Merge pull request #68 from noaa-ocs-modeling/develop

overwrite NEMS entries in `configure_nems.json` with configuration from their respective JSON files
noaa-ocs-modeling · Apr 8, 2021 · b6cd89d · b6cd89d
2 parents 5ba9c3a + 3a10ca9
commit b6cd89d
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Showing 51 changed files with 263 additions and 232 deletions.
diff --git a/coupledmodeldriver/generate/adcirc/configure.py b/coupledmodeldriver/generate/adcirc/configure.py
@@ -307,16 +307,21 @@ def read_directory(cls, directory: PathLike) -> 'NEMSADCIRCRunConfiguration':
             else:
                 raise FileNotFoundError(f'missing required configuration file "{filename}"')
 
+        driver, nems, slurm, adcirc = configurations
+
         forcings = []
         for configuration_class in cls.forcings:
             filename = directory / configuration_class.default_filename
             if filename.exists():
                 forcings.append(configuration_class.from_file(filename))
 
+        nems['models'] = [entry.nemspy_entry for entry in (adcirc, *forcings)
+                          if isinstance(entry, NEMSCapJSON)]
+
         return cls.from_configurations(
-            driver=configurations[0],
-            nems=configurations[1],
-            slurm=configurations[2],
-            adcirc=configurations[3],
+            driver=driver,
+            nems=nems,
+            slurm=slurm,
+            adcirc=adcirc,
             forcings=forcings,
         )
diff --git a/setup.py b/setup.py
@@ -78,7 +78,7 @@
     packages=find_packages(),
     python_requires='>=3.6',
     setup_requires=['dunamai', 'setuptools>=41.2'],
-    install_requires=['adcircpy>=1.0.28', 'nemspy>=0.6.13', 'numpy', 'requests'],
+    install_requires=['adcircpy>=1.0.29', 'nemspy>=0.6.13', 'numpy', 'requests'],
     extras_require={
         'testing': ['flake8', 'pytest', 'pytest-cov', 'wget'],
         'development': ['oitnb'],

diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/coldstart/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike/coldstart/fort.15
@@ -1,4 +1,4 @@
-created on 2021-04-07 17:49                                     ! RUNDES
+created on 2021-04-08 11:21                                     ! RUNDES
 Shinacock Inlet Coarse Grid                                     ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT
@@ -31,38 +31,38 @@ primitive_weighting_in_continuity_equation
 0                                                               ! CORI
 8                                                               ! NTIF
 Q1
-0.019256 6.49585E-05 0.695 1.14647 45.2841
+0.019256 6.49585E-05 0.695 1.1459 103.157
 O1
-0.100514 6.75977E-05 0.695 1.14647 51.0784
+0.100514 6.75977E-05 0.695 1.1459 272.96
 P1
-0.046843 7.25229E-05 0.706 1 322.487
+0.046843 7.25229E-05 0.706 1 131.152
 K1
-0.141565 7.29212E-05 0.736 1.09047 42.801
+0.141565 7.29212E-05 0.736 1.09012 234.173
 N2
-0.046398 0.00013788 0.693 0.972523 90.2443
+0.046398 0.00013788 0.693 0.972665 339.505
 M2
-0.242334 0.000140519 0.693 0.972523 96.0386
+0.242334 0.000140519 0.693 0.972665 149.308
 S2
 0.112841 0.000145444 0.693 1 0
 K2
-0.030704 0.000145842 0.693 1.23912 266.15
+0.030704 0.000145842 0.693 1.23794 288.895
 8
 Q1
-6.49585E-05 1.14647 45.2841
+6.49585E-05 1.1459 103.157
 O1
-6.75977E-05 1.14647 51.0784
+6.75977E-05 1.1459 272.96
 P1
-7.25229E-05 1 322.487
+7.25229E-05 1 131.152
 K1
-7.29212E-05 1.09047 42.801
+7.29212E-05 1.09012 234.173
 N2
-0.00013788 0.972523 90.2443
+0.00013788 0.972665 339.505
 M2
-0.000140519 0.972523 96.0386
+0.000140519 0.972665 149.308
 S2
 0.000145444 1 0
 K2
-0.000145842 1.23912 266.15
+0.000145842 1.23794 288.895
 Q1
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02

diff --git a/tests/data/reference/adcirc/hera_shinnecock_ike/runs/test_case_1/fort.15 b/tests/data/reference/adcirc/hera_shinnecock_ike/runs/test_case_1/fort.15
@@ -1,4 +1,4 @@
-created on 2021-04-07 17:50                                     ! RUNDES
+created on 2021-04-08 11:21                                     ! RUNDES
 Shinacock Inlet Coarse Grid                                     ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT
@@ -31,38 +31,38 @@ primitive_weighting_in_continuity_equation
 0                                                               ! CORI
 8                                                               ! NTIF
 Q1
-0.019256 6.49585E-05 0.695 1.14647 45.2841
+0.019256 6.49585E-05 0.695 1.1459 103.157
 O1
-0.100514 6.75977E-05 0.695 1.14647 51.0784
+0.100514 6.75977E-05 0.695 1.1459 272.96
 P1
-0.046843 7.25229E-05 0.706 1 322.487
+0.046843 7.25229E-05 0.706 1 131.152
 K1
-0.141565 7.29212E-05 0.736 1.09047 42.801
+0.141565 7.29212E-05 0.736 1.09012 234.173
 N2
-0.046398 0.00013788 0.693 0.972523 90.2443
+0.046398 0.00013788 0.693 0.972665 339.505
 M2
-0.242334 0.000140519 0.693 0.972523 96.0386
+0.242334 0.000140519 0.693 0.972665 149.308
 S2
 0.112841 0.000145444 0.693 1 0
 K2
-0.030704 0.000145842 0.693 1.23912 266.15
+0.030704 0.000145842 0.693 1.23794 288.895
 8
 Q1
-6.49585E-05 1.14647 45.2841
+6.49585E-05 1.1459 103.157
 O1
-6.75977E-05 1.14647 51.0784
+6.75977E-05 1.1459 272.96
 P1
-7.25229E-05 1 322.487
+7.25229E-05 1 131.152
 K1
-7.29212E-05 1.09047 42.801
+7.29212E-05 1.09012 234.173
 N2
-0.00013788 0.972523 90.2443
+0.00013788 0.972665 339.505
 M2
-0.000140519 0.972523 96.0386
+0.000140519 0.972665 149.308
 S2
 0.000145444 1 0
 K2
-0.000145842 1.23912 266.15
+0.000145842 1.23794 288.895
 Q1
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02

diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/coldstart/fort.15 b/tests/data/reference/adcirc/local_shinnecock_ike/coldstart/fort.15
@@ -1,4 +1,4 @@
-created on 2021-04-07 17:49                                     ! RUNDES
+created on 2021-04-08 11:21                                     ! RUNDES
 Shinacock Inlet Coarse Grid                                     ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT
@@ -31,38 +31,38 @@ primitive_weighting_in_continuity_equation
 0                                                               ! CORI
 8                                                               ! NTIF
 Q1
-0.019256 6.49585E-05 0.695 1.14647 45.2841
+0.019256 6.49585E-05 0.695 1.1459 103.157
 O1
-0.100514 6.75977E-05 0.695 1.14647 51.0784
+0.100514 6.75977E-05 0.695 1.1459 272.96
 P1
-0.046843 7.25229E-05 0.706 1 322.487
+0.046843 7.25229E-05 0.706 1 131.152
 K1
-0.141565 7.29212E-05 0.736 1.09047 42.801
+0.141565 7.29212E-05 0.736 1.09012 234.173
 N2
-0.046398 0.00013788 0.693 0.972523 90.2443
+0.046398 0.00013788 0.693 0.972665 339.505
 M2
-0.242334 0.000140519 0.693 0.972523 96.0386
+0.242334 0.000140519 0.693 0.972665 149.308
 S2
 0.112841 0.000145444 0.693 1 0
 K2
-0.030704 0.000145842 0.693 1.23912 266.15
+0.030704 0.000145842 0.693 1.23794 288.895
 8
 Q1
-6.49585E-05 1.14647 45.2841
+6.49585E-05 1.1459 103.157
 O1
-6.75977E-05 1.14647 51.0784
+6.75977E-05 1.1459 272.96
 P1
-7.25229E-05 1 322.487
+7.25229E-05 1 131.152
 K1
-7.29212E-05 1.09047 42.801
+7.29212E-05 1.09012 234.173
 N2
-0.00013788 0.972523 90.2443
+0.00013788 0.972665 339.505
 M2
-0.000140519 0.972523 96.0386
+0.000140519 0.972665 149.308
 S2
 0.000145444 1 0
 K2
-0.000145842 1.23912 266.15
+0.000145842 1.23794 288.895
 Q1
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02

diff --git a/tests/data/reference/adcirc/local_shinnecock_ike/runs/test_case_1/fort.15 b/tests/data/reference/adcirc/local_shinnecock_ike/runs/test_case_1/fort.15
@@ -1,4 +1,4 @@
-created on 2021-04-07 17:49                                     ! RUNDES
+created on 2021-04-08 11:21                                     ! RUNDES
 Shinacock Inlet Coarse Grid                                     ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT
@@ -31,38 +31,38 @@ primitive_weighting_in_continuity_equation
 0                                                               ! CORI
 8                                                               ! NTIF
 Q1
-0.019256 6.49585E-05 0.695 1.14647 45.2841
+0.019256 6.49585E-05 0.695 1.1459 103.157
 O1
-0.100514 6.75977E-05 0.695 1.14647 51.0784
+0.100514 6.75977E-05 0.695 1.1459 272.96
 P1
-0.046843 7.25229E-05 0.706 1 322.487
+0.046843 7.25229E-05 0.706 1 131.152
 K1
-0.141565 7.29212E-05 0.736 1.09047 42.801
+0.141565 7.29212E-05 0.736 1.09012 234.173
 N2
-0.046398 0.00013788 0.693 0.972523 90.2443
+0.046398 0.00013788 0.693 0.972665 339.505
 M2
-0.242334 0.000140519 0.693 0.972523 96.0386
+0.242334 0.000140519 0.693 0.972665 149.308
 S2
 0.112841 0.000145444 0.693 1 0
 K2
-0.030704 0.000145842 0.693 1.23912 266.15
+0.030704 0.000145842 0.693 1.23794 288.895
 8
 Q1
-6.49585E-05 1.14647 45.2841
+6.49585E-05 1.1459 103.157
 O1
-6.75977E-05 1.14647 51.0784
+6.75977E-05 1.1459 272.96
 P1
-7.25229E-05 1 322.487
+7.25229E-05 1 131.152
 K1
-7.29212E-05 1.09047 42.801
+7.29212E-05 1.09012 234.173
 N2
-0.00013788 0.972523 90.2443
+0.00013788 0.972665 339.505
 M2
-0.000140519 0.972523 96.0386
+0.000140519 0.972665 149.308
 S2
 0.000145444 1 0
 K2
-0.000145842 1.23912 266.15
+0.000145842 1.23794 288.895
 Q1
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02

diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/coldstart/fort.15 b/tests/data/reference/adcirc/stampede2_shinnecock_ike/coldstart/fort.15
@@ -1,4 +1,4 @@
-created on 2021-04-07 17:50                                     ! RUNDES
+created on 2021-04-08 11:21                                     ! RUNDES
 Shinacock Inlet Coarse Grid                                     ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT
@@ -31,38 +31,38 @@ primitive_weighting_in_continuity_equation
 0                                                               ! CORI
 8                                                               ! NTIF
 Q1
-0.019256 6.49585E-05 0.695 1.14647 45.2841
+0.019256 6.49585E-05 0.695 1.1459 103.157
 O1
-0.100514 6.75977E-05 0.695 1.14647 51.0784
+0.100514 6.75977E-05 0.695 1.1459 272.96
 P1
-0.046843 7.25229E-05 0.706 1 322.487
+0.046843 7.25229E-05 0.706 1 131.152
 K1
-0.141565 7.29212E-05 0.736 1.09047 42.801
+0.141565 7.29212E-05 0.736 1.09012 234.173
 N2
-0.046398 0.00013788 0.693 0.972523 90.2443
+0.046398 0.00013788 0.693 0.972665 339.505
 M2
-0.242334 0.000140519 0.693 0.972523 96.0386
+0.242334 0.000140519 0.693 0.972665 149.308
 S2
 0.112841 0.000145444 0.693 1 0
 K2
-0.030704 0.000145842 0.693 1.23912 266.15
+0.030704 0.000145842 0.693 1.23794 288.895
 8
 Q1
-6.49585E-05 1.14647 45.2841
+6.49585E-05 1.1459 103.157
 O1
-6.75977E-05 1.14647 51.0784
+6.75977E-05 1.1459 272.96
 P1
-7.25229E-05 1 322.487
+7.25229E-05 1 131.152
 K1
-7.29212E-05 1.09047 42.801
+7.29212E-05 1.09012 234.173
 N2
-0.00013788 0.972523 90.2443
+0.00013788 0.972665 339.505
 M2
-0.000140519 0.972523 96.0386
+0.000140519 0.972665 149.308
 S2
 0.000145444 1 0
 K2
-0.000145842 1.23912 266.15
+0.000145842 1.23794 288.895
 Q1
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02

diff --git a/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/test_case_1/fort.15 b/tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/test_case_1/fort.15
@@ -1,4 +1,4 @@
-created on 2021-04-07 17:50                                     ! RUNDES
+created on 2021-04-08 11:21                                     ! RUNDES
 Shinacock Inlet Coarse Grid                                     ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT
@@ -31,38 +31,38 @@ primitive_weighting_in_continuity_equation
 0                                                               ! CORI
 8                                                               ! NTIF
 Q1
-0.019256 6.49585E-05 0.695 1.14647 45.2841
+0.019256 6.49585E-05 0.695 1.1459 103.157
 O1
-0.100514 6.75977E-05 0.695 1.14647 51.0784
+0.100514 6.75977E-05 0.695 1.1459 272.96
 P1
-0.046843 7.25229E-05 0.706 1 322.487
+0.046843 7.25229E-05 0.706 1 131.152
 K1
-0.141565 7.29212E-05 0.736 1.09047 42.801
+0.141565 7.29212E-05 0.736 1.09012 234.173
 N2
-0.046398 0.00013788 0.693 0.972523 90.2443
+0.046398 0.00013788 0.693 0.972665 339.505
 M2
-0.242334 0.000140519 0.693 0.972523 96.0386
+0.242334 0.000140519 0.693 0.972665 149.308
 S2
 0.112841 0.000145444 0.693 1 0
 K2
-0.030704 0.000145842 0.693 1.23912 266.15
+0.030704 0.000145842 0.693 1.23794 288.895
 8
 Q1
-6.49585E-05 1.14647 45.2841
+6.49585E-05 1.1459 103.157
 O1
-6.75977E-05 1.14647 51.0784
+6.75977E-05 1.1459 272.96
 P1
-7.25229E-05 1 322.487
+7.25229E-05 1 131.152
 K1
-7.29212E-05 1.09047 42.801
+7.29212E-05 1.09012 234.173
 N2
-0.00013788 0.972523 90.2443
+0.00013788 0.972665 339.505
 M2
-0.000140519 0.972523 96.0386
+0.000140519 0.972665 149.308
 S2
 0.000145444 1 0
 K2
-0.000145842 1.23912 266.15
+0.000145842 1.23794 288.895
 Q1
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02

diff --git a/tests/data/reference/nems/hera_shinnecock_ike/coldstart/config.rc b/tests/data/reference/nems/hera_shinnecock_ike/coldstart/config.rc
@@ -1,2 +1,2 @@
-# `config.rc` generated with NEMSpy 1.2.6.post15.dev0+79ef4e6
+# `config.rc` generated with NEMSpy 1.2.8.post5.dev0+434c79d