diff --git a/.flake8 b/.flake8
index 05c5bac4..48d94a5f 100755
--- a/.flake8
+++ b/.flake8
@@ -1,5 +1,5 @@
 [flake8]
-ignore = E203, E266, E501, W503, F403
-max-line-length = 79
+ignore = E203, E266, E501, W503, F403, E741, B905
+max-line-length = 119
 max-complexity = 18
 select = B,C,E,F,W,T4,B9
diff --git a/.github/workflows/pydna_test_and_coverage_workflow.yml b/.github/workflows/pydna_test_and_coverage_workflow.yml
index 3306b839..2e2e4554 100644
--- a/.github/workflows/pydna_test_and_coverage_workflow.yml
+++ b/.github/workflows/pydna_test_and_coverage_workflow.yml
@@ -15,13 +15,11 @@ jobs:
       fail-fast: false
       matrix:
         os: ["macos-latest", "windows-latest"]
-        python-version: ["3.12", "3.11", "3.10", "3.9", "3.8"]
+        python-version: ["3.12", "3.11", "3.10", "3.9"]
         include:
-          - os: ubuntu-latest
-            python-version: "3.8"
-            codecov: true
           - os: ubuntu-latest
             python-version: "3.9"
+            codecov: true
           - os: ubuntu-latest
             python-version: "3.10"
           - os: ubuntu-latest
@@ -51,7 +49,6 @@ jobs:
         uses: snok/install-poetry@v1
         with:
           virtualenvs.prefer-active-python: true
-          version: ${{ matrix.python-version == '3.8' && '1.8.2' || 'latest' }}
       - name: 🔩 list Poetry settings
         run: poetry config --list
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 35444244..a86d6fb4 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,6 +7,8 @@ repos:
     args: [--branch, master]
   # Format yaml files
   - id: check-yaml
+  # Ignore conda build meta.yaml files
+    exclude: ^scripts/conda-build/meta.*\.yaml$
   # Fix end-of-file issues
   - id: end-of-file-fixer
   # Fix trailing whitespace
diff --git a/poetry.lock b/poetry.lock
index 680b24dd..178d32cd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,13 +2,13 @@
 
 [[package]]
 name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
 [[package]]
@@ -35,50 +35,47 @@ files = [
 
 [[package]]
 name = "asttokens"
-version = "2.4.1"
+version = "3.0.0"
 description = "Annotate AST trees with source code positions"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
-    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+    {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
+    {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
 ]
 
-[package.dependencies]
-six = ">=1.12.0"
-
 [package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=2,<4)"]
+test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.3.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.3.0-py3-none-any.whl", hash = "sha256:ac96cd038792094f438ad1f6ff80837353805ac950cd2aa0e0625ef19850c308"},
+    {file = "attrs-24.3.0.tar.gz", hash = "sha256:8f5c07333d543103541ba7be0e2ce16eeee8130cb0b3f9238ab904ce1e85baff"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "autopep8"
-version = "2.3.1"
+version = "2.3.2"
 description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "autopep8-2.3.1-py2.py3-none-any.whl", hash = "sha256:a203fe0fcad7939987422140ab17a930f684763bf7335bdb6709991dd7ef6c2d"},
-    {file = "autopep8-2.3.1.tar.gz", hash = "sha256:8d6c87eba648fdcfc83e29b788910b8643171c395d9c4bcf115ece035b9c9dda"},
+    {file = "autopep8-2.3.2-py2.py3-none-any.whl", hash = "sha256:ce8ad498672c845a0c3de2629c15b635ec2b05ef8177a6e7c91c74f3e9b51128"},
+    {file = "autopep8-2.3.2.tar.gz", hash = "sha256:89440a4f969197b69a995e4ce0661b031f455a9f776d2c5ba3dbd83466931758"},
 ]
 
 [package.dependencies]
@@ -87,32 +84,18 @@ tomli = {version = "*", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.16.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
-
 [package.extras]
 dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
-[[package]]
-name = "backcall"
-version = "0.2.0"
-description = "Specifications for callback functions passed in to an API"
-optional = false
-python-versions = "*"
-files = [
-    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
-    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
-]
-
 [[package]]
 name = "beautifulsoup4"
 version = "4.12.3"
@@ -136,38 +119,43 @@ lxml = ["lxml"]
 
 [[package]]
 name = "biopython"
-version = "1.83"
+version = "1.85"
 description = "Freely available tools for computational molecular biology."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.dependencies]
@@ -175,33 +163,33 @@ numpy = "*"
 
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 [package.dependencies]
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 [package.extras]
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-d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
+d = ["aiohttp (>=3.10)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 [package.dependencies]
-six = ">=1.9.0"
+tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""}
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "cai2"
@@ -255,74 +243,89 @@ scipy = "*"
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.12.14"
 description = "Python package for providing Mozilla's CA Bundle."
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 python-versions = ">=3.6"
 files = [
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 [[package]]
 name = "cffi"
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -341,112 +344,114 @@ files = [
 
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 [package.dependencies]
@@ -482,137 +487,157 @@ test = ["pytest"]
 
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@@ -638,33 +663,37 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
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@@ -691,35 +720,35 @@ files = [
 
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+version = "0.3.9"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 files = [
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 [[package]]
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 optional = false
 python-versions = ">=3.7"
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 [package.extras]
@@ -727,13 +756,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
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+version = "2.2.0"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = ">=3.5"
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 [package.extras]
@@ -741,13 +770,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
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-version = "2.19.1"
+version = "2.21.1"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
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 [package.extras]
@@ -755,19 +784,19 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
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 description = "A platform independent file lock."
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+typing = ["typing-extensions (>=4.12.2)"]
 
 [[package]]
 name = "flake8"
@@ -787,17 +816,17 @@ pyflakes = ">=3.2.0,<3.3.0"
 
 [[package]]
 name = "flake8-bugbear"
-version = "24.4.26"
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 description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle."
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 python-versions = ">=3.8.1"
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 [package.dependencies]
-attrs = ">=19.2.0"
+attrs = ">=22.2.0"
 flake8 = ">=6.0.0"
 
 [package.extras]
@@ -805,53 +834,61 @@ dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "pytest",
 
 [[package]]
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 [[package]]
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 [package.extras]
@@ -895,15 +932,18 @@ license = ["ukkonen"]
 
 [[package]]
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 description = "Internationalized Domain Names in Applications (IDNA)"
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+
 [[package]]
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 version = "1.4.1"
@@ -917,40 +957,48 @@ files = [
 
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 [package.dependencies]
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+type = ["pytest-mypy"]
 
 [[package]]
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-python-versions = ">=3.8"
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+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -965,13 +1013,13 @@ files = [
 
 [[package]]
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -998,71 +1046,69 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 
 [[package]]
 name = "ipython"
-version = "8.12.3"
+version = "8.18.1"
 description = "IPython: Productive Interactive Computing"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "ipython-8.12.3-py3-none-any.whl", hash = "sha256:b0340d46a933d27c657b211a329d0be23793c36595acf9e6ef4164bc01a1804c"},
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 ]
 
 [package.dependencies]
-appnope = {version = "*", markers = "sys_platform == \"darwin\""}
-backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
-pickleshare = "*"
-prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
+prompt-toolkit = ">=3.0.41,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
 typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
+all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
 notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
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-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath", "trio"]
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.5"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1073,51 +1119,48 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.21.1"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
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-importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
 jsonschema-specifications = ">=2023.03.6"
-pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
 referencing = ">=0.28.4"
 rpds-py = ">=0.7.1"
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
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+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.12.1"
+version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
-importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
 referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter-client"
-version = "8.6.1"
+version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1130,7 +1173,7 @@ traitlets = ">=5.3"
 
 [package.extras]
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+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
@@ -1165,131 +1208,140 @@ files = [
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.5"
+version = "1.4.7"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = true
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [[package]]
 name = "livereload"
-version = "2.6.3"
+version = "2.7.1"
 description = "Python LiveReload is an awesome tool for web developers"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
-six = "*"
-tornado = {version = "*", markers = "python_version > \"2.7\""}
+tornado = "*"
 
 [[package]]
 name = "markdown-it-py"
@@ -1317,127 +1369,122 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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 [package.dependencies]
@@ -1445,13 +1492,16 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
-numpy = ">=1.20,<2"
+kiwisolver = ">=1.3.1"
+numpy = ">=1.23"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
+[package.extras]
+dev = ["meson-python (>=0.13.1,<0.17.0)", "numpy (>=1.25)", "pybind11 (>=2.6,!=2.13.3)", "setuptools (>=64)", "setuptools_scm (>=7)"]
+
 [[package]]
 name = "matplotlib-inline"
 version = "0.1.7"
@@ -1509,15 +1559,18 @@ files = [
 
 [[package]]
 name = "mistune"
-version = "3.0.2"
+version = "3.1.0"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
+[package.dependencies]
+typing-extensions = {version = "*", markers = "python_version < \"3.11\""}
+
 [[package]]
 name = "mypy-extensions"
 version = "1.0.0"
@@ -1583,13 +1636,13 @@ testing-docutils = ["pygments", "pytest (>=8,<9)", "pytest-param-files (>=0.6.0,
 
 [[package]]
 name = "nbclient"
-version = "0.10.0"
+version = "0.10.2"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.9.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1600,23 +1653,23 @@ traitlets = ">=5.4"
 
 [package.extras]
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 [[package]]
 name = "nbconvert"
-version = "7.16.4"
+version = "7.16.5"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
 beautifulsoup4 = "*"
-bleach = "!=5.0.0"
+bleach = {version = "!=5.0.0", extras = ["css"]}
 defusedxml = "*"
 importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 jinja2 = ">=3.0"
@@ -1629,7 +1682,6 @@ nbformat = ">=5.7"
 packaging = "*"
 pandocfilters = ">=1.4.1"
 pygments = ">=2.4.1"
-tinycss2 = "*"
 traitlets = ">=5.1"
 
 [package.extras]
@@ -1707,127 +1759,96 @@ files = [
 
 [[package]]
 name = "networkx"
-version = "3.1"
+version = "3.2.1"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
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 [[package]]
 name = "nodeenv"
-version = "1.8.0"
+version = "1.9.1"
 description = "Node.js virtual environment builder"
 optional = false
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+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "pluggy"
@@ -2053,31 +2044,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
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-pyyaml = ">=5.1"
-virtualenv = ">=20.10.0"
-
-[[package]]
-name = "pre-commit"
-version = "3.7.1"
+version = "4.1.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
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 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -2089,13 +2062,13 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "prettytable"
-version = "3.11.0"
+version = "3.12.0"
 description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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@@ -2120,31 +2093,33 @@ wcwidth = "*"
 
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 [[package]]
 name = "ptyprocess"
@@ -2159,13 +2134,13 @@ files = [
 
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 [package.dependencies]
@@ -2264,28 +2236,27 @@ files = [
 
 [[package]]
 name = "pygments"
-version = "2.17.2"
+version = "2.19.1"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.extras]
-plugins = ["importlib-metadata"]
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.2.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = true
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -2293,23 +2264,23 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyperclip"
-version = "1.8.2"
+version = "1.9.0"
 description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)"
 optional = true
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "pytest"
-version = "8.1.1"
+version = "8.3.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2317,25 +2288,25 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=1.4,<2.0"
+pluggy = ">=1.5,<2"
 tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
-version = "5.0.0"
+version = "6.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
-coverage = {version = ">=5.2.1", extras = ["toml"]}
+coverage = {version = ">=7.5", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
@@ -2343,32 +2314,31 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "pytest-doctestplus"
-version = "1.2.1"
+version = "1.3.0"
 description = "Pytest plugin with advanced doctest features."
 optional = false
 python-versions = ">=3.8"
 files = [
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 packaging = ">=17.0"
 pytest = ">=4.6"
-setuptools = ">=30.3.0"
 
 [package.extras]
-test = ["numpy", "pytest-remotedata (>=0.3.2)", "sphinx"]
+test = ["numpy", "pytest-remotedata (>=0.3.2)", "setuptools (>=30.3.0)", "sphinx"]
 
 [[package]]
 name = "pytest-profiling"
-version = "1.7.0"
+version = "1.8.1"
 description = "Profiling plugin for py.test"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
@@ -2376,9 +2346,6 @@ gprof2dot = "*"
 pytest = "*"
 six = "*"
 
-[package.extras]
-tests = ["pytest-virtualenv"]
-
 [[package]]
 name = "python-dateutil"
 version = "2.9.0.post0"
@@ -2393,195 +2360,211 @@ files = [
 [package.dependencies]
 six = ">=1.5"
 
-[[package]]
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-version = "2024.1"
-description = "World timezone definitions, modern and historical"
-optional = false
-python-versions = "*"
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-
 [[package]]
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+version = "308"
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 python-versions = "*"
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 [[package]]
 name = "pyyaml"
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 description = "YAML parser and emitter for Python"
 optional = false
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 files = [
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+test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "seguid"
-version = "0.0.7"
+version = "0.1.0"
 description = "Sequence Globally Unique Identifier (SEGUID) Checksums for Linear, Circular, Single-Stranded and Double-Stranded Biological Sequences"
 optional = false
 python-versions = "<4.0,>=3.6"
 files = [
-    {file = "seguid-0.0.7-py3-none-any.whl", hash = "sha256:ac309eedcafe89fb89dba3106f1bfd9194f4bfcf1f3fb0af7b1579b86890a9ec"},
-    {file = "seguid-0.0.7.tar.gz", hash = "sha256:dfc9f8cf9768a003b07092fc7dc928c28da0f9019320a9ec0f01c8e67e52191c"},
+    {file = "seguid-0.1.0-py3-none-any.whl", hash = "sha256:cbc41af5a7aafa7e0bd966c99113cb0395848be9f59685c8713efe114c9c77c9"},
+    {file = "seguid-0.1.0.tar.gz", hash = "sha256:9dc6f602ec6d42099f1d26d047caf17da36dc5bff1c885418d1dbde559eca542"},
 ]
 
 [package.extras]
 pydivsufsort = ["pydivsufsort (>=0.0.14,<0.0.15)"]
 
-[[package]]
-name = "setuptools"
-version = "69.5.1"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "setuptools-69.5.1-py3-none-any.whl", hash = "sha256:c636ac361bc47580504644275c9ad802c50415c7522212252c033bd15f301f32"},
-    {file = "setuptools-69.5.1.tar.gz", hash = "sha256:6c1fccdac05a97e598fb0ae3bbed5904ccb317337a51139dcd51453611bbb987"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
-
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
-    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+    {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
 [[package]]
@@ -2893,38 +2884,39 @@ files = [
 
 [[package]]
 name = "sphinx"
-version = "7.1.2"
+version = "7.4.7"
 description = "Python documentation generator"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinx-7.1.2-py3-none-any.whl", hash = "sha256:d170a81825b2fcacb6dfd5a0d7f578a053e45d3f2b153fecc948c37344eb4cbe"},
-    {file = "sphinx-7.1.2.tar.gz", hash = "sha256:780f4d32f1d7d1126576e0e5ecc19dc32ab76cd24e950228dcf7b1f6d3d9e22f"},
+    {file = "sphinx-7.4.7-py3-none-any.whl", hash = "sha256:c2419e2135d11f1951cd994d6eb18a1835bd8fdd8429f9ca375dc1f3281bd239"},
+    {file = "sphinx-7.4.7.tar.gz", hash = "sha256:242f92a7ea7e6c5b406fdc2615413890ba9f699114a9c09192d7dfead2ee9cfe"},
 ]
 
 [package.dependencies]
-alabaster = ">=0.7,<0.8"
-babel = ">=2.9"
-colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.18.1,<0.21"
+alabaster = ">=0.7.14,<0.8.0"
+babel = ">=2.13"
+colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
+docutils = ">=0.20,<0.22"
 imagesize = ">=1.3"
-importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
-Jinja2 = ">=3.0"
-packaging = ">=21.0"
-Pygments = ">=2.13"
-requests = ">=2.25.0"
-snowballstemmer = ">=2.0"
+importlib-metadata = {version = ">=6.0", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.1"
+packaging = ">=23.0"
+Pygments = ">=2.17"
+requests = ">=2.30.0"
+snowballstemmer = ">=2.2"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = ">=2.0.0"
 sphinxcontrib-jsmath = "*"
 sphinxcontrib-qthelp = "*"
-sphinxcontrib-serializinghtml = ">=1.1.5"
+sphinxcontrib-serializinghtml = ">=1.1.9"
+tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
-test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"]
+lint = ["flake8 (>=6.0)", "importlib-metadata (>=6.0)", "mypy (==1.10.1)", "pytest (>=6.0)", "ruff (==0.5.2)", "sphinx-lint (>=0.9)", "tomli (>=2)", "types-docutils (==0.21.0.20240711)", "types-requests (>=2.30.0)"]
+test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
 
 [[package]]
 name = "sphinx-autobuild"
@@ -2947,13 +2939,13 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "3.0.0"
+version = "3.0.2"
 description = "Read the Docs theme for Sphinx"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "sphinx_rtd_theme-3.0.0-py2.py3-none-any.whl", hash = "sha256:1ffe1539957775bfa0a7331370de7dc145b6eac705de23365dc55c5d94bb08e7"},
-    {file = "sphinx_rtd_theme-3.0.0.tar.gz", hash = "sha256:905d67de03217fd3d76fbbdd992034ac8e77044ef8063a544dda1af74d409e08"},
+    {file = "sphinx_rtd_theme-3.0.2-py2.py3-none-any.whl", hash = "sha256:422ccc750c3a3a311de4ae327e82affdaf59eb695ba4936538552f3b00f4ee13"},
+    {file = "sphinx_rtd_theme-3.0.2.tar.gz", hash = "sha256:b7457bc25dda723b20b086a670b9953c859eab60a2a03ee8eb2bb23e176e5f85"},
 ]
 
 [package.dependencies]
@@ -2966,47 +2958,50 @@ dev = ["bump2version", "transifex-client", "twine", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.4"
+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
-    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
+    {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
+    {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+version = "2.0.0"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
-    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+    {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
+    {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.1"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -3039,32 +3034,34 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+version = "2.0.0"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
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-    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+    {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
+    {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+version = "2.0.0"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
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+    {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
+    {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
@@ -3102,13 +3099,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "tinycss2"
-version = "1.3.0"
+version = "1.4.0"
 description = "A tiny CSS parser"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "tinycss2-1.4.0-py3-none-any.whl", hash = "sha256:3a49cf47b7675da0b15d0c6e1df8df4ebd96e9394bb905a5775adb0d884c5289"},
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 ]
 
 [package.dependencies]
@@ -3120,33 +3117,63 @@ test = ["pytest", "ruff"]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:b82ebccc8c8a36f2094e969560a1b836758481f3dc360ce9a3277c65f374285e"},
+    {file = "tomli-2.2.1-cp312-cp312-win32.whl", hash = "sha256:889f80ef92701b9dbb224e49ec87c645ce5df3fa2cc548664eb8a25e03127a98"},
+    {file = "tomli-2.2.1-cp312-cp312-win_amd64.whl", hash = "sha256:7fc04e92e1d624a4a63c76474610238576942d6b8950a2d7f908a340494e67e4"},
+    {file = "tomli-2.2.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:f4039b9cbc3048b2416cc57ab3bda989a6fcf9b36cf8937f01a6e731b64f80d7"},
+    {file = "tomli-2.2.1-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:286f0ca2ffeeb5b9bd4fcc8d6c330534323ec51b2f52da063b11c502da16f30c"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a92ef1a44547e894e2a17d24e7557a5e85a9e1d0048b0b5e7541f76c5032cb13"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9316dc65bed1684c9a98ee68759ceaed29d229e985297003e494aa825ebb0281"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e85e99945e688e32d5a35c1ff38ed0b3f41f43fad8df0bdf79f72b2ba7bc5272"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:ac065718db92ca818f8d6141b5f66369833d4a80a9d74435a268c52bdfa73140"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
+    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
+    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
 name = "tornado"
-version = "6.4"
+version = "6.4.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
-python-versions = ">= 3.8"
+python-versions = ">=3.8"
 files = [
-    {file = "tornado-6.4-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:02ccefc7d8211e5a7f9e8bc3f9e5b0ad6262ba2fbb683a6443ecc804e5224ce0"},
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-    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e43bc2e5370a6a8e413e1e1cd0c91bedc5bd62a74a532371042a18ef19e10579"},
-    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f0251554cdd50b4b44362f73ad5ba7126fc5b2c2895cc62b14a1c2d7ea32f212"},
-    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:fd03192e287fbd0899dd8f81c6fb9cbbc69194d2074b38f384cb6fa72b80e9c2"},
-    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_i686.whl", hash = "sha256:88b84956273fbd73420e6d4b8d5ccbe913c65d31351b4c004ae362eba06e1f78"},
-    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:71ddfc23a0e03ef2df1c1397d859868d158c8276a0603b96cf86892bff58149f"},
-    {file = "tornado-6.4-cp38-abi3-win32.whl", hash = "sha256:6f8a6c77900f5ae93d8b4ae1196472d0ccc2775cc1dfdc9e7727889145c45052"},
-    {file = "tornado-6.4-cp38-abi3-win_amd64.whl", hash = "sha256:10aeaa8006333433da48dec9fe417877f8bcc21f48dda8d661ae79da357b2a63"},
-    {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"},
+    {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:e828cce1123e9e44ae2a50a9de3055497ab1d0aeb440c5ac23064d9e44880da1"},
+    {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:072ce12ada169c5b00b7d92a99ba089447ccc993ea2143c9ede887e0937aa803"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1a017d239bd1bb0919f72af256a970624241f070496635784d9bf0db640d3fec"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c36e62ce8f63409301537222faffcef7dfc5284f27eec227389f2ad11b09d946"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bca9eb02196e789c9cb5c3c7c0f04fb447dc2adffd95265b2c7223a8a615ccbf"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:304463bd0772442ff4d0f5149c6f1c2135a1fae045adf070821c6cdc76980634"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_i686.whl", hash = "sha256:c82c46813ba483a385ab2a99caeaedf92585a1f90defb5693351fa7e4ea0bf73"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:932d195ca9015956fa502c6b56af9eb06106140d844a335590c1ec7f5277d10c"},
+    {file = "tornado-6.4.2-cp38-abi3-win32.whl", hash = "sha256:2876cef82e6c5978fde1e0d5b1f919d756968d5b4282418f3146b79b58556482"},
+    {file = "tornado-6.4.2-cp38-abi3-win_amd64.whl", hash = "sha256:908b71bf3ff37d81073356a5fadcc660eb10c1476ee6e2725588626ce7e5ca38"},
+    {file = "tornado-6.4.2.tar.gz", hash = "sha256:92bad5b4746e9879fd7bf1eb21dce4e3fc5128d71601f80005afa39237ad620b"},
 ]
 
 [[package]]
@@ -3166,24 +3193,24 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "typing-extensions"
-version = "4.11.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
-    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.3.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"},
+    {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"},
 ]
 
 [package.extras]
@@ -3194,13 +3221,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.26.1"
+version = "20.29.1"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"},
-    {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"},
+    {file = "virtualenv-20.29.1-py3-none-any.whl", hash = "sha256:4e4cb403c0b0da39e13b46b1b2476e505cb0046b25f242bee80f62bf990b2779"},
+    {file = "virtualenv-20.29.1.tar.gz", hash = "sha256:b8b8970138d32fb606192cb97f6cd4bb644fa486be9308fb9b63f81091b5dc35"},
 ]
 
 [package.dependencies]
@@ -3236,13 +3263,13 @@ files = [
 
 [[package]]
 name = "wheel"
-version = "0.43.0"
+version = "0.45.1"
 description = "A built-package format for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "wheel-0.43.0-py3-none-any.whl", hash = "sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81"},
-    {file = "wheel-0.43.0.tar.gz", hash = "sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85"},
+    {file = "wheel-0.45.1-py3-none-any.whl", hash = "sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248"},
+    {file = "wheel-0.45.1.tar.gz", hash = "sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729"},
 ]
 
 [package.extras]
@@ -3250,18 +3277,22 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"},
+    {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [extras]
 clipboard = ["pyperclip"]
@@ -3271,5 +3302,5 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.8,<4.0"
-content-hash = "b65e47c09e07dea39463c0157452363e4c1c991150e4aa5db49a48ccbdfa4c27"
+python-versions = ">=3.9,<4.0"
+content-hash = "bab2cffcefa5498abd55f29a4572b09bcdca1beb336728a0af538bd6e0ccb7ef"
diff --git a/pyproject.toml b/pyproject.toml
index d92fb8f1..f39490bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [project]
 authors = [
-    {name = "Björn F. Johansson", email = "bjornjobb@gmail.com"},
-    {name = "Manuel Lera-Ramirez", email = "manulera14@gmail.com"}
+  { name = "Björn F. Johansson", email = "bjornjobb@gmail.com" },
+  { name = "Manuel Lera-Ramirez", email = "manulera14@gmail.com" },
 ]
 classifiers = [
   "Development Status :: 4 - Beta",
@@ -11,7 +11,6 @@ classifiers = [
   "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",
@@ -27,7 +26,10 @@ readme = "README.md"
 Changelog = "https://github.com/pydna-group/pydna/blob/master/docs/CHANGELOG.md#changelog"
 [tool.poetry]
 description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
-authors = ["Björn F. Johansson <bjornjobb@gmail.com>", "Manuel Lera-Ramirez <manulera14@gmail.com>"]
+authors = [
+  "Björn F. Johansson <bjornjobb@gmail.com>",
+  "Manuel Lera-Ramirez <manulera14@gmail.com>",
+]
 documentation = "https://pydna-group.github.io/pydna"
 homepage = "https://github.com/pydna-group/pydna#-pydna"
 license = "BSD"
@@ -37,21 +39,18 @@ repository = "https://github.com/pydna-group/pydna/tree/master"
 version = "6.0.0-a.24.post.17+b7b559bd66"
 [tool.poetry.dependencies]
 appdirs = ">=1.4.4"
-biopython = ">=1.80,<1.85"
+biopython = "1.85"
 cai2 = { version = ">=1.0.5", optional = true }
 matplotlib = { version = ">=3.4.3", optional = true }
 networkx = ">=2.8.8"
-numpy = [
-  { version = ">1.26", python = ">=3.9" },
-  { version = "<1.24", python = "<3.9" },
-]
+numpy = ">1.26"
 pillow = { version = ">=8.4.0", optional = true }
 prettytable = ">=3.5.0"
 pydivsufsort = ">=0.0.14"
 pyfiglet = "0.8.post1"
 pyparsing = { version = ">=2.4.7", optional = true }
 pyperclip = { version = ">=1.8.2", optional = true }
-python = ">=3.8,<4.0"
+python = ">=3.9,<4.0"
 requests = { version = ">=2.26.0", optional = true }
 scipy = [
   { version = ">=1.11.3", python = ">=3.12", optional = true },
@@ -88,19 +87,16 @@ sphinx-autobuild = "^2021.3.14"
 sphinx-rtd-theme = ">=1.3,<4.0"
 nbconvert = "^7.16.4"
 myst-parser = [
-  { version = ">3.0.0", python = "<3.10"},
-  { version = ">=4.0.0", python = ">=3.10"},
+  { version = ">3.0.0", python = "<3.10" },
+  { version = ">=4.0.0", python = ">=3.10" },
 ]
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.1.0"
 black = "^24.4.2"
-flake8-bugbear = [{ version = ">=24.4.21", python = ">=3.8.1" }]
-pre-commit = [
-  { version = ">3.6", python = ">=3.9" },
-  { version = "<3.6", python = "<3.9" },
-]
+pre-commit = ">3.6"
 nbstripout = "^0.7.1"
+flake8-bugbear = "^24.12.12"
 
 [tool.pytest.ini_options]
 minversion = "6.0.2"
diff --git a/scripts/conda-build/meta (copy).yaml b/scripts/conda-build/meta (copy).yaml
index 59817340..d669b6b7 100755
--- a/scripts/conda-build/meta (copy).yaml	
+++ b/scripts/conda-build/meta (copy).yaml	
@@ -10,7 +10,7 @@ source:
   path: .
 requirements:
     host:
-    - python>=3.8,<4.0
+    - python>=3.9,<4.0
     - pip
     - poetry-core
     - poetry-dynamic-versioning
diff --git a/scripts/conda-build/meta (copy2).yaml b/scripts/conda-build/meta (copy2).yaml
index be76e2d2..7a9f8cc4 100755
--- a/scripts/conda-build/meta (copy2).yaml	
+++ b/scripts/conda-build/meta (copy2).yaml	
@@ -11,7 +11,7 @@ source:
   path: .
 requirements:
     host:
-    - python >=3.8
+    - python >=3.9
     - pip
     - poetry
     - poetry-dynamic-versioning
diff --git a/scripts/conda-build/meta2.yaml b/scripts/conda-build/meta2.yaml
index 59817340..d669b6b7 100755
--- a/scripts/conda-build/meta2.yaml
+++ b/scripts/conda-build/meta2.yaml
@@ -10,7 +10,7 @@ source:
   path: .
 requirements:
     host:
-    - python>=3.8,<4.0
+    - python>=3.9,<4.0
     - pip
     - poetry-core
     - poetry-dynamic-versioning
diff --git a/scripts/conda-build/myenvironment.yaml b/scripts/conda-build/myenvironment.yaml
index c29cbfb1..86dd1f07 100644
--- a/scripts/conda-build/myenvironment.yaml
+++ b/scripts/conda-build/myenvironment.yaml
@@ -9,7 +9,7 @@
 ###############################################################################
 name: some-name-env
 dependencies:
-  - python>=3.8,<4.0
+  - python>=3.9,<4.0
   - conda-forge::appdirs>=1.4.4,<2.0.0
   - conda-forge::biopython>=1.80,<2.0
   - conda-forge::networkx>=2.8.8,<3.0.0
diff --git a/src/pydna/dseq.py b/src/pydna/dseq.py
index 0052120b..8225b577 100644
--- a/src/pydna/dseq.py
+++ b/src/pydna/dseq.py
@@ -1479,11 +1479,6 @@ def cutsite_is_valid(self, cutsite: CutSiteType) -> bool:
         enz = cutsite[1]
         watson, crick, ovhg = self.get_cut_parameters(cutsite, True)
 
-        # The cut positions fall within the sequence
-        # This could go into Biopython
-        if not self.circular and crick < 0 or crick > len(self):
-            return False
-
         # The overhang is double stranded
         overhang_dseq = self[watson:crick] if ovhg < 0 else self[crick:watson]
         if overhang_dseq.ovhg != 0 or overhang_dseq.watson_ovhg() != 0:
diff --git a/src/pydna/dseqrecord.py b/src/pydna/dseqrecord.py
index 83d848fd..2d35ee9d 100644
--- a/src/pydna/dseqrecord.py
+++ b/src/pydna/dseqrecord.py
@@ -788,9 +788,10 @@ def __mul__(self, number):
         if self.circular:
             raise TypeError("TypeError: can't multiply circular Dseqrecord.")
         if number > 0:
-            new = _copy.copy(self)
+            new = _copy.deepcopy(self)
             for i in range(1, number):
                 new += self
+            new._per_letter_annotations = self._per_letter_annotations
             return new
         else:
             return self.__class__("")
@@ -1061,7 +1062,10 @@ def upper(self):
         pydna.dseqrecord.Dseqrecord.lower"""
 
         upper = _copy.deepcopy(self)
+        # This is because the @seq.setter methods otherwise sets the _per_letter_annotations to an empty dict
+        prev_per_letter_annotation = upper._per_letter_annotations
         upper.seq = upper.seq.upper()
+        upper._per_letter_annotations = prev_per_letter_annotation
         return upper
 
     def lower(self):
@@ -1092,7 +1096,9 @@ def lower(self):
 
         """
         lower = _copy.deepcopy(self)
+        prev_per_letter_annotation = lower._per_letter_annotations
         lower.seq = lower.seq.lower()
+        lower._per_letter_annotations = prev_per_letter_annotation
         return lower
 
     def orfs(self, minsize=300):
diff --git a/src/pydna/seqrecord.py b/src/pydna/seqrecord.py
index 26251e94..88a970a7 100755
--- a/src/pydna/seqrecord.py
+++ b/src/pydna/seqrecord.py
@@ -50,10 +50,29 @@ class SeqRecord(_SeqRecord):
     nicer output in the IPython shell.
     """
 
-    def __init__(self, seq, *args, id="id", name="name", description="description", **kwargs):
+    def __init__(
+        self,
+        seq,
+        id="id",
+        name="name",
+        description="description",
+        dbxrefs=None,
+        features=None,
+        annotations=None,
+        letter_annotations=None,
+    ):
         if isinstance(seq, str):
             seq = _Seq(seq)
-        super().__init__(seq, *args, id=id, name=name, description=description, **kwargs)
+        super().__init__(
+            seq,
+            id=id,
+            name=name,
+            description=description,
+            dbxrefs=dbxrefs,
+            features=features,
+            annotations=annotations,
+            letter_annotations=letter_annotations,
+        )
         self._fix_attributes()
 
     def _fix_attributes(self):
@@ -612,7 +631,7 @@ def removeprefix(text, prefix):
 
         if format == "pydnafasta":
             return _pretty_str(
-                f">{self.id} {len(self)} bp {dict(((True,'circular'),(False,'linear')))[self.seq.circular]}\n{str(self.seq)}\n"
+                f">{self.id} {len(self)} bp {dict(((True, 'circular'), (False, 'linear')))[self.seq.circular]}\n{str(self.seq)}\n"
             )
         if format == "primer":
             return _pretty_str(
diff --git a/tests/test_module_dseq.py b/tests/test_module_dseq.py
index 504ac13d..770fe9bf 100644
--- a/tests/test_module_dseq.py
+++ b/tests/test_module_dseq.py
@@ -116,16 +116,16 @@ def test_initialization():
 
     obj2 = Dseq("gata")
 
-    assert obj2.circular == False
+    assert not obj2.circular
 
-    l = Dseq("gt")
-    c = l.looped()
+    lin_seq = Dseq("gt")
+    cir_seq = lin_seq.looped()
 
-    assert not l.circular
-    assert c.circular
+    assert not lin_seq.circular
+    assert cir_seq.circular
 
-    assert Dseq("gt", circular=False) == l
-    assert Dseq("gt", circular=True) == c
+    assert Dseq("gt", circular=False) == lin_seq
+    assert Dseq("gt", circular=True) == cir_seq
 
     assert Dseq.from_string("A") == Dseq("A")
     assert Dseq.from_string("A", circular=True) == Dseq("A", circular=True)
@@ -218,7 +218,7 @@ def test_Dseq_cutting_adding():
         ovhg=0,
     )
 
-    f, d, l = c.cut((EcoRI, PstI))
+    f, d, _ = c.cut((EcoRI, PstI))
 
     assert d.watson == "GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG"
     assert d.crick == "AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA"
@@ -554,11 +554,6 @@ def test_dseq():
 
 def test_Dseq_slicing():
     from pydna.dseq import Dseq
-    from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
     from Bio.Restriction import BamHI
 
     a = Dseq("ggatcc", "ggatcc", 0)
@@ -947,7 +942,7 @@ def test_apply_cut():
 def test_cutsite_is_valid():
 
     from pydna.dseq import Dseq
-    from Bio.Restriction import EcoRI, BsaI, PacI, NmeDI, Acc65I, NotI, BamHI, EcoRV
+    from Bio.Restriction import EcoRI, PacI, NmeDI, EcoRV
 
     # Works for circular case
     seqs = ["GAATTC", "TTAATTAAC", "GATATC"]
@@ -977,7 +972,7 @@ def test_cutsite_is_valid():
                 assert len(dseq.get_cutsites([enz])) == 1
 
     # Special cases:
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 0, 0)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, 0)
     assert len(dseq.get_cutsites([NmeDI])) == 2
     # Remove left cutting place
     assert len(dseq[2:].get_cutsites([NmeDI])) == 1
@@ -987,27 +982,27 @@ def test_cutsite_is_valid():
     assert len(dseq[2:-2].get_cutsites([NmeDI])) == 0
 
     # overhang left side
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", -2, 0)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", -2, 0)
     assert len(dseq.get_cutsites([NmeDI])) == 1
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 2, 0)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 2, 0)
     assert len(dseq.get_cutsites([NmeDI])) == 1
 
     # overhang right side
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 0, 2)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, 2)
     assert len(dseq.get_cutsites([NmeDI])) == 1
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 0, -2)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, -2)
     assert len(dseq.get_cutsites([NmeDI])) == 1
 
     # overhang both sides
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 2, 2)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 2, 2)
     assert len(dseq.get_cutsites([NmeDI])) == 0
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", -2, -2)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", -2, -2)
     assert len(dseq.get_cutsites([NmeDI])) == 0
 
     # overhang on recognition site removes both cutting places
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 16, 0)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 16, 0)
     assert len(dseq.get_cutsites([NmeDI])) == 0
-    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA", 0, 16)
+    dseq = Dseq.from_full_sequence_and_overhangs("AAAAAATTTTTTTGCCGGCAAAAAAAATTTTT", 0, 16)
     assert len(dseq.get_cutsites([NmeDI])) == 0
 
 
diff --git a/tests/test_module_dseqrecord.py b/tests/test_module_dseqrecord.py
index 07d44e2a..a169162a 100644
--- a/tests/test_module_dseqrecord.py
+++ b/tests/test_module_dseqrecord.py
@@ -2,7 +2,6 @@
 # -*- coding: utf-8 -*-
 
 import pytest
-from pydna import _PydnaWarning
 
 
 def test_orfs():
@@ -73,7 +72,6 @@ def test_initialization():
     from pydna.dseq import Dseq
     from pydna.dseqrecord import Dseqrecord
     from pydna.readers import read
-    from pydna.utils import eq
 
     from Bio.Seq import Seq
     from Bio.SeqRecord import SeqRecord as Srec
@@ -93,8 +91,8 @@ def test_initialization():
         assert str(b.seq.crick) == "aaat"
         assert str(b.seq) == "attt"
         assert str(b.seq) == "attt"
-        assert b.seq.circular == False
-        assert b.circular == False
+        assert b.seq.circular is False
+        assert b.circular is False
 
     a = []
     a.append(Dseqrecord("attt", circular=True))
@@ -109,8 +107,8 @@ def test_initialization():
         assert str(b.seq.crick) == "aaat"
         assert str(b.seq) == "attt"
         assert str(b.seq) == "attt"
-        assert b.circular == True
-        assert b.seq.circular == True
+        assert b.circular is True
+        assert b.seq.circular is True
 
     a = []
     a.append(Dseqrecord(Dseq("attt", circular=True), circular=True))
@@ -143,8 +141,8 @@ def test_initialization():
     assert isinstance(dsr.seq, Dseq)
     assert dsr.seq.watson == "attt"
     assert dsr.seq.crick == "taaa"
-    assert dsr.circular == False
-    assert dsr.seq.circular == False
+    assert dsr.circular is False
+    assert dsr.seq.circular is False
     assert str(dsr.seq) == "attta"
 
     dsr = Dseqrecord(ds, circular=True)
@@ -152,13 +150,13 @@ def test_initialization():
     assert isinstance(dsr.seq, Dseq)
     assert dsr.seq.watson == "attt"
     assert dsr.seq.crick == "aaat"
-    assert dsr.circular == True
-    assert dsr.seq.circular == True
+    assert dsr.circular is True
+    assert dsr.seq.circular is True
     assert str(dsr.seq) == "attt"
 
     a = []
     ds = Dseq("attt", "caaa")
-    assert ds.circular == False
+    assert ds.circular is False
     assert ds.ovhg == -1
 
     a.append(Dseqrecord(ds, circular=False))
@@ -204,8 +202,7 @@ def test_initialization():
 
     b = a + a
 
-    for f in b.features:
-        assert b.features[0].extract(a).seq.watson == "CG"
+    assert b.features[0].extract(a).seq.watson == "CG"
     feature = a.features[0]
 
     s = Dseq("agctt", "agcta")
@@ -241,39 +238,33 @@ def test_initialization():
 
 
 def test_linear_circular():
-    from pydna.dseq import Dseq
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
 
     """ test Dseqrecord linear & circular property"""
     a = Dseqrecord("attt")
     a.stamp()
     assert a.stamp()
     a = Dseqrecord("attt", circular=False)
-    assert a.circular == False
-    assert a.rc().circular == False
+    assert a.circular is False
+    assert a.rc().circular is False
 
     a = Dseqrecord("attt", circular=True)
 
-    assert a.circular == True
-    assert a.rc().circular == True
-    assert a.seq.circular == True
+    assert a.circular is True
+    assert a.rc().circular is True
+    assert a.seq.circular is True
 
     a = Dseqrecord("attt", circular=True)
 
-    assert a.circular == True
-    assert a.rc().circular == True
-    assert a.seq.circular == True
+    assert a.circular is True
+    assert a.rc().circular is True
+    assert a.seq.circular is True
 
     a = Dseqrecord("attt", circular=False)
 
-    assert a.circular == False
-    assert a.rc().circular == False
-    assert a.seq.circular == False
+    assert a.circular is False
+    assert a.rc().circular is False
+    assert a.seq.circular is False
 
 
 def test_stamp():
@@ -311,13 +302,7 @@ def test_stamp():
 
 
 def test_revcomp():
-    from pydna.dseq import Dseq
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
 
     #      ----
     #     attcccgggg
@@ -367,7 +352,7 @@ def test_extract_feature():
 
     s = Dseqrecord("tttGGATCCaaa")
     s.add_feature(3, 9)
-    s.extract_feature(0).seq == Dseqrecord("GGATCC").seq
+    assert s.extract_feature(0).seq == Dseqrecord("GGATCC").seq
 
 
 def test_find():
@@ -395,12 +380,12 @@ def test_str():
     s.annotations = {"date": "03-JAN-2018"}
     assert (
         str(s)
-        == "Dseqrecord\ncircular: False\nsize: 12\nID: id\nName: name\nDescription: description\nNumber of features: 0\n/date=03-JAN-2018\nDseq(-12)\ntttGGATCCaaa\naaaCCTAGGttt"
+        == "Dseqrecord\ncircular: False\nsize: 12\nID: id\nName: name\nDescription: description\nNumber of features: 0\n/date=03-JAN-2018\nDseq(-12)\ntttGGATCCaaa\naaaCCTAGGttt"  # noqa: B950
     )
     s = s.looped()
     assert (
         str(s)
-        == "Dseqrecord\ncircular: True\nsize: 12\nID: id\nName: name\nDescription: description\nNumber of features: 0\n/date=03-JAN-2018\nDseq(o12)\ntttGGATCCaaa\naaaCCTAGGttt"
+        == "Dseqrecord\ncircular: True\nsize: 12\nID: id\nName: name\nDescription: description\nNumber of features: 0\n/date=03-JAN-2018\nDseq(o12)\ntttGGATCCaaa\naaaCCTAGGttt"  # noqa: B950
     )
 
 
@@ -472,27 +457,23 @@ def test_write():
 
 
 def test_write_same_seq_to_existing_file(monkeypatch):
-    import builtins
     from unittest.mock import patch
     from unittest.mock import mock_open
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
 
     s = Dseqrecord("Ggatcc", circular=True)
 
     monkeypatch.setattr("pydna.dseqrecord._os.path.isfile", lambda x: True)
     m = mock_open(read_data=s.format())
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         s.write(filename="Ggatcc.gb")
 
 
 def test_write_different_file_to_existing_file(monkeypatch):
-    import builtins
     from unittest.mock import patch
     from unittest.mock import mock_open
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
 
     s = Dseqrecord("Ggatcc", circular=True)
     d = Dseqrecord("GgatcA", circular=True)
@@ -506,11 +487,9 @@ def test_write_different_file_to_existing_file(monkeypatch):
 
 
 def test_write_different_file_to_stamped_existing_file(monkeypatch):
-    import builtins
     from unittest.mock import patch
     from unittest.mock import mock_open
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
 
     new = Dseqrecord("Ggatcc", circular=True)
     new.stamp()
@@ -523,38 +502,36 @@ def test_write_different_file_to_stamped_existing_file(monkeypatch):
     monkeypatch.setattr("pydna.dseqrecord._os.rename", lambda x, y: True)
     m = mock_open(read_data=old.format())
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     new = Dseqrecord("Ggatcc", circular=True)
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     new.description = "cSEGUID_NNNNNNNNNNNNNNNNNNNNNNNNNNN_2018-06-01T05:05:51.778066"
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     new.description = "cSEGUID_N"
 
     m = mock_open(read_data=old.format())
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     assert m.called
     # m.write().assert_called_once_with(new.format())
-    assert m.call_count == 4  #  6
+    assert m.call_count == 4  # 6
     assert m.mock_calls[0]
     assert m.mock_calls[4]
 
 
 def test_write_different_file_to_stamped_existing_file2(monkeypatch):
-    import builtins
     from unittest.mock import patch
     from unittest.mock import mock_open
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
 
     new = Dseqrecord("Ggatcc", circular=True)
     new.stamp()
@@ -567,23 +544,23 @@ def test_write_different_file_to_stamped_existing_file2(monkeypatch):
     monkeypatch.setattr("pydna.dseqrecord._os.rename", lambda x, y: True)
     m = mock_open(read_data=old.format())
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     new = Dseqrecord("Ggatcc", circular=True)
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     new.description = "cSEGUID_NNNNNNNNNNNNNNNNNNNNNNNNNNN_2018-06-01T05:05:51.778066"
 
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     new.description = "cSEGUID_N"
 
     m = mock_open(read_data=old.format())
-    with patch("builtins.open", m) as d:
+    with patch("builtins.open", m):
         new.write(filename="Ggatcc.gb")
 
     assert m.called
@@ -599,7 +576,7 @@ def test_write_different_file_to_stamped_existing_file2(monkeypatch):
 # call().__exit__(None, None, None),
 # call('Ggatcc.gb', 'w'),
 # call().__enter__(),
-# call().write('LOCUS       name                       6 bp    DNA     circular UNK 01-JUN-2018\nDEFINITION  cSEGUID_N\n            cSEGUID_6WVYnCK97MOPMOlbLHvMnd4XIEY_2018-06-01T06:05:08.951398.\nACCESSION   id\nVERSION     id\nKEYWORDS    .\nSOURCE      .\n  ORGANISM  .\n            .\nFEATURES             Location/Qualifiers\nORIGIN\n        1 ggatcc\n//'),
+# call().write('LOCUS       name                       6 bp    DNA     circular UNK 01-JUN-2018\nDEFINITION  cSEGUID_N\n            cSEGUID_6WVYnCK97MOPMOlbLHvMnd4XIEY_2018-06-01T06:05:08.951398.\nACCESSION   id\nVERSION     id\nKEYWORDS    .\nSOURCE      .\n  ORGANISM  .\n            .\nFEATURES             Location/Qualifiers\nORIGIN\n        1 ggatcc\n//'),  # noqa: B950
 # call().__exit__(None, None, None)]
 
 
@@ -672,14 +649,7 @@ def test_cut_add():
     from pydna.dseqrecord import Dseqrecord
     from pydna.readers import read
     from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
-
-    from Bio.Seq import Seq
-    from Bio.Restriction import BamHI, EcoRI, PstI, EcoRV, SmaI
-
-    from Bio.SeqUtils.CheckSum import seguid
+    from Bio.Restriction import BamHI, EcoRI, PstI, SmaI
 
     a = Dseqrecord("GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC").seq
     b = a.cut(BamHI)[1]
@@ -690,13 +660,13 @@ def test_cut_add():
 
     pUC19 = read("pUC19.gb")
 
-    assert pUC19.circular == True
+    assert pUC19.circular is True
 
     assert len(pUC19) == 2686
     assert len(pUC19.seq.watson) == 2686
     assert len(pUC19.seq.crick) == 2686
 
-    assert pUC19.seq.circular == True
+    assert pUC19.seq.circular is True
 
     pUC19_SmaI = pUC19.cut(SmaI)
     assert len(pUC19_SmaI) == 1
@@ -708,7 +678,7 @@ def test_cut_add():
     pUC19_SmaI_a = pUC19_SmaI.seq + a
 
     assert not pUC19_SmaI_a.circular
-    assert pUC19_SmaI_a.circular == False
+    assert pUC19_SmaI_a.circular is False
 
     pUC19_SmaI_a = pUC19_SmaI_a.looped()
     assert len(pUC19_SmaI_a) == 2778
@@ -730,11 +700,11 @@ def test_cut_add():
 
     assert len(pUC19_BamHI_a.watson) == len(pUC19_BamHI_a.crick) == 2772
 
-    assert pUC19_BamHI_a.circular == False
+    assert pUC19_BamHI_a.circular is False
 
     pUC19_BamHI_a = pUC19_BamHI_a.looped()
 
-    assert pUC19_BamHI_a.circular == True
+    assert pUC19_BamHI_a.circular is True
 
     assert eq(pUC19_BamHI_a, read("pUC19-BamHI-a.gb"))
 
@@ -742,7 +712,7 @@ def test_cut_add():
 
     pUC19_BamHI_a_rc = pUC19_BamHI_a_rc.looped()
 
-    assert pUC19_BamHI_a.circular == True
+    assert pUC19_BamHI_a.circular is True
 
     assert eq(pUC19_BamHI_a_rc, read("pUC19-BamHI-a-rc.gb"))
 
@@ -789,11 +759,6 @@ def test_cut_add():
 def test_Dseqrecord_cutting_adding_2():
     from pydna.dseq import Dseq
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
 
     a = (
         Dseqrecord(
@@ -828,14 +793,8 @@ def test_Dseqrecord_cutting_adding_2():
 
 
 def test_Dseqrecord_cutting_adding_3():
-    from pydna.dseq import Dseq
-    from pydna.dseqrecord import Dseqrecord
     from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
-    from Bio.Restriction import KpnI, BamHI, Acc65I, NlaIV, EcoRI, EcoRV
+    from Bio.Restriction import Acc65I
 
     a = read(
         """
@@ -938,13 +897,7 @@ def test_Dseqrecord_cutting_adding_3():
 
 
 def test_Dseqrecord_cutting_adding_4():
-    from pydna.dseq import Dseq
-    from pydna.dseqrecord import Dseqrecord
     from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
     from Bio.Restriction import KpnI, Acc65I, NlaIV, EcoRI, EcoRV
 
     a = read(
@@ -1337,7 +1290,7 @@ def test_figure():
 
     linearDseqrecord.features.append(SeqFeature(SimpleLocation(14, 17, 1) + SimpleLocation(20, 23, 1), type="test"))
 
-    expect = "Dseqrecord(-37)\ngatcggtaccgatc\x1b[48;5;11mATG\x1b[0mAAA\x1b[48;5;11mTAA\x1b[0mgatcGGGCCCgatc\nctagccatggctagTACTTTATTctagCCCGGGctag"
+    expect = "Dseqrecord(-37)\ngatcggtaccgatc\x1b[48;5;11mATG\x1b[0mAAA\x1b[48;5;11mTAA\x1b[0mgatcGGGCCCgatc\nctagccatggctagTACTTTATTctagCCCGGGctag"  # noqa: B950
     assert linearDseqrecord.figure() == expect
 
     # short feature linear
@@ -1578,7 +1531,7 @@ def test_figure():
     circularDseqrecord.add_feature(32, 5)
     assert (
         circularDseqrecord.figure()
-        == "Dseqrecord(o37)\n\x1b[48;5;11mgatcg\x1b[0mgtaccgatcATGAAATAAgatcGGGCC\x1b[48;5;11mCgatc\x1b[0m\nctagccatggctagTACTTTATTctagCCCGGGctag"
+        == "Dseqrecord(o37)\n\x1b[48;5;11mgatcg\x1b[0mgtaccgatcATGAAATAAgatcGGGCC\x1b[48;5;11mCgatc\x1b[0m\nctagccatggctagTACTTTATTctagCCCGGGctag"  # noqa: B950
     )
 
     feat = Dseq.from_representation(
@@ -1612,7 +1565,7 @@ def test_figure():
     circularDseqrecord = circularDseqrecord.rc()
     assert (
         circularDseqrecord.figure()
-        == "Dseqrecord(o37)\ngatcGGGCCCgatcTTATTTCATgatcggtaccgatc\n\x1b[48;5;11mctagC\x1b[0mCCGGGctagAATAAAGTActagccatg\x1b[48;5;11mgctag\x1b[0m"
+        == "Dseqrecord(o37)\ngatcGGGCCCgatcTTATTTCATgatcggtaccgatc\n\x1b[48;5;11mctagC\x1b[0mCCGGGctagAATAAAGTActagccatg\x1b[48;5;11mgctag\x1b[0m"  # noqa: B950
     )
 
     feat = Dseq.from_representation(
@@ -1713,7 +1666,6 @@ def test_synced():
 
 
 def test_map_pCR_MCT1_HA46():
-    from pydna.dseqrecord import Dseqrecord
     from pydna.readers import read
 
     pCR_MCT1_HA46 = read("pCR_MCT1_HA46.gb")
@@ -2042,8 +1994,6 @@ def test_shifted():
 def test_looped():
     from pydna.dseq import Dseq
     from pydna.dseqrecord import Dseqrecord
-
-    from Bio import BiopythonDeprecationWarning
     import warnings
 
     warnings.simplefilter("always")
@@ -2150,11 +2100,6 @@ def test_lower():
 def test_map():
     from pydna.dseq import Dseq
     from pydna.dseqrecord import Dseqrecord
-    from pydna.readers import read
-    from pydna.utils import eq
-
-    from Bio.Seq import Seq
-    from Bio.SeqRecord import SeqRecord as Srec
     from Bio.SeqIO import read as abiread
 
     traces = []
@@ -2223,8 +2168,6 @@ def test_assemble_YEp24PGK_XK():
     """
     test YEp24PGK_XK
     """
-    import pytest
-    import sys
 
     from pydna.readers import read
     from pydna.utils import eq
@@ -2294,11 +2237,11 @@ def find_feature_by_id(f: Dseqrecord, id: str) -> SeqFeature:
                     assert new_locs == sorted(["[0:3](+)", "[0:4](+)", "[11:14](+)", "[10:14](+)"])
                 elif strand == -1:
                     assert new_locs == sorted(["[0:3](-)", "[0:4](-)", "[11:14](-)", "[10:14](-)"])
-                if strand == None:
+                if strand is None:
                     assert new_locs == sorted(["[0:3]", "[0:4]", "[11:14]", "[10:14]"])
 
 
-def test_apply_cut():
+def test_apply_cut2():
 
     from pydna.dseqrecord import Dseqrecord
     from Bio.SeqFeature import SeqFeature, SimpleLocation
@@ -2328,7 +2271,7 @@ def find_feature_by_id(f: Dseqrecord, id: str) -> SeqFeature:
                     assert new_locs == sorted(["[0:3](+)", "[0:4](+)", "[11:14](+)", "[10:14](+)"])
                 elif strand == -1:
                     assert new_locs == sorted(["[0:3](-)", "[0:4](-)", "[11:14](-)", "[10:14](-)"])
-                if strand == None:
+                if strand is None:
                     assert new_locs == sorted(["[0:3]", "[0:4]", "[11:14]", "[10:14]"])