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Adapt ESMValTool to new configuration #3761

Merged
merged 34 commits into from
Oct 22, 2024
Merged

Adapt ESMValTool to new configuration #3761

merged 34 commits into from
Oct 22, 2024

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schlunma
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@schlunma schlunma commented Oct 2, 2024 •
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Description

This PR adapt all parts of ESMValTool to the new configuration (see ESMValGroup/ESMValCore#2448).

Deprecation

Similar to the corresponding ESMValCore PR, this PR deprecates the command line option --config_file for esmvaltool data format/download/prepare. This option is scheduled for removal in version 2.14.0. Please use the option config_dir instead.

Example:

Old syntax:

esmvaltool data format --config_file=~/my/config/file.yml WOA

New syntax:

esmvaltool data format --config_dir=~/my/config/ WOA

See ESMValGroup/ESMValCore#2448 and ESMValGroup/ESMValCore#2371 for further details.

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@schlunma schlunma added the requires new ESMValCore release A new release of ESMValCore is needed to solve this issue/merge this pull request.. label Oct 2, 2024
@schlunma schlunma added this to the v2.12.0 milestone Oct 2, 2024
@schlunma schlunma self-assigned this Oct 2, 2024
@valeriupredoi valeriupredoi mentioned this pull request Oct 3, 2024
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@schlunma schlunma added deprecated feature and removed requires new ESMValCore release A new release of ESMValCore is needed to solve this issue/merge this pull request.. labels Oct 7, 2024
@schlunma schlunma marked this pull request as ready for review October 7, 2024 13:18
@schlunma schlunma requested a review from a team as a code owner October 7, 2024 13:18
bouweandela
bouweandela reviewed Oct 15, 2024
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doc/sphinx/source/community/dataset.rst Outdated
#. Download the data following the instructions included in the script and place
it in the ``RAWOBS`` path specified in your ``config-user.yml``
#. Download the data following the instructions included in the script and
place it in the ``RAWOBS`` `rootpath` specified in your :ref:`configuration
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Use double backticks around rootpath to make it monospace (a single backtick is italic and the convention is to use monospace for things that have to be typed exactly like that)

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Yeah, I am always unsure about this. Numpy recommends to enclose parameter names in single backticks, and they seem to be aware of the different meanings of single backticks in markdown and reST. I've also seen the usage of italic font for parameters in Numpy's (and other project's) API documentation (e.g., bins here). That's why I used single backticks here.

However, I can totally see your point about the double backticks. As long as we use one convention consistently (and we're currently certainly not doing that), I guess both are fine? So maybe we should just once and for all decide on one and continue to use that?

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Changed in ce62d9f and 75e2b33

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Thanks! I assumed our convention was to use monospace font for things that need to be written exactly like that to work and all the other cases were people who just forgot that in .rst you need double backticks to create monospace fonts. Maybe we need to write this in our contributor docs somewhere too. From the text you linked it looks like numpy plans to adopt the same convention, but are working on some feature to make that work with single backticks:

This guide continues to recommended that parameter names be enclosed within single backticks. Currently, this may cause parameter names to render improperly and cause warnings, but numpydoc will soon release a feature that causes them to render as monospaced hyperlinks to the parameter documentation.

bouweandela
bouweandela requested changes Oct 15, 2024
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Nice work! Just a few comments on improving the formatting and possibly removing some unnecessary code from the recipe filler.

schlunma and others added 13 commits October 15, 2024 12:52
@schlunma @bouweandela
Expand environment variables when reading config dirs for CMORizer
dfcc120 
Co-authored-by: Bouwe Andela <[email protected]>
@schlunma
Do not use bare Exception
697e60f
@schlunma
Add FAQ how to read multiple config dirs
f31f9b7
@schlunma @bouweandela
Update esmvaltool/cmorizers/data/datasets.yml
d67b4bc 
Co-authored-by: Bouwe Andela <[email protected]>
@schlunma
remove "user" before configuration
cf85b57
@schlunma
Merge remote-tracking branch 'public/main' into new_config
2f842ec
@schlunma
Better line breaks in doc
51ef776
@schlunma
Merge branch 'main' into new_config
8725b41
@schlunma @bouweandela
Update doc/sphinx/source/recipes/recipe_oceans.rst
918471c 
Co-authored-by: Bouwe Andela <[email protected]>
@schlunma @bouweandela
Update doc/sphinx/source/recipes/recipe_shapeselect.rst
4db3491 
Co-authored-by: Bouwe Andela <[email protected]>
@schlunma
rootpath -> rootpath
ce62d9f
@schlunma
auxiliary_data_dir -> auxiliary_data_dir
75e2b33
@schlunma
Merge remote-tracking branch 'public/main' into new_config
c95184f
bouweandela
bouweandela reviewed Oct 21, 2024
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Thanks for making all the changes @schlunma! I believe there is one comment still outstanding: #3761 (comment), could you have a look?

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Thanks for making all the changes @schlunma! I believe there is one comment still outstanding: #3761 (comment), could you have a look?

Done in f0e7565

@bouweandela bouweandela merged commit 8f7982c into main Oct 22, 2024
7 of 8 checks passed
@bouweandela bouweandela deleted the new_config branch October 22, 2024 14:39
ehogan added a commit that referenced this pull request Nov 19, 2024
@ehogan
Merge branch 'main' into recipe_test_workflow_prototype
09490de 
* main: (31 commits)
  Update environment: pin `iris>=3.11`, unpin `cartopy` and allow for `numpy >=2` (#3811)
  Fix issue related to removal/change of private function imported in `diag_scripts/shared/_supermeans.py` (deprecation in iris=3.11) (#3810)
  Remove recipe filler utility (#3777)
  [Condalock] Update Linux condalock file (#3809)
  change authors name (#3806)
  [Condalock] Update Linux condalock file (#3798)
  Fix contourf plots for masked data (#3797)
  [Condalock] Update Linux condalock file (#3796)
  Add next release schedule (#3794)
  Use `transform_first=True` for contourf plots with Robinson projection to avoid cartopy bug (#3789)
  Pin pys2index >=0.1.5 in osx environment (#3792)
  Adding a CMORiser for CMAP data for pr (#3766)
  Adding pr, tauu, tauv, tos to NCEP2 CMORISer (#3765)
  Readthedocs configuration/builds: revert to miniconda before miniforge is available (#3785)
  Adapt ESMValTool to new configuration (#3761)
  Adding pr, tauu, tauv NOAA-CIRES-20CR-V2 CMORISER (#3763)
  update comment in conda lock creation Github action (#3788)
  [Condalock] Update Linux condalock file (#3786)
  update Docker builds badge in README (#3783)
  Pin mamba<2 for conda-lock: solution by Ben Mares @maresb (#3771)
  ...
ehogan added a commit that referenced this pull request Nov 19, 2024
@ehogan
Merge branch '3723_remove_rose_cylc' of github.com:ESMValGroup/ESMVal…
90c8ca1 
…Tool into 3723_remove_rose_cylc

* '3723_remove_rose_cylc' of github.com:ESMValGroup/ESMValTool: (31 commits)
  Update environment: pin `iris>=3.11`, unpin `cartopy` and allow for `numpy >=2` (#3811)
  Fix issue related to removal/change of private function imported in `diag_scripts/shared/_supermeans.py` (deprecation in iris=3.11) (#3810)
  Remove recipe filler utility (#3777)
  [Condalock] Update Linux condalock file (#3809)
  change authors name (#3806)
  [Condalock] Update Linux condalock file (#3798)
  Fix contourf plots for masked data (#3797)
  [Condalock] Update Linux condalock file (#3796)
  Add next release schedule (#3794)
  Use `transform_first=True` for contourf plots with Robinson projection to avoid cartopy bug (#3789)
  Pin pys2index >=0.1.5 in osx environment (#3792)
  Adding a CMORiser for CMAP data for pr (#3766)
  Adding pr, tauu, tauv, tos to NCEP2 CMORISer (#3765)
  Readthedocs configuration/builds: revert to miniconda before miniforge is available (#3785)
  Adapt ESMValTool to new configuration (#3761)
  Adding pr, tauu, tauv NOAA-CIRES-20CR-V2 CMORISER (#3763)
  update comment in conda lock creation Github action (#3788)
  [Condalock] Update Linux condalock file (#3786)
  update Docker builds badge in README (#3783)
  Pin mamba<2 for conda-lock: solution by Ben Mares @maresb (#3771)
  ...
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@bouweandela bouweandela bouweandela approved these changes

@valeriupredoi valeriupredoi Awaiting requested review from valeriupredoi

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