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Merge remote-tracking branch 'emc/develop' into feature/simplify_res
* emc/develop: CI maintenance updates and adding CI Unit Tests (NOAA-EMC#2740) Adds contents of constructor and initialize methods to marine LETKF class (NOAA-EMC#2635) Fix GDAS group B restart archiving (NOAA-EMC#2735) Add fcst dependency to ocnanalprep (NOAA-EMC#2728) Update (partially) global-workflow for orion+rocky9 (NOAA-EMC#2741)
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,64 @@ | ||
| name: CI Unit Tests | ||
| on: [pull_request, push, workflow_dispatch] | ||
|
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| jobs: | ||
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| ci_pytest: | ||
| runs-on: ubuntu-latest | ||
| name: Run unit tests on CI system | ||
| permissions: | ||
| checks: write | ||
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| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: 3.11.8 | ||
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| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl | ||
| python -m pip install --upgrade pip | ||
| pip install pytest | ||
| pip install wxflow | ||
| pip install wget | ||
| - name: Cache Rocoto Install | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: ~/rocoto | ||
| key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} | ||
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| - name: Install Rocoto | ||
| run: | | ||
| if [ ! -d "$HOME/rocoto/bin" ]; then | ||
| git clone https://github.com/christopherwharrop/rocoto.git $HOME/rocoto | ||
| cd $HOME/rocoto | ||
| ./INSTALL | ||
| fi | ||
| echo "$HOME/rocoto/bin" >> $GITHUB_PATH | ||
| - name: Run tests | ||
| shell: bash | ||
| run: | | ||
| sudo mkdir -p /scratch1/NCEPDEV | ||
| cd $GITHUB_WORKSPACE/sorc | ||
| git submodule update --init --recursive | ||
| ./link_workflow.sh | ||
| cd $GITHUB_WORKSPACE/ci/scripts/tests | ||
| ln -s ../wxflow | ||
| pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml | ||
| - name: Publish Test Results | ||
| if: always() | ||
| uses: EnricoMi/publish-unit-test-result-action@v2 | ||
| with: | ||
| files: ci/scripts/tests/test-results.xml | ||
| job_summary: true | ||
| comment_mode: off |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| defaults: | ||
| !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml | ||
| base: | ||
| HPC_ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} | ||
| ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} |
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| Original file line number | Diff line number | Diff line change |
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| from wxflow import Executable | ||
| from shutil import rmtree | ||
| import os | ||
| import copy | ||
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| _here = os.path.dirname(__file__) | ||
| HOMEgfs = os.sep.join(_here.split(os.sep)[:-3]) | ||
| RUNDIR = os.path.join(_here, 'testdata/RUNDIR') | ||
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| def test_create_experiment(): | ||
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| create_experiment_script = Executable(f'{HOMEgfs}/workflow/create_experiment.py') | ||
| yaml_dir = yaml_dir = os.path.join(HOMEgfs, 'ci/cases/pr') | ||
| env = os.environ.copy() | ||
| env['RUNTESTS'] = RUNDIR | ||
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| for case in os.listdir(yaml_dir): | ||
| if case.endswith('.yaml'): | ||
| with open(os.path.join(yaml_dir, case), 'r') as file: | ||
| file_contents = file.read() | ||
| if 'ICSDIR_ROOT' not in file_contents: | ||
| create_experiment = copy.deepcopy(create_experiment_script) | ||
| create_experiment.add_default_arg(['-y', f'../../cases/pr/{case}', '--overwrite']) | ||
| env['pslot'] = os.path.splitext(case)[0] | ||
| create_experiment(env=env) | ||
| assert (create_experiment.returncode == 0) | ||
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| rmtree(RUNDIR) |
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| Original file line number | Diff line number | Diff line change |
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| import sys | ||
| import os | ||
| from shutil import rmtree | ||
| import wget | ||
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| script_dir = os.path.dirname(os.path.abspath(__file__)) | ||
| sys.path.append(os.path.join(os.path.dirname(script_dir), 'utils')) | ||
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| from rocotostat import rocoto_statcount, rocotostat_summary, is_done, is_stalled, CommandNotFoundError | ||
| from wxflow import which | ||
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| test_data_url = 'https://noaa-nws-global-pds.s3.amazonaws.com/data/CI/' | ||
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| testdata_path = 'testdata/rocotostat' | ||
| testdata_full_path = os.path.join(script_dir, testdata_path) | ||
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| if not os.path.isfile(os.path.join(testdata_full_path, 'database.db')): | ||
| os.makedirs(testdata_full_path, exist_ok=True) | ||
| workflow_url = test_data_url + str(testdata_path) + '/workflow.xml' | ||
| workflow_destination = os.path.join(testdata_full_path, 'workflow.xml') | ||
| wget.download(workflow_url, workflow_destination) | ||
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| database_url = test_data_url + str(testdata_path) + '/database.db' | ||
| database_destination = os.path.join(testdata_full_path, 'database.db') | ||
| wget.download(database_url, database_destination) | ||
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| try: | ||
| rocotostat = which('rocotostat') | ||
| except CommandNotFoundError: | ||
| raise CommandNotFoundError("rocotostat not found in PATH") | ||
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| rocotostat.add_default_arg(['-w', os.path.join(testdata_path, 'workflow.xml'), '-d', os.path.join(testdata_path, 'database.db')]) | ||
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| def test_rocoto_statcount(): | ||
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| result = rocoto_statcount(rocotostat) | ||
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| assert result['SUCCEEDED'] == 20 | ||
| assert result['FAIL'] == 0 | ||
| assert result['DEAD'] == 0 | ||
| assert result['RUNNING'] == 0 | ||
| assert result['SUBMITTING'] == 0 | ||
| assert result['QUEUED'] == 0 | ||
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| def test_rocoto_summary(): | ||
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| result = rocotostat_summary(rocotostat) | ||
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| assert result['CYCLES_TOTAL'] == 1 | ||
| assert result['CYCLES_DONE'] == 1 | ||
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| def test_rocoto_done(): | ||
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| result = rocotostat_summary(rocotostat) | ||
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| assert is_done(result) | ||
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| rmtree(testdata_full_path) | ||
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| def test_rocoto_stalled(): | ||
| testdata_path = 'testdata/rocotostat_stalled' | ||
| testdata_full_path = os.path.join(script_dir, testdata_path) | ||
| xml = os.path.join(testdata_full_path, 'stalled.xml') | ||
| db = os.path.join(testdata_full_path, 'stalled.db') | ||
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| if not os.path.isfile(os.path.join(testdata_full_path, 'stalled.db')): | ||
| os.makedirs(testdata_full_path, exist_ok=True) | ||
| workflow_url = test_data_url + str(testdata_path) + '/stalled.xml' | ||
| database_url = test_data_url + str(testdata_path) + '/stalled.db' | ||
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| workflow_destination = os.path.join(testdata_full_path, 'stalled.xml') | ||
| wget.download(workflow_url, workflow_destination) | ||
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| database_destination = os.path.join(testdata_full_path, 'stalled.db') | ||
| wget.download(database_url, database_destination) | ||
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| rocotostat = which('rocotostat') | ||
| rocotostat.add_default_arg(['-w', xml, '-d', db]) | ||
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| result = rocoto_statcount(rocotostat) | ||
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| assert result['SUCCEEDED'] == 11 | ||
| assert is_stalled(result) | ||
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| rmtree(testdata_full_path) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| from wxflow import Executable, Configuration, ProcessError | ||
| from shutil import rmtree | ||
| import pytest | ||
| import os | ||
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| _here = os.path.dirname(__file__) | ||
| HOMEgfs = os.sep.join(_here.split(os.sep)[:-3]) | ||
| RUNDIR = os.path.join(_here, 'testdata/RUNDIR') | ||
| pslot = "C48_ATM" | ||
| account = "fv3-cpu" | ||
| foobar = "foobar" | ||
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| def test_setup_expt(): | ||
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| arguments = [ | ||
| "gfs", "forecast-only", | ||
| "--pslot", pslot, "--app", "ATM", "--resdetatmos", "48", | ||
| "--comroot", f"{RUNDIR}", "--expdir", f"{RUNDIR}", | ||
| "--idate", "2021032312", "--edate", "2021032312", "--overwrite" | ||
| ] | ||
| setup_expt_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_expt.py")) | ||
| setup_expt_script.add_default_arg(arguments) | ||
| setup_expt_script() | ||
| assert (setup_expt_script.returncode == 0) | ||
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| def test_setup_xml(): | ||
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| setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow/setup_xml.py")) | ||
| setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") | ||
| setup_xml_script() | ||
| assert (setup_xml_script.returncode == 0) | ||
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| cfg = Configuration(f"{RUNDIR}/{pslot}") | ||
| base = cfg.parse_config('config.base') | ||
| assert base.ACCOUNT == account | ||
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| assert "UNKNOWN" not in base.values() | ||
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| with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: | ||
| contents = file.read() | ||
| assert contents.count(account) > 5 | ||
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| rmtree(RUNDIR) | ||
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| def test_setup_xml_fail_config_env_cornercase(): | ||
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| script_content = ('''#!/usr/bin/env bash | ||
| export HOMEgfs=foobar | ||
| ../../../workflow/setup_xml.py "${1}"\n | ||
| ''') | ||
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| with open('run_setup_xml.sh', 'w') as file: | ||
| file.write(script_content) | ||
| os.chmod('run_setup_xml.sh', 0o755) | ||
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| try: | ||
| setup_xml_script = Executable(os.path.join(HOMEgfs, "ci", "scripts", "tests", "run_setup_xml.sh")) | ||
| setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") | ||
| setup_xml_script() | ||
| assert (setup_xml_script.returncode == 0) | ||
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| cfg = Configuration(f"{RUNDIR}/{pslot}") | ||
| base = cfg.parse_config('config.base') | ||
| assert base.ACCOUNT == account | ||
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| assert foobar not in base.values() | ||
| assert "UNKNOWN" not in base.values() | ||
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| with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: | ||
| contents = file.read() | ||
| assert contents.count(account) > 5 | ||
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| except ProcessError as e: | ||
| # We expect this fail becuse ACCOUNT=fv3-cpu in config.base and environment | ||
| pass | ||
| except Exception as e: | ||
| # If an exception occurs, pass the test with a custom message | ||
| pytest.fail(f"Expected exception occurred: {e}") | ||
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| finally: | ||
| # Cleanup code to ensure it runs regardless of test outcome | ||
| os.remove('run_setup_xml.sh') | ||
| try: | ||
| rmtree(RUNDIR) | ||
| except FileNotFoundError: | ||
| pass |
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