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Cutsite pairs rebased #199

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3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -70,3 +70,6 @@ docs/_build/
target/

.eggs

# mac files
.DS_Store
967 changes: 107 additions & 860 deletions poetry.lock

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101 changes: 52 additions & 49 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -1,102 +1,105 @@
[project]
name = "pydna"
dynamic = ["version"]
description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
authors = ["Björn F. Johansson<[email protected]>"]
classifiers = [
"Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Education",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Education",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
dynamic = ["version"]
name = "pydna"
readme = "README.md"
classifiers=["Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Education",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Education",
"Topic :: Scientific/Engineering :: Bio-Informatics", ]
[tool.poetry.urls]
Changelog = "https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog"
[tool.poetry]
name = "pydna"
version = "6.0.0-a.24.post.17+b7b559bd66"
description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
authors = ["BjornFJohansson <[email protected]>"]
description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
documentation = "https://pydna.readthedocs.io/?badge=latest"
homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
license = "BSD"
name = "pydna"
readme = "README.md"
homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
documentation = "https://pydna.readthedocs.io/?badge=latest"
repository = "https://github.com/BjornFJohansson/pydna/tree/dev_bjorn"
version = "6.0.0-a.24.post.17+b7b559bd66"
[tool.poetry.dependencies]
python = ">=3.8, <4.0"
appdirs = ">=1.4.4"
biopython = ">=1.80"
cai2 = {version = ">=1.0.5", optional = true}
matplotlib = {version = ">=3.4.3", optional = true}
networkx = ">=2.8.8"
pydivsufsort = ">=0.0.14"
seguid = ">=0.0.3"
prettytable = ">=3.5.0"
pyfiglet = "0.8.post1"
numpy = [
{version = ">=1.24.4", python = ">=3.8,<3.9"},
{version = ">=1.26.3", python = ">=3.9"}
{version = ">1.26", python = ">=3.9"},
{version = "<1.24", python = "<3.9"},
]
pyperclip = { version = ">=1.8.2", optional = true }
pillow = {version = ">=8.4.0", optional = true}
prettytable = ">=3.5.0"
pydivsufsort = ">=0.0.11"
pyfiglet = "0.8.post1"
pyparsing = {version = ">=2.4.7", optional = true}
pyperclip = {version = ">=1.8.2", optional = true}
python = ">=3.8,<4.0"
requests = {version = ">=2.26.0", optional = true}
scipy = [
{version = ">=1.9.3", python = ">=3.8,<3.9", optional = true },
{version = ">=1.11.4", python = ">=3.9", optional = true }
{version = ">=1.11.3", python = ">=3.12", optional = true},
{version = ">=1.9.3", python = "<3.12", optional = true},
]
matplotlib = { version = ">=3.4.3", optional = true }
pillow = { version = ">=8.4.0", optional = true }
pyparsing = { version = ">=2.4.7", optional = true }
requests = { version = ">=2.26.0", optional = true }
cai2 = { version = ">=1.0.5", optional = true }
poetry = "^1.7.1"
seguid = "^0.0.3"
[tool.poetry.extras]
clipboard = ["pyperclip"]
gel = ["scipy", "matplotlib", "pillow"]
download = ["pyparsing", "requests"]
express = ["cai2"]
gel = ["scipy", "matplotlib", "pillow"]
[build-system]
requires = ["poetry-core",
"poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"
requires = [
"poetry-core",
"poetry-dynamic-versioning",
]
[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "semver"
vcs = "git"
[tool.poetry-dynamic-versioning.substitution]
folders = [
{ path = "src"}
{path = "src"},
]
[tool.poetry.group.test] # This part can be left out
[tool.poetry.group.test.dependencies]
coverage = ">=7.1.0"
nbval = ">=0.9.6"
pytest = ">=7.2.0"
pytest-cov = ">=4.0.0"
pytest-doctestplus = ">=0.12.1"
pytest-profiling = ">=1.7.0"
coverage = ">=7.1.0"
nbval = ">=0.9.6"
requests-mock = ">=1.10.0"

[tool.poetry.group.docs.dependencies]
sphinx-autobuild = "^2021.3.14"
numpydoc = "^1.6.0"
sphinx-autobuild = "^2021.3.14"
sphinx-rtd-theme = ">=1.3,<3.0"

[tool.pytest.ini_options]
minversion = "6.0.2"
python_files = "test_*.py"
testpaths = [
"tests",
"src",
"tests",
"src",
]
[tool.black]
include = '\.pyi?$'
line-length = 119
target-version = ["py38", "py39", "py310", "py311", "py312"]
include = '\.pyi?$'
# 'extend-exclude' excludes files or directories in addition to the defaults
extend-exclude = '''
# A regex preceded with ^/ will apply only to files and directories
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