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Merge branch 'main' of github.com:esmvalgroup/esmvaltool into no-dist…
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…ributed-diagnostic-script
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bouweandela committed Jan 21, 2025
2 parents 70f7d57 + c84868e commit 9ff3f13
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10 changes: 6 additions & 4 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -90,8 +90,9 @@ commands:
# Install
. /opt/conda/etc/profile.d/conda.sh
mkdir /logs
mamba env create >> /logs/conda.txt 2>&1
mamba env create
conda activate esmvaltool
mamba list >> /logs/conda.txt
pip install << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
esmvaltool install Julia > /logs/install_julia.txt 2>&1
if [[ "<<parameters.flags>>" != *'--editable'* ]]
Expand Down Expand Up @@ -201,8 +202,9 @@ jobs:
# https://docs.esmvaltool.org/en/latest/quickstart/installation.html#install-from-source
. /opt/conda/etc/profile.d/conda.sh
mkdir /logs
mamba env create >> /logs/conda.txt 2>&1
mamba env create
conda activate esmvaltool
mamba list >> /logs/conda.txt
pip install --editable .[develop]
esmvaltool install Julia > /logs/install_julia.txt 2>&1
git clone https://github.com/ESMValGroup/ESMValCore $HOME/ESMValCore
Expand All @@ -216,8 +218,8 @@ jobs:
conda activate esmvaltool
mkdir -p ~/climate_data
esmvaltool config get_config_user
echo "search_esgf: when_missing" >> ~/.esmvaltool/config-user.yml
cat ~/.esmvaltool/config-user.yml
echo "search_esgf: when_missing" >> ~/.config/esmvaltool/config-user.yml
cat ~/.config/esmvaltool/config-user.yml
for recipe in esmvaltool/recipes/testing/recipe_*.yml; do
esmvaltool run "$recipe"
done
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3 changes: 2 additions & 1 deletion .codacy.yml
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Expand Up @@ -21,5 +21,6 @@ engines:
exclude_paths: [
'doc/sphinx/**',
'esmvaltool/cmor/tables/**',
'tests/**'
'tests/**',
'esmvaltool/utils/recipe_test_workflow/app/configure/bin/test_configure.py'
]
1 change: 1 addition & 0 deletions .github/CODEOWNERS
Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
esmvaltool/cmorizers @ESMValGroup/obs-maintainers
.github/workflows @valeriupredoi
esmvaltool/utils/recipe_test_workflow/ @alistairsellar @ehogan
78 changes: 78 additions & 0 deletions .github/workflows/check-rtw.yml
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@@ -0,0 +1,78 @@
# This workflow performs various validation steps for Cylc and Rose.
name: Check Recipe Test Workflow (RTW)

# Controls when the action will run
on:
# Triggers the workflow on push events
push:
paths:
- esmvaltool/utils/recipe_test_workflow/**

# Schedule this workflow to run at 04:00 every 10 days
schedule:
- cron: '0 4 */10 * *'

# Common variables are defined here
env:
RTW_ROOT_DIR: esmvaltool/utils/recipe_test_workflow

# Required shell entrypoint to have properly configured bash shell
defaults:
run:
shell: bash -l {0}

# A workflow run is made up of one or more jobs that can run
# sequentially or in parallel
jobs:
# This workflow contains a single job called "check-rtw"
check-rtw:
# The type of runner that the job will run on
runs-on: ubuntu-latest

# Steps represent a sequence of tasks that will be executed as part
# of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job
# can access it
- name: Checkout repository
uses: actions/checkout@v4

- name: Setup Cylc
uses: cylc/setup-cylc@v1
with:
cylc_rose: true

- name: Validate Cylc workflow
run: |
cd ${RTW_ROOT_DIR}
cylc validate . -O metoffice
- name: Run Cylc configuration linter
run: |
cd ${RTW_ROOT_DIR}
cylc lint
- name: Validate format of Rose configuration files
run: |
cd ${RTW_ROOT_DIR}
output="$(rose config-dump)"
msg="Run 'rose config-dump' to re-dump the Rose configuration files"
msg="${msg} in the common format, then commit the changes."
# The '-z' option returns true if 'output' is empty.
if [[ -z "${output}" ]]; then true; else echo "${msg}" && exit 1; fi
- name: Validate Rose configuration metadata
run: |
cd ${RTW_ROOT_DIR}
rose metadata-check -C meta/
- name: Run Rose configuration validation macros
run: |
cd ${RTW_ROOT_DIR}
rose macro -V
- name: Lint shell scripts
run: |
cd ${RTW_ROOT_DIR}
output=$(find . -name "*.sh" -exec shellcheck {} \;)
if [ "$output" ]; then echo "${output}" && exit 1; fi
3 changes: 2 additions & 1 deletion .github/workflows/create-condalock-file.yml
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Expand Up @@ -36,7 +36,8 @@ jobs:
conda --version
# setup-miniconda@v3 installs an old conda and mamba
# forcing a modern mamba updates both mamba and conda
# pin <2 due to https://github.com/ESMValGroup/ESMValTool/pull/3771
# unpin mamba after conda-lock=3 release
# see github.com/ESMValGroup/ESMValTool/issues/3782
conda install -c conda-forge "mamba>=1.4.8,<2"
conda config --show-sources
conda config --show
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50 changes: 50 additions & 0 deletions .github/workflows/cron_esmvalbot_test.yml
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@@ -0,0 +1,50 @@
name: Run Esmvalbot Test

on:
# push:
# branches:
# - cron_esmvalbot_test
# scheduled once every 2 weeks
schedule:
- cron: '0 4 */14 * *'

# Required shell entrypoint to have properly configured bash shell
defaults:
run:
shell: bash -l {0}

jobs:
run-esmvalbot:
runs-on: 'ubuntu-latest'
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Create empty commit on branch
run: |
git config user.name 'Valeriu Predoi'
git config user.email '[email protected]'
git commit --allow-empty -m "empty commit"
# Automated PR where we run "@esmvalbot please run examples/recipe_python.yml"
# as comment in the PR
# see https://github.com/marketplace/actions/create-pull-request
- name: Create Auto PR
uses: peter-evans/create-pull-request@v7
with:
token: ${{ secrets.GITHUB_TOKEN }}
commit-message: empty message
# defaults are GH bot: # ${{ github.actor }} <${{ github.actor }}@users.noreply.github.com>
committer: Valeriu Predoi <[email protected]>
author: Valeriu Predoi <[email protected]>
signoff: false
branch: run-esmvalbot
delete-branch: true
title: '[EsmvalbotTest] Periodic reminder to run an esmvalbot test'
body: 'Automatic PR; please DO NOT merge! This is for testing Esmvalbot only. @valeriupredoi @bouweandela @schlunma please run an ESMValBot test here; if the bot runs fine, please close the auto PR, if it has issues, please open a Github issue and tag @valeriupredoi. Many thanks :beers:'
labels: |
testing
esmvalbot
automatedPR
assignees: valeriupredoi
reviewers: valeriupredoi
draft: true
32 changes: 19 additions & 13 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,22 @@ version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-22.04
os: ubuntu-lts-latest
tools:
# updated and deployed from Aug 1, 2023
python: "mambaforge-22.9"
# try miniforge3 when available? see github.com/ESMValGroup/ESMValTool/issues/3779
# DO NOT use mambaforge-*; that is currently sunsetted
python: "miniconda-latest"
jobs:
pre_create_environment:
# update mamba just in case
- mamba update --yes --quiet --name=base mamba 'zstd=1.5.2'
- mamba --version
- mamba list --name=base
post_create_environment:
- conda run -n ${CONDA_DEFAULT_ENV} mamba list
# use conda run executable wrapper to have all env variables
- conda run -n ${CONDA_DEFAULT_ENV} mamba --version
- conda run -n ${CONDA_DEFAULT_ENV} pip install . --no-deps
post_checkout:
# The ESMValTool repository is shallow i.e., has a .git/shallow,
# therefore complete the repository with a full history in order
# to allow setuptools-scm to correctly auto-discover the version.
- git fetch --unshallow
- git fetch --all
pre_install:
- git stash
post_install:
- git stash pop

# Declare the requirements required to build your docs
conda:
Expand All @@ -33,6 +34,11 @@ sphinx:
configuration: doc/sphinx/source/conf.py
fail_on_warning: true

python:
install:
- method: pip
path: .

# If using Sphinx, optionally build your docs in additional formats such as PDF
formats:
- pdf
32 changes: 26 additions & 6 deletions .zenodo.json
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Expand Up @@ -81,13 +81,17 @@
"name": "Berg, Peter",
"orcid": "0000-0002-1469-2568"
},
{
"affiliation": "Met Office, UK",
"name": "Billows, Chris"
},
{
"affiliation": "DLR, Germany",
"name": "Bock, Lisa",
"orcid": "0000-0001-7058-5938"
},
{
"affiliation": "MetOffice, UK",
"affiliation": "Met Office, UK",
"name": "Bodas-Salcedo, Alejandro",
"orcid": "0000-0002-7890-2536"
},
Expand Down Expand Up @@ -142,21 +146,29 @@
"name": "Docquier, David"
},
{
"affiliation": "MetOffice, UK",
"affiliation": "Met Office, UK",
"name": "Dreyer, Laura"
},
{
"affiliation": "DKRZ, Germany",
"name": "Ehbrecht, Carsten"
},
{
"affiliation": "MetOffice, UK",
"affiliation": "Met Office, UK",
"name": "Earnshaw, Paul"
},
{
"affiliation": "Met Office, UK",
"name": "Geddes, Theo"
},
{
"affiliation": "University of Bremen, Germany",
"name": "Gier, Bettina"
},
{
"affiliation": "Met Office, UK",
"name": "Gillett, Ed"
},
{
"affiliation": "BSC, Spain",
"name": "Gonzalez-Reviriego, Nube",
Expand Down Expand Up @@ -191,6 +203,10 @@
"name": "Heuer, Helge",
"orcid": "0000-0003-2411-7150"
},
{
"affiliation": "Met Office, UK",
"name": "Hogan, Emma"
},
{
"affiliation": "BSC, Spain",
"name": "Hunter, Alasdair",
Expand Down Expand Up @@ -227,7 +243,7 @@
"orcid": "0000-0001-6085-5914"
},
{
"affiliation": "MetOffice, UK",
"affiliation": "Met Office, UK",
"name": "Little, Bill"
},
{
Expand Down Expand Up @@ -279,7 +295,7 @@
"name": "Sandstad, Marit"
},
{
"affiliation": "MetOffice, UK",
"affiliation": "Met Office, UK",
"name": "Sellar, Alistair"
},
{
Expand All @@ -305,6 +321,10 @@
"name": "Swaminathan, Ranjini",
"orcid": "0000-0001-5853-2673"
},
{
"affiliation": "Met Office, UK",
"name": "Tomkins, Katherine"
},
{
"affiliation": "BSC, Spain",
"name": "Torralba, Verónica"
Expand Down Expand Up @@ -387,7 +407,7 @@
"orcid": "0000-0003-3780-0784"
},
{
"affiliation": "MetOffice, UK",
"affiliation": "Met Office, UK",
"name": "Munday, Gregory",
"orcid": "0000-0003-4750-9923"
}
Expand Down
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