Merge pull request #175 from UC-Davis-molecular-computing/dev

v0.16.0

.github/workflows/docs-check.yml

@@ -5,9 +5,17 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: ammaraskar/sphinx-action@master
+    - uses: actions/[email protected]
+    - name: Set up Python
+      uses: actions/setup-python@v2
       with:
-        docs-folder: "doc/"
-        pre-build-command: "pip3 install sphinx_rtd_theme"
-        build-command: "sphinx-build -T -E -W -b html . _build"
+          python-version: '3.x'
+    - name: Install Sphinx
+      run: |
+        python -m pip install --upgrade pip
+        pip install sphinx sphinx_rtd_theme
+    - name: Move to docs folder and build
+      run: |
+        cd doc
+        pwd
+        sphinx-build -T -E -W -b html . _build

.github/workflows/release.yml

@@ -3,7 +3,7 @@ name: "release"
 on:
   push:
     branches:
-      - "master"
+      - "main"
 
 jobs:
   release:

doc/conf.py

@@ -59,7 +59,14 @@ def extract_version(filename: str):
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    # 'sphinx.ext.napoleon',
+]
+
+# next line puts type of each function parameter next to description of parameter
+autodoc_typehints = "description"
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

examples/1_staple_1_helix_origami_position_nondefault.py

@@ -3,14 +3,16 @@
 
 def create_design() -> sc.Design:
     length = 9
+    pitch90_group = sc.HelixGroup(pitch=90)
     helices = [
-        sc.Helix(max_offset=length, major_ticks=[2, 5], position=sc.Position3D(x=1, y=2, z=3), pitch=90)]
+        sc.Helix(max_offset=length, major_ticks=[2, 5], position=sc.Position3D(x=1, y=2, z=3), group='pitch90')]
     stap_ss = sc.Domain(0, True, 0, length)
     scaf_ss = sc.Domain(0, False, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]
-    design = sc.Design(helices=helices, strands=strands, grid=sc.Grid.none)
+    design = sc.Design(helices=helices, groups={
+                       'pitch90': pitch90_group}, strands=strands)
     design.assign_dna(scaf, 'AACT' * (length // 4))
 
     return design

examples/4_helix_grid_none.py

@@ -4,10 +4,10 @@
 def create_design() -> sc.Design:
     length = 10
     helices = [
-        sc.Helix(max_offset=length, position=sc.Position3D(x=0, y=0, z=2.5), pitch=0, roll=0, yaw=0),
-        sc.Helix(max_offset=length, position=sc.Position3D(x=3, y=3, z=0), pitch=0, roll=0, yaw=0),
-        sc.Helix(max_offset=length, position=sc.Position3D(x=8, y=-3, z=0), pitch=0, roll=0, yaw=0),
-        sc.Helix(max_offset=length, position=sc.Position3D(x=11, y=1, z=0), pitch=0, roll=0, yaw=0),
+        sc.Helix(max_offset=length, position=sc.Position3D(x=0, y=0, z=2.5), roll=0),
+        sc.Helix(max_offset=length, position=sc.Position3D(x=3, y=3, z=0), roll=0),
+        sc.Helix(max_offset=length, position=sc.Position3D(x=8, y=-3, z=0), roll=0),
+        sc.Helix(max_offset=length, position=sc.Position3D(x=11, y=1, z=0), roll=0),
     ]
     stap_ss = sc.Domain(0, True, 0, length)
     scaf_ss = sc.Domain(0, False, 0, length)

examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc

@@ -1,10 +1,16 @@
 {
-  "version": "0.15.0",
-  "grid": "none",
+  "version": "0.16.0",
+  "groups": {
+    "pitch90": {
+      "position": {"x": 0, "y": 0, "z": 0},
+      "pitch": 90,
+      "grid": "none"
+    }
+  },
   "helices": [
     {
+      "group": "pitch90",
       "position": {"x": 1, "y": 2, "z": 3},
-      "pitch": 90,
       "major_ticks": [2, 5]
     }
   ],