Merge pull request #142 from Exabyte-io/feature/SOF-7266

feature/SOF-7266 chore: start basis arrays from 0
Exabyte-io · Feb 21, 2024 · 8857e0f · 8857e0f
2 parents cba5311 + e33900d
commit 8857e0f
Showing 14 changed files with 36 additions and 36 deletions.
diff --git a/express/parsers/apps/espresso/formats/txt.py b/express/parsers/apps/espresso/formats/txt.py
@@ -333,8 +333,8 @@ def initial_basis(self, text):
          Example:
             {
                 'units': 'angstrom',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [2.1095228, 1.49165, 3.6538]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [2.1095228, 1.49165, 3.6538]}]
              }
         """
         alat = self._get_alat(text)
@@ -436,14 +436,14 @@ def _basis_convergence(self, text):
             [
                 {
                     'units': 'crystal',
-                    'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                    'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                    'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                    'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
                  },
                 ...
                 {
                     'units': 'crystal',
-                    'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                    'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                    'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                    'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
                  }
             ]
         """
@@ -462,8 +462,8 @@ def _extract_basis_from_bfgs_blocks(self, text):
         Example:
             {
                 'units': 'crystal',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
              }
         """
         basis = {"units": "crystal", "elements": [], "coordinates": []}

diff --git a/express/parsers/apps/espresso/formats/xml/xml_base.py b/express/parsers/apps/espresso/formats/xml/xml_base.py
@@ -139,8 +139,8 @@ def final_basis(self):
         Example:
             {
                 'units': 'angstrom',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
              }
         """
         pass
diff --git a/express/parsers/apps/espresso/formats/xml/xml_pre64.py b/express/parsers/apps/espresso/formats/xml/xml_pre64.py
@@ -165,8 +165,8 @@ def final_basis(self):
         Example:
             {
                 'units': 'angstrom',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
              }
         """
         elements, coordinates = [], []

diff --git a/express/parsers/apps/vasp/formats/txt.py b/express/parsers/apps/vasp/formats/txt.py
@@ -111,14 +111,14 @@ def _basis_convergence(self, text, atom_names):
             [
                 {
                     'units': 'crystal',
-                    'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                    'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                    'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                    'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
                  },
                 ...
                 {
                     'units': 'crystal',
-                    'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                    'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
+                    'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                    'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
                  }
             ]
         """

diff --git a/express/parsers/apps/vasp/formats/xml.py b/express/parsers/apps/vasp/formats/xml.py
@@ -292,8 +292,8 @@ def final_basis(self):
         Example:
             {
                 'units': 'angstrom',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [1.11, 0.78, 1.93]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [1.11, 0.78, 1.93]}]
              }
         """
         lattice = self.final_lattice_vectors()

diff --git a/express/parsers/mixins/ionic.py b/express/parsers/mixins/ionic.py
@@ -42,8 +42,8 @@ def initial_basis(self):
         Example:
             {
                 'units': 'crystal',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.25, 0.25, 0.25]}]
              }
         """
         pass
@@ -81,8 +81,8 @@ def final_basis(self):
         Example:
             {
                 'units': 'crystal',
-                'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
-                'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}]
+                'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
+                'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.25, 0.25, 0.25]}]
              }
         """
         pass

diff --git a/express/parsers/structure.py b/express/parsers/structure.py
@@ -158,8 +158,8 @@ def basis(self):
         """
         return {
             "units": "crystal",
-            "elements": [{"id": i + 1, "value": v.species_string} for i, v in enumerate(self.structure.sites)],
-            "coordinates": [{"id": i + 1, "value": v.frac_coords.tolist()} for i, v in enumerate(self.structure.sites)],
+            "elements": [{"id": i, "value": v.species_string} for i, v in enumerate(self.structure.sites)],
+            "coordinates": [{"id": i, "value": v.frac_coords.tolist()} for i, v in enumerate(self.structure.sites)],
         }
 
     def space_group_symbol(self):

diff --git a/express/properties/utils.py b/express/properties/utils.py
@@ -26,4 +26,4 @@ def to_array_with_ids(array):
     Returns:
         list
     """
-    return [{"id": index + 1, "value": value} for index, value in enumerate(array)]
+    return [{"id": index, "value": value} for index, value in enumerate(array)]
diff --git a/tests/fixtures/data.py b/tests/fixtures/data.py
diff --git a/tests/fixtures/espresso/v5_4/references.py b/tests/fixtures/espresso/v5_4/references.py
diff --git a/tests/fixtures/nwchem/references.py b/tests/fixtures/nwchem/references.py
@@ -14,10 +14,10 @@
 
 BASIS = {
     "units": "angstrom",
-    "elements": [{"id": 1, "value": "O"}, {"id": 2, "value": "H"}, {"id": 3, "value": "H"}],
+    "elements": [{"id": 0, "value": "O"}, {"id": 1, "value": "H"}, {"id": 2, "value": "H"}],
     "coordinates": [
-        {"id": 1, "value": [0.00000000, 0.00000000, 0.22143053]},
-        {"id": 2, "value": [0.00000000, 1.43042809, -0.88572213]},
-        {"id": 3, "value": [0.00000000, -1.43042809, -0.88572213]},
+        {"id": 0, "value": [0.00000000, 0.00000000, 0.22143053]},
+        {"id": 1, "value": [0.00000000, 1.43042809, -0.88572213]},
+        {"id": 2, "value": [0.00000000, -1.43042809, -0.88572213]},
     ],
 }
diff --git a/tests/unit/properties/non_scalar/test_atomic_forces.py b/tests/unit/properties/non_scalar/test_atomic_forces.py
@@ -5,7 +5,7 @@
 ATOMIC_FORCES = {
     "units": "eV/angstrom",
     "name": "atomic_forces",
-    "values": [{"id": 1, "value": [-3.9e-07, -2.4e-07, 0.0]}, {"id": 2, "value": [3.9e-07, 2.4e-07, 0.0]}],
+    "values": [{"id": 0, "value": [-3.9e-07, -2.4e-07, 0.0]}, {"id": 1, "value": [3.9e-07, 2.4e-07, 0.0]}],
 }
 
 

diff --git a/tests/unit/properties/non_scalar/test_magnetic_moments.py b/tests/unit/properties/non_scalar/test_magnetic_moments.py
@@ -5,7 +5,7 @@
 MAGNETIC_MOMENTS = {
     "units": "uB",
     "name": "magnetic_moments",
-    "values": [{"id": 1, "value": [0, 0, 1.235]}, {"id": 2, "value": [0, 0, -1.235]}],
+    "values": [{"id": 0, "value": [0, 0, 1.235]}, {"id": 1, "value": [0, 0, -1.235]}],
 }
 
 

diff --git a/tests/unit/properties/non_scalar/test_workflow.py b/tests/unit/properties/non_scalar/test_workflow.py
@@ -13,9 +13,9 @@ def setUp(self):
     def tearDown(self):
         super().setUp()
 
-    @mock.patch("express.properties.workflow.os")
-    def test_pyml_workflow(self, mock_os):
-        mock_os.listdir.return_value = MOCK_BASENAMES
+    @mock.patch("express.properties.workflow.os.listdir")
+    def test_pyml_workflow(self, mock_os_listdir):
+        mock_os_listdir.return_value = MOCK_BASENAMES
 
         name = NAME
         parser = PARSER