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

timurbazhirov · web-flow · commit 8857e0f4ebe2 · 2024-02-20T18:27:43.000-08:00
feature/SOF-7266 chore: start basis arrays from 0
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
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:1b5922e129683c921c2ab96ff9d4e6d26b7701c95587a8f67b19c536c4ae2011
+oid sha256:c6dfc86c91e91091a18ae8006cb9ba5d6d7e0935111273d1396ca78be82297df
 size 23287
diff --git a/tests/fixtures/espresso/v5_4/references.py b/tests/fixtures/espresso/v5_4/references.py
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:daa02db7be6eae56bbe3dabb3326e97014240de97e71aa26acedf97ff3656122
+oid sha256:25cb7690bac1b36a0ed787cfca62706d58614c2a1cbdb7ad5774c010bec9b072
 size 144655
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

Original file line number	Diff line number	Diff line change
`@@ -333,8 +333,8 @@ def initial_basis(self, text):`
`333`	`333`	`Example:`
`334`	`334`	`{`
`335`	`335`	`'units': 'angstrom',`
`336`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`337`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [2.1095228, 1.49165, 3.6538]}]`
	`336`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`337`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [2.1095228, 1.49165, 3.6538]}]`
`338`	`338`	`}`
`339`	`339`	`"""`
`340`	`340`	`alat = self._get_alat(text)`
`@@ -436,14 +436,14 @@ def _basis_convergence(self, text):`
`436`	`436`	`[`
`437`	`437`	`{`
`438`	`438`	`'units': 'crystal',`
`439`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`440`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`439`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`440`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`441`	`441`	`},`
`442`	`442`	`...`
`443`	`443`	`{`
`444`	`444`	`'units': 'crystal',`
`445`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`446`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`445`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`446`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`447`	`447`	`}`
`448`	`448`	`]`
`449`	`449`	`"""`
`@@ -462,8 +462,8 @@ def _extract_basis_from_bfgs_blocks(self, text):`
`462`	`462`	`Example:`
`463`	`463`	`{`
`464`	`464`	`'units': 'crystal',`
`465`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`466`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`465`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`466`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`467`	`467`	`}`
`468`	`468`	`"""`
`469`	`469`	`basis = {"units": "crystal", "elements": [], "coordinates": []}`
Original file line number	Diff line number	Diff line change
`@@ -139,8 +139,8 @@ def final_basis(self):`
`139`	`139`	`Example:`
`140`	`140`	`{`
`141`	`141`	`'units': 'angstrom',`
`142`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`143`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`142`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`143`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`144`	`144`	`}`
`145`	`145`	`"""`
`146`	`146`	`pass`
Original file line number	Diff line number	Diff line change
`@@ -165,8 +165,8 @@ def final_basis(self):`
`165`	`165`	`Example:`
`166`	`166`	`{`
`167`	`167`	`'units': 'angstrom',`
`168`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`169`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`168`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`169`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`170`	`170`	`}`
`171`	`171`	`"""`
`172`	`172`	`elements, coordinates = [], []`
Original file line number	Diff line number	Diff line change
`@@ -111,14 +111,14 @@ def _basis_convergence(self, text, atom_names):`
`111`	`111`	`[`
`112`	`112`	`{`
`113`	`113`	`'units': 'crystal',`
`114`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`115`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`114`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`115`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`116`	`116`	`},`
`117`	`117`	`...`
`118`	`118`	`{`
`119`	`119`	`'units': 'crystal',`
`120`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`121`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]`
	`120`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`121`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]`
`122`	`122`	`}`
`123`	`123`	`]`
`124`	`124`	`"""`
Original file line number	Diff line number	Diff line change
`@@ -292,8 +292,8 @@ def final_basis(self):`
`292`	`292`	`Example:`
`293`	`293`	`{`
`294`	`294`	`'units': 'angstrom',`
`295`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`296`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [1.11, 0.78, 1.93]}]`
	`295`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`296`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [1.11, 0.78, 1.93]}]`
`297`	`297`	`}`
`298`	`298`	`"""`
`299`	`299`	`lattice = self.final_lattice_vectors()`
Original file line number	Diff line number	Diff line change
`@@ -42,8 +42,8 @@ def initial_basis(self):`
`42`	`42`	`Example:`
`43`	`43`	`{`
`44`	`44`	`'units': 'crystal',`
`45`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`46`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}]`
	`45`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`46`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.25, 0.25, 0.25]}]`
`47`	`47`	`}`
`48`	`48`	`"""`
`49`	`49`	`pass`
`@@ -81,8 +81,8 @@ def final_basis(self):`
`81`	`81`	`Example:`
`82`	`82`	`{`
`83`	`83`	`'units': 'crystal',`
`84`		`- 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],`
`85`		`- 'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}]`
	`84`	`+ 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],`
	`85`	`+ 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.25, 0.25, 0.25]}]`
`86`	`86`	`}`
`87`	`87`	`"""`
`88`	`88`	`pass`