Merge branch 'main' into handle_cubelist

.github/workflows/conda-lock.yml

@@ -47,12 +47,12 @@ jobs:
             # Developer lock files.
             cp "requirements/environment.yml" "${{ runner.temp }}/${py_ver}_dev_environment.yml"
             echo -e "\n  - python = $py_ver" >> "${{ runner.temp }}/${py_ver}_dev_environment.yml"
-            conda-lock --channel conda-forge --kind explicit --file "${{ runner.temp }}/${py_ver}_dev_environment.yml" --platform linux-64 --filename-template "requirements/locks/py$(echo $py_ver | sed 's/\.//')-lock-linux-64.txt" &
+            conda-lock --channel conda-forge --kind explicit --file "${{ runner.temp }}/${py_ver}_dev_environment.yml" --platform linux-64 --filename-template "requirements/locks/py$(echo $py_ver | sed 's/\.//')-lock-linux-64.txt"
 
             # Workflow lock files.
             cp "cset-workflow/requirements/environment.yml" "${{ runner.temp }}/${py_ver}_workflow_environment.yml"
             echo -e "\n  - python = $py_ver" >> "${{ runner.temp }}/${py_ver}_workflow_environment.yml"
-            conda-lock --channel conda-forge --kind explicit --file "${{ runner.temp }}/${py_ver}_workflow_environment.yml" --platform linux-64 --filename-template "cset-workflow/requirements/locks/py$(echo $py_ver | sed 's/\.//')-lock-linux-64.txt" &
+            conda-lock --channel conda-forge --kind explicit --file "${{ runner.temp }}/${py_ver}_workflow_environment.yml" --platform linux-64 --filename-template "cset-workflow/requirements/locks/py$(echo $py_ver | sed 's/\.//')-lock-linux-64.txt"
           done
           wait
 
@@ -66,28 +66,50 @@ jobs:
           done
 
       - name: Generate GitHub App Token
-        uses: actions/create-github-app-token@5d869da34e18e7287c1daad50e0b8ea0f506ce69
+        uses: actions/create-github-app-token@c1a285145b9d317df6ced56c09f525b5c2b6f755
         id: app-token
         with:
           app-id: ${{ secrets.AUTH_APP_ID }}
           private-key: ${{ secrets.AUTH_APP_PRIVATE_KEY }}
 
       - name: Create pull requests
+        env:
+          source_ref: ${{ github.ref }}
+          source_ref_type: ${{ github.ref_type }}
         run: |
           shopt -s globstar
+
+          # Display any changes in the log.
           git diff --name-status
-          if $(sha256sum --status -c ${{ runner.temp }}/lock_file_hashes); then
+
+          # Exit early if there are no changes.
+          if $(sha256sum --status -c ${{ runner.temp }}/lock_file_hashes)
+          then
             echo "Lock files unchanged. Skipping pull request..."
             exit 0
           fi
-          # Update lock_file_hashes so pushed branch name is unique.
-          sha256sum **/locks/*.txt > ${{ runner.temp }}/lock_file_hashes
+
+          # Commit changed lockfiles.
           git add **/locks/*.txt
           git commit -m "[CI] Update conda lock files"
+
+          # Update lock_file_hashes so pushed branch name is unique.
+          sha256sum **/locks/*.txt > ${{ runner.temp }}/lock_file_hashes
           remote_branch_name="conda-lock-$(sha256sum ${{ runner.temp }}/lock_file_hashes | head -c 8)"
+
+          # If running from a branch target the created PR at that branch.
+          if [[ $source_ref_type = branch ]]
+          then
+            base_branch_name="$source_ref"
+          else
+            base_branch_name="main"
+          fi
+
+          # Push branch to GitHub.
           git push --set-upstream origin "conda-lock-files:${remote_branch_name}"
+
           # Create PR on GitHub using GitHub REST API.
-          request_body='{"title":"[CI] Update conda lock files","body":"Created automatically by GitHub Actions.","base":"main","head":"'"${remote_branch_name}"'"}'
+          request_body='{"title":"[CI] Update conda lock files","body":"Created automatically by GitHub Actions.","base":"'"${base_branch_name}"'","head":"'"${remote_branch_name}"'"}'
           curl -LsS --fail-with-body \
             -X POST \
             -H "Accept: application/vnd.github+json" \

.github/workflows/documentation.yml

@@ -20,7 +20,7 @@ jobs:
 
       - name: Cache conda environment
         id: conda-env-cache
-        uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57
         with:
           key: conda|${{runner.os}}-${{runner.arch}}|${{hashFiles('requirements/locks/py312-lock-linux-64.txt')}}
           path: |
@@ -48,7 +48,7 @@ jobs:
           sphinx-build -b html --color "docs/source" "docs/build/html"
           echo '::endgroup::'
 
-      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+      - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: html-docs
           path: docs/build/html/

.github/workflows/pre-commit-update.yml

@@ -35,7 +35,7 @@ jobs:
           pre-commit autoupdate --freeze
 
       - name: Generate GitHub App Token
-        uses: actions/create-github-app-token@5d869da34e18e7287c1daad50e0b8ea0f506ce69
+        uses: actions/create-github-app-token@c1a285145b9d317df6ced56c09f525b5c2b6f755
         id: app-token
         with:
           app-id: ${{ secrets.AUTH_APP_ID }}

.github/workflows/pull_request_checks.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Cache conda environment
         id: conda-env-cache
-        uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57
         with:
           key: conda|${{runner.os}}-${{runner.arch}}|${{ hashFiles(format('requirements/locks/{0}-lock-linux-64.txt', matrix.py-ver)) }}
           path: |
@@ -44,11 +44,11 @@ jobs:
         run: |
           # Install package and run pytest.
           echo '::group::Installing local package'
-          python3 -m pip install -e .
+          python3 -m pip install .
           echo '::endgroup::'
           pytest --verbose --cov --cov-append --cov-config=pyproject.toml
           mv .coverage ".coverage.${{ matrix.py-ver }}"
-      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+      - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: coverage-data-${{ matrix.py-ver }}
           path: .coverage.*
@@ -104,7 +104,7 @@ jobs:
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
         with:
           python-version: "3.x"
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a
+      - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57
         with:
           key: pre-commit|${{runner.os}}-${{runner.arch}}|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
           path: ~/.cache/pre-commit
@@ -123,7 +123,7 @@ jobs:
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
       - name: Cache conda environment
         id: conda-env-cache
-        uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57
         with:
           key: conda|${{runner.os}}-${{runner.arch}}|${{hashFiles('requirements/locks/py312-lock-linux-64.txt')}}
           path: |
@@ -148,7 +148,7 @@ jobs:
           sphinx-build -b html --color -W --keep-going "docs/source" "docs/build/html"
           echo '::endgroup::'
       - name: Upload documentation artifact
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: html-docs
           path: docs/build/html/

.github/workflows/release.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Build package
         run: python3 -m build
 
-      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+      - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: packages
           path: dist/

.github/workflows/weekly-checks.yml

@@ -14,7 +14,7 @@ jobs:
 
       - name: Cache conda environment
         id: conda-env-cache
-        uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57
         with:
           key: conda|${{runner.os}}-${{runner.arch}}|${{hashFiles('requirements/locks/py312-lock-linux-64.txt')}}
           path: |
@@ -44,7 +44,7 @@ jobs:
           echo '::group::Checking for broken hyperlinks'
           sphinx-build -b linkcheck --color -W --keep-going "docs/source" "docs/build/linkcheck"
           echo '::endgroup::'
-      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+      - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: html-docs
           path: docs/build/html/

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 859e42ab7d54544f32d4f73bbc2136a7d9094f54  # frozen: v0.8.1
+    rev: 89c421dff2e1026ba12cdb9ebd731f4a83aa8021  # frozen: v0.8.6
     hooks:
       - id: ruff
         args: [ --fix, --show-fixes, --exit-non-zero-on-fix ]

cset-workflow/includes/aoa_diag.cylc

@@ -0,0 +1,19 @@
+{% if AOA_DIAG|default(False) %}
+{% for model in models %}
+{% for plev in AOA_PLEV %}
+[runtime]
+    [[aoa_diag_m{{model["number"]}}_plev{{plev}}]]
+    inherit = PROCESS
+    execution time limit = PT60M
+
+        [[[directives]]]
+        --mem=12000
+        --ntasks=12
+
+        [[[environment]]]
+        CSET_RECIPE_NAME = "ageofair.yaml"
+        CSET_ADDOPTS = "--AOA_PLEV={{plev}} --AOA_CYCLIC={{AOA_CYCLIC}} --MODEL_NAME='{{model["name"]}}'"
+        MODEL_NUMBER = {{model["number"]}}
+{% endfor %}
+{% endfor %}
+{% endif %}

cset-workflow/includes/plot_spatial_plevel_model_field.cylc

@@ -5,6 +5,8 @@
 [runtime]
     [[generic_plevel_spatial_plot_sequence_m{{model_number}}_{{sanitise_task_name(field)}}_lv{{sanitise_task_name(plevel)}}]]
     inherit = PROCESS
+        [[[directives]]]
+        --mem=4000
         [[[environment]]]
         CSET_RECIPE_NAME = "generic_plevel_spatial_plot_sequence.yaml"
         CSET_ADDOPTS = """

cset-workflow/meta/diagnostics/rose-meta.conf

@@ -464,3 +464,45 @@ help=Set to True if you want a one-to-one line; false if not.
 type=python_boolean
 compulsory=true
 sort-key=qq1h
+
+[template variables=AOA_DIAG]
+ns=Diagnostics/Other
+title=Run age of air diagnostic on specified pressure levels.
+description=Run the age of air diagnostic on model data.
+help=The age of air diagnostic provides a qualtitative view of how old air is within
+     the domain, by calculating a back trajectory at each grid point at each lead time
+     to determine when air entered through the lateral boundary. This is useful for
+     diagnosing how quickly air ventilates the domain, depending on its size and the
+     prevailing meteorology.
+     The diagnostic uses the u, v and w components of wind, along with geopotential height to
+     perform the back trajectory. Data is first regridded to 0.5 degrees.
+     Note: the code here does not consider sub-grid transport, and only uses the postprocessed
+     velocity fields and geopotential height. Its applicability is for large-scale flow O(1000 km),
+     and not small scale flow where mixing is likely to play a larger role.
+type=python_boolean
+compulsory=true
+trigger=template variables=AOA_PLEV: True;
+        template variables=AOA_CYCLIC: True;
+sort-key=aoa1
+
+[template variables=AOA_PLEV]
+ns=Diagnostics/Other
+title=AOA: Pressure Levels
+description=List of pressure levels to calculate the age of air diagnostic.
+help=The pressure levels must be specified in hPa, where the variables (U,V,W,Z)
+     exist on the pressure level.
+type=python_list
+compulsory=true
+sort-key=aoa2
+
+[template variables=AOA_CYCLIC]
+ns=Diagnostics/Other
+title=AOA: Use Cyclic Option
+description=If True, LAM is considered cyclic in the east/west direction.
+help=This option when True, will allow back trajectories to advect through the east/
+     west boundary and continue through the other side of the domain. This is useful
+     for large domains such as the cyclic tropical channel, where there is no east/
+     west boundary.
+type=python_boolean
+compulsory=true
+sort-key=aoa3

cset-workflow/meta/rose-meta.conf

@@ -50,19 +50,12 @@ help=This is passed through to the plotting operators and sets the resolution
 type=integer
 compulsory=true
 
-[template variables=WEB_DIR]
-ns=General
-description=Path to directory that is served by the webserver.
-help=This will probably be under $HOME/public_html or similar. You will want to
-    ensure a subfolder is used as multiple files will be written here.
-type=quoted
-compulsory=true
-sort-key=web2
-
 [template variables=WEB_ADDR]
 ns=General
 title=Website address
-description=The address at which the website is served.
+description=The address at which the website is served. It should be specified
+           to the directory level above WEB_DIR (e.g.
+           https://example.com/~username if WEB_DIR is $HOME/public_html/CSET).
 help=This should be the address where your public_html or equivalent is served.
     It might include a partial path, such as your username.
 
@@ -74,7 +67,8 @@ sort-key=web1
 [template variables=WEB_DIR]
 ns=General
 title=Web directory
-description=Path to directory that is served by the webserver.
+description=Path to directory that is served by the webserver
+           (e.g: $HOME/public_html/CSET).
 help=This will probably be under $HOME/public_html or similar. You will want to
     ensure a subfolder is used as it will be replaced with a symbolic link.