Commit MOM_parameter_doc.* into docs folder of config

payu/git_utils.py

@@ -102,7 +102,7 @@ def commit(self,
         untracked_files = [Path(self.repo_path) / path
                            for path in self.repo.untracked_files]
         for path in paths_to_commit:
-            if self.repo.git.diff(None, path) or path in untracked_files:
+            if self.repo.git.diff(None, path) or Path(path) in untracked_files:
                 self.repo.index.add([path])
                 changes = True
 

payu/models/cesm_cmeps.py

@@ -19,7 +19,7 @@
 from payu.fsops import mkdir_p, make_symlink
 from payu.models.model import Model
 from payu.models.fms import fms_collate
-from payu.models.mom6 import mom6_add_parameter_files
+from payu.models.mom6 import mom6_add_parameter_files, mom6_save_docs_files
 
 NUOPC_CONFIG = "nuopc.runconfig"
 NUOPC_RUNSEQ = "nuopc.runseq"
@@ -272,6 +272,11 @@ def _setup_checks(self):
         return True
 
     def archive(self):
+
+        # Move any the MOM_parameter_docs output back into the control repo and commit it for documentation
+        if 'mom' in self.components.values() :
+            mom6_save_docs_files(self)
+
         super().archive()
 
         mkdir_p(self.restart_path)
@@ -387,14 +392,16 @@ class AccessOm3(CesmCmeps):
     def get_components(self):
         super().get_components()
 
-        assert self.components["atm"] == "datm", (
-            "Access-OM3 comprises a data atmosphere model, but the atmospheric model in nuopc.runconfig is set "
-            f"to {self.components['atm']}."
-        )
-        assert self.components["rof"] == "drof", (
-            "Access-OM3 comprises a data runoff model, but the runoff model in nuopc.runconfig is set "
-            f"to {self.components['rof']}."
-        )
+        if (self.components["atm"] != "datm") :
+            raise RuntimeError(
+                "Access-OM3 comprises a data atmosphere model, but the atmospheric model in nuopc.runconfig is set "
+                f"to {self.components['atm']}."
+            )
+        if (self.components["rof"] != "drof") :
+            raise RuntimeError(
+                "Access-OM3 comprises a data runoff model, but the runoff model in nuopc.runconfig is set "
+                f"to {self.components['rof']}."
+            )
 
 
 class Runconfig:

payu/models/mom6.py

@@ -13,11 +13,17 @@
 
 # Extensions
 import f90nml
+import shutil
+from warnings import warn
+from glob import glob
 
 # Local
+from payu.fsops import mkdir_p
 from payu.models.fms import Fms
 from payu.models.mom_mixin import MomMixin
+from payu.git_utils import GitRepository
 
+MOM6_DOCS = "MOM_parameter_doc.*"
 
 def mom6_add_parameter_files(model):
     """Add parameter files defined in input.nml to model configuration files.
@@ -41,6 +47,26 @@ def mom6_add_parameter_files(model):
         else:
             model.config_files.extend(filenames)
 
+def mom6_save_docs_files(model):
+    """Add docs files created as MOM output back to the control directory"""
+    docs_folder = os.path.join(model.control_path, 'docs')
+    mkdir_p(docs_folder)
+
+    # copy everything that matches MOM_parameter_doc.* to the control dir
+    for f in glob(os.path.join(model.work_path, MOM6_DOCS)):
+        try:
+            shutil.copy(f, docs_folder)
+        except Exception as e:
+            warn(e)
+
+    if model.expt.runlog.enabled: #if runlog true, default to true
+        # commit new files to the control dir
+        repo = GitRepository(repo_path = model.control_path)
+
+        repo.commit(
+            commit_message = "payu archive: documentation of MOM6 run-time configuration" ,
+            paths_to_commit = glob(os.path.join(docs_folder, MOM6_DOCS))
+        )
 
 class Mom6(MomMixin, Fms):
     """Interface to GFDL's MOM6 ocean model."""
@@ -93,3 +119,10 @@ def init_config(self):
             input_nml['SIS_input_nml']['input_filename'] = input_type
 
         f90nml.write(input_nml, input_fpath, force=True)
+
+    def archive(self):
+        # Move any the MOM_parameter_docs output back into the control repo 
+        # and commit it for documentation
+        mom6_save_docs_files(self)
+
+        super().archive()

test/common.py

@@ -7,8 +7,6 @@
 
 import yaml
 
-import payu
-
 # Namespace clash if import setup_cmd.runcmd as setup. For
 # consistency use payu_ prefix for all commands
 from payu.subcommands.init_cmd import runcmd as payu_init

test/models/access-om3/test_access_om3.py

@@ -1,7 +1,6 @@
 import copy
 import os
 import shutil
-from pathlib import Path
 import pytest
 
 import payu
@@ -421,4 +420,3 @@ def test_get_restart_datetime_badcal(start_dt, calendar, cmeps_calendar, expecte
 
     teardown_cmeps_config()
     remove_expt_archive_dirs(type='restart')
-

test/models/test_mom6.py

@@ -1,6 +1,6 @@
-import copy
 import os
 import shutil
+from pathlib import Path
 
 import pytest
 import f90nml
@@ -11,6 +11,7 @@
 from test.common import tmpdir, ctrldir, labdir, expt_workdir, ctrldir_basename
 from test.common import write_config, write_metadata
 from test.common import make_random_file, make_inputs, make_exe
+from test.test_git_utils import create_new_repo
 
 verbose = True
 
@@ -126,6 +127,146 @@ def test_mom6_add_parameter_files(input_nml,
     # Tidy up input.nml
     os.remove(input_nml_fp)
 
+@pytest.fixture
+def mom_parameter_doc(request):
+
+    with cd(ctrldir):
+        lab = payu.laboratory.Laboratory(lab_path=str(labdir))
+        expt = payu.experiment.Experiment(lab, reproduce=False)
+        model = expt.models[0]
+
+   # Create docs
+    if (request.param != None) :
+        for file in request.param:
+            filename = os.path.join(model.work_path, file)
+            make_random_file(filename, 8)
+
+    yield model
+
+    # and Tidy up 
+    if (request.param != None) :
+        for file in request.param:
+            filename = os.path.join(model.work_path, file)
+            os.remove(filename)
+
+
+@pytest.mark.parametrize(
+        "mom_parameter_doc", 
+        [["MOM_parameter_doc.all","MOM_parameter_doc.debug","MOM_parameter_docs.debug"]],
+        indirect=True
+)
+@pytest.mark.filterwarnings("error")
+def test_mom6_save_doc_files(mom_parameter_doc):
+    # Confirm that mom6_save_doc_filse moves files names MOM_parameter_doc.* into the docs folder of a config
+    # and doesn't move files that don't match that name
+
+    # don't try and commit during tests
+    mom_parameter_doc.expt.runlog.enabled = False
+
+    # Function to test
+    payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
+
+    # Check MOM_parameter_doc.* are added to control_path
+    for file in ["MOM_parameter_doc.all","MOM_parameter_doc.debug"]:
+        filename = os.path.join(mom_parameter_doc.control_path, "docs", file)
+        assert os.path.isfile(filename)==True , "Payu did not move MOM_parameter_doc.* files into docs folder"
+        os.remove(filename)
+
+    # Check fake files are not added to control_path
+    for file in ["MOM_parameter_docs.debug"]:
+        filename = os.path.join(mom_parameter_doc.control_path, "docs", file)
+        assert os.path.isfile(filename)==False, "Payu incorrectly moved MOM_parameter_docs.* files into docs folder"
+
+
+@pytest.mark.parametrize(
+        "mom_parameter_doc", 
+        [["MOM_parameter_doc.layout"]],
+        indirect=True
+)
+@pytest.mark.filterwarnings("error")
+def test_mom6_commit_doc_files(mom_parameter_doc):
+    # Confirm that mom6_save_doc_files commits files named MOM_parameter_doc.* into the docs folder of a config
+    mom_parameter_doc.expt.runlog.enabled = True
+
+    #init a git repo
+    repo = create_new_repo(Path(mom_parameter_doc.control_path))
+    initial_commit = repo.head.commit
+
+    # Function to test
+    payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
+
+    # Check files are added to control_path
+    for file in ["MOM_parameter_doc.layout"]:
+        filename = os.path.join(mom_parameter_doc.control_path, "docs", file)
+        assert os.path.isfile(filename)==True , "docs/MOM_parameter_doc.* do not exist"
+        os.remove(filename)
+
+    assert repo.head.commit != initial_commit,  "Payu did not commit MOM_parameter_doc.layout"
+
+    # Confirm it doesn't commit twice if unchanged
+    initial_commit = repo.head.commit
+    payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
+
+    assert repo.head.commit == initial_commit,  "Payu commit MOM_parameter_doc incorrectly"
+
+    # Confirm it does commit twice correctly
+    file = "MOM_parameter_doc.all"
+    filename = os.path.join(mom_parameter_doc.work_path, file)
+    make_random_file(filename, 8)
+
+    payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
+
+    assert repo.head.commit != initial_commit,  "Payu did not commit MOM_parameter_doc.all"
+
+    # and Tidy up 
+    filename = os.path.join(mom_parameter_doc.work_path, file)
+    os.remove(filename)
+
+
+@pytest.mark.parametrize(
+        "mom_parameter_doc", 
+        [["MOM_parameter_doc.layout"]],
+        indirect=True
+)
+@pytest.mark.filterwarnings("error")
+def test_mom6_not_commit_doc_files(mom_parameter_doc):
+    # Confirm that mom6_save_doc_files doesn't commits files if runlog is False
+
+    mom_parameter_doc.expt.runlog.enabled = False
+
+    #init a git repo
+    repo = create_new_repo(Path(mom_parameter_doc.control_path))
+    initial_commit = repo.head.commit
+
+    # Function to test
+    payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
+
+    # Check files are added to control_path
+    for file in ["MOM_parameter_doc.layout"]:
+        filename = os.path.join(mom_parameter_doc.control_path, "docs", file)
+        assert os.path.isfile(filename)==True , "docs/MOM_parameter_doc.* do not exist"
+        os.remove(filename)
+
+    assert repo.head.commit == initial_commit,  "Payu incorrectly committed MOM_parameter_docs.layout"
+
+@pytest.mark.parametrize(
+        "mom_parameter_doc", 
+        [None],
+        indirect=True
+)
+@pytest.mark.filterwarnings("error")
+def test_mom6_not_commit_doc_files(mom_parameter_doc):
+    # Confirm that mom6_save_doc_files doesn't commits files if runlog is False
+
+    #init a git repo
+    repo = create_new_repo(Path(mom_parameter_doc.control_path))
+    initial_commit = repo.head.commit
+
+    # Function to test
+    payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
+
+    assert repo.head.commit == initial_commit,  "Payu incorrectly committed with no docs to add"
+
 
 def test_setup():
     input_nml = {

test/test_setup.py

@@ -257,3 +257,36 @@ def test_check_payu_version_configured_invalid_version(minimum_version):
 
             with pytest.raises(ValueError):
                 expt.check_payu_version()
+
+
+
+# model.expt.runlog.enabled is used in code for writing runlog
+# it can be set as runlog:true or runlog:enable:true in config.yaml
+@pytest.mark.parametrize(
+        "runlog, enabled", 
+        [   
+            (None, True), #default is True
+            (True, True), 
+            (False, False), 
+            ({"enable":True}, True),
+            ({"enable":False}, False)
+         ]
+)
+@pytest.mark.filterwarnings("error")
+def test_runlog_enable(runlog, enabled):
+    config = copy.deepcopy(config_orig)
+    if runlog == None:
+        config.pop('runlog') #remove from config for default case
+    else:
+        config['runlog'] = runlog
+
+    write_config(config)
+
+    make_inputs()
+
+    with cd(ctrldir):
+        lab = payu.laboratory.Laboratory(lab_path=str(labdir))
+        expt = payu.experiment.Experiment(lab, reproduce=False)
+        model = expt.models[0]
+
+    assert model.expt.runlog.enabled == enabled