ESMValCore 2.14.0rc2__tar.gz → 2.15.0rc2__tar.gz

esmvalcore-2.15.0rc2/.circleci/config.yml

@@ -0,0 +1,134 @@
+---
+version: 2.1
+
+orbs:
+  codecov: codecov/codecov@6.0.0
+  pixi: prefix-dev/pixi@0.1.0
+
+jobs:
+  test:
+    # Run tests.
+    docker:
+      - image: cimg/base:current
+    resource_class: large
+    steps:
+      - checkout
+      - pixi/pixi_setup
+      - run:
+          name: Check dependencies are compatible
+          command: pixi run --as-is pip check
+      - run:
+          name: Run tests
+          command: |
+            pixi run --as-is test --cov -n 4 --durations=10 --junitxml=test-reports/report.xml
+      - run:
+          name: Test the command line interface
+          command: |
+            pixi run --as-is esmvaltool version
+            pixi run --as-is esmvaltool -- --help
+            pixi run --as-is esmvaltool config list
+            pixi run --as-is esmvaltool config show
+      - codecov/upload:
+          files: "test-reports/coverage.xml"
+          disable_search: true
+      - store_test_results:
+          path: test-reports/report.xml
+      - run:
+          name: Compress pytest artifacts
+          command: tar -cvzf pytest.tar.gz -C /tmp/pytest-of-$(whoami)/ .
+      - store_artifacts:
+          path: pytest.tar.gz
+      - run:
+          name: Compress test-report artifacts
+          command: tar -cvzf test-reports.tar.gz test-reports/
+      - store_artifacts:
+          path: test-reports.tar.gz
+
+  test_with_upstream_developments:
+    # Test with development versions of upstream packages.
+    docker:
+      - image: cimg/base:current
+    resource_class: large
+    steps:
+      - checkout
+      - pixi/pixi_setup
+      - run:
+          name: Install development versions of upstream packages
+          command: |
+            pixi run --as-is pip install \
+              git+https://github.com/esgf2-us/intake-esgf \
+              git+https://github.com/euro-cordex/py-cordex \
+              git+https://github.com/SciTools/cartopy \
+              git+https://github.com/SciTools/cf-units \
+              git+https://github.com/SciTools/iris \
+              git+https://github.com/SciTools/iris-grib \
+              git+https://github.com/SciTools/nc-time-axis \
+              git+https://github.com/SciTools/ncdata \
+              git+https://github.com/SciTools/iris-esmf-regrid \
+              git+https://github.com/SciTools/python-stratify
+      - run:
+          name: Run tests
+          command: |
+            pixi run --as-is test -n 4 --junitxml=test-reports/report.xml
+      - run:
+          name: Test the command line interface
+          command: |
+            pixi run --as-is esmvaltool version
+            pixi run --as-is esmvaltool -- --help
+      - store_test_results:
+          path: test-reports/report.xml
+      - run:
+          name: Compress pytest artifacts
+          command: tar -cvzf pytest.tar.gz -C /tmp/pytest-of-$(whoami)/ .
+      - store_artifacts:
+          path: pytest.tar.gz
+      - run:
+          name: Compress test-report artifacts
+          command: tar -cvzf test-reports.tar.gz test-reports/
+      - store_artifacts:
+          path: test-reports.tar.gz
+
+  test_installation_from_conda:
+    # Test installation from conda-forge.
+    docker:
+      - image: mambaorg/micromamba
+    resource_class: medium
+    steps:
+      - run:
+          name: Install ESMValCore from conda
+          command: |
+            micromamba create -y --name esmvalcore esmvalcore
+            micromamba env export --name esmvalcore
+            micromamba run --name esmvalcore esmvaltool -- --help
+            micromamba run --name esmvalcore esmvaltool version
+
+  build_documentation:
+    # Test building documentation.
+    docker:
+      - image: cimg/base:current
+    resource_class: small
+    steps:
+      - checkout
+      - pixi/pixi_setup
+      - run:
+          name: Build documentation
+          command: pixi run --as-is doc --fail-on-warning --show-traceback
+
+workflows:
+  commit:
+    jobs:
+      - test
+
+  nightly:
+    triggers:
+      - schedule:
+          cron: "0 0 * * *"
+          filters:
+            branches:
+              only:
+                - main
+    jobs:
+      - build_documentation
+      - test
+      - test_installation_from_conda
+      - test_with_upstream_developments

esmvalcore-2.15.0rc2/.dockerignore

@@ -0,0 +1,9 @@
+
+**/__pycache__
+.*
+doc
+tests
+ESMValCore.egg-info
+
+!.git
+!.zenodo.json

esmvalcore-2.15.0rc2/.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

esmvalcore-2.15.0rc2/.github/ISSUE_TEMPLATE/data_issue_report.md

@@ -0,0 +1,38 @@
+---
+name: Dataset issue report
+about: Create a report about a problematic dataset
+title: 'Dataset problem: '
+labels: ''
+assignees: valeriupredoi
+
+---
+
+**Describe the dataset issue**
+A clear and concise description of what the problem with the data is is. Here are some guidelines that you can use
+right out the box by filling in the blanks. If needed we will assist you with writing a fix.
+Please check the [ESGF errata service](https://errata.ipsl.fr/static/index.html) to
+see if the problem has already been reported and report it there if it is not.
+Please link to the errata issue in your report here.
+
+- Data file has been changed by you in any way (if you answer yes the issue will be void and closed, we are not
+supporting custom-made datasets that present problems, it is your resposability to fix those problems):
+- Project (CMIP7/CMIP6/obs4MIPs/CORDEX/OBS/etc.):
+- Full dataset description (fill out as many as you know, please):
+  - dataset:
+  - ensemble:
+  - experiment:
+  - mip:
+  - grid:
+  - variable used:
+  - version:
+- Problems encountered (please describe what the actual problems are: e.g. wrong standard name, issue with dimensions):
+- Pointer to existing copy of data on ESGF node (it would be very useful if you could provide a physical
+fullpath to the file(s) that are causing the problem, e.g. on CEDA Jasmin or DKRZ):
+- Other notes and mentions:
+
+**Please attach**
+  - The recipe that you are trying to run, you can find a copy in the `run` directory in the output directory
+  - The `main_log_debug.txt` file, this can also be found in the `run` directory in the output directory
+  - Attach a text file with the output of `ncdump -h /path/to/file.nc`
+
+Cheers :beer:

esmvalcore-2.15.0rc2/.github/workflows/build-and-deploy-on-pypi.yml

@@ -0,0 +1,63 @@
+# Workflow from https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Build and publish Python 🐍 distribution 📦 to PyPI
+
+permissions: {}
+
+on:
+  release:
+    types: [published]
+  push:
+    # Use this for testing the package build.
+    branches:
+      - main
+      - v[0-9]+.[0-9]+.x # matches release branches like v2.12.x
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ESMValCore
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

esmvalcore-2.15.0rc2/.github/workflows/citation_file_validator.yml

@@ -0,0 +1,28 @@
+# workflow that performs a validity check of CITATION.cff file
+# author: Abel Siqueira, GH: @abelsiqueira
+
+name: CFF File Validator
+
+permissions: {}
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+  schedule:
+    - cron: "0 0 1 * *"
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    if: github.repository == 'ESMValGroup/ESMValCore' # avoid GAs in forks
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          persist-credentials: false
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/cffconvert-github-action@4cf11baa70a673bfdf9dad0acc7ee33b3f4b6084 # 2.0.0
+        with:
+          args: "--validate"

esmvalcore-2.15.0rc2/.github/workflows/install-from-conda.yml

@@ -0,0 +1,45 @@
+---
+name: Install from Conda
+
+permissions: {}
+
+# runs on a push on main and at the end of every day
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: "0 4 * * *"
+
+# Required shell entrypoint to have properly configured bash shell
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  install:
+    runs-on: ${{ matrix.os }}
+    if: github.repository == 'ESMValGroup/ESMValCore'
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+        python-version:
+          - "3.12"
+          - "3.13"
+          - "3.14"
+    name: Install ESMValCore with Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    steps:
+      - uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476  # v3.0.0
+        with:
+          environment-name: esmvalcore
+          create-args: >-
+            python=${{ matrix.python-version }}
+            esmvalcore
+      - name: Verify installation
+        run: |
+          pip check
+          esmvaltool --help
+          esmvaltool version

esmvalcore-2.15.0rc2/.github/workflows/run-tests-monitor.yml

@@ -0,0 +1,53 @@
+---
+name: Monitor Tests
+
+permissions: {}
+
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: "0 0 * * *" # nightly
+
+# Required shell entrypoint to have properly configured bash shell
+defaults:
+  run:
+    shell: pixi run bash -e {0}
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.os }}
+    if: github.repository == 'ESMValGroup/ESMValCore' # avoid GAs in forks
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+        environment:
+          - test-py312
+          - test-py313
+          - test-py314
+    name: ${{ matrix.os }} ${{ matrix.environment }}
+    steps:
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
+        with:
+          frozen: true
+          environments: ${{ matrix.environment }}
+      - name: Install pytest-monitor
+        run: pip install pytest-monitor
+      - name: Run tests
+        run: pytest -n 2 --db ../.pymon
+      - name: Parse monitor information
+        run: python tests/parse_pymon.py
+      - name: Upload artifacts
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: Test_reports_${{ matrix.os }}_${{ matrix.environment }}
+          path: test-reports

esmvalcore-2.15.0rc2/.github/workflows/run-tests.yml

@@ -0,0 +1,58 @@
+---
+name: Test
+
+permissions: {}
+
+# runs on a push on main and at the end of every day
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: "0 0 * * *" # nightly
+
+defaults:
+  run:
+    shell: pixi run bash -e {0}
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    if: github.repository == 'ESMValGroup/ESMValCore'
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+        environment:
+          - test-py312
+          - test-py313
+          - test-py314
+          - test-r
+    name: ${{ matrix.os }} ${{ matrix.environment }}
+    steps:
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
+        with:
+          frozen: true
+          environments: ${{ matrix.environment }}
+      - name: Check dependencies are compatible
+        run: pip check
+      - name: Check code quality
+        run: pre-commit run -a
+      - name: Run tests
+        run: pytest -n 2 --durations=10
+      - name: Upload artifacts
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: Test_reports_${{ matrix.os }}_${{ matrix.environment }}
+          path: test-reports
+      - name: Check the command line interface
+        run: |
+          esmvaltool version
+          esmvaltool -- --help

esmvalcore-2.15.0rc2/.github/workflows/stale.yml

@@ -0,0 +1,41 @@
+name: Close stale issues and pull requests
+
+permissions: {}
+
+on:
+  schedule:
+    # Run once a day
+    - cron: "30 1 * * *"
+
+jobs:
+  stale:
+    if: "github.repository == 'ESMValGroup/ESMValCore'"
+    permissions:
+      actions: write
+      issues: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # v10.3.0
+        with:
+          days-before-issue-stale: 720
+          days-before-pr-stale: 180
+          days-before-close: 60
+          ascending: true
+          operations-per-run: 300
+          stale-issue-message: |
+            In order to maintain a backlog of relevant issues, we automatically label them as stale after 720 days of inactivity.
+
+            If this issue is still important to you, please comment below to remove the stale label. Otherwise, this issue will be automatically closed in 60 days.
+          stale-pr-message: |
+            In order to maintain a backlog of relevant pull requests, we automatically label them as stale after 180 days of inactivity.
+
+            If this pull request is still important to you, please comment below to remove the stale label. Otherwise, this pull request will be automatically closed in 60 days. If this pull request only suffers from a lack of reviewers, please tag the @<span></span>ESMValGroup/technical-lead-development-team so they can help you find a suitable reviewer.
+          close-issue-message: |
+            This stale issue has been automatically closed due to a lack of community activity.
+
+            If you still care about this issue, please re-open it. If you do not have sufficient permissions for this, tag the @<span></span>ESMValGroup/technical-lead-development-team in a comment below including a short message that this issue is still relevant to you. They will re-open it on your behalf.
+          close-pr-message: |
+            This stale pull request has been automatically closed due to a lack of community activity.
+
+            If you still care about this pull request, please re-open it. If you do not have sufficient permissions for this, tag the @<span></span>ESMValGroup/technical-lead-development-team in a comment below including a short message that this pull request is still relevant to you. They will re-open it on your behalf.

esmvalcore-2.15.0rc2/.github/workflows/update-lockfiles.yml

@@ -0,0 +1,40 @@
+# Workflow documentation: https://pixi.prefix.dev/v0.32.0/advanced/updates_github_actions/#how-to-use
+name: Update lockfiles
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: 0 5 1 * *
+
+jobs:
+  pixi-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11  # v0.9.6
+        with:
+          run-install: false
+      - name: Update lockfiles
+        run: |
+          set -o pipefail
+          pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1 # v8.1.1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Update pixi lockfile
+          title: Update pixi lockfile
+          body-path: diff.md
+          branch: update-pixi
+          base: main
+          labels: pixi
+          delete-branch: true
+          add-paths: pixi.lock

esmvalcore-2.15.0rc2/.gitignore

@@ -0,0 +1,119 @@
+# Autogenerated files
+_sidebar.rst.inc
+jupyter_execute/
+
+# Distribution / packaging
+.Python
+build/
+_build/
+c
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+env/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+*.orig
+*.tmp
+MANIFEST
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Created by editors
+*~
+\#*
+\.\#*
+*.swp
+
+# Created by PyCharm
+.idea/
+
+# eclipse/pydev
+.project
+.pydevproject
+.settings
+
+#Create by VSCode
+.vscode
+
+#pytest
+.cache
+.pytest_cache
+.pymon
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.mypy_cache
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+*.tmp
+*.orig
+/c
+/tests/data/**
+test-reports/
+/test_bash.sh
+/python_test_out.txt
+
+# Auto generated doc
+_sidebar.rst.inc
+
+# Documentation build
+html/
+
+# Data files
+*.nc
+*.nc4
+*.grb
+*.grib
+*.RData
+*.Rdata
+*.Rhistory
+*.rdata
+*.pkl
+
+# ESMF log files
+*.ESMF_LogFile
+
+# AI
+.github/instructions/codacy.instructions.md
+CLAUDE.md
+
+# pixi environments
+.pixi
+.pixi/*
+!.pixi/config.toml