Merge pull request #76 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Jun 9, 2020 · ed2693f · ed2693f
2 parents 9c66609 + 2bfd802
commit ed2693f
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diff --git a/README.md b/README.md
@@ -49,11 +49,11 @@ Once Python is installed, there are two ways you can install the scadnano Python
     in your PYTHONPATH (e.g., in the same directory as the scripts you are running):
 
     * *required*: [scadnano.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/scadnano.py) 
-    * *required*: [scadnano_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/scadnano_version.py) 
     * *optional*: [modifications.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. 
     * *optional*: [origami_rectangle.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano.
-
-    Unfortunately, the scadnano package depends on the Python package [xlwt](https://pypi.org/project/xlwt/), so xlwt must be installed. To install, type `pip install xlwt` at the command line. If this does not work, then you can comment out the line `import xlwt` in `scadnano.py`, but then you will not be able to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences.
+    * *optional*: [scadnano_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/scadnano_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.)
+    
+    Unfortunately, the scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line.
 
 
 

diff --git a/dist/scadnano-0.8.2.tar.gz b/dist/scadnano-0.8.2.tar.gz
diff --git a/dist/scadnano-0.8.3.tar.gz b/dist/scadnano-0.8.3.tar.gz
diff --git a/doc/conf.py b/doc/conf.py
@@ -21,8 +21,12 @@
 sys.path.insert(0, os.path.abspath('../scadnano'))
 # print(sys.path)
 
-# from scadnano import current_version
-current_version = "0.8.1"
+# current_version = "0.8.1"
+# this is ugly, but appears to be standard practice:
+# https://stackoverflow.com/questions/17583443/what-is-the-correct-way-to-share-package-version-with-setup-py-and-the-package/17626524#17626524
+__version__ = open("../scadnano/_version.py").readlines()[-1].split()[-1].strip("\"'")
+
+
 
 # Type "make html" at the command line to generate the documentation.
 
@@ -34,10 +38,9 @@
 author = 'David Doty'
 
 # The full version, including alpha/beta/rc tags
-# version = '0.7.0'
 # release = '0.7.0'
-version = current_version
-release = current_version
+version = __version__
+release = __version__
 
 # -- General configuration ---------------------------------------------------
 

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
@@ -1,27 +1,107 @@
 {
-  "version": "0.8.0",
+  "version": "0.8.2",
   "grid": "square",
   "helices": [
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-    {"max_offset": 512, "grid_position": [0, 3], "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]},
-    {"max_offset": 512, "grid_position": [0, 4], "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]},
-    {"max_offset": 512, "grid_position": [0, 5], "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]},
-    {"max_offset": 512, "grid_position": [0, 6], "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]},
-    {"max_offset": 512, "grid_position": [0, 7], "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]},
-    {"max_offset": 512, "grid_position": [0, 8], "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]},
-    {"max_offset": 512, "grid_position": [0, 9], "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]},
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+    {
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+    },
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+      "grid_position": [0, 1],
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+    },
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+    },
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+    },
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+      "grid_position": [0, 4],
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+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 5],
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+    },
+    {
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+      "grid_position": [0, 6],
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+    },
+    {
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+      "grid_position": [0, 7],
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+    },
+    {
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+      "grid_position": [0, 8],
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+    },
+    {
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+      "grid_position": [0, 9],
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+    },
+    {
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+      "grid_position": [0, 10],
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+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 11],
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+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 12],
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+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 13],
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+    },
+    {
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+      "grid_position": [0, 14],
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+    },
+    {
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+      "grid_position": [0, 15],
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+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 16],
+      "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]
+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 17],
+      "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]
+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 18],
+      "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]
+    },
+    {
+      "max_offset": 512,
+      "grid_position": [0, 19],
+      "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]
+    }
   ],
   "strands": [
     {

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": "0.8.0",
+  "version": "0.8.2",
   "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": "0.8.0",
+  "version": "0.8.2",
   "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": "0.8.0",
+  "version": "0.8.2",
   "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": "0.8.0",
+  "version": "0.8.2",
   "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": "0.8.0",
+  "version": "0.8.2",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},