Add pyproject.toml

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt-get install -qq phyml
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade pip setuptools>=77.0.3 wheel
         pip install --only-binary=numpy,scipy numpy scipy
         pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
         pip install -r requirements.txt

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Datasnakes
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -2,7 +2,7 @@
 #exclude OrthoEvol/Manager/TODO.py
 
 # Include the README file
-include README.rst
+include README.md
 
 # Include the requirements file
 include requirements.txt
@@ -18,11 +18,10 @@ recursive-include OrthoEvol/Cookies *
 recursive-include OrthoEvol/Manager/config *
 
 # Include docs
-include Docs/docs/source/*.rst
-include Docs/docs/source/Makefile
-include Docs/docs/source/conf.py
-include Docs/createdocs.py
-include Docs/README.md
+include docs/docs/source/*.rst
+include docs/docs/source/Makefile
+include docs/docs/source/conf.py
+include docs/README.md
 
 # Include tests
-include Tests/*
+include tests/*

README.md

@@ -1,40 +1,28 @@
-[![CI](https://github.com/datasnakes/OrthoEvolution/actions/workflows/ci.yml/badge.svg)](https://github.com/datasnakes/OrthoEvolution/actions/workflows/ci.yml)
-
-[![PyPI](https://badge.fury.io/py/OrthoEvol.svg)](https://badge.fury.io/py/OrthoEvol)
-
-[![Documentation](https://readthedocs.org/projects/orthoevolution/badge/?version=latest)](http://orthoevolution.readthedocs.io/en/latest/?badge=latest)
-
-[![Coverage](https://codecov.io/gh/datasnakes/OrthoEvolution/branch/main/graph/badge.svg)](https://codecov.io/gh/datasnakes/OrthoEvolution)
-
-[![Last Commit](https://badgen.net/github/last-commit/datasnakes/OrthoEvolution)](https://github.com/datasnakes/OrthoEvolution/commits/main)
+[![CI](https://github.com/datasnakes/OrthoEvolution/actions/workflows/ci.yml/badge.svg)](https://github.com/datasnakes/OrthoEvolution/actions/workflows/ci.yml) [![PyPI](https://badge.fury.io/py/OrthoEvol.svg)](https://badge.fury.io/py/OrthoEvol) [![Documentation](https://readthedocs.org/projects/orthoevolution/badge/?version=latest)](http://orthoevolution.readthedocs.io/en/latest/?badge=latest) [![Coverage](https://codecov.io/gh/datasnakes/OrthoEvolution/branch/main/graph/badge.svg)](https://codecov.io/gh/datasnakes/OrthoEvolution) [![Last Commit](https://badgen.net/github/last-commit/datasnakes/OrthoEvolution)](https://github.com/datasnakes/OrthoEvolution/commits/main)
 
 # OrthoEvolution
 
 OrthoEvolution is an **easy to use** and comprehensive Python package
-which aids in the **analysis and visualization of comparative
-evolutionary genetics** related projects such as the **inference of
-orthologs**.
+which aids in the **analysis and visualization of comparative evolutionary genetics** related 
+projects such as the **inference of orthologs**.
 
 **Current Version:** 1.0.0b2
 
 ## Overview
 
-This package focuses on **inferring orthologs** using NCBI\'s blast,
+This package focuses on **inferring orthologs** using NCBI's blast,
 various sequence alignment strategies, and phylogenetics analyses
 including PAML, PhyML, ete3, and more tools.
 
-Ultimately, the goal of this project is to create a **reusable
-pipeline** for the inference of orthologs in order to ensure
-reproducibility of data as well as improve the management and analysis
+Ultimately, the goal of this project is to create a **reusable pipeline** for the 
+inference of orthologs in order to ensure reproducibility of data as well as improve the management and analysis
 of (what can be) large datasets. The Cookies, Manager, Pipeline, and
 Tools modules act as a framework for our workflow, while the Orthologs
 module provides access to specific functions for our various ortholog
 inference projects.
 
-View our [read the
-docs](http://orthoevolution.readthedocs.io/en/latest/) and feel free to
-also read [this related
-paper](https://www.frontiersin.org/articles/10.3389/fnhum.2014.00283/full)
+View our [read the docs](http://orthoevolution.readthedocs.io/en/latest/) and feel free to
+also read [this related paper](https://www.frontiersin.org/articles/10.3389/fnhum.2014.00283/full)
 to gain more insight into this project/python package.
 
 ## Installation
@@ -79,9 +67,11 @@ directory](https://github.com/datasnakes/OrthoEvolution/tree/main/examples)
 for working examples and scripts demonstrating how to utilize this
 package.
 
-The examples include: - Standalone scripts for common workflows -
-Example data files - GUI implementations (Tkinter and PyWebView) -
-Pipeline demonstrations
+The examples include:
+- Standalone scripts for common workflows
+- Example data files
+- GUI implementations (Tkinter and PyWebView)
+- Pipeline demonstrations
 
 ### Running a pre-configured local blast
 
@@ -199,11 +189,8 @@ pytest tests
 
 This package was created by the Datasnakes.
 
-- Rob Gilmore \| Github: [\@grabear](https://github.com/grabear) \|
-  [✉](mailto:robgilmore127@gmail.com)
-- Shaurita Hutchins \| Github:
-  [\@sdhutchins](https://github.com/sdhutchins) \|
-  [✉](mailto:sdhutchins@outlook.com)
+- Rob Gilmore | Github: [@grabear](https://github.com/grabear) | [✉](mailto:robgilmore127@gmail.com)
+- Shaurita D. Hutchins | Github: [@sdhutchins](https://github.com/sdhutchins) | [✉](mailto:sdhutchins@outlook.com)
 
 If you would like to contribute to this package, install the package in
 development mode:
@@ -212,20 +199,17 @@ development mode:
 pip install -e .
 ```
 
-Check out our [contributing
-guidelines](https://github.com/datasnakes/OrthoEvolution/blob/main/CONTRIBUTING.rst)
+Check out our [contributing guidelines](https://github.com/datasnakes/OrthoEvolution/blob/main/CONTRIBUTING.rst)
 for more information.
 
 ## License
 
-This project is licensed under the MIT License. See the
-[LICENSE](https://github.com/datasnakes/OrthoEvolution/blob/main/LICENSE)
+This project is licensed under the MIT License. See the [LICENSE](https://github.com/datasnakes/OrthoEvolution/blob/main/LICENSE)
 file for details.
 
 ## Citations
 
-We\'re thankful to have a resource such as
-[Biopython](http://biopython.org/wiki/Biopython), which inspired this
+We're thankful to have a resource such as [Biopython](http://biopython.org/wiki/Biopython), which inspired this
 package.
 
 *Cock, P.J.A. et al. Biopython: freely available Python tools for

docs/docs/source/conf.py

@@ -24,15 +24,36 @@
 # Add project root to path
 sys.path.insert(0, os.path.abspath('../../../'))
 
-# Read version from setup.py automatically
+# Read version from pyproject.toml automatically
 def get_version():
-    """Extract version from setup.py."""
-    setup_path = os.path.join(os.path.dirname(__file__), '../../../setup.py')
-    with open(setup_path, 'r') as f:
-        content = f.read()
-        match = re.search(r"version\s*=\s*['\"]([^'\"]+)['\"]", content)
-        if match:
-            return match.group(1)
+    """Extract version from pyproject.toml."""
+    pyproject_path = os.path.join(os.path.dirname(__file__), '../../../pyproject.toml')
+
+    # Try using tomli (Python 3.11+) or tomllib (Python 3.11+)
+    try:
+        import tomllib
+        with open(pyproject_path, 'rb') as f:
+            data = tomllib.load(f)
+            version = data.get('project', {}).get('version')
+            if version:
+                return version
+    except ImportError:
+        # Fall back to tomli for older Python versions
+        try:
+            import tomli
+            with open(pyproject_path, 'rb') as f:
+                data = tomli.load(f)
+                version = data.get('project', {}).get('version')
+                if version:
+                    return version
+        except ImportError:
+            # Last resort: regex parsing
+            with open(pyproject_path, 'r') as f:
+                content = f.read()
+                match = re.search(r'version\s*=\s*["\']([^"\']+)["\']', content)
+                if match:
+                    return match.group(1)
+
     return '1.0.0b2'  # fallback
 
 # -- General configuration ------------------------------------------------
@@ -70,7 +91,7 @@ def get_version():
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# Automatically read version from setup.py
+# Automatically read version from pyproject.toml
 _version = get_version()
 # The short X.Y version.
 version = _version

docs/requirements-docs.txt

@@ -1,3 +1,4 @@
 # Documentation build dependencies for Read the Docs
 sphinx
 pypandoc
+tomli; python_version < "3.11"

docs/update_docs.py

@@ -24,23 +24,44 @@
 from typing import List, Dict
 
 
-def get_version_from_setup():
-    """Extract version from setup.py.
+def get_version_from_pyproject():
+    """Extract version from pyproject.toml.
 
-    :return: Version string from setup.py
+    :return: Version string from pyproject.toml
     """
-    setup_path = Path(__file__).parent.parent / 'setup.py'
-    with open(setup_path, 'r') as f:
-        content = f.read()
-        match = re.search(r"version\s*=\s*['\"]([^'\"]+)['\"]", content)
-        if match:
-            return match.group(1)
-    raise ValueError("Could not find version in setup.py")
+    pyproject_path = Path(__file__).parent.parent / 'pyproject.toml'
+
+    # Try using tomli (Python 3.11+) or tomllib (Python 3.11+)
+    try:
+        import tomllib
+        with open(pyproject_path, 'rb') as f:
+            data = tomllib.load(f)
+            version = data.get('project', {}).get('version')
+            if version:
+                return version
+    except ImportError:
+        # Fall back to tomli for older Python versions
+        try:
+            import tomli
+            with open(pyproject_path, 'rb') as f:
+                data = tomli.load(f)
+                version = data.get('project', {}).get('version')
+                if version:
+                    return version
+        except ImportError:
+            # Last resort: regex parsing
+            with open(pyproject_path, 'r') as f:
+                content = f.read()
+                match = re.search(r'version\s*=\s*["\']([^"\']+)["\']', content)
+                if match:
+                    return match.group(1)
+
+    raise ValueError("Could not find version in pyproject.toml")
 
 
 def update_conf_py():
     """Update conf.py with current version (already automated in conf.py)."""
-    print("✓ conf.py automatically reads version from setup.py")
+    print("✓ conf.py automatically reads version from pyproject.toml")
 
 
 def convert_readmes():
@@ -251,7 +272,7 @@ def main():
 
     # Get current version
     try:
-        version = get_version_from_setup()
+        version = get_version_from_pyproject()
         print(f"\nCurrent version: {version}")
     except ValueError as e:
         print(f"✗ {e}")

pyproject.toml

@@ -0,0 +1,95 @@
+[build-system]
+requires = ["setuptools >= 77.0.3", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "OrthoEvol"
+version = "1.0.0b2"
+description = "This package aids in the analysis of orthologous genes."
+readme = "README.md"
+requires-python = ">=3.9"
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = [
+    "bioinformatics",
+    "science",
+    "evolution",
+    "orthology",
+    "psychiatry",
+    "genetics"
+]
+authors = [
+    {name = "Rob Gilmore", email = "robgilmore127@gmail.com"},
+    {name = "Shaurita D. Hutchins", email = "sdhutchins@outlook.com"}
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Programming Language :: Python :: 3",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Unix",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Framework :: Flask",
+    "Framework :: Cookiecutter"
+]
+
+dependencies = [
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "tqdm==4.66.3",
+    "ete3==3.0.0b35",
+    "pandas>=0.25.3",
+    "openpyxl>=2.5.0",
+    "pexpect==4.4.0",
+    "slacker==0.9.42",
+    "biopython>=1.79,<1.84",
+    "tablib>=0.11.5",
+    "mygene>=3.0.0",
+    "cookiecutter",
+    "Flask",
+    "Flask-Login",
+    "Flask-Mail",
+    "Flask-SQLAlchemy",
+    "Flask-WTF",
+    "treelib==1.3.5",
+    "psutil>=5.6.7",
+    "luigi",
+    "logzero>=1.5.0",
+    "xmltodict>=0.11.0",
+    "plotly>=3.10.0",
+    "pyyaml>=3.12",
+    "werkzeug>=3.1.4"
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+    "pytest-runner"
+]
+
+[project.scripts]
+orthoevol = "OrthoEvol.Orthologs.command_line:main"
+
+[project.urls]
+Homepage = "https://github.com/datasnakes/OrthoEvolution"
+Documentation = "https://orthoevolution.readthedocs.io/"
+Repository = "https://github.com/datasnakes/OrthoEvolution"
+"Bug Reports" = "https://github.com/datasnakes/OrthoEvolution/issues"
+Releases = "https://github.com/datasnakes/OrthoEvolution/releases"
+
+[tool.setuptools]
+packages = {find = {exclude = ["docs", "examples", "tests"]}}
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.package-data]
+"*" = ["*.md", "*.txt", "*.yml", "*.yaml", "*.json", "*.cfg"]

setup.cfg

@@ -1,6 +1,3 @@
-[metadata]
-description-file = README.rst
-
 [flake8]
 max-line-length = 100