Dev

.github/workflows/python-package.yml

@@ -13,7 +13,7 @@ on:
 jobs:
   build:
 
-    runs-on: [ubuntu-latest, macos-latest, windows-2019]
+    runs-on: [ubuntu-latest]
     strategy:
       fail-fast: false
       matrix:
@@ -36,6 +36,6 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+    - name: Test with unittest
       run: |
-        pytest
+        python -m unittest discover -s tests

.github/workflows/python-publish.yml

@@ -50,12 +50,7 @@ jobs:
     # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
     environment:
       name: pypi
-      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
-      # url: https://pypi.org/p/YOURPROJECT
-      #
-      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
-      # ALTERNATIVE: exactly, uncomment the following line instead:
-      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+      url: https://pypi.org/p/sbol2build/
 
     steps:
       - name: Retrieve release distributions
@@ -67,4 +62,5 @@ jobs:
       - name: Publish release distributions to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
           packages-dir: dist/

.readthedocs.yaml

@@ -0,0 +1,25 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt 
+

SBOL2Build.ipynb

@@ -939,7 +939,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 117,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -973,7 +973,7 @@
    ],
    "source": [
     "pro_in_bb_doc = sbol2.Document()\n",
-    "pro_in_bb_doc.read('Test/pro_in_bb.xml')\n",
+    "pro_in_bb_doc.read('tests/test_files/test_files/pro_in_bb.xml')\n",
     "md = pro_in_bb_doc.getModuleDefinition(\"https://sbolcanvas.org/module1\")\n",
     "assembly_plan = sbol2.ModuleDefinition('insert_assembly_plan')\n",
     "\n",
@@ -1188,7 +1188,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -1223,7 +1223,7 @@
    ],
    "source": [
     "bb_doc = sbol2.Document()\n",
-    "bb_doc.read('Test/backbone.xml')\n",
+    "bb_doc.read('tests/test_files/backbone.xml')\n",
     "\n",
     "md = bb_doc.getModuleDefinition(\"https://sbolcanvas.org/module1\")\n",
     "assembly_plan = sbol2.ModuleDefinition('bb_assembly_plan')\n",
@@ -1600,7 +1600,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 44,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -1660,7 +1660,7 @@
     "temp_doc = sbol2.Document()\n",
     "reactants_list = []\n",
     "assembly_plan = sbol2.ModuleDefinition('assembly_plan')\n",
-    "parts = ['Test/pro_in_bb.xml','Test/rbs_in_bb.xml', 'Test/cds_in_bb.xml', 'Test/terminator_in_bb.xml']\n",
+    "parts = ['tests/test_files/pro_in_bb.xml','tests/test_files/rbs_in_bb.xml', 'tests/test_files/cds_in_bb.xml', 'tests/test_files/terminator_in_bb.xml']\n",
     "\n",
     "for i, part in enumerate(parts):\n",
     "    temp_doc.read(part)\n",
@@ -1676,7 +1676,7 @@
     "\n",
     "    reactants_list.append(extracts_tuple_list[0][0])\n",
     "\n",
-    "temp_doc.read('Test/backbone.xml')\n",
+    "temp_doc.read('tests/test_files/backbone.xml')\n",
     "# run digestion, extract component + sequence, add to ligation_doc, reactants_list\n",
     "md = temp_doc.getModuleDefinition('https://sbolcanvas.org/module1')\n",
     "extracts_tuple_list, assembly_plan = backbone_digestion(md, [bsai], assembly_plan, temp_doc)\n",

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,32 @@
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../src')) #adjust file path
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'SBOL2Build'
+copyright = '2025, Ryan Greer'
+author = 'Ryan Greer'
+release = '0.0b1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [ "sphinx.ext.autodoc", "sphinx.ext.viewcode"]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'furo'
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,25 @@
+.. SBOL2Build documentation master file, created by
+   sphinx-quickstart on Mon Apr 14 14:04:32 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SBOL2Build's documentation!
+======================================
+
+SBOL2Build is a Python library for assisting in the planning, documentation, and distribution of DNA assembly plans using the Synthetic Biology Open Language 2.3 data standard. 
+
+It was developed to support build functionality and workflows in `SynBioSuite <https://synbiosuite.org/>`_, based off the `SBOL Best Practices <https://github.com/SynBioDex/SBOL-examples/tree/main/SBOL/best-practices/BP011/>`_.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+API Reference
+=============
+
+.. automodule:: sbol2build.sbol2build
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx
+furo

notebooks/test_notebook.ipynb

@@ -40,11 +40,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "pro = s2b.dna_componentdefinition_with_sequence2('promoter', 'acgt')"
+    "pro = s2b.dna_componentdefinition_with_sequence('promoter', 'acgt')"
    ]
   },
   {
@@ -98,7 +98,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "GLLDB",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -112,7 +112,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

requirements.txt

@@ -0,0 +1,3 @@
+sbol2
+biopython
+pydna