Merge pull request #66 from UC-Davis-molecular-computing/dev

bumped version to 0.7.2

README.md

@@ -45,10 +45,11 @@ Once Python is installed, there are two ways you can install the scadnano Python
 
 2. download
 
-    As a simple alternative, you can download and place the following file(s) (located in the [scadnano/](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/tree/master/scadnano) subfolder)
+    As a simple alternative, you can download and place the following files (located in the [scadnano/](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/tree/master/scadnano) subfolder)
     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.
 

doc/conf.py

@@ -16,11 +16,13 @@
 import os
 import sys
 
-import scadnano_version
+
 
 sys.path.insert(0, os.path.abspath('../scadnano'))
 # print(sys.path)
 
+import scadnano_version
+
 # Type "make html" at the command line to generate the documentation.
 
 

scadnano/origami_rectangle.py

@@ -5,6 +5,7 @@
 
 from dataclasses import dataclass, field
 
+# from . import scadnano as sc
 import scadnano as sc
 from enum import Enum, auto
 

scadnano/scadnano.py

@@ -57,13 +57,6 @@
 import xlwt
 
 
-# TODO: make explicit rules about when strands can be added and sequences assigned.
-#  For instance, if we add a strand to overlap one that already has a DNA sequence sequence assigned,
-#  should the complement be automatically assigned?
-
-# TODO: see if :param the_parameter: and :return: can be used with Sphinx
-
-
 def _pairwise(iterable):
     """s -> (s0,s1), (s1,s2), (s2, s3), ..."""
     a, b = itertools.tee(iterable)
@@ -299,9 +292,12 @@ class Grid(str, enum.Enum):
 ##########################################################################
 # constants
 
-import scadnano_version
-current_version: str = scadnano_version.current_version
-initial_version: str = scadnano_version.initial_version
+# from . import scadnano_version
+# import scadnano_version
+# current_version: str = scadnano_version.current_version
+# initial_version: str = scadnano_version.initial_version
+current_version: str = "0.7.2"
+initial_version: str = "0.0.1" 
 
 default_idt_scale = "25nm"
 default_idt_purification = "STD"

scadnano/scadnano_version.py

@@ -0,0 +1,2 @@
+current_version = "0.7.2"
+initial_version = "0.0.1"

setup.py

@@ -8,9 +8,11 @@
 # not including the README.md file and not formatting it as Markdown on PyPI
 # https://setuptools.readthedocs.io/en/latest/setuptools.html
 
-from setuptools import setup, find_packages
+from setuptools import setup
 
-from scadnano_version import current_version
+# import scadnano.scadnano_version as sv
+
+# from scadnano.scadnano_version import current_version
 
 # read the contents of your README file
 from os import path
@@ -21,10 +23,10 @@
 
 setup(name='scadnano',
       packages=['scadnano'],
-      version=current_version,
-      # version='0.7.0',
-      download_url=f'https://github.com/UC-Davis-molecular-computing/scadnano-python-package/archive/v{current_version}.zip',
-      # download_url=f'https://github.com/UC-Davis-molecular-computing/scadnano-python-package/archive/v0.7.0.zip',
+      # version=sv.current_version,
+      version='0.7.2',
+      # download_url=f'https://github.com/UC-Davis-molecular-computing/scadnano-python-package/archive/v{sv.current_version}.zip',
+      download_url=f'https://github.com/UC-Davis-molecular-computing/scadnano-python-package/archive/v0.7.0.zip',
       license='MIT',
       description="Python scripting library for generating designs readable by scadnano.",
       author="David Doty",

tests/scadnano_tests.py

@@ -621,7 +621,7 @@ def test_from_json__helices_non_default_indices_mixed_with_default(self):
         self.design_pre_json = sc.DNADesign(helices=helices, strands=[s1, s2], grid=sc.square)
 
         json_str = self.design_pre_json.to_json()
-        print(json_str)
+
         json_map = json.loads(json_str)
         design = sc.DNADesign._from_scadnano_json(json_map)
 

tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna

@@ -1,5 +1,5 @@
 {
-  "version": "0.7.0",
+  "version": "0.7.2",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna

@@ -1,5 +1,5 @@
 {
-  "version": "0.7.0",
+  "version": "0.7.2",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna

@@ -1,5 +1,5 @@
 {
-  "version": "0.7.0",
+  "version": "0.7.2",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna

@@ -1,5 +1,5 @@
 {
-  "version": "0.7.0",
+  "version": "0.7.2",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna

@@ -1,5 +1,5 @@
 {
-  "version": "0.7.0",
+  "version": "0.7.2",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},