Bug fix helix number was badly set in cadnano export

.gitignore

@@ -1,3 +1,4 @@
+*.DS_Store
 *.pyc
 __pyache__/*
 /venv/

scadnano/scadnano.py

@@ -4706,7 +4706,8 @@ def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -
         """Creates blank cadnanov2 helices in and initialized all their fields.
         """
         helices_ids_reverse = {}
-        for i, helix in self.helices.items():
+        i = 0
+        for _, helix in self.helices.items():
             helix_dct: Dict[str, Any] = OrderedDict()
             helix_dct['num'] = helix.idx
 
@@ -4732,6 +4733,7 @@ def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -
 
             helices_ids_reverse[helix_dct['num']] = i
             dct['vstrands'].append(helix_dct)
+            i += 1
         return helices_ids_reverse
 
     def to_cadnano_v2(self) -> Dict[str, Any]:

tests/scadnano_tests.py

@@ -610,6 +610,13 @@ def test_circular_auto_staple_hex(self) -> None:
         design.write_scadnano_file(directory=self.output_path,
                                    filename=f'{file_name}.{sc.default_scadnano_file_extension}')
 
+    def test_paranemic_crossover(self) -> None:
+        file_name = "test_paranemic_crossover"
+        design = sc.Design.from_cadnano_v2(directory=self.input_path,
+                                           filename=file_name + ".json")
+        design.write_scadnano_file(directory=self.output_path,
+                                   filename=f'{file_name}.{sc.default_scadnano_file_extension}')
+
 
 class TestExportDNASequences(unittest.TestCase):
 
@@ -1034,6 +1041,12 @@ def test_big_circular_staples(self) -> None:
         design.export_cadnano_v2(directory=self.output_path,
                                  filename='test_big_circular_staples.json')
 
+    def test_paranemic_crossover(self) -> None:
+        design = sc.Design.from_scadnano_file(
+            os.path.join(self.input_path, f'test_paranemic_crossover.{self.ext}'))
+        design.export_cadnano_v2(directory=self.output_path,
+                                 filename='test_paranemic_crossover.json')
+
     def test_bad_cases(self) -> None:
         """ We do not handle Loopouts and design where the parity of the helix
         does not correspond to the direction.

tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_circular_strand.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "grid": "square",
   "helices": [
     {"max_offset": 24, "grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_export_design_with_helix_group.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "groups": {
     "east": {
       "position": {"x": 10, "y": 0, "z": 0},

tests_inputs/cadnano_v2_export/test_export_design_with_helix_group_not_same_grid.sc

@@ -1,5 +1,5 @@
 {
-  "version": "0.16.1",
+  "version": "0.16.2",
   "groups": {
     "east": {
       "position": {"x": 10, "y": 0, "z": 0},