bumped version to v0.8.0

UC-Davis-molecular-computing · Jun 4, 2020 · f327b0d · f327b0d
1 parent c2c394c
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diff --git a/dist/scadnano-0.8.0.tar.gz b/dist/scadnano-0.8.0.tar.gz
diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 512, "grid_position": [0, 0], "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501]},

diff --git a/examples/output_designs/16_helix_origami_rectangle.dna b/examples/output_designs/16_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.dna b/examples/output_designs/16_helix_origami_rectangle_idt.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 512, "grid_position": [0, 0], "major_ticks": [11, 22, 32, 40, 48, 58, 69, 79, 90, 100, 111, 121, 132, 142, 153, 163, 174, 184, 195, 205, 216, 226, 237, 247, 258, 268, 279, 289, 300, 310, 321, 331, 342, 352, 363, 373, 384, 394, 405, 415, 426, 436, 447, 457, 468, 478]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/1_staple_1_helix_origami.dna b/examples/output_designs/1_staple_1_helix_origami.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0], "major_ticks": [2, 5]}

diff --git a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]}

diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"position": {"x": 3, "y": 2, "z": 1}, "pitch": 90, "major_ticks": [2, 5]}

diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.dna b/examples/output_designs/1_staple_1_helix_origami_roll.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0], "roll": 90}

diff --git a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 304, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},
@@ -12,18 +12,30 @@
       "display_connector": false,
       "location": "5'"
     },
-    "/5Biosg/": {
-      "display_text": "B",
-      "idt_text": "/5Biosg/",
-      "display_connector": false,
-      "location": "5'"
-    },
     "/3Bio/": {
       "display_text": "B",
       "idt_text": "/3Bio/",
       "display_connector": false,
       "location": "3'"
     },
+    "/iCy3/": {
+      "display_text": "Cy3",
+      "idt_text": "/iCy3/",
+      "display_connector": false,
+      "location": "internal"
+    },
+    "/iCy5/": {
+      "display_text": "Cy5",
+      "idt_text": "/iCy5/",
+      "display_connector": false,
+      "location": "internal"
+    },
+    "/5Biosg/": {
+      "display_text": "B",
+      "idt_text": "/5Biosg/",
+      "display_connector": false,
+      "location": "5'"
+    },
     "/iBiodT/": {
       "display_text": "B",
       "idt_text": "/iBiodT/",
@@ -36,18 +48,6 @@
       "idt_text": "/3Cy3Sp/",
       "display_connector": false,
       "location": "3'"
-    },
-    "/iCy5/": {
-      "display_text": "Cy5",
-      "idt_text": "/iCy5/",
-      "display_connector": false,
-      "location": "internal"
-    },
-    "/iCy3/": {
-      "display_text": "Cy3",
-      "idt_text": "/iCy3/",
-      "display_connector": false,
-      "location": "internal"
     }
   },
   "strands": [

diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/3_helix_deletions_insertions.dna b/examples/output_designs/3_helix_deletions_insertions.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 64, "grid_position": [0, 0]},

diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "none",
   "helices": [
     {"position": {"x": 0, "y": 0, "z": 0}},

diff --git a/examples/output_designs/56_helix_origami_rectangle.dna b/examples/output_designs/56_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 160, "grid_position": [0, 0]},

diff --git a/examples/output_designs/64_helix_origami_rectangle.dna b/examples/output_designs/64_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 128, "grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.dna b/examples/output_designs/6_helix_6_col_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_bundle_honeycomb.dna b/examples/output_designs/6_helix_bundle_honeycomb.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 1295, "grid_position": [1, 1]},

diff --git a/examples/output_designs/6_helix_origami_rectangle.dna b/examples/output_designs/6_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

diff --git a/examples/output_designs/add_deletions_to_24_helix_rectangle.dna b/examples/output_designs/add_deletions_to_24_helix_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "e",
   "helices": [
     {"max_offset": 304, "grid_position": [0, -3]},

diff --git a/examples/output_designs/empty.dna b/examples/output_designs/empty.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [],
   "strands": []

diff --git a/examples/output_designs/hairpin.dna b/examples/output_designs/hairpin.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]}

diff --git a/examples/output_designs/helices_out_of_order_nonconsecutive.dna b/examples/output_designs/helices_out_of_order_nonconsecutive.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "none",
   "helices": [
     {"max_offset": 20, "grid_position": [0, 2], "idx": 2},

diff --git a/examples/output_designs/hex_lattice_10x10.dna b/examples/output_designs/hex_lattice_10x10.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "hex",
   "helices": [
     {"max_offset": 16, "grid_position": [0, 0]},

diff --git a/examples/output_designs/hex_lattice_10x10_with_negative.dna b/examples/output_designs/hex_lattice_10x10_with_negative.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "hex",
   "helices": [
     {"max_offset": 16, "grid_position": [-4, -4]},

diff --git a/examples/output_designs/honeycomb_lattice_10x10.dna b/examples/output_designs/honeycomb_lattice_10x10.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 16, "grid_position": [0, 0]},

diff --git a/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna b/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 16, "grid_position": [-4, -4]},

diff --git a/examples/output_designs/idt-plates-explicit.dna b/examples/output_designs/idt-plates-explicit.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/long_range_crossovers.dna b/examples/output_designs/long_range_crossovers.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/loopouts_all_types.dna b/examples/output_designs/loopouts_all_types.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/many_big_helices.dna b/examples/output_designs/many_big_helices.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"max_offset": 2000, "grid_position": [0, 0]},

diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},
@@ -18,6 +18,12 @@
       "display_connector": false,
       "location": "internal"
     },
+    "/5Biosg/": {
+      "display_text": "B",
+      "idt_text": "/5Biosg/",
+      "display_connector": false,
+      "location": "5'"
+    },
     "/iBiodT/": {
       "display_text": "B",
       "idt_text": "/iBiodT/",
@@ -30,12 +36,6 @@
       "idt_text": "/3Cy3Sp/",
       "display_connector": false,
       "location": "3'"
-    },
-    "/5Biosg/": {
-      "display_text": "B",
-      "idt_text": "/5Biosg/",
-      "display_connector": false,
-      "location": "5'"
     }
   },
   "strands": [

diff --git a/examples/output_designs/proposal.dna b/examples/output_designs/proposal.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "none",
   "helices": [
     {"max_offset": 512, "position": {"x": 0, "y": 0, "z": 0}},

diff --git a/examples/output_designs/sst-motif-3_2.dna b/examples/output_designs/sst-motif-3_2.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "major_tick_distance": 10,
   "helices": [

diff --git a/examples/output_designs/sst-motif-4_1.dna b/examples/output_designs/sst-motif-4_1.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.7.4",
+  "version": "0.8.0",
   "grid": "square",
   "major_tick_distance": 10,
   "helices": [

diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py
@@ -298,7 +298,7 @@ class Grid(str, enum.Enum):
 # import scadnano_version
 # current_version: str = scadnano_version.current_version
 # initial_version: str = scadnano_version.initial_version
-current_version: str = "0.7.4"
+current_version: str = "0.8.0"
 initial_version: str = "0.0.1"
 
 default_idt_scale = "25nm"