Merge branch '72-nitrous-oxide' of github.com:pmlmodelling/ersem-dev …

…into 72-nitrous-oxide
pmlmodelling · Aug 4, 2022 · 2d7b0ce · 2d7b0ce
2 parents f4d8cef + 0fce61d
commit 2d7b0ce
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Showing 6 changed files with 729 additions and 696 deletions.
diff --git a/.github/workflows/ersem.yml b/.github/workflows/ersem.yml
@@ -22,8 +22,8 @@ jobs:
           run: ./github-actions/pyfabm-ersem/pyfabm-ersem-dep-debian.sh
         - name: Building and installing PyFABM-ERSEM
           run: |
-              branch=$(git branch --show-current)
-              ./github-actions/pyfabm-ersem/pyfabm-ersem-build.sh $branch
+              BRANCH=${{ github.head_ref }}
+              ./github-actions/pyfabm-ersem/pyfabm-ersem-build.sh $BRANCH
         - name: Running pyfabm tutorial
           run: |
               python -m pip install matplotlib
@@ -44,8 +44,8 @@ jobs:
           run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
-              branch=$(git branch --show-current)
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $branch
+              BRANCH=${{ github.head_ref }}
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $BRANCH
         - name: Running tutorial
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh
@@ -69,8 +69,8 @@ jobs:
           run: ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-dep-debian.sh
         - name: Building and installing FABM0d-GOTM-ERSEM
           run: |
-              branch=$(git branch --show-current)
-              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh $branch
+              BRANCH=${{ github.head_ref }}
+              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh -b $BRANCH
         - name: Running tutorial
           run: |
               ./github-actions/fabm0d-gotm-ersem/aquarium-tut-config-setup.sh
@@ -93,8 +93,8 @@ jobs:
           run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
-              branch=$(git branch --show-current)
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg""
+              BRANCH=${{ github.head_ref }}
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg"" -b $BRANCH
         - name: Running config
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-profiling.sh

diff --git a/github-actions/fabm0d-gotm-ersem/expected.json b/github-actions/fabm0d-gotm-ersem/expected.json
diff --git a/github-actions/fabm0d-gotm-ersem/test_aquarium.py b/github-actions/fabm0d-gotm-ersem/test_aquarium.py
@@ -10,6 +10,7 @@
 
 import aquarium_tut
 
+
 class AquariumTests(unittest.TestCase):
     """
     Aquarium 0D model tests
@@ -28,6 +29,7 @@ def setUp(self, mock_show):
             self.expected = json.load(fp)
         self.value_dict = aquarium_tut.main(self.model_path)
 
+
     def test_dates_value(self):
         """
         Checks the dates (dates) values are the same
@@ -41,46 +43,46 @@ def test_light_value(self):
         values are the same
         """
         name = "light_parEIR"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])
 
     def test_temp_value(self):
         """
         Checks the temp (temp) values are the same
         """
         name = "temp"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])
 
     def test_salt_value(self):
         """
         Checks the salinity (salt) values are the same
         """
         name = "salt"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])
 
     def test_phosphorus_value(self):
         """
         Checks the phosphate phosphorus (N1_p) values are the same
         """
         name = "N1_p"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])
 
     def test_nitrogen_value(self):
         """
         Checks the nitrate nitrogen (N3_n) values are the same
         """
         name = "N3_n"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])
 
     def test_bcarbon_value(self):
         """
         Checks the bacteria carbon (B1_c) values are the same
         """
         name = "B1_c"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])
 
     def test_ncarbon_value(self):
         """
         Checks the nanophytoplankton carbon (P2_c) values are the same
         """
         name = "B1_c"
-        assert np.array_equal(self.expected[name], self.value_dict[name])
+        assert np.allclose(self.expected[name], self.value_dict[name])