Merge pull request #123 from UC-Davis-molecular-computing/dev

Dev

README.md

@@ -60,10 +60,12 @@ If you are using Python 3.6 and do not wish to upgrade, you can install a packag
 Python 3.7 provides the
 [dataclasses module](https://docs.python.org/3/library/dataclasses.html) automatically.
 
-Once Python is installed (and the dataclasses backport if you have Python version 3.6), there are two ways you can install the scadnano Python package:
+
 
 ### Installing the scadnano Python package
 
+Once Python is installed (and the dataclasses backport if you have Python version 3.6), there are two ways you can install the scadnano Python package:
+
 1. pip (recommended)
 
     Use [pip](https://pypi.org/project/pip/) to install the package by executing the following at the command line:
@@ -109,8 +111,7 @@ Once Python is installed (and the dataclasses backport if you have Python versio
     * *required*: [scadnano.py](scadnano/scadnano.py) 
     * *optional*: [modifications.py](scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. 
     * *optional*: [origami_rectangle.py](scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano.
-    * *optional*: [_version.py](scadnano/_version.py) This ensures that the current version number is written into any `.sc` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.)
-
+    
     To download them, right-click on "Raw" near the top and select (in Chrome or Firefox) "Save link as...":
     ![](images/download_raw_screenshot.png)
     

doc/conf.py

@@ -21,10 +21,29 @@
 sys.path.insert(0, os.path.abspath('../scadnano'))
 # print(sys.path)
 
-# current_version = "0.8.1"
+# from scadnano.scadnano_version import current_version
 # 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("\"'")
+# __version__ = open("scadnano/_version.py").readlines()[-1].split()[-1].strip("\"'")
+
+
+# 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
+def extract_version(filename: str):
+    with open(filename) as f:
+        lines = f.readlines()
+    version_comment = '# version line; WARNING: do not remove or change this line or comment'
+    for line in lines:
+        if version_comment in line:
+            idx = line.index(version_comment)
+            line_prefix = line[:idx]
+            parts = line_prefix.split('=')
+            stripped_parts = [part.strip() for part in parts]
+            version_str = stripped_parts[-1].replace('"', '')
+            return version_str
+    raise AssertionError(f'could not find version in {filename}')
+
+__version__ = extract_version('../scadnano/scadnano.py')
 
 
 

examples/16_helix_origami_barrel_from_algoSST_paper.py

@@ -248,7 +248,7 @@ def assign_dna_to_unzipper_toeholds(design):
         design.assign_dna(strand, seq)
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     the_design = create_design()
     the_design.write_scadnano_file(directory='output_designs')
     the_design.write_idt_bulk_input_file(directory='idt')

examples/16_helix_origami_rectangle.py

@@ -7,6 +7,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/16_helix_origami_rectangle_idt.py

@@ -7,7 +7,7 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')
     design.write_idt_bulk_input_file(directory='idt')

examples/16_helix_origami_rectangle_no_seq.py

@@ -7,6 +7,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/16_helix_origami_rectangle_no_seq_no_twist.py

@@ -8,6 +8,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/16_helix_origami_rectangle_no_twist.py

@@ -7,6 +7,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py

@@ -144,7 +144,7 @@ def add_adapters(design):
 #         design.assign_dna(tile, seq)
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')
     design.write_idt_bulk_input_file(directory='idt')

examples/16_helix_origami_rectangle_shifted_seam_no_seq.py

@@ -7,6 +7,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/1_staple_1_helix_origami.py

@@ -13,6 +13,6 @@ def create_design():
 
     return design
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/1_staple_1_helix_origami_idt_duplicate_names.py

@@ -19,6 +19,6 @@ def create_design():
 
     return design
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_idt_bulk_input_file(directory='idt')

examples/1_staple_1_helix_origami_mismatches.py

@@ -18,6 +18,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/1_staple_1_helix_origami_position_nondefault.py

@@ -16,6 +16,6 @@ def create_design():
     return design
 
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')

examples/1_staple_1_helix_origami_roll.py

@@ -15,6 +15,6 @@ def create_design():
 
     return design
 
-if not sc.in_browser() and __name__ == '__main__':
+if __name__ == '__main__':
     design = create_design()
     design.write_scadnano_file(directory='output_designs')