diff --git a/.github/workflows/conda-lock.yml b/.github/workflows/conda-lock.yml index e236ed01d..f83b4d41e 100644 --- a/.github/workflows/conda-lock.yml +++ b/.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" \ diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 5a082275c..367f75836 100644 --- a/.github/workflows/documentation.yml +++ b/.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/ diff --git a/.github/workflows/pre-commit-update.yml b/.github/workflows/pre-commit-update.yml index 0777119f1..2989555c8 100644 --- a/.github/workflows/pre-commit-update.yml +++ b/.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: ${{ secrets.AUTH_APP_ID }} diff --git a/.github/workflows/pull_request_checks.yml b/.github/workflows/pull_request_checks.yml index 101abf38e..7ee9eb490 100644 --- a/.github/workflows/pull_request_checks.yml +++ b/.github/workflows/pull_request_checks.yml @@ -24,7 +24,7 @@ jobs: - name: Cache conda environment id: conda-env-cache - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a + uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 with: key: conda|${{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}}|${{hashFiles('requirements/locks/py312-lock-linux-64.txt')}} path: | @@ -148,7 +148,7 @@ jobs: sphinx-build -b html --color -W --keep-going "docs/source" "docs/build/html" echo '::endgroup::' - name: Upload documentation artifact - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 + uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b with: name: html-docs path: docs/build/html/ diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index e359494ec..c1cee6080 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -27,7 +27,7 @@ jobs: - name: Build package run: python3 -m build - - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 + - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b with: name: packages path: dist/ diff --git a/.github/workflows/weekly-checks.yml b/.github/workflows/weekly-checks.yml index 64b644ceb..807969916 100644 --- a/.github/workflows/weekly-checks.yml +++ b/.github/workflows/weekly-checks.yml @@ -14,7 +14,7 @@ jobs: - name: Cache conda environment id: conda-env-cache - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a + uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 with: key: conda|${{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/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1093050b4..8065b3605 100644 --- a/.pre-commit-config.yaml +++ b/.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 ] diff --git a/cset-workflow/includes/aoa_diag.cylc b/cset-workflow/includes/aoa_diag.cylc new file mode 100644 index 000000000..e50e82d06 --- /dev/null +++ b/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 %} diff --git a/cset-workflow/includes/plot_spatial_plevel_model_field.cylc b/cset-workflow/includes/plot_spatial_plevel_model_field.cylc index 18b85b7d4..c85f60c0f 100644 --- a/cset-workflow/includes/plot_spatial_plevel_model_field.cylc +++ b/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 = """ diff --git a/cset-workflow/meta/diagnostics/rose-meta.conf b/cset-workflow/meta/diagnostics/rose-meta.conf index 36370eed1..f53192079 100644 --- a/cset-workflow/meta/diagnostics/rose-meta.conf +++ b/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 diff --git a/cset-workflow/meta/rose-meta.conf b/cset-workflow/meta/rose-meta.conf index da61317af..b81e15e5c 100644 --- a/cset-workflow/meta/rose-meta.conf +++ b/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. diff --git a/cset-workflow/requirements/locks/py310-lock-linux-64.txt b/cset-workflow/requirements/locks/py310-lock-linux-64.txt index 8499c727d..6d9eff919 100644 --- a/cset-workflow/requirements/locks/py310-lock-linux-64.txt +++ b/cset-workflow/requirements/locks/py310-lock-linux-64.txt @@ -5,28 +5,28 @@ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda#f730d54ba9cd543666d7220c9f7ed563 -https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-hef167b5_0.conda#54fe76ab3d0189acaef95156874db7f9 +https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda#2c2fae981fd2afd00812c92ac47d023d https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb9d3cd8_2.conda#98514fe74548d768907ce7a13f680e8f https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb9d3cd8_2.conda#c63b5e52939e795ba8d26e35d767a843 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.3-hb9d3cd8_1.conda#ee228789a85f961d14567252a03e725f -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244 -https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.4-hb9d3cd8_0.conda#e2775acf57efd5af15b8e3d1d74d72d3 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda#720523eb0d6a9b0f6120c16b2aa4e7de +https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.2-h3394656_1.conda#b34c2833a1f56db610aeb27f206d800d https://conda.anaconda.org/conda-forge/linux-64/cartopy-0.24.0-py310h5eaa309_0.conda#ca4d935c1715f95b6e86846ad1675a2b https://conda.anaconda.org/conda-forge/linux-64/cf-units-3.3.0-py310hf462985_0.conda#c31938674e4cda43617a4d70f99ffd0c https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.4-py310hf462985_1.conda#c2d5289e6cbcecf2c549e01772fe5274 https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.1-py310h3788b33_0.conda#f993b13665fc2bb262b30217c815d137 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda#8f5b0b297b59e1ac160ad4beec99dbee -https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.55.0-py310h89163eb_0.conda#b1f20c0aa91d0e67e773e67076f01cc6 +https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.55.3-py310h89163eb_1.conda#c81251a712a36b477ed2330ec0e1a299 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.12-hb9ae30d_0.conda#201db6c2d9a3c5e46573ac4cb2e92f4f https://conda.anaconda.org/conda-forge/linux-64/geos-3.13.0-h5888daf_0.conda#40b4ab956c90390e407bb177f8a58bab https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c https://conda.anaconda.org/conda-forge/linux-64/graphviz-12.0.0-hba01fac_0.conda#953e31ea00d46beb7e64a79fc291ec44 -https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h6470451_5.conda#1483ba046164be27df7f6eddbcec3a12 +https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h8ee276e_7.conda#28a9681054948a7d7e96a7b8fe9b604e https://conda.anaconda.org/conda-forge/linux-64/gts-0.7.6-h977cf35_4.conda#4d8df0b0db060d33c9a702ada998a8fe -https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8 +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-10.1.0-h0b3b770_0.conda#ab1d7d56034814f4c3ed9f69f8c68806 https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h2a13503_7.conda#bd77f8da987968ec3927990495dc22e4 https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.4-nompi_h2d575fe_105.conda#d76fff0092b6389a12134ddebc0929bd https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 @@ -37,13 +37,13 @@ https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672 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argument parsing, setting up logging, top level error capturing, + and execution of the desired subcommand. + """ + # Read arguments from the command line and CSET_ADDOPTS environment variable + # into an args object. + parser = setup_argument_parser() + cli_args = raw_cli_args[1:] + shlex.split(os.getenv("CSET_ADDOPTS", "")) + args, unparsed_args = parser.parse_known_args(cli_args) + + setup_logging(args.verbose) + + # Down here so runs after logging is setup. + logging.debug("CLI Arguments: %s", cli_args) + + if args.subparser is None: + print("Please choose a command.", file=sys.stderr) + parser.print_usage() + sys.exit(127) + + try: + # Execute the specified subcommand. + args.func(args, unparsed_args) + except ArgumentError as err: + # Error message for when needed template variables are missing. + print(err, file=sys.stderr) + parser.print_usage() + sys.exit(127) + except Exception as err: + # Provide slightly nicer error messages for unhandled exceptions. + print(err, file=sys.stderr) + # Display the time and full traceback when debug logging. + logging.debug("An unhandled exception occurred.") + if logging.root.isEnabledFor(logging.DEBUG): + raise + sys.exit(1) + + +def setup_argument_parser() -> argparse.ArgumentParser: + """Create argument parser for CSET CLI.""" parser = argparse.ArgumentParser( prog="cset", description="Convective Scale Evaluation Tool" ) @@ -134,41 +174,17 @@ def main(): ) parser_recipe_id.set_defaults(func=_recipe_id_command) - cli_args = sys.argv[1:] + shlex.split(os.getenv("CSET_ADDOPTS", "")) - args, unparsed_args = parser.parse_known_args(cli_args) - - # Setup logging. - logging.captureWarnings(True) - loglevel = calculate_loglevel(args) - logger = logging.getLogger() - logger.setLevel(min(loglevel, logging.INFO)) - stderr_log = logging.StreamHandler() - stderr_log.addFilter(lambda record: record.levelno >= loglevel) - stderr_log.setFormatter(logging.Formatter("%(asctime)s %(levelname)s %(message)s")) - logger.addHandler(stderr_log) - - # Down here so runs after logging is setup. - logging.debug("CLI Arguments: %s", cli_args) + return parser - if args.subparser is None: - print("Please choose a command.", file=sys.stderr) - parser.print_usage() - sys.exit(127) - - try: - # Execute the specified subcommand. - args.func(args, unparsed_args) - except ArgumentError as err: - logging.error(err) - parser.print_usage() - sys.exit(3) - -def calculate_loglevel(args) -> int: - """Calculate the logging level to apply. +def setup_logging(verbosity: int): + """Configure logging level, format and output stream. Level is based on verbose argument and the LOGLEVEL environment variable. """ + logging.captureWarnings(True) + + # Calculate logging level. try: name_to_level = logging.getLevelNamesMapping() except AttributeError: @@ -176,17 +192,25 @@ def calculate_loglevel(args) -> int: # implementation detail for older versions. name_to_level = logging._nameToLevel # Level from CLI flags. - if args.verbose >= 2: - loglevel = logging.DEBUG - elif args.verbose == 1: - loglevel = logging.INFO + if verbosity >= 2: + cli_loglevel = logging.DEBUG + elif verbosity == 1: + cli_loglevel = logging.INFO else: - loglevel = logging.WARNING - return min( - loglevel, - # Level from environment variable. - name_to_level.get(os.getenv("LOGLEVEL"), logging.ERROR), - ) + cli_loglevel = logging.WARNING + # Level from environment variable. + env_loglevel = name_to_level.get(os.getenv("LOGLEVEL"), logging.ERROR) + loglevel = min(cli_loglevel, env_loglevel) + + # Configure the root logger. + logger = logging.getLogger() + # Record everything at least INFO for the log file. + logger.setLevel(min(loglevel, logging.INFO)) + stderr_log = logging.StreamHandler() + # Filter stderr log to just what is requested. + stderr_log.addFilter(lambda record: record.levelno >= loglevel) + stderr_log.setFormatter(logging.Formatter("%(asctime)s %(levelname)s %(message)s")) + logger.addHandler(stderr_log) def _bake_command(args, unparsed_args): diff --git a/src/CSET/operators/__init__.py b/src/CSET/operators/__init__.py index f447aa6bb..0b70e4f32 100644 --- a/src/CSET/operators/__init__.py +++ b/src/CSET/operators/__init__.py @@ -27,11 +27,13 @@ import CSET.operators from CSET._common import parse_recipe from CSET.operators import ( + ageofair, aggregate, collapse, constraints, convection, filters, + mesoscale, misc, plot, read, @@ -42,6 +44,7 @@ # Exported operators & functions to use elsewhere. __all__ = [ + "ageofair", "aggregate", "collapse", "constraints", @@ -49,6 +52,7 @@ "execute_recipe", "filters", "get_operator", + "mesoscale", "misc", "plot", "read", diff --git a/src/CSET/operators/_utils.py b/src/CSET/operators/_utils.py index 8522c6ebe..239b6b77f 100644 --- a/src/CSET/operators/_utils.py +++ b/src/CSET/operators/_utils.py @@ -66,6 +66,42 @@ def get_cube_yxcoordname(cube: iris.cube.Cube) -> tuple[str, str]: return (y_coords[0], x_coords[0]) +def is_spatialdim(cube: iris.cube.Cube) -> bool: + """Determine whether a cube is has two spatial dimension coordinates. + + If cube has both spatial dims, it will contain two unique coordinates + that explain space (latitude and longitude). The coordinates have to + be iterable/contain usable dimension data, as cubes may contain these + coordinates as scalar dimensions after being collapsed. + + Arguments + --------- + cube: iris.cube.Cube + An iris cube which will be checked to see if it contains coordinate + names that match a pre-defined list of acceptable coordinate names. + + Returns + ------- + bool + If true, then the cube has a spatial projection and thus can be plotted + as a map. + """ + # Acceptable horizontal coordinate names. + X_COORD_NAMES = ["longitude", "grid_longitude", "projection_x_coordinate", "x"] + Y_COORD_NAMES = ["latitude", "grid_latitude", "projection_y_coordinate", "y"] + + # Get a list of coordinate names for the cube + coord_names = [coord.name() for coord in cube.dim_coords] + x_coords = [coord for coord in coord_names if coord in X_COORD_NAMES] + y_coords = [coord for coord in coord_names if coord in Y_COORD_NAMES] + + # If there is one coordinate for both x and y direction return True. + if len(x_coords) == 1 and len(y_coords) == 1: + return True + else: + return False + + def is_transect(cube: iris.cube.Cube) -> bool: """Determine whether a cube is a transect. diff --git a/src/CSET/operators/ageofair.py b/src/CSET/operators/ageofair.py new file mode 100644 index 000000000..bd087ef21 --- /dev/null +++ b/src/CSET/operators/ageofair.py @@ -0,0 +1,474 @@ +# © Crown copyright, Met Office (2022-2024) and CSET contributors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Age of air operator. + +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. +""" + +import datetime +import logging +import multiprocessing +import os +import tempfile +from functools import partial +from math import asin, cos, radians, sin, sqrt + +import numpy as np +from iris.cube import Cube +from scipy.ndimage import gaussian_filter + +from CSET.operators._utils import get_cube_yxcoordname + + +def _calc_dist(coord_1, coord_2): + """Calculate distance between two coordinate tuples. + + Arguments + ---------- + coord_1: tuple + A tuple containing (latitude, longitude) coordinate floats + coord_2: tuple + A tuple containing (latitude, longitude) coordinate floats + + Returns + ------- + distance: float + Distance between the two coordinate points in meters + + Notes + ----- + The function uses the Haversine approximation to calculate distance in metres. + + """ + # Approximate radius of earth in m + # Source: https://nssdc.gsfc.nasa.gov/planetary/factsheet/earthfact.html + radius = 6378000 + + # Extract coordinates and convert to radians + lat1 = radians(coord_1[0]) + lon1 = radians(coord_1[1]) + lat2 = radians(coord_2[0]) + lon2 = radians(coord_2[1]) + + # Find out delta latitude, longitude + dlon = lon2 - lon1 + dlat = lat2 - lat1 + + # Compute distance + a = sin(dlat / 2) ** 2 + cos(lat1) * cos(lat2) * sin(dlon / 2) ** 2 + c = 2 * asin(sqrt(a)) + distance = radius * c + + return distance + + +def _aoa_core( + x_arr: np.ndarray, + y_arr: np.ndarray, + z_arr: np.ndarray, + g_arr: np.ndarray, + lats: np.ndarray, + lons: np.ndarray, + dt: int, + plev_idx: int, + timeunit: str, + cyclic: bool, + tmpdir: str, + lon_pnt: int, +): + """AOA multiprocessing core. + + Runs the core age of air code on a specific longitude point (all latitudes) for + parallelisation. + + Arguments + --------- + x_arr: np.ndarray + A numpy array containing x wind data. + y_arr: np.ndarray + A numpy array containing y wind data. + z_arr: np.ndarray + A numpy array containing w wind data. + g_arr: np.ndarray + A numpy array containing geopotential height data. + lats: np.ndarray + A numpy array containing latitude points. + lons: np.ndarray + A numpy array containing longitude points. + dt: int + Gap between time intervals + plev_idx: int + Index of pressure level requested to run back trajectories on. + timeunit: str + Units of time, currently only accepts 'hour' + cyclic: bool + Whether to wrap at east/west boundaries. See compute_ageofair for a fuller description. + tmpdir: str + Path to store intermediate data + lon_pnt: int + Longitude point to extract and run back trajectories on for parallelisation. + """ + # Initialise empty array to store age of air for this latitude strip. + ageofair_local = np.zeros((x_arr.shape[0], x_arr.shape[2])) + logging.debug("Working on %s", lon_pnt) + + # Ignore leadtime 0 as this is trivial. + for leadtime in range(1, x_arr.shape[0]): + # Initialise leadtime slice with current leadtime. + ageofair_local[leadtime, :] = leadtime * dt + for lat_pnt in range(0, x_arr.shape[2]): + # Gridpoint initialised as within LAM by construction. + outside_lam = False + + # If final column, look at dist from prev column, otherwise look at next column. + if lon_pnt == len(lons) - 1: + ew_spacing = _calc_dist( + (lats[lat_pnt], lons[lon_pnt]), (lats[lat_pnt], lons[lon_pnt - 1]) + ) + else: + ew_spacing = _calc_dist( + (lats[lat_pnt], lons[lon_pnt]), (lats[lat_pnt], lons[lon_pnt + 1]) + ) + + # If final row, look at dist from row column, otherwise look at next row. + if lat_pnt == len(lats) - 1: + ns_spacing = _calc_dist( + (lats[lat_pnt], lons[lon_pnt]), (lats[lat_pnt - 1], lons[lon_pnt]) + ) + else: + ns_spacing = _calc_dist( + (lats[lat_pnt], lons[lon_pnt]), (lats[lat_pnt + 1], lons[lon_pnt]) + ) + + # Go through past timeslices + for n in range(0, leadtime): + # First step back, so we use i,j coords to find out parcel location + # in terms of array point + if n == 0: + x = lon_pnt + y = lat_pnt + z = plev_idx + + # Only seek preceding wind if its inside domain. + if not outside_lam: + # Get vector profile at current time - nearest whole gridpoint. + u = x_arr[leadtime - n, int(z), int(y), int(x)] + v = y_arr[leadtime - n, int(z), int(y), int(x)] + w = z_arr[leadtime - n, int(z), int(y), int(x)] + g = g_arr[leadtime - n, int(z), int(y), int(x)] + + # First, compute horizontal displacement using inverse of horizontal vector + # Convert m/s to m/[samplingrate]h, then m -> model gridpoints + if timeunit == "hour": + du = ((u * 60 * 60 * dt) / ew_spacing) * -1.0 + dv = ((v * 60 * 60 * dt) / ns_spacing) * -1.0 + dz = (w * 60 * 60 * dt) * -1.0 + + # Get column of geopot height. + g_col = g_arr[(leadtime - n), :, int(y), int(x)] + + # New geopotential height of parcel - store 'capacity' between timesteps as vertical motions smaller. + if n == 0: + new_g = g + dz + pre_g = new_g + else: + new_g = pre_g + dz + + # Calculate which geopot level is closest to new geopot level. + z = np.argmin(np.abs(g_col - new_g)) + + # Update x,y location based on displacement. Z already updated + x = x + du + y = y + dv + + # If it is now outside domain, then save age and don't process further with outside LAM flag. + # Support cyclic domains like K-SCALE, where x coord out of domain gets moved through dateline. + if cyclic: + if ( + x < 0 + ): # as for example -0.3 would still be in domain, but x_arr.shape-0.3 would result in index error + x = x_arr.shape[3] + x # wrap back around dateline + elif x >= x_arr.shape[3]: + x = x_arr.shape[3] - x + else: + if x < 0 or x >= x_arr.shape[3]: + ageofair_local[leadtime, lat_pnt] = n * dt + outside_lam = True + + if y < 0 or y >= x_arr.shape[2]: + ageofair_local[leadtime, lat_pnt] = n * dt + outside_lam = True + + # Save 3d array containing age of air + np.save(tmpdir + f"/aoa_frag_{lon_pnt:04d}.npy", ageofair_local) + + +def compute_ageofair( + XWIND: Cube, + YWIND: Cube, + WWIND: Cube, + GEOPOT: Cube, + plev: int, + cyclic: bool = False, + multicore=True, +): + """Compute back trajectories for a given forecast. + + This allows us to determine when air entered through the boundaries. This will run on all available + lead-times, and thus return an age of air cube of shape ntime, nlat, nlon. It supports multiprocesing, + by iterating over longitude, or if set as None, will run on a single core, which is easier for debugging. + This function supports ensembles, where it will check if realization dimension exists and if so, loop + over this axis. + + Arguments + ---------- + XWIND: Cube + An iris cube containing the x component of wind on pressure levels, on a 0p5 degree grid. + Requires 4 dimensions, ordered time, pressure, latitude and longitude. Must contain at + least 2 time points to compute back trajectory. + YWIND: Cube + An iris cube in the same format as XWIND. + WWIND: Cube + An iris cube in the same format as XWIND. + GEOPOT: Cube + An iris cube in the same format as XWIND. + plev: int + The pressure level of which to compute the back trajectory on. The function will search to + see if this exists and if not, will raise an exception. + cyclic: bool + If cyclic is True, then the code will assume no east/west boundary and if a back trajectory + reaches the boundary, it will emerge out of the other side. This option is useful for large + domains such as the K-SCALE tropical channel, where there are only north/south boundaries in + the domain. + multicore: bool + If true, split up age of air diagnostic to use multiple cores (defaults to number of cores available to the process), otherwise run + using a single process, which is easier to debug if developing the code. + + Returns + ------- + ageofair_cube: Cube + An iris cube of the age of air data, with 3 dimensions (time, latitude, longitude). + + Notes + ----- + The age of air diagnostic was used in Warner et al. (2023) [Warneretal2023]_ to identify the relative + role of spin-up from initial conditions and lateral boundary conditions over tropical Africa to explore + the impact of new data assimilation techniques. A further paper is currently in review ([Warneretal2024]_) + which applies the diagnostic more widely to the Australian ACCESS convection-permitting models. + + References + ---------- + .. [Warneretal2023] Warner, J.L., Petch, J., Short, C., Bain, C., 2023. Assessing the impact of an NWP warm-start + system on model spin-up over tropical Africa. QJ, 149( 751), pp.621-636. doi:10.1002/qj.4429 + .. [Warneretal2024] Diagnosing lateral boundary spin-up in regional models using an age of air diagnostic + James L. Warner, Charmaine N. Franklin, Belinda Roux, Shaun Cooper, Susan Rennie, Vinod + Kumar. + Submitted for Quarterly Journal of the Royal Meteorological Society. + + """ + # Set up temporary directory to store intermediate age of air slices. + tmpdir = tempfile.TemporaryDirectory(dir=os.getenv("CYLC_TASK_WORK_DIR")) + logging.info("Made tmpdir %s", tmpdir.name) + + # Check that all cubes are of same size (will catch different dimension orders too). + if not XWIND.shape == YWIND.shape == WWIND.shape == GEOPOT.shape: + raise ValueError("Cubes are not the same shape") + + # Get time units and assign for later + if str(XWIND.coord("time").units).startswith("hours since "): + timeunit = "hour" + else: + raise NotImplementedError("Unsupported time base") + + # Make data non-lazy to speed up code. + logging.info("Making data non-lazy...") + x_arr = XWIND.data + y_arr = YWIND.data + z_arr = WWIND.data + g_arr = GEOPOT.data + + # Get coord points + lat_name, lon_name = get_cube_yxcoordname(XWIND) + lats = XWIND.coord(lat_name).points + lons = XWIND.coord(lon_name).points + time = XWIND.coord("time").points + + # Get time spacing of cube to determine whether the spacing in time is the + # same throughout the cube. If not, then not supported. + dt = XWIND.coord("time").points[1:] - XWIND.coord("time").points[:-1] + if np.all(dt == dt[0]): + dt = dt[0] + else: + raise NotImplementedError("Time intervals are not consistent") + + # Some logic to determine which index each axis is, and check for ensembles. + dimension_mapping = {} + for coord in XWIND.dim_coords: + dim_index = XWIND.coord_dims(coord.name())[0] + dimension_mapping[coord.name()] = dim_index + + if "realization" in dimension_mapping: + ensemble_mode = True + if dimension_mapping != { + "realization": 0, + "time": 1, + "pressure": 2, + lat_name: 3, + lon_name: 4, + }: + raise ValueError( + f"Dimension mapping not correct, ordered {dimension_mapping}" + ) + else: + ensemble_mode = False + if dimension_mapping != {"time": 0, "pressure": 1, lat_name: 2, lon_name: 3}: + raise ValueError( + f"Dimension mapping not correct, ordered {dimension_mapping}" + ) + + # Smooth vertical velocity to 2sigma (standard for 0.5 degree). + logging.info("Smoothing vertical velocity...") + if ensemble_mode: + z_arr = gaussian_filter(z_arr, 2, mode="nearest", axes=(3, 4)) + else: + z_arr = gaussian_filter(z_arr, 2, mode="nearest", axes=(2, 3)) + + # Get array index for user specified pressure level. + if plev not in XWIND.coord("pressure").points: + raise IndexError(f"Can't find plev {plev} in {XWIND.coord('pressure').points}") + + # Find corresponding pressure level index + plev_idx = np.where(XWIND.coord("pressure").points == plev)[0][0] + + # Initialise cube containing age of air. + if ensemble_mode: + ageofair_cube = Cube( + np.zeros( + ( + len(XWIND.coord("realization").points), + len(time), + len(lats), + len(lons), + ) + ), + long_name="age_of_air", + units="hours", + dim_coords_and_dims=[ + (XWIND.coord("realization"), 0), + (XWIND.coord("time"), 1), + (XWIND.coord(lat_name), 2), + (XWIND.coord(lon_name), 3), + ], + ) + else: + ageofair_cube = Cube( + np.zeros((len(time), len(lats), len(lons))), + long_name="age_of_air", + units="hours", + dim_coords_and_dims=[ + (XWIND.coord("time"), 0), + (XWIND.coord(lat_name), 1), + (XWIND.coord(lon_name), 2), + ], + ) + + # Unix API for getting set of usable CPUs. + # See https://docs.python.org/3/library/os.html#os.cpu_count + if multicore: + num_usable_cores = len(os.sched_getaffinity(0)) + + logging.info("STARTING AOA DIAG...") + start = datetime.datetime.now() + + # Main call for calculating age of air diagnostic + if ensemble_mode: + for e in range(0, len(XWIND.coord("realization").points)): + logging.info(f"Working on member {e}") + + # Multiprocessing on each longitude slice + func = partial( + _aoa_core, + np.copy(x_arr[e, :, :, :, :]), + np.copy(y_arr[e, :, :, :, :]), + np.copy(z_arr[e, :, :, :, :]), + np.copy(g_arr[e, :, :, :, :]), + lats, + lons, + dt, + plev_idx, + timeunit, + cyclic, + tmpdir.name, + ) + if multicore: + with multiprocessing.Pool(num_usable_cores) as pool: + pool.map(func, range(0, XWIND.shape[4])) + else: + # Convert to list to ensure everything is processed. + list(map(func, range(0, XWIND.shape[4]))) + + for i in range(0, XWIND.shape[4]): + file = f"{tmpdir.name}/aoa_frag_{i:04}.npy" + ageofair_cube.data[e, :, :, i] = np.load(file) + + else: + # Multiprocessing on each longitude slice + func = partial( + _aoa_core, + np.copy(x_arr), + np.copy(y_arr), + np.copy(z_arr), + np.copy(g_arr), + lats, + lons, + dt, + plev_idx, + timeunit, + cyclic, + tmpdir.name, + ) + if multicore: + with multiprocessing.Pool(num_usable_cores) as pool: + pool.map(func, range(0, XWIND.shape[3])) + else: + # Convert to list to ensure everything is processed. + list(map(func, range(0, XWIND.shape[3]))) + + for i in range(0, XWIND.shape[3]): + file = f"{tmpdir.name}/aoa_frag_{i:04}.npy" + ageofair_cube.data[:, :, i] = np.load(file) + + # Verbose for time taken to run, and collate tmp ndarrays into final cube, and return + logging.info( + "AOA DIAG DONE, took %s s", + (datetime.datetime.now() - start).total_seconds(), + ) + + # Clean tmpdir + tmpdir.cleanup() + + return ageofair_cube diff --git a/src/CSET/operators/constraints.py b/src/CSET/operators/constraints.py index fa8e80dda..438555115 100644 --- a/src/CSET/operators/constraints.py +++ b/src/CSET/operators/constraints.py @@ -92,6 +92,14 @@ def generate_level_constraint( Returns ------- constraint: iris.Constraint + + Notes + ----- + Due to the specification of ``coordinate`` as an argument any iterable + coordinate can be stratified with this function. Therefore, + ``"realization"`` is a valid option. Subsequently, ``levels`` specifies the + ensemble members, or group of ensemble members you wish to constrain your + results over. """ # If asterisks, then return all levels for given coordinate. if levels == "*": diff --git a/src/CSET/operators/filters.py b/src/CSET/operators/filters.py index 298e83d6e..fdd70ffbf 100644 --- a/src/CSET/operators/filters.py +++ b/src/CSET/operators/filters.py @@ -14,11 +14,56 @@ """Operators to perform various kind of filtering.""" +import logging from typing import Union import iris import iris.cube import iris.exceptions +import numpy as np + + +def apply_mask( + original_field: iris.cube.Cube, + mask: iris.cube.Cube, +) -> iris.cube.Cube: + """Apply a mask to given data as a masked array. + + Parameters + ---------- + original_field: iris.cube.Cube + The field to be masked. + mask: iris.cube.Cube + The mask being applied to the original field. + + Returns + ------- + masked_field: iris.cube.Cube + A cube of the masked field. + + Notes + ----- + The mask is first converted to 1s and NaNs before multiplication with + the original data. + + As discussed in generate_mask, you can combine multiple masks in a + recipe using other functions before applying the mask to the data. + + Examples + -------- + >>> land_points_only = apply_mask(temperature, land_mask) + """ + # Ensure mask is only 1s or NaNs. + mask.data[mask.data == 0] = np.nan + mask.data[~np.isnan(mask.data)] = 1 + logging.info( + "Mask set to 1 or 0s, if addition of multiple masks results" + "in values > 1 these are set to 1." + ) + masked_field = original_field.copy() + masked_field.data *= mask.data + masked_field.attributes["mask"] = f"mask_of_{original_field.name()}" + return masked_field def filter_cubes( @@ -93,3 +138,68 @@ def filter_multiple_cubes( "The constraints don't produce a single cube per constraint." ) from err return filtered_cubes + + +def generate_mask( + mask_field: iris.cube.Cube, + condition: str, + value: float, +) -> iris.cube.Cube: + """Generate a mask to remove data not meeting conditions. + + Parameters + ---------- + mask_field: iris.cube.Cube + The field to be used for creating the mask. + condition: str + The type of condition applied, six available options: + '==','!=','<','<=','>', and '>='. + value: float + The value on the right hand side of the condition. + + Returns + ------- + mask: iris.cube.Cube + Mask meeting the condition applied. + + Raises + ------ + ValueError: Unexpected value for condition. Expected ==, !=, >, >=, <, <=. + Got {condition}. + Raised when condition is not supported. + + Notes + ----- + The mask is created in the opposite sense to numpy.ma.masked_arrays. This + method was chosen to allow easy combination of masks together outside of + this function using misc.addition or misc.multiplication depending on + applicability. The combinations can be of any fields such as orography > + 500 m, and humidity == 100 %. + + The conversion to a masked array occurs in the apply_mask routine, which + should happen after all relevant masks have been combined. + + Examples + -------- + >>> land_mask = generate_mask(land_sea_mask,'==',1) + """ + mask = mask_field.copy() + mask.data = np.zeros(mask.data.shape) + match condition: + case "==": + mask.data[mask_field.data == value] = 1 + case "!=": + mask.data[mask_field.data != value] = 1 + case ">": + mask.data[mask_field.data > value] = 1 + case ">=": + mask.data[mask_field.data >= value] = 1 + case "<": + mask.data[mask_field.data < value] = 1 + case "<=": + mask.data[mask_field.data <= value] = 1 + case _: + raise ValueError("""Unexpected value for condition. Expected ==, !=, + >, >=, <, <=. Got {condition}.""") + mask.attributes["mask"] = f"mask_for_{mask_field.name()}_{condition}_{value}" + return mask diff --git a/src/CSET/operators/mesoscale.py b/src/CSET/operators/mesoscale.py new file mode 100644 index 000000000..900a12f36 --- /dev/null +++ b/src/CSET/operators/mesoscale.py @@ -0,0 +1,117 @@ +# © Crown copyright, Met Office (2022-2024) and CSET contributors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +"""A module containing different diagnostics for mesoscales. + +The diagnostics here are applicable at mesoscales and apply generally +rather than for specific aspects of mesoscale meteorology (e.g. convection). +For specific aspects, the user is referred to other modules available in +CSET. + +""" + +import logging + +import iris +from scipy.ndimage import gaussian_filter, uniform_filter + +from CSET.operators._utils import get_cube_yxcoordname + + +def spatial_perturbation_field( + original_field: iris.cube.Cube, + apply_gaussian_filter: bool = True, + filter_scale: int = 40, +) -> iris.cube.Cube: + """Calculate a spatial perturbation field. + + Parameters + ---------- + original_field: iris.cube.Cube + Iris cube containing data to smooth, supporting multiple dimensions + (at least two spatial dimensions must be supplied, i.e. 2D). + apply_gaussian_filter: boolean, optional + If set to True a Gaussian filter is applied; if set to False + a Uniform filter is applied. + Default is True. + filter_scale: int, optional + Scale at which to define the filter in grid boxes. If the + filter is a Gaussian convolution this value represents the + standard deviation of the Gaussian kernel. + Default is 40 grid boxes. + + Returns + ------- + pert_field: iris.cube.Cube + An iris cube of the spatial perturbation field. + + Notes + ----- + In mesoscale meteorology the perturbation field is more important than the + balanced flows for process understanding. This function is designed + to create spatial perturbation fields based on smoothing with a Gaussian + kernel or a uniform kernel. + + The kernels are defined by the filter_scale, which for mesoscale + perturbations should be between an approximate cloud separation distance, + of 30 km, and synoptic scale variations (1000 km). In practice any + value between these ranges should provided broadly consistent results (e.g. + [Flacketal2016]_). The Gaussian kernel will give greater importance to + areas closer to the event and will produce a smooth perturbation field. + The uniform kernel will produce a smooth perturbation field but will not + give local features as much prominence. + + Caution should be applied to boundaries, particularly if the domain is of + variable resolution, as some numerical artifacts could be introduced. + + References + ---------- + .. [Flacketal2016] Flack, D.L.A., Plant, R.S., Gray, S.L., Lean, H.W., + Keil, C. and Craig, G.C. (2016) "Characterisation of Convective + Regimes over the British Isles." Quarterly Journal of the Royal + Meteorological Society, vol. 142, 1541-1553. doi:10.1002/qj.2758 + + Examples + -------- + >>> Temperature_perturbation = meso.spatial_perturbation_fields(Temp, + gaussian_filter=True,filter_scale=40) + >>> iplt.pcolormesh(Temperature_perturabtion[0,:,:],cmap=mpl.cm.bwr) + >>> plt.gca().coastlines('10m') + >>> plt.clim(-5,5) + >>> plt.colorbar() + >>> plt.show() + + """ + pert_field = original_field.copy() + # find axes of spatial coordinates in field + coords = [coord.name() for coord in original_field.coords()] + # axes tuple containing latitude, longitude coordinate name. + axes = ( + coords.index(get_cube_yxcoordname(original_field)[0]), + coords.index(get_cube_yxcoordname(original_field)[1]), + ) + # apply convolution depending on type used + if apply_gaussian_filter: + filter_type = "Gaussian" + logging.info("Gaussian filter applied.") + pert_field.data -= gaussian_filter(original_field.data, filter_scale, axes=axes) + else: + logging.info("Uniform filter applied.") + filter_type = "Uniform" + pert_field.data -= uniform_filter(original_field.data, filter_scale, axes=axes) + # provide attributes to cube to indicate spatial perturbation field + pert_field.attributes["perturbation_field"] = ( + f"{filter_type}_with_{str(filter_scale)}_grid_point_filter_scale" + ) + return pert_field diff --git a/src/CSET/operators/read.py b/src/CSET/operators/read.py index 73f439ec3..0ed7661c4 100644 --- a/src/CSET/operators/read.py +++ b/src/CSET/operators/read.py @@ -83,6 +83,8 @@ def read_cube( if len(cubes) == 1: return cubes[0] else: + # Log cube details so you can see why they are not merging. + logging.debug("Non-merging cubes:\n%s", "\n".join(str(cube) for cube in cubes)) raise ValueError( f"Constraint doesn't produce single cube. {constraint}\n{cubes}" ) @@ -198,6 +200,8 @@ def callback(cube: iris.cube.Cube, field, filename: str): _lfric_normalise_callback(cube, field, filename) _lfric_time_coord_fix_callback(cube, field, filename) _longitude_fix_callback(cube, field, filename) + _fix_spatialcoord_name_callback(cube) + _fix_pressurecoord_name_callback(cube) return callback @@ -276,7 +280,7 @@ def _lfric_normalise_callback(cube: iris.cube.Cube, field, filename): # Remove unwanted attributes. cube.attributes.pop("timeStamp", None) cube.attributes.pop("uuid", None) - # There might also be a "name" attribute to ditch, which is the filename. + cube.attributes.pop("name", None) # Sort STASH code list. stash_list = cube.attributes.get("um_stash_source") @@ -333,6 +337,52 @@ def _longitude_fix_callback(cube: iris.cube.Cube, field, filename): return cube +def _fix_spatialcoord_name_callback(cube: iris.cube.Cube): + """Check latitude and longitude coordinates name. + + This is necessary as some models define their grid as 'grid_latitude' and 'grid_longitude' + and this means that recipes will fail - particularly if the user is comparing multiple models + where the spatial coordinate names differ. + """ + import CSET.operators._utils as utils + + # Check if cube is spatial. + if not utils.is_spatialdim(cube): + # Don't modify non-spatial cubes. + return cube + + # Get spatial coords. + y_name, x_name = utils.get_cube_yxcoordname(cube) + + if y_name in ["latitude"] and cube.coord(y_name).units in [ + "degrees", + "degrees_north", + "degrees_south", + ]: + cube.coord(y_name).rename("grid_latitude") + if x_name in ["longitude"] and cube.coord(x_name).units in [ + "degrees", + "degrees_west", + "degrees_east", + ]: + cube.coord(x_name).rename("grid_longitude") + + +def _fix_pressurecoord_name_callback(cube: iris.cube.Cube): + """Rename pressure_level coordinate to pressure if it exists. + + This problem was raised because the AIFS model data from ECMWF + defines the pressure coordinate with the name 'pressure_level' rather + than compliant CF coordinate names + """ + # We only want to modify instances where the coordinate system is actually + # latitude/longitude, and not touch the cube if the coordinate system is say + # meters. + for coord in cube.dim_coords: + if coord.name() == "pressure_level": + coord.rename("pressure") + + def _check_input_files(input_path: Path | str, filename_pattern: str) -> Iterable[Path]: """Get an iterable of files to load, and check that they all exist. diff --git a/src/CSET/operators/regrid.py b/src/CSET/operators/regrid.py index 59b08d52d..242003c52 100644 --- a/src/CSET/operators/regrid.py +++ b/src/CSET/operators/regrid.py @@ -158,7 +158,7 @@ def regrid_onto_xyspacing( y_coord, x_coord = get_cube_yxcoordname(cube) # List of supported grids - check if it is compatible - supported_grids = (iris.coord_systems.GeogCS,) + supported_grids = (iris.coord_systems.GeogCS, iris.coord_systems.RotatedGeogCS) if not isinstance(cube.coord(x_coord).coord_system, supported_grids): raise NotImplementedError( f"Does not currently support {cube.coord(x_coord).coord_system} regrid method" diff --git a/src/CSET/recipes/Example_Gaussian_Spatial_Perturbation.yaml b/src/CSET/recipes/Example_Gaussian_Spatial_Perturbation.yaml new file mode 100644 index 000000000..78cbbbb25 --- /dev/null +++ b/src/CSET/recipes/Example_Gaussian_Spatial_Perturbation.yaml @@ -0,0 +1,28 @@ +category: Surface Spatial Plot +title: Mesoscale Gaussian Filter Spatial Perturbation Plot +description: | + Creates a spatial map of a perturbation field based on a Gaussian filter + over a specified halfwidth in number of grid points. + +steps: + - operator: read.read_cubes + + - operator: mesoscale.spatial_perturbation_field + original_field: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: surface_air_temperature + cell_method_constraint: + operator: constraints.generate_cell_methods_constraint + cell_methods: [] + Gaussian_filter: True + filter_scale: 40 + + - operator: plot.spatial_pcolormesh_plot + sequence_coordinate: time + + - operator: write.write_cube_to_nc + overwrite: True diff --git a/src/CSET/recipes/Example_Uniform_Spatial_Perturbation.yaml b/src/CSET/recipes/Example_Uniform_Spatial_Perturbation.yaml new file mode 100644 index 000000000..c78033302 --- /dev/null +++ b/src/CSET/recipes/Example_Uniform_Spatial_Perturbation.yaml @@ -0,0 +1,28 @@ +category: Surface Spatial Plot +title: Mesoscale Uniform Filter Spatial Perturbation Plot +description: | + Creates a spatial map of a perturbation field based on a uniform filter + over a specified filter scale in number of grid points. + +steps: + - operator: read.read_cubes + + - operator: mesoscale.spatial_perturbation_field + original_field: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: surface_air_temperature + cell_method_constraint: + operator: constraints.generate_cell_methods_constraint + cell_methods: [] + Gaussian_filter: False + filter_scale: 40 + + - operator: plot.spatial_pcolormesh_plot + sequence_coordinate: time + + - operator: write.write_cube_to_nc + overwrite: True diff --git a/src/CSET/recipes/ageofair.yaml b/src/CSET/recipes/ageofair.yaml new file mode 100644 index 000000000..a2cf0b7ed --- /dev/null +++ b/src/CSET/recipes/ageofair.yaml @@ -0,0 +1,88 @@ +category: Diagnostics +title: $MODEL_NAME Age of Air Diagnostic at $AOA_PLEV +description: | + Extracts data required for, and calculates the age of air diagnostic on a given pressure levels. This is then plotted on a map projection for each lead-time. + 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. + +steps: + - operator: read.read_cubes + + - operator: ageofair.compute_ageofair + XWIND: + operator: regrid.regrid_onto_xyspacing + xspacing: 0.5 + yspacing: 0.5 + method: Linear + toregrid: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: x_wind + pressure_level_constraint: + operator: constraints.generate_level_constraint + coordinate: pressure + levels: "*" + YWIND: + operator: regrid.regrid_onto_xyspacing + xspacing: 0.5 + yspacing: 0.5 + method: Linear + toregrid: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: y_wind + pressure_level_constraint: + operator: constraints.generate_level_constraint + coordinate: pressure + levels: "*" + WWIND: + operator: regrid.regrid_onto_xyspacing + xspacing: 0.5 + yspacing: 0.5 + method: Linear + toregrid: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: upward_air_velocity + pressure_level_constraint: + operator: constraints.generate_level_constraint + coordinate: pressure + levels: "*" + GEOPOT: + operator: regrid.regrid_onto_xyspacing + xspacing: 0.5 + yspacing: 0.5 + method: Linear + toregrid: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: geopotential_height + pressure_level_constraint: + operator: constraints.generate_level_constraint + coordinate: pressure + levels: "*" + + plev: $AOA_PLEV + cyclic: $AOA_CYCLIC + + - operator: write.write_cube_to_nc + overwrite: True + + - operator: plot.spatial_contour_plot diff --git a/src/CSET/recipes/example_combined_mask_addition.yaml b/src/CSET/recipes/example_combined_mask_addition.yaml new file mode 100644 index 000000000..9e14eb9af --- /dev/null +++ b/src/CSET/recipes/example_combined_mask_addition.yaml @@ -0,0 +1,50 @@ +category: Quick Look +title: Example adding masks for 'OR' type filters +description: | + Generates and applies two masks, and adds them together for more complex stratified analysis. + Examples would include masking for variables outside a range, e.g. temperature < 273 K or temperature + > 313 K. Addition of masks would be akin to finding a probability of two events happening at the same time in different places. + +steps: + - operator: read.read_cubes + + - operator: filters.apply_mask + original_field: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: surface_air_temperature + cell_method_constraint: + operator: constraints.generate_cell_methods_constraint + cell_methods: [] + masks: + operator: misc.addition + addend_1: + operator: filters.generate_mask + mask_field: + operator: filters.filter_cubes + constraint: + operator: constraints.generate_var_constraint + varname: surface_altitude + condition: '<' + value: 500 + addend_2: + operator: filters.generate_mask + mask_field: + operator: filters.filter_cubes + constraint: + operator: constraints.generate_var_constraint + varname: surface_altitude + condition: '>' + value: 200 + + - operator: collapse.collapse + coordinate: [grid_latitude, grid_longitude] + method: MEAN + + - operator: write.write_cube_to_nc + overwrite: True + + - operator: plot.plot_line_series diff --git a/src/CSET/recipes/example_combined_mask_multiplication.yaml b/src/CSET/recipes/example_combined_mask_multiplication.yaml new file mode 100644 index 000000000..e7c725cde --- /dev/null +++ b/src/CSET/recipes/example_combined_mask_multiplication.yaml @@ -0,0 +1,50 @@ +category: Quick Look +title: Example adding masks for 'AND' type filters +description: | + Generates and applies two masks, and multiplies them together for more complex stratified analysis. + Examples would include masking for temperature > 273 K and orography > 500 m. Multiplication of masks + would be akin to finding a probability of two events happening at the same time in the same place. + +steps: + - operator: read.read_cubes + + - operator: filters.apply_mask + original_field: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: surface_air_temperature + cell_method_constraint: + operator: constraints.generate_cell_methods_constraint + cell_methods: [] + masks: + operator: misc.multiplication + multiplicand: + operator: filters.generate_mask + mask_field: + operator: filters.filter_cubes + constraint: + operator: constraints.generate_var_constraint + varname: surface_altitude + condition: '>' + value: 500 + multiplier: + operator: filters.generate_mask + mask_field: + operator: filters.filter_cubes + constraint: + operator: constraints.generate_var_constraint + varname: surface_air_temperature + condition: '<=' + value: 273 + + - operator: collapse.collapse + coordinate: [grid_latitude, grid_longitude] + method: MEAN + + - operator: write.write_cube_to_nc + overwrite: True + + - operator: plot.plot_line_series diff --git a/src/CSET/recipes/example_simple_mask.yaml b/src/CSET/recipes/example_simple_mask.yaml new file mode 100644 index 000000000..d39d8d683 --- /dev/null +++ b/src/CSET/recipes/example_simple_mask.yaml @@ -0,0 +1,36 @@ +category: Quick Look +title: Example simple mask application +description: Generates and applies a simple mask to a field for stratified analysis. + +steps: + - operator: read.read_cubes + + - operator: filters.apply_mask + original_field: + operator: filters.filter_cubes + constraint: + operator: constraints.combine_constraints + variable_constraint: + operator: constraints.generate_var_constraint + varname: surface_air_temperature + cell_method_constraint: + operator: constraints.generate_cell_methods_constraint + cell_methods: [] + masks: + operator: filters.generate_mask + mask_field: + operator: filters.filter_cubes + constraint: + operator: constraints.generate_var_constraint + varname: surface_altitude + condition: '>=' + value: 500 + + - operator: collapse.collapse + coordinate: [grid_latitude, grid_longitude] + method: MEAN + + - operator: write.write_cube_to_nc + overwrite: True + + - operator: plot.plot_line_series diff --git a/src/CSET/recipes/example_spatial_plot_of_mask.yaml b/src/CSET/recipes/example_spatial_plot_of_mask.yaml new file mode 100644 index 000000000..c2e7b8883 --- /dev/null +++ b/src/CSET/recipes/example_spatial_plot_of_mask.yaml @@ -0,0 +1,21 @@ +category: Surface Spatial Plot +title: Example plot of a mask +description: | + Generates a mask and then provides a spatial map of the mask. + +steps: + - operator: read.read_cubes + + - operator: filters.generate_mask + mask_field: + operator: filters.filter_cubes + constraint: + operator: constraints.generate_var_constraint + varname: surface_altitude + condition: '>=' + value: 500 + + - operator: plot.spatial_pcolormesh_plot + + - operator: write.write_cube_to_nc + overwrite: True diff --git a/src/CSET/recipes/generic_surface_histogram_series.yaml b/src/CSET/recipes/generic_surface_histogram_series.yaml index ed34358a0..56372b912 100644 --- a/src/CSET/recipes/generic_surface_histogram_series.yaml +++ b/src/CSET/recipes/generic_surface_histogram_series.yaml @@ -1,5 +1,5 @@ category: Histogram -title: $VARNAME Surface Level Histogram Plot +title: $MODEL_NAME $VARNAME Surface Level Histogram Plot description: | Extracts and plots the probability density of surface `$VARNAME`. It uses [`plt.hist`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.hist.html) diff --git a/tests/operators/test_ageofair.py b/tests/operators/test_ageofair.py new file mode 100644 index 000000000..ae2646d73 --- /dev/null +++ b/tests/operators/test_ageofair.py @@ -0,0 +1,239 @@ +# © Crown copyright, Met Office (2022-2024) and CSET contributors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +"""Tests for age of air operator.""" + +import iris +import iris.cube +import numpy as np +import pytest + +import CSET.operators.ageofair as ageofair + + +@pytest.fixture() +def xwind() -> iris.cube.Cube: + """Get regridded xwind to run tests on.""" + return iris.load_cube("tests/test_data/ageofair/aoa_in_rgd.nc", "x_wind") + + +@pytest.fixture() +def ywind() -> iris.cube.Cube: + """Get regridded ywind to run tests on.""" + return iris.load_cube("tests/test_data/ageofair/aoa_in_rgd.nc", "y_wind") + + +@pytest.fixture() +def wwind() -> iris.cube.Cube: + """Get regridded wwind to run tests on.""" + return iris.load_cube( + "tests/test_data/ageofair/aoa_in_rgd.nc", "upward_air_velocity" + ) + + +@pytest.fixture() +def geopot() -> iris.cube.Cube: + """Get regridded geopotential height to run tests on.""" + return iris.load_cube( + "tests/test_data/ageofair/aoa_in_rgd.nc", "geopotential_height" + ) + + +@pytest.fixture() +def ens_regridded() -> iris.cube.CubeList: + """Get regridded ensemble cubelist to run tests on.""" + return iris.load("tests/test_data/ageofair/aoa_in_ens.nc") + + +@pytest.fixture() +def ens_regridded_out() -> iris.cube.Cube: + """Get age of air ensemble output to check results are consistent.""" + return iris.load("tests/test_data/ageofair/aoa_out_ens.nc") + + +def test_calc_dist(): + """Test distance calculated from calc_dist in age of air calculation. + + Allow a tolerance of 20km (as we expect some error). + """ + # London and Johannesburg coordinates to 2 decimal places. + london_coords = (51.51, -0.13) + johanbg_coords = (-26.21, 28.03) + + dist = ageofair._calc_dist(london_coords, johanbg_coords) + actual_distance = 9068670 # Air line according to Google?! + + assert np.allclose(dist, actual_distance, rtol=1e-06, atol=20000) + + +def test_aoa_nocyclic(xwind, ywind, wwind, geopot): + """Test case when not cyclic.""" + assert np.allclose( + ageofair.compute_ageofair( + xwind, ywind, wwind, geopot, plev=500, cyclic=False + ).data, + iris.load_cube("tests/test_data/ageofair/aoa_out_nocyclic.nc").data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_aoa_cyclic_parallelthreads(xwind, ywind, wwind, geopot): + """Test case when cyclic with parallel threads.""" + assert np.allclose( + ageofair.compute_ageofair( + xwind, + ywind, + wwind, + geopot, + plev=500, + cyclic=True, + multicore=True, + ).data, + iris.load_cube("tests/test_data/ageofair/aoa_out_cyclic.nc").data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_aoa_cyclic_singlethread(xwind, ywind, wwind, geopot): + """Test case when cyclic with no parallelisation.""" + assert np.allclose( + ageofair.compute_ageofair( + xwind, + ywind, + wwind, + geopot, + plev=500, + cyclic=True, + multicore=False, + ).data, + iris.load_cube("tests/test_data/ageofair/aoa_out_cyclic.nc").data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_aoa_mismatched_size(xwind, ywind, wwind, geopot): + """Mismatched array size raises error.""" + ywind = ywind[:, :, 1:, :] + with pytest.raises(ValueError): + ageofair.compute_ageofair(xwind, ywind, wwind, geopot, plev=500, cyclic=True) + + +def test_aoa_timefreq(xwind, ywind, wwind, geopot): + """Variable time intervals raises NotImplemented error.""" + with pytest.raises(NotImplementedError): + ageofair.compute_ageofair( + xwind[[1, 2, 4, 5], :, :, :], + ywind[[1, 2, 4, 5], :, :, :], + wwind[[1, 2, 4, 5], :, :, :], + geopot[[1, 2, 4, 5], :, :, :], + plev=500, + cyclic=True, + ) + + +def test_aoa_timeunits(xwind, ywind, wwind, geopot): + """Time intervals that are not hourly raises NotImplemented error.""" + xwind.coord("time").units = "days since 1970-01-01 00:00:00" + with pytest.raises(NotImplementedError): + ageofair.compute_ageofair(xwind, ywind, wwind, geopot, plev=500, cyclic=True) + + +def test_aoa_plevreq(xwind, ywind, wwind, geopot): + """Pressure level requested that doesn't exist raises Index error.""" + with pytest.raises(IndexError): + ageofair.compute_ageofair(xwind, ywind, wwind, geopot, plev=123, cyclic=True) + + +def test_aoa_ens(ens_regridded): + """Test case including vertical velocity and not cyclic for ensemble data.""" + assert np.allclose( + ageofair.compute_ageofair( + ens_regridded.extract("x_wind")[0], + ens_regridded.extract("y_wind")[0], + ens_regridded.extract("upward_air_velocity")[0], + ens_regridded.extract("geopotential_height")[0], + plev=200, + cyclic=False, + ).data, + iris.load_cube("tests/test_data/ageofair/aoa_out_ens.nc").data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_aoa_ens_multicore(ens_regridded): + """Test case with ensembles ensuring that single core and multicore produce identical values.""" + assert np.allclose( + ageofair.compute_ageofair( + ens_regridded.extract("x_wind")[0], + ens_regridded.extract("y_wind")[0], + ens_regridded.extract("upward_air_velocity")[0], + ens_regridded.extract("geopotential_height")[0], + plev=200, + cyclic=False, + multicore=True, + ).data, + ageofair.compute_ageofair( + ens_regridded.extract("x_wind")[0], + ens_regridded.extract("y_wind")[0], + ens_regridded.extract("upward_air_velocity")[0], + ens_regridded.extract("geopotential_height")[0], + plev=200, + cyclic=False, + multicore=False, + ).data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_aoa_misordered_dims(xwind, ywind, wwind, geopot): + """Dimensions in input cubes do not match expected ordering.""" + xwind.transpose([0, 1, 3, 2]) + ywind.transpose([0, 1, 3, 2]) + wwind.transpose([0, 1, 3, 2]) + geopot.transpose([0, 1, 3, 2]) + with pytest.raises(ValueError): + ageofair.compute_ageofair( + xwind, + ywind, + wwind, + geopot, + plev=500, + cyclic=True, + ) + + +def test_aoa_misordered_dims_ens(ens_regridded): + """Dimensions in input cubes do not match expected ordering.""" + xwind = ens_regridded.extract("x_wind")[0] + ywind = ens_regridded.extract("y_wind")[0] + wwind = ens_regridded.extract("upward_air_velocity")[0] + geopot = ens_regridded.extract("geopotential_height")[0] + xwind.transpose([0, 1, 2, 4, 3]) + ywind.transpose([0, 1, 2, 4, 3]) + wwind.transpose([0, 1, 2, 4, 3]) + geopot.transpose([0, 1, 2, 4, 3]) + with pytest.raises(ValueError): + ageofair.compute_ageofair( + xwind, + ywind, + wwind, + geopot, + plev=500, + cyclic=True, + ) diff --git a/tests/operators/test_filters.py b/tests/operators/test_filters.py index 8eefe3b78..a35352c75 100644 --- a/tests/operators/test_filters.py +++ b/tests/operators/test_filters.py @@ -15,6 +15,7 @@ """Test filter operators.""" import iris.cube +import numpy as np import pytest from CSET.operators import constraints, filters @@ -176,3 +177,103 @@ def test_generate_level_constraint_returnallmodlev(load_verticalcoord_cubelist): assert expected_coordstr in repr( load_verticalcoord_cubelist.extract(constraint_1)[0].coords ) + + +def test_generate_mask_fail_wrong_condition(cube): + """Fails for a wrong condition.""" + with pytest.raises(ValueError): + filters.generate_mask(cube, "!<", 10) + + +def test_generate_mask_equal_to(cube): + """Generates a mask with values equal to a specified value.""" + mask = cube.copy() + mask.data = np.zeros(mask.data.shape) + mask.data[cube.data == 276] = 1 + assert np.allclose( + filters.generate_mask(cube, "==", 276).data, + mask.data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_generate_mask_not_equal_to(cube): + """Generates a mask with values not equal to a specified value.""" + mask = cube.copy() + mask.data = np.zeros(mask.data.shape) + mask.data[cube.data != 276] = 1 + assert np.allclose( + filters.generate_mask(cube, "!=", 276).data, + mask.data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_generate_mask_greater_than(cube): + """Generates a mask with values greater than a specified value.""" + mask = cube.copy() + mask.data = np.zeros(mask.data.shape) + mask.data[cube.data > 276] = 1 + assert np.allclose( + filters.generate_mask(cube, ">", 276).data, + mask.data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_generate_mask_greater_equal_to(cube): + """Generates a mask with values greater than or equal to a specified value.""" + mask = cube.copy() + mask.data = np.zeros(mask.data.shape) + mask.data[cube.data >= 276] = 1 + assert np.allclose( + filters.generate_mask(cube, ">=", 276).data, + mask.data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_generate_mask_less_than(cube): + """Generates a mask with values less than a specified value.""" + mask = cube.copy() + mask.data = np.zeros(mask.data.shape) + mask.data[cube.data < 276] = 1 + assert np.allclose( + filters.generate_mask(cube, "<", 276).data, + mask.data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_generate_mask_less_equal_to(cube): + """Generates a mask with values less than or equal to a specified value.""" + mask = cube.copy() + mask.data = np.zeros(mask.data.shape) + mask.data[cube.data <= 276] = 1 + assert np.allclose( + filters.generate_mask(cube, "<=", 276).data, + mask.data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_apply_mask(cube): + """Apply a mask to a cube.""" + mask = filters.generate_mask(cube, "==", 276) + mask.data[mask.data == 0] = np.nan + mask.data[~np.isnan(mask.data)] = 1 + test_data = cube.copy() + test_data.data *= mask.data + assert np.allclose( + filters.apply_mask(cube, mask).data, + test_data.data, + rtol=1e-06, + atol=1e-02, + equal_nan=True, + ) diff --git a/tests/operators/test_mesoscale.py b/tests/operators/test_mesoscale.py new file mode 100644 index 000000000..cbb1311d5 --- /dev/null +++ b/tests/operators/test_mesoscale.py @@ -0,0 +1,75 @@ +# © Crown copyright, Met Office (2022-2024) and CSET contributors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +"""Test mesoscale operators.""" + +import numpy as np +from scipy.ndimage import gaussian_filter, uniform_filter + +import CSET.operators.mesoscale as mesoscale +from CSET.operators._utils import get_cube_yxcoordname + + +def test_spatial_perturbation_field_gaussian(cube): + """Test smoothing a cube with a Gaussian filter.""" + calculated = cube.copy() + coords = [coord.name() for coord in cube.coords()] + axes = ( + coords.index(get_cube_yxcoordname(cube)[0]), + coords.index(get_cube_yxcoordname(cube)[1]), + ) + calculated.data -= gaussian_filter(cube.data, 40, axes=axes) + assert np.allclose( + calculated.data, + mesoscale.spatial_perturbation_field(cube).data, + rtol=1e-06, + atol=1e-02, + ) + + calculated_2 = cube.copy() + calculated_2.data -= gaussian_filter(cube.data, 100, axes=axes) + assert np.allclose( + calculated_2.data, + mesoscale.spatial_perturbation_field(cube, filter_scale=100).data, + rtol=1e-06, + atol=1e-02, + ) + + +def test_spatial_perturbation_field_uniform(cube): + """Test smoothing a cube with a uniform filter.""" + calculated = cube.copy() + coords = [coord.name() for coord in cube.coords()] + axes = ( + coords.index(get_cube_yxcoordname(cube)[0]), + coords.index(get_cube_yxcoordname(cube)[1]), + ) + calculated.data -= uniform_filter(cube.data, 40, axes=axes) + assert np.allclose( + calculated.data, + mesoscale.spatial_perturbation_field(cube, apply_gaussian_filter=False).data, + rtol=1e-06, + atol=1e-02, + ) + + calculated_2 = cube.copy() + calculated_2.data -= uniform_filter(cube.data, 100, axes=axes) + assert np.allclose( + calculated_2.data, + mesoscale.spatial_perturbation_field( + cube, apply_gaussian_filter=False, filter_scale=100 + ).data, + rtol=1e-06, + atol=1e-02, + ) diff --git a/tests/operators/test_read.py b/tests/operators/test_read.py index 9197cb919..b03029f9f 100644 --- a/tests/operators/test_read.py +++ b/tests/operators/test_read.py @@ -240,3 +240,36 @@ def test_lfric_time_coord_fix_callback_no_time(): cube = iris.cube.Cube([0, 0, 0], aux_coords_and_dims=[(length_coord, 0)]) read._lfric_time_coord_fix_callback(cube, None, None) assert len(cube.coords("time")) == 0 + + +def test_pressurecoordfix_callback(): + """Check that pressure_level is renamed to pressure if it exists.""" + cube = iris.load_cube("tests/test_data/transect_test_umpl.nc") + cube.coord("pressure").rename("pressure_level") + read._fix_pressurecoord_name_callback(cube) + assert ( + repr(cube.coords()) + == "[, , , , , ]" + ) + + +def test_spatialcoordrename_callback(): + """Check that spatial coord gets renamed if it is not grid_latitude.""" + # This cube contains 'latitude' and 'longitude' + cube = iris.load_cube("tests/test_data/transect_test_umpl.nc") + read._fix_spatialcoord_name_callback(cube) + assert ( + repr(cube.coords()) + == "[, , , , , ]" + ) + + +def test_spatialcoordnotexist_callback(): + """Check that spatial coord returns cube if cube does not contain spatial coordinates.""" + cube = iris.load_cube("tests/test_data/transect_test_umpl.nc") + cube = cube[:, :, 0, 0] # Remove spatial dimcoords + read._fix_spatialcoord_name_callback(cube) + assert ( + repr(cube.coords()) + == "[, , , , , ]" + ) diff --git a/tests/operators/test_utils.py b/tests/operators/test_utils.py index 7270a3962..7f81f9ca6 100644 --- a/tests/operators/test_utils.py +++ b/tests/operators/test_utils.py @@ -14,6 +14,7 @@ """Tests for common operator functionality across CSET.""" +import iris import pytest import CSET.operators._utils as operator_utils @@ -21,14 +22,14 @@ def test_missing_coord_get_cube_yxcoordname_x(regrid_rectilinear_cube): """Missing X coordinate raises error.""" - regrid_rectilinear_cube.remove_coord("longitude") + regrid_rectilinear_cube.remove_coord("grid_longitude") with pytest.raises(ValueError): operator_utils.get_cube_yxcoordname(regrid_rectilinear_cube) def test_missing_coord_get_cube_yxcoordname_y(regrid_rectilinear_cube): """Missing Y coordinate raises error.""" - regrid_rectilinear_cube.remove_coord("longitude") + regrid_rectilinear_cube.remove_coord("grid_longitude") with pytest.raises(ValueError): operator_utils.get_cube_yxcoordname(regrid_rectilinear_cube) @@ -36,8 +37,8 @@ def test_missing_coord_get_cube_yxcoordname_y(regrid_rectilinear_cube): def test_get_cube_yxcoordname(regrid_rectilinear_cube): """Check that function returns tuple containing horizontal dimension names.""" assert (operator_utils.get_cube_yxcoordname(regrid_rectilinear_cube)) == ( - "latitude", - "longitude", + "grid_latitude", + "grid_longitude", ) @@ -58,3 +59,16 @@ def test_is_transect_correctcoord(transect_source_cube): # Retain only time and latitude coordinate, so it passes the first spatial coord test. transect_source_cube_slice = transect_source_cube[:, :, :, 0] assert operator_utils.is_transect(transect_source_cube_slice) + + +def test_is_spatialdim_false(): + """Check that is spatial test returns false if cube does not contain spatial coordinates.""" + cube = iris.load_cube("tests/test_data/transect_test_umpl.nc") + cube = cube[:, :, 0, 0] # Remove spatial dimcoords + assert not operator_utils.is_spatialdim(cube) + + +def test_is_spatialdim_true(): + """Check that is spatial test returns true if cube contains spatial coordinates.""" + cube = iris.load_cube("tests/test_data/transect_test_umpl.nc") + assert operator_utils.is_spatialdim(cube) diff --git a/tests/test_cli.py b/tests/test_cli.py index f422316e6..6daa6bf92 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -17,45 +17,132 @@ In many ways these are integration tests. """ -import os +import logging import subprocess from pathlib import Path from uuid import uuid4 import pytest +import CSET +import CSET.operators -def test_command_line_help(): - """Check that help commands work.""" - subprocess.run(["cset", "--help"], check=True) + +def test_command_line_invocation(): + """Check invocation via different entrypoints. + + Uses subprocess to validate the external interface. + """ + # Invoke via cset command subprocess.run(["cset", "--version"], check=True) + # Invoke via __main__.py + subprocess.run(["python3", "-m", "CSET", "--version"], check=True) + + +# Every other test should not use the command line interface, but rather stay +# within python to ensure coverage measurement. +def test_argument_parser(): + """Tests the argument parser behaves appropriately.""" + parser = CSET.setup_argument_parser() + # Test verbose flag. + args = parser.parse_args(["recipe-id", "-r", "recipe.yaml"]) + assert args.verbose == 0 + args = parser.parse_args(["-v", "recipe-id", "-r", "recipe.yaml"]) + assert args.verbose == 1 + args = parser.parse_args(["-vv", "recipe-id", "-r", "recipe.yaml"]) + assert args.verbose == 2 + + +def test_setup_logging(): + """Tests the logging setup at various verbosity levels.""" + root_logger = logging.getLogger() + # Log level gets pinned at a minimum of INFO for file output. + CSET.setup_logging(0) + assert root_logger.level == logging.INFO + # -v + CSET.setup_logging(1) + assert root_logger.level == logging.INFO + # -vv + CSET.setup_logging(2) + assert root_logger.level == logging.DEBUG + + +def test_main_no_subparser(capsys): + """Appropriate error when no subparser is given.""" + with pytest.raises(SystemExit) as sysexit: + CSET.main(["cset"]) + assert sysexit.value.code == 127 + assert capsys.readouterr().err == "Please choose a command.\n" + + +def test_main_unhandled_exception_normal(capsys): + """Appropriate error when an unhandled exception occurs.""" + with pytest.raises(SystemExit) as sysexit: + CSET.main( + [ + "cset", + "bake", + "--recipe=/non-existent/recipe.yaml", + "--input-dir=/dev/null", + "--output-dir=/dev/null", + ] + ) + assert sysexit.value.code == 1 + assert ( + capsys.readouterr().err + == "[Errno 2] No such file or directory: '/non-existent/recipe.yaml'\n" + ) - # Gain coverage of __main__.py - subprocess.run(["python3", "-m", "CSET", "-h"], check=True) - # Test verbose options. This is really just to up the coverage number. - subprocess.run(["cset", "-v"]) - subprocess.run(["cset", "-vv"]) +def test_main_unhandled_exception_debug(caplog, capsys): + """Appropriate error when an unhandled exception occurs under debug mode.""" + with pytest.raises(FileNotFoundError): + CSET.main( + [ + "cset", + "-vv", + "bake", + "--recipe=/non-existent/recipe.yaml", + "--input-dir=/dev/null", + "--output-dir=/dev/null", + ] + ) + assert ( + "[Errno 2] No such file or directory: '/non-existent/recipe.yaml'\n" + in capsys.readouterr().err + ) + log_record = caplog.records[-1] + assert log_record.message == "An unhandled exception occurred." + assert log_record.levelno == logging.DEBUG -def test_bake_recipe_execution(tmp_path): +def test_bake_recipe_execution(monkeypatch): """Test running CSET recipe from the command line.""" - subprocess.run( + bake_ran = False + + def _bake_test(args, unparsed_args): + nonlocal bake_ran + bake_ran = True + assert args.input_dir == Path("/dev/null") + assert args.output_dir == Path("/dev/null") + assert args.recipe == Path("tests/test_data/noop_recipe.yaml") + + monkeypatch.setattr(CSET, "_bake_command", _bake_test) + CSET.main( [ "cset", "bake", - f"--input-dir={os.devnull}", - f"--output-dir={tmp_path}", + "--input-dir=/dev/null", + "--output-dir=/dev/null", "--recipe=tests/test_data/noop_recipe.yaml", - ], - check=True, + ] ) -def test_bake_invalid_args(): +def test_bake_invalid_args(capsys): """Invalid arguments give non-zero exit code.""" - with pytest.raises(subprocess.CalledProcessError): - subprocess.run( + with pytest.raises(SystemExit) as sysexit: + CSET.main( [ "cset", "bake", @@ -63,17 +150,20 @@ def test_bake_invalid_args(): "--input-dir=/tmp", "--output-dir=/tmp", "--not-a-real-option", - ], - check=True, + ] ) + assert sysexit.value.code == 127 + assert capsys.readouterr().err == "Unknown argument: --not-a-real-option\n" -def test_bake_invalid_args_input_dir(): +def test_bake_invalid_args_input_dir(capsys): """Missing required input-dir argument for bake.""" - with pytest.raises(subprocess.CalledProcessError): - subprocess.run( - ["cset", "bake", "--recipe=foo", "--output-dir=/tmp"], check=True - ) + with pytest.raises(SystemExit) as sysexit: + CSET.main(["cset", "bake", "--recipe=foo", "--output-dir=/tmp"]) + assert sysexit.value.code == 2 + assert capsys.readouterr().err.endswith( + "cset bake: error: the following arguments are required: -i/--input-dir\n" + ) def test_graph_creation(tmp_path: Path): @@ -84,116 +174,89 @@ def test_graph_creation(tmp_path: Path): # Run with output path specified output_file = tmp_path / f"{uuid4()}.svg" - subprocess.run( - ( + CSET.main( + [ "cset", "graph", "-o", str(output_file), "--recipe=tests/test_data/noop_recipe.yaml", - ), - check=True, + ] ) assert output_file.is_file() output_file.unlink() def test_graph_details(tmp_path: Path): - """Generate a graph with details with details.""" + """Generate a graph with details.""" output_file = tmp_path / f"{uuid4()}.svg" - subprocess.run( - ( + CSET.main( + [ "cset", "graph", "--details", "-o", str(output_file), "--recipe=tests/test_data/noop_recipe.yaml", - ), - check=True, + ] ) assert output_file.is_file() def test_cookbook_cwd(tmp_working_dir): """Unpacking the recipes into the current working directory.""" - subprocess.run(["cset", "cookbook", "CAPE_ratio_plot.yaml"], check=True) + CSET.main(["cset", "cookbook", "CAPE_ratio_plot.yaml"]) assert Path("CAPE_ratio_plot.yaml").is_file() def test_cookbook_path(tmp_path: Path): """Unpacking the recipes into a specified directory.""" - subprocess.run( - ["cset", "cookbook", "--output-dir", tmp_path, "CAPE_ratio_plot.yaml"], - check=True, + CSET.main( + ["cset", "cookbook", "--output-dir", str(tmp_path), "CAPE_ratio_plot.yaml"] ) assert (tmp_path / "CAPE_ratio_plot.yaml").is_file() -def test_cookbook_list_available_recipes(): +def test_cookbook_list_available_recipes(capsys): """List all available recipes.""" - proc = subprocess.run( - ["cset", "cookbook", "--details"], capture_output=True, check=True - ) + CSET.main(["cset", "cookbook", "--details"]) + stdout = capsys.readouterr().out # Check start. - assert proc.stdout.startswith(b"Available recipes:\n") + assert stdout.startswith("Available recipes:\n") # Check has some recipes. - assert len(proc.stdout.splitlines()) > 3 + assert len(stdout.splitlines()) > 3 -def test_cookbook_detail_recipe(): +def test_cookbook_detail_recipe(capsys): """Show detail of a recipe.""" - proc = subprocess.run( - [ - "cset", - "cookbook", - "--details", - "CAPE_ratio_plot.yaml", - ], - capture_output=True, - check=True, - ) - assert proc.stdout.startswith(b"\n\tCAPE_ratio_plot.yaml\n") + CSET.main(["cset", "cookbook", "--details", "CAPE_ratio_plot.yaml"]) + assert capsys.readouterr().out.startswith("\n\tCAPE_ratio_plot.yaml\n") def test_cookbook_non_existent_recipe(tmp_path): """Non-existent recipe give non-zero exit code.""" - with pytest.raises(subprocess.CalledProcessError): - subprocess.run( - ["cset", "cookbook", "--output-dir", tmp_path, "non-existent.yaml"], - check=True, + with pytest.raises(SystemExit) as sysexit: + CSET.main( + ["cset", "cookbook", "--output-dir", str(tmp_path), "non-existent.yaml"] ) + assert sysexit.value.code == 1 -def test_recipe_id(): +def test_recipe_id(capsys): """Get recipe ID for a recipe.""" - p = subprocess.run( - ["cset", "recipe-id", "-r", "tests/test_data/noop_recipe.yaml"], - check=True, - capture_output=True, - ) - assert p.stdout == b"noop\n" + CSET.main(["cset", "recipe-id", "-r", "tests/test_data/noop_recipe.yaml"]) + assert capsys.readouterr().out == "noop\n" -def test_recipe_id_no_title(): +def test_recipe_id_no_title(capsys): """Get recipe id for recipe without a title.""" - p = subprocess.run( - ["cset", "recipe-id", "-r", "tests/test_data/ensemble_air_temp.yaml"], - check=True, - capture_output=True, - ) + CSET.main(["cset", "recipe-id", "-r", "tests/test_data/ensemble_air_temp.yaml"]) # UUID output + newline. - assert len(p.stdout) == 37 + assert len(capsys.readouterr().out) == 37 -def test_cset_addopts(): +def test_cset_addopts(capsys, monkeypatch): """Lists in CSET_ADDOPTS environment variable don't crash the parser.""" - environment = dict(os.environ) - environment["CSET_ADDOPTS"] = "--LIST='[1, 2, 3]'" - p = subprocess.run( - ["cset", "recipe-id", "-r", "tests/test_data/addopts_test_recipe.yaml"], - check=True, - capture_output=True, - env=environment, - ) - assert p.stdout == b"list_1_2_3\n" + monkeypatch.setenv("CSET_ADDOPTS", "--LIST='[1, 2, 3]'") + CSET.main(["cset", "recipe-id", "-r", "tests/test_data/addopts_test_recipe.yaml"]) + assert capsys.readouterr().out == "list_1_2_3\n" diff --git a/tests/test_data/ageofair/aoa_in.nc b/tests/test_data/ageofair/aoa_in.nc new file mode 100644 index 000000000..1a40a6564 Binary files /dev/null and b/tests/test_data/ageofair/aoa_in.nc differ diff --git a/tests/test_data/ageofair/aoa_in_ens.nc b/tests/test_data/ageofair/aoa_in_ens.nc new file mode 100644 index 000000000..6254155a3 Binary files /dev/null and b/tests/test_data/ageofair/aoa_in_ens.nc differ diff --git a/tests/test_data/ageofair/aoa_in_rgd.nc b/tests/test_data/ageofair/aoa_in_rgd.nc new file mode 100644 index 000000000..139778938 Binary files /dev/null and b/tests/test_data/ageofair/aoa_in_rgd.nc differ diff --git a/tests/test_data/ageofair/aoa_out.nc b/tests/test_data/ageofair/aoa_out.nc new file mode 100644 index 000000000..8ad6c5eb8 Binary files /dev/null and b/tests/test_data/ageofair/aoa_out.nc differ diff --git a/tests/test_data/ageofair/aoa_out_cyclic.nc b/tests/test_data/ageofair/aoa_out_cyclic.nc new file mode 100644 index 000000000..29230a056 Binary files /dev/null and b/tests/test_data/ageofair/aoa_out_cyclic.nc differ diff --git a/tests/test_data/ageofair/aoa_out_ens.nc b/tests/test_data/ageofair/aoa_out_ens.nc new file mode 100644 index 000000000..c5aca3070 Binary files /dev/null and b/tests/test_data/ageofair/aoa_out_ens.nc differ diff --git a/tests/test_data/ageofair/aoa_out_nocyclic.nc b/tests/test_data/ageofair/aoa_out_nocyclic.nc new file mode 100644 index 000000000..331ffad88 Binary files /dev/null and b/tests/test_data/ageofair/aoa_out_nocyclic.nc differ diff --git a/tests/test_recipes.py b/tests/test_recipes.py index da8126e67..b7edbd708 100644 --- a/tests/test_recipes.py +++ b/tests/test_recipes.py @@ -18,28 +18,28 @@ import pytest -import CSET.recipes +from CSET import recipes def test_recipe_files_in_tree(): """Get recipes in directory containing sub-directories.""" - files = CSET.recipes._recipe_files_in_tree(input_dir=Path("tests")) + files = recipes._recipe_files_in_tree(input_dir=Path("tests")) assert Path("tests/test_data/noop_recipe.yaml") in files def test_recipe_files_in_tree_from_package(): """Get a recipe from inside the CSET package.""" - files = CSET.recipes._recipe_files_in_tree() + files = recipes._recipe_files_in_tree() assert any("CAPE_ratio_plot.yaml" == path.name for path in files) def test_unpack(tmp_path: Path): """Unpack recipes.""" - CSET.recipes.unpack_recipe(tmp_path, "CAPE_ratio_plot.yaml") + recipes.unpack_recipe(tmp_path, "CAPE_ratio_plot.yaml") assert (tmp_path / "CAPE_ratio_plot.yaml").is_file() # Unpack everything and check a warning is produced when files collide. with pytest.warns(): - CSET.recipes.unpack_recipe(tmp_path, "CAPE_ratio_plot.yaml") + recipes.unpack_recipe(tmp_path, "CAPE_ratio_plot.yaml") def test_unpack_recipes_exception_collision(tmp_path: Path): @@ -47,7 +47,7 @@ def test_unpack_recipes_exception_collision(tmp_path: Path): file_path = tmp_path / "regular_file" file_path.touch() with pytest.raises(FileExistsError): - CSET.recipes.unpack_recipe(file_path, "CAPE_ratio_plot.yaml") + recipes.unpack_recipe(file_path, "CAPE_ratio_plot.yaml") def test_unpack_recipes_exception_permission(): @@ -56,32 +56,30 @@ def test_unpack_recipes_exception_permission(): Will fail if tests are run as root, but no one should do that, right? """ with pytest.raises(OSError): - CSET.recipes.unpack_recipe( - Path("/usr/bin/cset"), "extract_instant_air_temp.yaml" - ) + recipes.unpack_recipe(Path("/usr/bin/cset"), "extract_instant_air_temp.yaml") def test_get_recipe_file(): """Get a recipe file from a specific location.""" - file = CSET.recipes._get_recipe_file("noop_recipe.yaml", Path("tests/test_data")) + file = recipes._get_recipe_file("noop_recipe.yaml", Path("tests/test_data")) assert file.is_file() def test_get_recipe_file_missing(): """Exception raised when recipe file not in location.""" with pytest.raises(FileNotFoundError): - CSET.recipes._get_recipe_file("non-existent", Path("tests/test_data")) + recipes._get_recipe_file("non-existent", Path("tests/test_data")) def test_get_recipe_file_in_package(): """Get a recipe file from a the default location inside the package.""" - file = CSET.recipes._get_recipe_file("CAPE_ratio_plot.yaml") + file = recipes._get_recipe_file("CAPE_ratio_plot.yaml") assert file.is_file() def test_list_available_recipes(capsys): """Display available recipes.""" - CSET.recipes.list_available_recipes() + recipes.list_available_recipes() # Read stdout and stderr. captured_output = capsys.readouterr() # Check start. @@ -92,7 +90,7 @@ def test_list_available_recipes(capsys): def test_detail_recipe(capsys): """Show detail of a recipe.""" - CSET.recipes.detail_recipe("CAPE_ratio_plot.yaml") + recipes.detail_recipe("CAPE_ratio_plot.yaml") # Read stdout and stderr. captured_output = capsys.readouterr() assert captured_output.out.startswith("\n\tCAPE_ratio_plot.yaml\n")