Merge pull request #313 from UC-Davis-molecular-computing/dev

Dev

Author: dave-doty

.github/workflows/run_unit_tests.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.7, 3.8, 3.9, "3.10", "3.11" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
 
     steps:
       - uses: actions/checkout@v2
@@ -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

README.md

@@ -65,7 +65,7 @@ pip install scadnano
 Read below for troubleshooting suggestions if that didn't work.
 
 ### Getting Python
-The scadnano Python package requires Python version 3.7 or later.
+The scadnano Python package requires Python version 3.9 or later.
 
 To check your current version of Python, open a command line and type
 
@@ -79,7 +79,7 @@ If it is version 2.7 or below, type
 python3 --version
 ```
 
-If that fails, or reports Python version 3.6 or below, you will have to install a later version of Python. Follow [this link](https://www.python.org/downloads/) to install Python. You may also use an alternative Python distribution, such as [Anaconda](https://www.anaconda.com/products/individual#Downloads).
+If that fails, or reports Python version 3.8 or below, you will have to install a later version of Python. Follow [this link](https://www.python.org/downloads/) to install Python. You may also use an alternative Python distribution, such as [Anaconda](https://www.anaconda.com/products/individual#Downloads).
 
 
 
@@ -123,17 +123,11 @@ Once Python is installed, there are two ways you can install the scadnano Python
     ```
     pip 19.3.1 from ...lib\site-packages\pip (python 3.8)
     ```
-    If the version of Python at the end is Python 3.7 or higher, you are good. If it is version 2.7 or lower, type
+    If the version of Python at the end is Python 3.9 or higher, you are good. If it is version 2.7 or lower, type
     ```
     pip3 --version
     ```
-    If that works and shows Python 3.7 or higher, you are good, but you should type `pip3` in the subsequent instructions instead of `pip`.
-    
-    If it shows Python 3.6, install the [dataclasses backport module](https://pypi.org/project/dataclasses/) via
-    ```
-    pip install dataclasses
-    ```
-    If it shows Python 3.5 or lower, then you will need to upgrade your Python version (recommended Python 3.7 or higher).
+    If that works and shows Python 3.9 or higher, you are good, but you should type `pip3` in the subsequent instructions instead of `pip`.
 
     
 2. download

environment.yml

@@ -3,8 +3,7 @@ name: scadnano-test
 channels:
   - defaults
 dependencies:
-  - python=3.7
-  - xlwt=1.3.0=py37_0
+  - python=3.9
   - 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": "0.19.5",
+  "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}
+      ]
+    }
+  ]
+}