MetOffice · jfrost-mo · Jan 30, 2024 · Dec 19, 2023 · Dec 19, 2023 · Dec 19, 2023
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,12 +5,6 @@
 
 version: 2
 updates:
-  # Check for python dependency updates.
-  - package-ecosystem: "pip" # See documentation for possible values
-    directory: "/" # Location of package manifests
-    schedule:
-      interval: "weekly"
-
   # Check for GitHub Actions updates.
   - package-ecosystem: "github-actions"
     directory: "/"

diff --git a/.github/workflows/conda-lock.yml b/.github/workflows/conda-lock.yml
@@ -23,11 +23,7 @@ jobs:
         run: python3 -m pip install tox tox-conda conda-lock
 
       - name: Update conda
-        run: |
-          conda update -q conda
-          # Install and use libmamba solver as it is much faster.
-          conda install -q -n base conda-libmamba-solver
-          conda config --set solver libmamba
+        run: conda update -q conda
 
       - name: Hash existing lock files
         run: sha256sum **/locks/*.txt > ${{ runner.temp }}/lock_file_hashes

diff --git a/.github/workflows/pull_request_checks.yml b/.github/workflows/pull_request_checks.yml
@@ -34,7 +34,7 @@ jobs:
           PY_COLORS: "1"
         run: |
           python3 -m pip install -e .
-          pytest --verbose --cov --cov-append
+          pytest --verbose --cov --cov-append --cov-config=pyproject.toml
           mv .coverage ".coverage.${{ matrix.py-ver }}"
       - uses: actions/upload-artifact@v4
         with:
@@ -50,19 +50,12 @@ jobs:
       contents: read
       pull-requests: write
     steps:
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - name: Get week number for cache
-        id: week
-        run: echo "week=$(date '+W%V')" >> $GITHUB_OUTPUT
-      - uses: actions/cache@v4
-        with:
-          key: coverage-report|${{ env.pythonLocation }}|${{ steps.week.outputs.week }}
-          path: ~/.cache/pip
       - name: Install coverage
         run: python3 -m pip install coverage
-      - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
           pattern: coverage-data-*
@@ -84,10 +77,13 @@ jobs:
           if ! gh pr comment --edit-last ${{ github.head_ref }} --body-file ${{ runner.temp }}/cov-report.md ; then
             gh pr comment ${{ github.head_ref }} --body-file ${{ runner.temp }}/cov-report.md
           fi
+      - name: Check 95% minimum coverage
+        run: coverage report --fail-under=95
 
   pre-commit:
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -98,7 +94,6 @@ jobs:
           path: ~/.cache/pre-commit
       - name: Set up pre-commit
         run: python3 -m pip install pre-commit
-      - uses: actions/checkout@v4
       - name: Run pre-commit
         run: pre-commit run --show-diff-on-failure --color=always --all-files
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,3 @@
+prune .github
+prune cset-workflow
+exclude .gitignore .pre-commit-config.yaml .git-blame-ignore-revs
diff --git a/cset-workflow/app/build_conda/bin/build_conda_env.sh b/cset-workflow/app/build_conda/bin/build_conda_env.sh
@@ -20,7 +20,7 @@ else
 fi
 
 # Find environment definition file, abort if not found.
-env_lock_file="${CYLC_WORKFLOW_RUN_DIR}/requirements/locks/py311-lock-linux-64.txt"
+env_lock_file="${CYLC_WORKFLOW_RUN_DIR}/requirements/locks/py312-lock-linux-64.txt"
 if [[ -f "$env_lock_file" ]]; then
   echo "Using environment file $env_lock_file"
 else

diff --git a/cset-workflow/app/install_local_cset/bin/install-local-cset.py b/cset-workflow/app/install_local_cset/bin/install-local-cset.py
@@ -35,5 +35,5 @@
                 check=True,
             )
 
-print("Using CSET version:")
-subprocess.run(("cset", "--version"), check=True)
+result = subprocess.run(("cset", "--version"), check=True, capture_output=True)
+print(f"Using CSET version: {result.stdout}")
diff --git a/cset-workflow/app/install_website_skeleton/file/html/double.html b/cset-workflow/app/install_website_skeleton/file/html/double.html
@@ -12,10 +12,7 @@
 
 <body>
     <nav class="topbar">
-        <div>
-            <h1>CSET</h1>
-            <div>TODO: Think of a tagline</div>
-        </div>
+        <h1>CSET</h1>
         <menu>
             <li><a href="index.html"><button>Home</button></a></li>
             <li><a href="single.html"><button>Single plot</button></a></li>

diff --git a/cset-workflow/app/install_website_skeleton/file/html/index.html b/cset-workflow/app/install_website_skeleton/file/html/index.html
@@ -12,10 +12,7 @@
 
 <body>
     <nav class="topbar">
-        <div>
-            <h1>CSET</h1>
-            <div>TODO: Think of a tagline</div>
-        </div>
+        <h1>CSET</h1>
         <menu>
             <li><a href="index.html"><button>Home</button></a></li>
             <li><a href="single.html"><button>Single plot</button></a></li>

diff --git a/cset-workflow/app/install_website_skeleton/file/html/plots/test/index.html b/cset-workflow/app/install_website_skeleton/file/html/plots/test/index.html
diff --git a/cset-workflow/app/install_website_skeleton/file/html/plots/test/plot.png b/cset-workflow/app/install_website_skeleton/file/html/plots/test/plot.png
diff --git a/cset-workflow/app/install_website_skeleton/file/html/single.html b/cset-workflow/app/install_website_skeleton/file/html/single.html
@@ -12,10 +12,7 @@
 
 <body>
     <nav class="topbar">
-        <div>
-            <h1>CSET</h1>
-            <div>TODO: Think of a tagline</div>
-        </div>
+        <h1>CSET</h1>
         <menu>
             <li><a href="index.html"><button>Home</button></a></li>
             <li><a href="single.html"><button>Single plot</button></a></li>

diff --git a/cset-workflow/app/install_website_skeleton/file/html/static/style.css b/cset-workflow/app/install_website_skeleton/file/html/static/style.css
@@ -79,7 +79,7 @@ a:hover {
   display: flex;
   flex-wrap: wrap;
   justify-content: space-between;
-  box-shadow: 0 4px 4px grey;
+  border-bottom: 1px solid black;
   padding: 0.5em 1em;
 }
 

diff --git a/cset-workflow/app/run_cset_recipe/bin/run-cset-recipe.py b/cset-workflow/app/run_cset_recipe/bin/run-cset-recipe.py
@@ -53,7 +53,7 @@ def append_to_index(index_path: Path, record: dict):
         json.dump(index, fp)
 
 
-input_file = (
+input_path = (
     Path(
         f"{os.getenv('CYLC_WORKFLOW_SHARE_DIR')}/cycle/{os.getenv('CYLC_TASK_CYCLE_POINT')}/input_path"
     )
@@ -63,8 +63,25 @@ def append_to_index(index_path: Path, record: dict):
 plot_id = str(uuid4())
 output_directory = Path.cwd() / plot_id
 
-# Takes recipe from CSET_RECIPE environment variable.
-subprocess.run(("cset", "-v", "bake", input_file, output_directory), check=True)
+# Takes recipe from CSET_RECIPE environment variable if not given.
+cset_recipe = os.getenv("CSET_RECIPE_NAME")
+if cset_recipe:
+    subprocess.run(("cset", "-v", "cookbook", cset_recipe), check=True)
+else:
+    cset_recipe = Path("recipe.yaml")
+    cset_recipe.write_bytes(os.getenvb("CSET_RECIPE"))
+
+subprocess.run(
+    (
+        "cset",
+        "-v",
+        "bake",
+        f"--recipe={cset_recipe}",
+        f"--input-dir={input_path}",
+        f"--output-dir={output_directory}",
+    ),
+    check=True,
+)
 
 with open(output_directory / "meta.json", "rt", encoding="UTF=8") as fp:
     recipe_meta = json.load(fp)
@@ -73,7 +90,6 @@ def append_to_index(index_path: Path, record: dict):
 # TODO: Save model in meta.json. Currently this always returns "Unknown".
 source_model = recipe_meta.get("model", "Unknown")
 
-# TODO: Give archive a meaningful name, probably a slugified title.
 archive_path = output_directory / "diagnostic.zip"
 with zipfile.ZipFile(archive_path, "w", compression=zipfile.ZIP_DEFLATED) as archive:
     for path in output_directory.rglob("*"):

diff --git a/cset-workflow/app/send_email/bin/send-email.py b/cset-workflow/app/send_email/bin/send-email.py
@@ -16,13 +16,20 @@ def get_home_page_addr():
     if len(path) == 1:
         path = os.getenv("WEB_DIR").split("/Public/")
     if len(path) == 1:
-        raise RuntimeError("Cannot determine web address.")
-    return f"{os.getenv('WEB_ADDR').strip('/')}/{path[-1]}"
+        raise ValueError("Cannot determine web address.")
+    try:
+        base_address = os.getenv("WEB_ADDR", "").strip("/")
+    except AttributeError as err:
+        raise ValueError("WEB_ADDR not set.") from err
+    return f"{base_address}/{path[-1]}"
 
 
 if __name__ == "__main__":
     subject = "CSET webpage ready"
-    body = f"""The webpage for your run of CSET is now ready. You can view it here:\n{get_home_page_addr()}"""
+    try:
+        body = f"The webpage for your run of CSET is now ready. You can view it here:\n{get_home_page_addr()}"
+    except ValueError:
+        body = "The webpage for your run of CSET is now ready, though the address could not be determined.\nCheck that WEB_ADDR and WEB_DIR are set correctly, then consider filing a bug report at https://github.com/MetOffice/CSET"
     subprocess.run(
         f'printf "{body}" | mail -s "{subject}" -S "from=notifications" "$USER"',
         check=True,

diff --git a/cset-workflow/includes/deterministic_plot_cape_ratio.cylc b/cset-workflow/includes/deterministic_plot_cape_ratio.cylc
@@ -9,38 +9,5 @@
     script = rose task-run -v --app-key=run_cset_recipe
     execution time limit = PT15M
         [[[environment]]]
-        CSET_RECIPE = """
-title: CAPE ratio plot
-description: |
-  Extracts data required for, and calculates the CAPE ratio diagnostic, plotting on a map.
-
-steps:
-  - operator: read.read_cubes
-
-  - operator: convection.cape_ratio
-    SBCAPE:
-        operator: filters.filter_cubes
-        constraint:
-            operator: constraints.generate_stash_constraint
-            stash: m01s20i114
-    MUCAPE:
-        operator: filters.filter_cubes
-        constraint:
-            operator: constraints.generate_stash_constraint
-            stash: m01s20i112
-    MUCIN:
-        operator: filters.filter_cubes
-        constraint:
-            operator: constraints.generate_stash_constraint
-            stash: m01s20i113
-    MUCIN_thresh: -75
-
-  - operator: filters.filter_cubes
-    constraint:
-        operator: constraints.generate_time_constraint
-        time_start: 2020-07-30T13:00Z
-
-  - operator: plot.postage_stamp_contour_plot
-
-  - operator: write.write_cube_to_nc
-"""
+        CSET_RECIPE_NAME = "CAPE_ratio_plot.yaml"
+        CSET_ADDOPTS = "--TIME={{CAPE_RATIO_TIME}}"
diff --git a/cset-workflow/install_restricted_files.sh b/cset-workflow/install_restricted_files.sh
@@ -36,7 +36,14 @@ fi
 # Don't copy some files, like README.md or top-level hidden files.
 rm "${tempdir}/README.md"
 
-cp -rv "${tempdir}"/* .
+if [[ -z "${1-}" ]]
+then
+  target_directory="$PWD"
+else
+  target_directory="$1"
+fi
+
+cp -rv "${tempdir}"/* "${target_directory}"
 
-# Clean up
+# Clean up, must force here to remove .git folder.
 rm -rf "${tempdir}"