Oligos

.gitignore

@@ -22,3 +22,4 @@
 # recursively re-ignore
 __pycache__
 *.egg-info/
+docs/build

README.md

@@ -1,15 +1,14 @@
-# PyTemplate
+# DesignerDNA
 [![build status][buildstatus-image]][buildstatus-url]
 
-[buildstatus-image]: https://github.com/Spill-Tea/PyTemplate/actions/workflows/python-app.yml/badge.svg?branch=main
-[buildstatus-url]: https://github.com/Spill-Tea/PyTemplate/actions?query=branch%3Amain
+[buildstatus-image]: https://github.com/Spill-Tea/DesignerDNA/actions/workflows/python-app.yml/badge.svg?branch=main
+[buildstatus-url]: https://github.com/Spill-Tea/DesignerDNA/actions?query=branch%3Amain
 
-Python Project Template. Be sure to create a template directly
-from github.
+DesignerDNA - Design DNA sequences with intent.
 
 <!-- omit in toc -->
 ## Table of Contents
-- [PyTemplate](#pytemplate)
+- [DesignerDNA](#designerdna)
   - [Installation](#installation)
   - [For Developers](#for-developers)
   - [License](#license)
@@ -19,29 +18,30 @@ from github.
 Clone the repository and pip install.
 
 ```bash
-git clone https://github.com/Spill-Tea/PyTemplate.git
-cd PyTemplate
+git clone https://github.com/Spill-Tea/DesignerDNA.git
+cd DesignerDNA
 pip install .
 ```
 
 Alternatively, you may install directly from github.
 ```bash
-pip install git+https://github.com/Spill-Tea/PyTemplate@main
+pip install git+https://github.com/Spill-Tea/DesignerDNA@main
 ```
 
 
 ## For Developers
-After cloning the repository, create a new virtual environment and run the following commands:
+After cloning the repository, create a new virtual environment and run the following
+commands:
 
 ```bash
 pip install -e ".[dev]"
 pre-commit install
 pre-commit run --all-files
 ```
 
-Running unit tests locally is straightforward with tox. Make sure
-you have all python versions available required for your project
-The `p` flag is not required, but it runs tox environments in parallel.
+Running unit tests locally is straightforward with tox. Make sure you have all python
+versions available required for your project. The `p` flag is not required, but it runs
+tox environments in parallel.
 ```bash
 tox -p
 ```

tests/unit/test_version.py → docs/source/_ext/styles.py

@@ -27,16 +27,55 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-"""Example unit tests."""
+"""Custom Pygment styles."""
 
-from PyTemplate import __version__
+from typing import ClassVar
 
+from pygments.style import Style
+from pygments.token import (
+    Comment,
+    Error,
+    Keyword,
+    Name,
+    Number,
+    Operator,
+    Punctuation,
+    String,
+    _TokenType,
+)
 
-def test_version_type():
-    """Test defined version is a string."""
-    assert isinstance(__version__, str), "Expected string format version"
 
+class VSCodeDarkPlus(Style):
+    """VSCode Dark+ Style."""
 
-def test_version_value():
-    """Test version string starts with the letter v."""
-    assert __version__.lower().startswith("v"), "Expected version to begin with `v`"
+    background_color: str = "#1E1E1E"
+
+    styles: ClassVar[dict[_TokenType, str]] = {
+        Number: "#B6CEA9",
+        Operator: "#D4D4D4",
+        Operator.Word: "#C586C0",
+        Comment: "#6D9957",
+        Comment.Preproc: "#639BD4",
+        Keyword.Namespace: "#C287A0",
+        # Keyword.Reserved: "#C287A0",
+        Keyword.Reserved: "#639BD4",
+        Keyword.Type: "#61C8B0",
+        Keyword.Constant: "#4FC1FF",
+        # Keyword: "#639BD4",
+        Keyword: "#C586C0",
+        Name: "#7FD0FD",
+        Name.Class: "#61C8B0",
+        Name.Namespace: "#61C8B0",
+        Name.Function: "#DCDCAA",
+        # Name.Builtin: "#DCDCAA",
+        Name.Builtin: "#4EC9B0",
+        Name.Type: "#4EC9B0",
+        Name.Builtin.Pseudo: "#9CDCFE",
+        Name.Variable: "#9CDCFE",
+        Name.Variable.Class: "#61C8B0",
+        Name.Variable.Magic: "#DCDCAA",
+        Name.Exception: "#61C8B0",
+        Error: "#61C8B0",
+        String: "#C9937A",
+        Punctuation: "#F9C922",
+    }

docs/source/api/designer_dna.rst

@@ -0,0 +1,21 @@
+designer\_dna package
+=====================
+
+Submodules
+----------
+
+designer\_dna.oligos module
+---------------------------
+
+.. automodule:: designer_dna.oligos
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Module contents
+---------------
+
+.. automodule:: designer_dna
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/modules.rst

@@ -0,0 +1,7 @@
+designer_dna
+============
+
+.. toctree::
+   :maxdepth: 4
+
+   designer_dna

docs/source/conf.py

@@ -1,18 +1,42 @@
-# Configuration file for the Sphinx documentation builder.
+# BSD 3-Clause License
 #
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# Copyright (c) 2025, Spill-Tea
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from
+#    this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+"""Sphinx configuration file."""
 
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 import os
 import sys
 
 
 sys.path.insert(0, os.path.abspath("../src/"))
+sys.path.append(os.path.abspath("./_ext"))  # Required for custom extensions
 
-
-project = "PyTemplate"
+project = "DesignerDNA"
 copyright = "2025, Jason C Del Rio (Spill-Tea)"
 author = "Jason C Del Rio (Spill-Tea)"
 release = "v0.0.1"
@@ -38,3 +62,4 @@
 html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]
 html_css_files = ["custom.css"]
+pygments_style = "styles.VSCodeDarkPlus"

docs/source/index.rst

@@ -1,29 +1,17 @@
-.. PyTemplate documentation master file, created by
-   sphinx-quickstart on Thu Jun 12 22:11:46 2025.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+DesignerDNA documentation
+=========================
 
-PyTemplate documentation
-========================
-
-Add your content using ``reStructuredText`` syntax. See the
-`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
-documentation for details.
-
-.. automodule:: PyTemplate.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
+Design, fiddle, and optimize DNA sequences.
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
-   api
+   api/modules
 
 
 Indices and tables
 ==================
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
+* :ref:`search`

pyproject.toml

@@ -1,39 +1,46 @@
 [build-system]
-requires = ["setuptools>=67.6.1"]
+requires = ["setuptools>=67.6.1", "cython>=3.0.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "PyTemplate"
+name = "designer_dna"
 authors = [{ name = "Jason C Del Rio", email = "spillthetea917@gmail.com" }]
 maintainers = [{ name = "Jason C Del Rio", email = "spillthetea917@gmail.com" }]
 description = "Project description here."
 license = { file = "LICENSE" }
-requires-python = ">=3.7"
-keywords = ["keyword1", "keyword2"]
-classifiers = ["Programming Language :: Python :: 3"]
+requires-python = ">=3.11"
+keywords = ["DNA", "design", "ligation", "optimization"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
 dynamic = ["version", "readme", "dependencies"]
 
 [project.urls]
-homepage = "https://github.com/Spill-Tea/PyTemplate"
-issues = "https://github.com/Spill-Tea/PyTemplate/issues"
+homepage = "https://github.com/Spill-Tea/DesignerDNA"
+issues = "https://github.com/Spill-Tea/DesignerDNA/issues"
 
 [tool.setuptools.dynamic]
-version = { attr = "PyTemplate.__version__" }
+version = { attr = "designer_dna.__version__" }
 readme = { file = ["README.md"], content-type = "text/markdown" }
 dependencies = { file = ["requirements.txt"] }
 
 [tool.setuptools]
-package-dir = { "" = "src" }
+package-dir = { "" = "src"}
 
 [tool.setuptools.packages.find]
 where = ["src"]
-exclude = ["benchmarks", "docs", "tests"]
+exclude = ["benchmarks", "build", "docs", "tests", "scripts"]
 
 [tool.setuptools.package-data]
 "*" = ["py.typed", "*.pyi"]
+"designer_dna.headers" = ["*.h", "*.pxd"]
 
 [project.optional-dependencies]
-dev = ["PyTemplate[doc,test,lint,type]", "tox", "pre-commit"]
+dev = ["designer_dna[doc,test,lint,type,commit]", "tox"]
+commit = ["pre-commit"]
 doc = ["sphinx", "sphinx-rtd-theme"]
 test = ["pytest", "coverage", "pytest-xdist"]
 lint = ["pylint", "ruff"]
@@ -46,7 +53,7 @@ addopts = "-n auto -rA"
 [tool.coverage.run]
 parallel = true
 branch = true
-source = ["PyTemplate"]
+source = ["designer_dna"]
 disable_warnings = ["no-data-collected", "module-not-imported"]
 
 [tool.coverage.paths]
@@ -61,14 +68,14 @@ skip_empty = true
 exclude_also = ["def __repr__", 'if __name__ == "__main__"']
 
 [tool.mypy]
-mypy_path = "PyTemplate"
+mypy_path = "designer_dna"
 warn_unused_ignores = true
 allow_redefinition = false
 force_uppercase_builtins = true
 
 [tool.pylint.main]
 # extension-pkg-whitelist = []
-ignore = ["tests", "dist", "build"]
+ignore = ["dist", "build"]
 fail-under = 9.0
 jobs = 0
 limit-inference-results = 100
@@ -86,8 +93,10 @@ module-naming-style = "any"
 [tool.pylint.format]
 max-line-length = 88
 
-# [tool.pylint."messages control"]
-# disable = []
+[tool.pylint."messages control"]
+disable = [
+  "R1731" # consider-using-max-builtin
+]
 
 [tool.ruff]
 line-length = 88
@@ -118,6 +127,7 @@ ignore = [
   "D213",    # multi-line-summary-second-line (D213)
   "PLR0913", # too-many-arguments (PLR0913)
   "C408",    # unnecessary-collection-call (C408)
+  "PYI021",  # docstring-in-stub (PYI021)
 ]
 
 [tool.ruff.lint.pydocstyle]
@@ -128,7 +138,7 @@ lines-after-imports = 2
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = [
-  "E402", # Import Statement not at Top of File
+  "E402", # Import Statement not at top of file
   "F401", # Unused Imports
 ]
 "tests/*.py" = [