Merge branch '309-account-for-helix-group-rotation-properly-in-oxdnao…

…xview-export' of https://github.com/UC-Davis-molecular-computing/scadnano-python-package into 309-account-for-helix-group-rotation-properly-in-oxdnaoxview-export

.github/workflows/run_unit_tests.yml

@@ -21,8 +21,8 @@ jobs:
         with:
           activate-conda: true
       - name: Install openpyxl,tabulate with conda
-        run: conda install openpyxl=3.0.10 tabulate=0.8.10
+        run: conda install openpyxl=3.1 tabulate=0.9
       - name: Install docutils with conda
-        run: conda install docutils=0.16
+        run: conda install docutils=0.18
       - name: Test with unittest
         run: python -m unittest -v tests/scadnano_tests.py

environment.yml

@@ -4,7 +4,6 @@ channels:
   - defaults
 dependencies:
   - python=3.7
-  - xlwt=1.3.0=py37_0
   - pip
   - pip:
     - sphinx

examples/1_staple_1_helix_origami_roll.py

@@ -1,5 +1,3 @@
-import math
-
 import scadnano as sc
 
 def create_design() -> sc.Design:

examples/2_staple_2_helix_helixgroup_geometry.py

@@ -0,0 +1,24 @@
+import scadnano as sc
+
+
+def create_design() -> sc.Design:
+    group0 = sc.HelixGroup(grid=sc.square)
+    group1 = sc.HelixGroup(grid=sc.square, geometry=sc.Geometry(bases_per_turn=18),
+                           position=sc.Position3D(0, 3, 0))
+    groups = {"group 0": group0, "group 1": group1}
+    helices = [sc.Helix(idx=idx, max_offset=40, group=group) for idx, group in
+               [(0, "group 0"), (1, "group 1")]]
+    design = sc.Design(helices=helices, groups=groups, strands=[])
+    design.draw_strand(0, 0).move(40)
+    design.draw_strand(0, 40).move(-40)
+    design.draw_strand(1, 0).move(40)
+    design.draw_strand(1, 40).move(-40)
+
+    return design
+
+
+if __name__ == '__main__':
+    d = create_design()
+    d.write_scadnano_file(directory='output_designs')
+    d.from_scadnano_file('output_designs/2_staple_2_helix_helixgroup_geometry.sc')
+    print(f'design: {d.to_json()}')

examples/idt-plates-explicit.py

@@ -45,7 +45,7 @@ def main() -> None:
     design = create_design()
     design.write_scadnano_file(directory='output_designs')
     design.write_idt_bulk_input_file(directory='idt')
-    design.write_idt_plate_excel_file(directory='idt', use_default_plates=False, only_strands_with_idt=True)
+    design.write_idt_plate_excel_file(directory='idt', use_default_plates=False, only_strands_with_vendor_fields=True)
 
 
 if __name__ == '__main__':

examples/output_designs/2_staple_2_helix_helixgroup_geometry.sc

@@ -0,0 +1,46 @@
+{
+  "version": "0.19.4",
+  "groups": {
+    "group 0": {
+      "position": {"x": 0, "y": 0, "z": 0},
+      "grid": "square"
+    },
+    "group 1": {
+      "position": {"x": 0, "y": 3, "z": 0},
+      "grid": "square",
+      "geometry": {
+        "bases_per_turn": 18
+      }
+    }
+  },
+  "helices": [
+    {"group": "group 0", "grid_position": [0, 0]},
+    {"group": "group 1", "grid_position": [0, 0]}
+  ],
+  "strands": [
+    {
+      "color": "#f74308",
+      "domains": [
+        {"helix": 0, "forward": true, "start": 0, "end": 40}
+      ]
+    },
+    {
+      "color": "#57bb00",
+      "domains": [
+        {"helix": 0, "forward": false, "start": 0, "end": 40}
+      ]
+    },
+    {
+      "color": "#888888",
+      "domains": [
+        {"helix": 1, "forward": true, "start": 0, "end": 40}
+      ]
+    },
+    {
+      "color": "#32b86c",
+      "domains": [
+        {"helix": 1, "forward": false, "start": 0, "end": 40}
+      ]
+    }
+  ]
+}

tests/scadnano_tests.py

@@ -1282,7 +1282,7 @@ def test_write_idt_plate_excel_file(self) -> None:
         # add 10 strands in excess of 3 plates
         for plate_type in [sc.PlateType.wells96, sc.PlateType.wells384]:
             num_strands = 3 * plate_type.num_wells_per_plate() + 10
-            filename = f'test_excel_export_{plate_type.num_wells_per_plate()}.xlsx'
+            filename = f'tests/test_excel_export_{plate_type.num_wells_per_plate()}.xlsx'
             max_offset = num_strands * strand_len
             helices = [sc.Helix(max_offset=max_offset) for _ in range(1)]
             design = sc.Design(helices=helices, strands=[], grid=sc.square)
@@ -1307,7 +1307,10 @@ def test_write_idt_plate_excel_file(self) -> None:
 
                 self.assertEqual(expected_wells + 1, sheet.max_row)
 
-            os.remove(filename)
+            try:
+                os.remove(filename)
+            except PermissionError as e:
+                print(f'could not remove file "{filename}" due to permission error')
 
     def test_export_dna_sequences_extension_5p(self) -> None:
         design = sc.Design(helices=[sc.Helix(max_offset=100)])