iris/tests/results/netcdf/netcdf_merc_false.cml

* Update cml for new test data

* Bump test data version for cirrus

* What's new

* Bump peter-evans/create-pull-request from 3.13.0 to 3.14.0 (#4608)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3.13.0 to 3.14.0.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/89265e8d24a5dea438a2577fdc409a11e9f855ca...18f7dc018cc2cd597073088f7c7591b9d1c02672)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Revert plotting-vs-y (#4601)

* revert plotting-vs-y

* whatsnew

* Bump actions/stale from 4.1.0 to 5 (#4612)

Bumps [actions/stale](https://github.com/actions/stale) from 4.1.0 to 5.
- [Release notes](https://github.com/actions/stale/releases)
- [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/stale/compare/v4.1.0...v5)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/checkout from 2 to 3 (#4611)

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...v3)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Use crs.globe in _crs_distance_differentials() (#4605)

* Use crs.globe in _crs_distance_differentials(), add a relevant test, update whatsnew

* add a ref to the issue and PR

* add dennis (#4614)

* Final offline benchmark migration (#4562)

* Overnight benchmarks remove ambiguity between file and commit names. (#4620)

* purge deploy key (#4615)

* Remove no_clobber task from Refresh lockfiles Action (#4618)

* Remove no_clobber task from Refresh lockfiles Action

* review actions - add extra infor to pr message

* Scalar Scatter Plot (#4616)

* add failing test

* pass test

* initial review actions

* test 2nd arg scalar

* whatsnew

* Updated environment lockfiles (#4624)

Co-authored-by: Lockfile bot <noreply@github.com>

* Overnight benchmarks - find a valid issue assignee (#4627)

* Overnight benchmarks find a valid issue assignee.

* Overnight benchmarks safer check for a valid issue assignee.

* Votable Issues (#4617)

* Create test2.yml

* gha test

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* Update refresh-votable-issues.yml

* initial

* tidy

* updated whatsnew

* removed defunct ext links

* Update docs/src/votable_issues.rst

Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com>

* added suggestion to subscribe to voted issues.

* Renamed votable to voted.  Layout tweaks to the voted issues page.

Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com>

* Avoid dimensionality mismatch between data array and CF variables. (#4610)

* Sperf & Cperf Benchmarks (#4621)

* Update version to 3.2.1 and fix whatsnew (#4635)

* Improve Small Benchmark Accuracy (#4636)

* Remove another memory benchmark that's smaller than the noise level.

* Fixed import benchmarks.

* Updated GHA frequency and table name for Voted Issues (#4641)

* updated gha frequency and table name

* added new ignore for linkcheck

* use conda-lock -k explicit (#4644)

* Bump actions/cache from 2 to 3 (#4650)

Bumps [actions/cache](https://github.com/actions/cache) from 2 to 3.
- [Release notes](https://github.com/actions/cache/releases)
- [Commits](https://github.com/actions/cache/compare/v2...v3)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump peter-evans/create-pull-request from 3.14.0 to 4 (#4652)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3.14.0 to 4.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/18f7dc018cc2cd597073088f7c7591b9d1c02672...d6d5519d05f5814158ef015b8448f2f74648c421)

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

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Fix aggregated_by mdtol/masked constant problem (#4246)

* add failing test

* pass test

* whatsnew

* remove redundant copy call

* Make iris.tests.stock.simple_1d respect bounds arg (#4658)

* Make iris.tests.stock.simple_1d respect bounds arg

* What's new

* What's new

* Improved check for valid user in overnight BM run. (#4659)

* Preserve position when replacing Axes with GeoAxes (#4273)

* preserve position

* add test

* comment to clarify test

* whatsnew

* use original position

* Lazy Percentile Aggregator (#3901)

* implement lazy percentile

* fix map_complete_blocks tests

* fix legacy masked type no mask tests

* add test for map_complete_blocks on dask array

* handle axis expressed as sequence

* fix docstring

* add lazy_aggregate method and mdtol handling

* reshape for multi-dim collapse

* mdtol handling for added trailing dimension

* update aggregator instance docstring

* simplify array reshape

* factor out array reshaping as decorator

* reduce repetition in tests

* PERCENTILE multi-axis tests

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* review: remove docstring kwarg; define _real_percentile

* review: blank line for note

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* review: generalise MaskedCalcMixin

* review: remove stray as_lazy_data calls

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* review: use MultiAxisMixin in both lazy classes

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* Fix nearest_neighbour_index for edge case where requested point is float and bounds are int (#4245)

* add failing test

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* Roughly functional, but lots of tests to fix.

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* --no-edit

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* 'Deep' benchmarks to catch scaling with field count (#4654)

* 'Deep' benchmarks to catch scaling with field count

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* Automatic reversal of DimCoord bounds (#4466)

* first pass at ensuring contiguous bounds

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* Reorder Constraints sections of user guide, add time bounds example (#4656)

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* Bump peter-evans/create-pull-request from 4.0.0 to 4.0.1 (#4675)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.0 to 4.0.1.
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* tweak whatsnew (#4682)

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* Update percentile tests (#4684)

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* Bump actions/download-artifact from 2 to 3 (#4686)

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* Bump actions/upload-artifact from 2 to 3 (#4687)

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* Bump peter-evans/create-pull-request from 4.0.1 to 4.0.2 (#4688)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.1 to 4.0.2.
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* Add dynamic matrix to refresh lockfile job (#4573)

* Add dynamic matrix to refresh lockfile job

* review actions

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* Comment rendering (#4689)

* used numpy docstrings to fix docs rendering

* comment rejig

* apply numpydoc strings

* corrected notes

* updated docstring guidance.

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* review actions.

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* Cache regular points generation (#4698)

* Cache regular points generation

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* Git ignore the benchmarks data folder

* Update path and description

* Catch `AttributeError` from removing `CFReader._dataset` when it doesn't exist (#4646)

* Implement full Mercator parameter support (#4609)

* Changes to coord_systems

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* Define both standard_parallel and scale_factor... but leave one None

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* Test updates and additions

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* Add evertrol to whatsnew of #4646 given #4705 (#4709)

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* credit Will's epic review (#4711)

* add bullet (#4715)

* Weighted `aggregated_by` (#4589)

* First suggestion for weighted aggregated_by

* Added lazy weighted aggregation

* Added first tests for weighted aggregated_by

* Added further tests and allowed returned kwarg

* Added unit tests for weighted aggregated_by

* Moved _get_aggregator_fn to iris.analyis

* Reused 'returned' keyword

* Added test for lazy output if 'returned' is used

* Removed checksum=False from tests

* Expanded test for lazy aggregation since PERCENTILE is lazy now

* Added schlunma to common links

* Addaux speedup (#4718)

* Attempt faster add-aux-fact

* Added whatsnew draft.

* Put PR ref into whatsnew.

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* Remove time_return benchmarks. (#4717)

* Credit reviewer in what's new contributions. (#4705)

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* Change Cell equality to equate nans (fixes #4681) (#4701)

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* Netcdf saving: workaround known netcdf bug. (#4407)

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* Added tests for all the different places where code was fixed.

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* Review changes.

* Updated environment lockfiles (#4724)

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* MAX_RUN into docs (#4726)

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* transform_points test

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* In datums, unknown means None

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* Bump peter-evans/create-pull-request from 4.0.2 to 4.0.3 (#4733)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.2 to 4.0.3.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
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* Updated environment lockfiles (#4732)

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* Replace nose with pytest (#4734)

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* Remove Mule monkey patch. (#4738)

* climatology doc tweak (#4740)

* Mesh docs - include examples of converting different mesh formats. (#4739)

* Mesh docs - include examples of converting different mesh formats.

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* Add sample images to mesh conversion examples.

* Mesh conversion examples - fix bullet points.

* Mesh conversion examples - print meshes.

* Whats New entry.

* Mesh conversion examples - more detailed comments.

* Gallery: update NEMO example (#4741)

* update nemo example

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* Extend any kwarg array

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* Set stacklevel to get more useful FutureWarning

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* Only generate crs and globe on demand, handle attr setting

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* Permit fast percentile with mdtol=0 (#4755)

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* Interpolate all points at once rather than sequentially

* This splits the internals of cube.interpolate in an effort not to make so much superfluous data, but is slow

* Generate the extra values then discard them, but with minimal looping

* Updated docstrings to clarify behaviour

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* Update error thrown for aux coord over interpolated and uninterpolated dimensions, and add unit tests

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* Add failing test for brackets within comments

* Fix test

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* Add additional failing test for multiple axis methods

* Handle multiple axis cell methods

* Update docstring to reflect eventual choices

* Add warnings to function, and test them

* Significantly simpler warning checks

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* Developer documentation on available testing conveniences

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* Update to be easily usable without code links working

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* Cubelist contain only cubes -- resurrected (#4767)

* ensure cubelists only contain cubes

* address __iadd__ and __setitem__

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* Replace CubeList init with new. Cube testing duck-type.

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* Updated environment lockfiles (#4775)

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* Redirect whatsnew to latest (#4727)

* Redirect whatsnew

* Get the top bar working too

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* Update release docs

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* Bump peter-evans/create-pull-request from 4.0.3 to 4.0.4 (#4783)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.3 to 4.0.4.
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---
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* Updated environment lockfiles (#4782)

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* Fix whatsnew (#4784)

* Fix whatsnew

* Instead of changing 3.0.rst, rename 'whatsnew.rst' to 'index.rst'

* Missed one

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* Permit Stereographic saving

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* Add mesh details to cube printout. (#4778)

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* Test repr-html of string attributes.

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* Review change : fix string truncation/quoting.

* Retire use of the New labels. (#4801)

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* Scripted Logo Generation, take two (#3935)

* Added logo generation Python script.

* Replace lambda scale_func.n

* Matched current logo appearance.

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* Renamed land_mask to land_clip.

* Make new svg instead of faffing with reformatting existing.

* Refactor out 'style' in attributes.

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* Environment variable logo names.

* Removed banner width calculation to avoid font dependency.

* Refactored to also generate rotating logos.

* Replace plt.tightlayout with plt.subplots_adjust.

* Replaced OrderedDicts with dicts (not needed >=Py3.6).

* Numpy standard import form.

* Replaced animated SVG with precusor files for animated GIF.

* Corrected logo URL to source from ReadTheDocs site.

* Changes to better match 'hand-created' logo.

* Fixed logo rotate zip title.

* Relocated logo generation script to SciTools/marketing.

* update links (#3942)

* update links

* added s to http

* Added logo generation Python script.

* Replace lambda scale_func.n

* Matched current logo appearance.

* Simplified gradient code.

* Renamed land_mask to land_clip.

* Make new svg instead of faffing with reformatting existing.

* Refactor out 'style' in attributes.

* File header.

* Integrated logo generation script into Sphinx docs generation.

* Environment variable logo names.

* Removed banner width calculation to avoid font dependency.

* Refactored to also generate rotating logos.

* Replace plt.tightlayout with plt.subplots_adjust.

* Replaced OrderedDicts with dicts (not needed >=Py3.6).

* Numpy standard import form.

* Replaced animated SVG with precusor files for animated GIF.

* Corrected logo URL to source from ReadTheDocs site.

* Changes to better match 'hand-created' logo.

* Fixed logo rotate zip title.

* Relocated logo generation script to SciTools/marketing.

* Include version string in logo generation.

* Reference official logo generation code.

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* Fix README docs reference.

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* fix composite gha (#4809)

* fix composite gha

* bump gha cache_build to force purge

* Whats new entry for SVG logo. (#4810)

* Updated environment lockfiles (#4815)

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* add gha workflow badges (#4813)

* address npy disable cpu features warning (#4811)

* Ensure tests use ncgen/ncdump from the Python env; rationalise uses of ncgen. (#4794)

* Ensure tests use ncgen/ncdump from the Python env; rationalise uses of ncgen a bit.

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* Rationalise use of ncgen and avoid subprocess 'shell=True'.

* Review changes: revert to importing iris.tests first.

* Tidy routines slightly.

* Fix subprocess call.

* Added whatsnew.

* Limit memory benchmark result to 5Mb minimum (#4818)

* docs: cirrus-ci to gha (#4821)

* docs: cirrus-ci to gha

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* Allow passing of method keyword to numpy.percentile (#4791)

* allow passing of method keyword to numpy.percentile

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* Use images from test data

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* Oops, missed it. There now

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This reverts commit bdca27cd301fff9de034f14db9da991dac43facf.

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* Add whats new entry for 4734 (#4908)

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Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.4 to 4.1.1.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/923ad837f191474af6b1721408744feb989a4c27...18f90432bedd2afd6a825469ffd38aa24712a91d)

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

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