pep8 included for toml file:

pyproject.toml

@@ -12,42 +12,39 @@ authors = [
 maintainers = [
   {name = "maintainers_name", email = "[email protected]" }
 ]
-dependencies = [
-    "Sphinx = \"4.5.0\"",
-    "coverage",
-    "flake8",
-    "isort",
-    "matplotlib = \"3.5.3\"",
-    "nbmake",
-    "numpy <= 1.22.0",
-    "pytest-cov",
-    "pytest-xdist",
-    "pytest = \"7.1.2\"",
-    "scipy",
-    "setuptools = \"65.5.1\"",
-    "sphinx",
-    "taichi = \"1.6.0\"",
-    "toml",
-    "tox",
-    "yapf",
-    "ipywidgets",
-    "pyvista",
-    "trimesh",
-    "PyMCubes",
-    "scikit-image",
-    "path"
-]
-
-[project.urls] 
-"Homepage" = "https://github.com/PolyPhyHub/PolyPhy"
-"Bug Reports" = "https://github.com/PolyPhyHub/PolyPhy/issues"
 
 [build-system]
-# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
 requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-# For smarter version schemes and other configuration options,
-# check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.poetry.dependencies]
+Sphinx = "4.5.0"
+coverage = "*"
+flake8 = "*"
+isort = "*"
+matplotlib = "3.5.3"
+nbmake = "*"
+numpy = "<=1.22.0"
+pytest-cov = "*"
+pytest-xdist = "*"
+pytest = "7.1.2"
+scipy = "*"
+setuptools = "65.5.1"
+sphinx = "*"
+taichi = "1.6.0"
+toml = "*"
+tox = "*"
+yapf = "*"
+ipywidgets = "*"
+pyvista = "*"
+trimesh = "*"
+PyMCubes = "*"
+scikit-image = "*"
+path = "*"
+
+[tool.poetry.dev-dependencies]
+
+[tool.poetry.extras]