Merge pull request #5 from samsrabin/fates-auto-params-ssr

Improvements and fix for fates-auto-params

.git-blame-ignore-revs

@@ -21,6 +21,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630
 025d5e7c2e80263717fb029101d65cbbf261c3c4
 a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
+0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands

@@ -1,16 +1,7 @@
 ./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
 ./xmlchange BFBFLAG="TRUE"
 
-CASE=`./xmlquery CASE --value`
 SRCROOT=`./xmlquery SRCROOT --value`
-
-#CIME_OUTPUT_ROOT=`./xmlquery CIME_OUTPUT_ROOT --value`
-# CASEDIR=`./xmlquery CASEROOT --value`
-# env_test.xml IS NOT AVAILABLE TESTROOT=`./xmlquery TESTROOT --value`
-# env_test.xml IS NOT AVAILABLE TESTID=`./xmlquery TESTID --value`
-# env_test.xml IS NOT AVAILABLE TESTARGV=`./xmlquery TEST_ARGV --value`
-
-FATESDIR=$SRCROOT/src/fates
-FATESPARAMFILE=${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc
+. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
 
 ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl

cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands

@@ -1,7 +1,6 @@
-CASE=`./xmlquery CASE --value`
 SRCROOT=`./xmlquery SRCROOT --value`
-FATESDIR=$SRCROOT/src/fates
-FATESPARAMFILE=${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc
+. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
+CASE=`./xmlquery CASE --value`
 
 $FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts
 $FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts

cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands

@@ -1,5 +1,3 @@
-CASE=`./xmlquery CASE --value`
 SRCROOT=`./xmlquery SRCROOT --value`
-FATESDIR=$SRCROOT/src/fates
-FATESPARAMFILE=${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc
+. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
 $FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts

cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands

@@ -1,5 +1,3 @@
-CASE=`./xmlquery CASE --value`
 SRCROOT=`./xmlquery SRCROOT --value`
-FATESDIR=$SRCROOT/src/fates
-FATESPARAMFILE=${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc
+. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
 $FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts

cime_config/testdefs/testmods_dirs/clm/_scripts/README

@@ -0,0 +1,2 @@
+This directory contains scripts that can be called in
+shell_commands of multiple testmods.

cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh

@@ -0,0 +1,11 @@
+# This script should be called in shell_commands with
+#    . "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
+# where the leading period ensures it's run in the same shell.
+
+CASE=`./xmlquery CASE --value`
+FATESDIR="${SRCROOT}/src/fates"
+FATESPARAMDIR="${SRCROOT}/src/fates/parameter_files/binaries"
+mkdir -p "${FATESPARAMDIR}"
+FATESPARAMFILE="${FATESPARAMDIR}/${CASE}-params.nc"
+
+# No exit status because it should be called in the same shell.

python/ctsm/run_sys_tests.py

@@ -249,7 +249,7 @@ def run_sys_tests(
         else:
             raise RuntimeError("None of suite_name, testfile or testlist were provided")
         if not running_ctsm_py_tests:
-            _try_systemtests(testname_list)
+            _check_py_env(testname_list)
         _run_create_test(
             cime_path=cime_path,
             test_args=test_args,
@@ -708,20 +708,60 @@ def _run_test_suite(
         )
 
 
-def _try_systemtests(testname_list):
+def _get_testmod_list(test_attributes, unique=False):
+    # Isolate testmods, producing a list like
+    # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...]
+    # Handles test attributes passed in from run_sys_tests calls using -t, -f, or -s
+
+    testmods = []
+    for test_attribute in test_attributes:
+        for dot_split in test_attribute.split("."):
+            slash_replaced = dot_split.replace("/", "-")
+            newline_replaced = slash_replaced.replace("\n", "")
+            for ddash_split in newline_replaced.split("--"):
+                if "clm-" in ddash_split and (ddash_split not in testmods or not unique):
+                    testmods.append(ddash_split)
+
+    return testmods
+
+
+def _check_py_env(test_attributes):
     err_msg = " can't be loaded. Do you need to activate the ctsm_pylib conda environment?"
     # Suppress pylint import-outside-toplevel warning because (a) we only want to import
     # this when certain tests are requested, and (b) the import needs to be in a try-except
     # block to produce a nice error message.
     # pylint: disable=import-outside-toplevel disable
     # Suppress pylint unused-import warning because the import itself IS the use.
     # pylint: disable=unused-import disable
-    if any("FSURDATMODIFYCTSM" in t for t in testname_list):
+    # Suppress pylint import-error warning because the whole point here is to check
+    # whether import is possible.
+    # pylint: disable=import-error disable
+
+    # Check requirements for FSURDATMODIFYCTSM, if needed
+    if any("FSURDATMODIFYCTSM" in t for t in test_attributes):
         try:
             import ctsm.modify_input_files.modify_fsurdat
         except ModuleNotFoundError as err:
             raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err
 
+    # Check that list for any testmods that use modify_fates_paramfile.py
+    testmods_to_check = [
+        "clm-FatesColdSeedDisp",
+        "clm-FatesColdTwoStream",
+        "clm-FatesColdTwoStreamNoCompFixedBioGeo",
+    ]
+    testmods = _get_testmod_list(test_attributes)
+    if any(t in testmods_to_check for t in testmods):
+        # This bit is needed because it's outside the top-level python/ directory.
+        fates_dir = os.path.join(
+            os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "src", "fates"
+        )
+        sys.path.insert(1, fates_dir)
+        try:
+            import tools.modify_fates_paramfile
+        except ModuleNotFoundError as err:
+            raise ModuleNotFoundError("modify_fates_paramfile" + err_msg) from err
+
 
 def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests):
     test_data = get_tests_from_xml(xml_machine=machine_name, xml_category=suite_name)
@@ -730,7 +770,8 @@ def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests):
             "No tests found for suite {} on machine {}".format(suite_name, machine_name)
         )
     if not running_ctsm_py_tests:
-        _try_systemtests([t["testname"] for t in test_data])
+        _check_py_env([t["testname"] for t in test_data])
+        _check_py_env([t["testmods"] for t in test_data if "testmods" in t.keys()])
     compilers = sorted({one_test["compiler"] for one_test in test_data})
     logger.info("Running with compilers: %s", compilers)
     return compilers

python/ctsm/test/test_unit_run_sys_tests.py

@@ -16,7 +16,7 @@
 
 from ctsm import add_cime_to_path  # pylint: disable=unused-import
 from ctsm import unit_testing
-from ctsm.run_sys_tests import run_sys_tests
+from ctsm.run_sys_tests import run_sys_tests, _get_testmod_list
 from ctsm.machine_defaults import MACHINE_DEFAULTS
 from ctsm.machine import create_machine
 from ctsm.joblauncher.job_launcher_factory import JOB_LAUNCHER_FAKE
@@ -269,6 +269,57 @@ def test_withDryRun_nothingDone(self):
         self.assertEqual(os.listdir(self._scratch), [])
         self.assertEqual(machine.job_launcher.get_commands(), [])
 
+    def test_getTestmodList_suite(self):
+        """Ensure that _get_testmod_list() works correctly with suite-style input"""
+        input = [
+            "clm/default",
+            "clm/default",
+            "clm/crop",
+            "clm/cropMonthlyOutput",
+        ]
+        target = [
+            "clm-default",
+            "clm-default",
+            "clm-crop",
+            "clm-cropMonthlyOutput",
+        ]
+        output = _get_testmod_list(input, unique=False)
+        self.assertEqual(output, target)
+
+    def test_getTestmodList_suite_unique(self):
+        """Ensure that _get_testmod_list() works correctly with unique=True"""
+        input = [
+            "clm/default",
+            "clm/default",
+            "clm/crop",
+            "clm/cropMonthlyOutput",
+        ]
+        target = [
+            "clm-default",
+            "clm-crop",
+            "clm-cropMonthlyOutput",
+        ]
+
+        output = _get_testmod_list(input, unique=True)
+        self.assertEqual(output, target)
+
+    def test_getTestmodList_testname(self):
+        """Ensure that _get_testmod_list() works correctly with full test name(s) specified"""
+        input = [
+            "ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-crop",
+            "ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-default",
+        ]
+        target = ["clm-crop", "clm-default"]
+        output = _get_testmod_list(input)
+        self.assertEqual(output, target)
+
+    def test_getTestmodList_twomods(self):
+        """Ensure that _get_testmod_list() works correctly with full test name(s) specified and two mods in one test"""
+        input = ["ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-default--clm-crop"]
+        target = ["clm-default", "clm-crop"]
+        output = _get_testmod_list(input)
+        self.assertEqual(output, target)
+
 
 if __name__ == "__main__":
     unit_testing.setup_for_tests()