Extend testing to handle dumping rho and sigma remapped diagnostics a…

…s well as z. mom-ocean#328

ice_ocean_SIS2/Baltic/MOM_input

@@ -61,6 +61,8 @@ NK = 63                         !   [nondim]
                                 ! The number of model layers.
 
 DIAG_REMAP_Z_GRID_DEF = "FILE:OM3_zgrid.nc,zw,zt"
+DIAG_REMAP_RHO_GRID_DEF = "UNIFORM"
+DIAG_REMAP_SIGMA_GRID_DEF = "UNIFORM"
 
 ! === module MOM_verticalGrid ===
 ! Parameters providing information about the vertical grid.

tools/tests/conftest.py

@@ -23,8 +23,6 @@ def pytest_generate_tests(metafunc):
     Parameterize tests. Presently handles those that have 'exp' as an argument.
     """
 
-    print("Calling pytest_generate_tests")
-
     if 'exp' in metafunc.fixturenames:
         if metafunc.config.option.full:
             # Run tests on all experiments.
@@ -49,13 +47,14 @@ def exp(request):
     """
     exp = request.param
 
-    # Run the experiment to get latest code changes. This will do nothing if
-    # the experiment has already been run.
+    # Run the experiment to get latest code changes, and updates to the
+    # available_diags. This will do nothing if the experiment has already been
+    # run.
     exp.run()
     # Dump all available diagnostics, if they haven't been already.
     if not exp.has_dumped_diags:
         # Before dumping we delete old ones if they exist.
-        diags = exp.get_available_diags()
+        diags = exp.parse_available_diags()
         for d in diags:
             try:
                 os.remove(d.output)
@@ -66,6 +65,20 @@ def exp(request):
         exp.has_dumped_diags = True
     return exp
 
+
+@pytest.fixture(scope='session')
+def exp_diags_not_dumped():
+
+    exp = experiment_dict['ice_ocean_SIS2/Baltic']
+
+    # Run the experiment to get latest code changes, and updates to the
+    # available_diags. This will do nothing if the experiment has already been
+    # run.
+    exp.run()
+
+    return exp
+
+
 def restore_after_test():
     """
     Restore experiment state after running a test.

tools/tests/dump_all_diagnostics.py

@@ -29,14 +29,15 @@ def dump_diags(exp, diags):
     with open(os.path.join(exp.path, 'diag_table'), 'w') as f:
         print('All {} diags'.format(exp.name), file=f)
         print('1 1 1 0 0 0', file=f)
-        for d in diags:
-            print('"{}_{}", 0, "seconds", 1, "seconds",' \
-                  '"time"'.format(d.model, d.name), file=f)
+        for fname in list(set([d.filename for d in diags])):
+            print('"{}", 0, "seconds", 1, "seconds",' \
+                  '"time"'.format(fname), file=f)
         for d in diags:
             m = d.model
             n = d.name
-            print('"{}", "{}", "{}", "{}_{}", "all",' \
-                  '.false., "none", 2'.format(m, n, n, m, n), file=f)
+            fname = d.filename
+            print('"{}", "{}", "{}", "{}", "all",' \
+                  '.false., "none", 2'.format(m, n, n, fname, n), file=f)
     return exp.force_run()
 
 def main():

tools/tests/experiment.py

@@ -5,6 +5,7 @@
 import os
 import re
 import shlex
+import random
 import subprocess as sp
 import run_config as rc
 from model import Model
@@ -17,18 +18,33 @@
 
 class Diagnostic:
 
-    def __init__(self, model, name, path):
+    def __init__(self, model, name, path, packed=True):
         self.model = model
         self.name = name
         self.full_name = '{}_{}'.format(model, name)
-        self.output = os.path.join(path, '00010101.{}.nc'.format(self.full_name))
+        self.run_path = path
+
+        # Hack to deal with FMS limitations, see https://github.com/NOAA-GFDL/FMS/issues/27
+        # Use fewer different files for diagnostics.
+        if packed:
+            letter = self.name[0]
+            self.packed_filename = '{}_{}'.format(self.model, letter)
+
+        self.unpacked_filename = '{}_{}'.format(self.model, self.name)
+
+        if packed:
+            self.filename = self.packed_filename
+        else:
+            self.filename = self.unpacked_filename
+
+        self.output = os.path.join(path, '00010101.{}.nc'.format(self.filename))
 
     def __eq__(self, other):
-        return ((self.model, self.name, self.output) ==
-                (other.model, other.name, other.output))
+        return ((self.model, self.name) ==
+                (other.model, other.name))
 
     def __hash__(self):
-        return hash(self.model + self.name + self.output)
+        return hash(self.full_name)
 
 
 # Unfinished diagnostics are those which have been registered but have not been
@@ -101,6 +117,7 @@ def __init__(self, id, platform='raijin', compiler='gnu', build='DEBUG', memory_
         self.has_run = False
         # Another thing to avoid repeating.
         self.has_dumped_diags = False
+        self.diags_parsed = False
 
     def build_model(self):
         """
@@ -146,11 +163,19 @@ def force_run(self):
 
         return ret
 
-    def _parse_available_diags(self):
+    def parse_available_diags(self, packed=True):
         """
-        Create a list of available diags for the experiment by parsing
-        available_diags.000001 and SIS.available_diags.
+        Return a list of the available diagnostics for this experiment by
+        parsing available_diags.000001 and SIS.available_diags.
+
+        The 'packed' argument is used to pack many diagnostics into a few
+        output files. Without this each diagnostic is in it's own file.
+
+        The experiment needs to have been run before calling this.
         """
+
+        assert self.has_run
+
         mom_av_file = os.path.join(self.path, 'available_diags.000000')
         sis_av_file = os.path.join(self.path, 'SIS.available_diags')
 
@@ -164,20 +189,14 @@ def _parse_available_diags(self):
                 # Pull out the model name and variable name.
                 matches = re.findall('^\"(\w+)\", \"(\w+)\".*$',
                                      f.read(), re.MULTILINE)
-                diags.extend([Diagnostic(m, d, self.path) for m, d in matches])
-        return diags
-
-    def get_available_diags(self):
-        """
-        Return a list of the available diagnostics for this experiment.
-
-        The experiment needs to have been run before calling this.
-        """
-
-        assert self.has_run
+                for m, d in matches:
+                    if m[-5:] == '_zold':
+                        diags.append(Diagnostic(m, d, self.path, packed=False))
+                    else:
+                        diags.append(Diagnostic(m, d, self.path, packed))
 
         # Lists of available and unfinished diagnostics.
-        self.available_diags = self._parse_available_diags()
+        self.available_diags = diags
         self.unfinished_diags = [Diagnostic(m, d, self.path) \
                                  for m, d in _unfinished_diags]
         # Available diags is not what you think! Need to remove the unfinished
@@ -187,8 +206,27 @@ def get_available_diags(self):
         # It helps with testing and human readability if this is sorted.
         self.available_diags.sort(key=lambda d: d.full_name)
 
+        self.diags_parsed = True
+
+        return self.available_diags
+
+    def get_diags(self):
+
+        assert self.has_run
+        assert self.diags_parsed
+
         return self.available_diags
 
+    def get_diags_dict(self):
+
+        diags = self.get_diags()
+
+        d = {}
+        for diag in diags:
+            d[diag.full_name] = diag
+
+        return d
+
     def get_unfinished_diags(self):
         """
         Return a list of the unfinished diagnostics for this experiment.