Repository: AstraZeneca/jazzy (language: python)

Issue:
IndexError when processing a single hydrogen
**Describe the bug**
When a single hydrogen molecule is processed by the calculate_polar_strength_map() function, the code raises a IndexError because the neighbour list is zero for this molecule.

**To Reproduce**
```
Steps to reproduce the behavior:
>>> import jazzy
>>> from jazzy.api import deltag_from_smiles
>>> deltag_from_smiles("[H]")
[09:18:56] WARNING: not removing hydrogen atom without neighbors
[09:18:56] WARNING: not removing hydrogen atom without neighbors
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/kdxr003/.local/lib/python3.8/site-packages/jazzy/api.py", line 113, in deltag_from_smiles
    atomic_map = calculate_polar_strength_map(
  File "/home/kdxr003/.local/lib/python3.8/site-packages/jazzy/core.py", line 231, in calculate_polar_strength_map
    if nbr[0].GetAtomicNum() == 6:
IndexError: tuple index out of range
```

**Expected behavior**
A single hydrogen cannot produce hydrogen bond, hence, there its strength can be assumed to be zero. Also, it does not make any sense to run this calculation on this compound. The code can be changed to have ```if nbr: do stuff```

**Screenshots**
Not needed.

**Additional context**
Add any other context about the problem here.

Update dependencies for compatibility in integration
**Is your feature request related to a problem? Please describe.**
ERROR: kallisto 1.0.9 has requirement scipy==1.9.2, but you'll have scipy 1.10.1 which is incompatible.
ERROR: jazzy 0.0.11 has requirement click==8.0.4, but you'll have click 8.1.7 which is incompatible.
ERROR: jazzy 0.0.11 has requirement rdkit<=2022.9.5, but you'll have rdkit 2023.3.3 which is incompatible.

**Describe the solution you'd like**
Release constraints and verify that the library is functioning as expected.



Discussion / hints:

Fix patch:
diff --git a/README.rst b/README.rst
index 681692d..768e533 100644
--- a/README.rst
+++ b/README.rst
@@ -61,17 +61,6 @@ Features
 * Command-line interface
 
 
-Requirements
-------------
-
-.. code:: console
-
-   click         # Composable command line interface toolkit
-   kallisto      # Atomic and molecular featurizer
-   numpy         # NumPy array computing package
-   rdkit         # Chemoinformatics toolkit
-
-
 Installation via PyPI
 ---------------------
 
diff --git a/poetry.lock b/poetry.lock
index b5d1158..d9b6df1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,9 +1,10 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -13,13 +14,14 @@ files = [
 
 [[package]]
 name = "alembic"
-version = "1.10.2"
+version = "1.12.0"
 description = "A database migration tool for SQLAlchemy."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "alembic-1.10.2-py3-none-any.whl", hash = "sha256:8b48368f6533c064b39c024e1daba15ae7f947eac84185c28c06bbe1301a5497"},
-    {file = "alembic-1.10.2.tar.gz", hash = "sha256:457eafbdc0769d855c2c92cbafe6b7f319f916c80cf4ed02b8f394f38b51b89d"},
+    {file = "alembic-1.12.0-py3-none-any.whl", hash = "sha256:03226222f1cf943deee6c85d9464261a6c710cd19b4fe867a3ad1f25afda610f"},
+    {file = "alembic-1.12.0.tar.gz", hash = "sha256:8e7645c32e4f200675e69f0745415335eb59a3663f5feb487abfa0b30c45888b"},
 ]
 
 [package.dependencies]
@@ -34,26 +36,28 @@ tz = ["python-dateutil"]
 
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
+category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "autopage"
 version = "0.5.1"
 description = "A library to provide automatic paging for console output"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -65,6 +69,7 @@ files = [
 name = "babel"
 version = "2.12.1"
 description = "Internationalization utilities"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -79,6 +84,7 @@ pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
 name = "bandit"
 version = "1.7.5"
 description = "Security oriented static analyser for python code."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -100,143 +106,154 @@ yaml = ["PyYAML"]
 
 [[package]]
 name = "black"
-version = "21.12b0"
+version = "22.12.0"
 description = "The uncompromising code formatter."
+category = "dev"
 optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.7"
 files = [
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-    {file = "black-21.12b0.tar.gz", hash = "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3"},
+    {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
+    {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
+    {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
+    {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
+    {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
+    {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
+    {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
+    {file = "black-22.12.0-cp38-cp38-win_amd64.whl", hash = "sha256:82d9fe8fee3401e02e79767016b4907820a7dc28d70d137eb397b92ef3cc5bfc"},
+    {file = "black-22.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:101c69b23df9b44247bd88e1d7e90154336ac4992502d4197bdac35dd7ee3320"},
+    {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
+    {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
+    {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
 ]
 
 [package.dependencies]
-click = ">=7.1.2"
+click = ">=8.0.0"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.9.0,<1"
+pathspec = ">=0.9.0"
 platformdirs = ">=2"
-tomli = ">=0.2.6,<2.0.0"
-typing-extensions = [
-    {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
-    {version = ">=3.10.0.0,<3.10.0.1 || >3.10.0.1", markers = "python_version >= \"3.10\""},
-]
+tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
 d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
-python2 = ["typed-ast (>=1.4.3)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
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+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
 name = "cfgv"
-version = "3.3.1"
+version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
+category = "dev"
 optional = false
-python-versions = ">=3.6.1"
+python-versions = ">=3.8"
 files = [
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+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
 ]
 
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 name = "charset-normalizer"
-version = "3.1.0"
+version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "dev"
 optional = false
 python-versions = ">=3.7.0"
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 ]
 
 [[package]]
 name = "classify-imports"
 version = "4.2.0"
 description = "Utilities for refactoring imports in python-like syntax."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -246,13 +263,14 @@ files = [
 
 [[package]]
 name = "click"
-version = "8.0.4"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
+category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -260,13 +278,14 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "cliff"
-version = "4.2.0"
+version = "4.3.0"
 description = "Command Line Interface Formulation Framework"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -279,13 +298,14 @@ stevedore = ">=2.0.1"
 
 [[package]]
 name = "cmaes"
-version = "0.9.1"
+version = "0.10.0"
 description = "Lightweight Covariance Matrix Adaptation Evolution Strategy (CMA-ES) implementation for Python 3."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -298,6 +318,7 @@ cmawm = ["scipy"]
 name = "cmd2"
 version = "2.4.3"
 description = "cmd2 - quickly build feature-rich and user-friendly interactive command line applications in Python"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -320,6 +341,7 @@ validate = ["flake8", "mypy", "types-pkg-resources"]
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -331,6 +353,7 @@ files = [
 name = "colorlog"
 version = "6.7.0"
 description = "Add colours to the output of Python's logging module."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -346,71 +369,64 @@ development = ["black", "flake8", "mypy", "pytest", "types-colorama"]
 
 [[package]]
 name = "coverage"
-version = "7.2.7"
+version = "7.3.1"
 description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -423,6 +439,7 @@ toml = ["tomli"]
 name = "darglint"
 version = "1.8.1"
 description = "A utility for ensuring Google-style docstrings stay up to date with the source code."
+category = "dev"
 optional = false
 python-versions = ">=3.6,<4.0"
 files = [
@@ -432,19 +449,21 @@ files = [
 
 [[package]]
 name = "distlib"
-version = "0.3.6"
+version = "0.3.7"
 description = "Distribution utilities"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "docutils"
 version = "0.18.1"
 description = "Docutils -- Python Documentation Utilities"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -454,32 +473,34 @@ files = [
 
 [[package]]
 name = "dparse"
-version = "0.6.2"
+version = "0.6.3"
 description = "A parser for Python dependency files"
+category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
 packaging = "*"
-toml = "*"
+tomli = {version = "*", markers = "python_version < \"3.11\""}
 
 [package.extras]
 conda = ["pyyaml"]
-pipenv = ["pipenv"]
+pipenv = ["pipenv (<=2022.12.19)"]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.1"
+version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -487,23 +508,28 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.10.7"
+version = "3.12.3"
 description = "A platform independent file lock."
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "filelock-3.10.7.tar.gz", hash = "sha256:892be14aa8efc01673b5ed6589dbccb95f9a8596f0507e232626155495c18105"},
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 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.7.1", markers = "python_version < \"3.11\""}
+
 [package.extras]
-docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "flake8"
 version = "4.0.1"
 description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -520,6 +546,7 @@ pyflakes = ">=2.4.0,<2.5.0"
 name = "flake8-bandit"
 version = "3.0.0"
 description = "Automated security testing with bandit and flake8."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -537,6 +564,7 @@ pycodestyle = "*"
 name = "flake8-bugbear"
 version = "22.12.6"
 description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -555,6 +583,7 @@ dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "tox"]
 name = "flake8-docstrings"
 version = "1.7.0"
 description = "Extension for flake8 which uses pydocstyle to check docstrings"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -570,6 +599,7 @@ pydocstyle = ">=2.1"
 name = "flake8-polyfill"
 version = "1.0.2"
 description = "Polyfill package for Flake8 plugins"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -584,6 +614,7 @@ flake8 = "*"
 name = "flake8-rst-docstrings"
 version = "0.3.0"
 description = "Python docstring reStructuredText (RST) validator for flake8"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -603,6 +634,7 @@ develop = ["build", "twine"]
 name = "gitdb"
 version = "4.0.10"
 description = "Git Object Database"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -615,22 +647,27 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.31"
+version = "3.1.36"
 description = "GitPython is a Python library used to interact with Git repositories"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "GitPython-3.1.31-py3-none-any.whl", hash = "sha256:f04893614f6aa713a60cbbe1e6a97403ef633103cdd0ef5eb6efe0deb98dbe8d"},
-    {file = "GitPython-3.1.31.tar.gz", hash = "sha256:8ce3bcf69adfdf7c7d503e78fd3b1c492af782d58893b650adb2ac8912ddd573"},
+    {file = "GitPython-3.1.36-py3-none-any.whl", hash = "sha256:8d22b5cfefd17c79914226982bb7851d6ade47545b1735a9d010a2a4c26d8388"},
+    {file = "GitPython-3.1.36.tar.gz", hash = "sha256:4bb0c2a6995e85064140d31a33289aa5dce80133a23d36fcd372d716c54d3ebf"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
+[package.extras]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar", "virtualenv"]
+
 [[package]]
 name = "greenlet"
 version = "2.0.2"
 description = "Lightweight in-process concurrent programming"
+category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 files = [
@@ -702,13 +739,14 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "identify"
-version = "2.5.22"
+version = "2.5.28"
 description = "File identification library for Python"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.22-py2.py3-none-any.whl", hash = "sha256:f0faad595a4687053669c112004178149f6c326db71ee999ae4636685753ad2f"},
-    {file = "identify-2.5.22.tar.gz", hash = "sha256:f7a93d6cf98e29bd07663c60728e7a4057615068d7a639d132dc883b2d54d31e"},
+    {file = "identify-2.5.28-py2.py3-none-any.whl", hash = "sha256:87816de144bf46d161bd5b3e8f5596b16cade3b80be537087334b26bc5c177f3"},
+    {file = "identify-2.5.28.tar.gz", hash = "sha256:94bb59643083ebd60dc996d043497479ee554381fbc5307763915cda49b0e78f"},
 ]
 
 [package.extras]
@@ -718,6 +756,7 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -729,6 +768,7 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -738,13 +778,14 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.1.0"
+version = "6.8.0"
 description = "Read metadata from Python packages"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-6.1.0-py3-none-any.whl", hash = "sha256:ff80f3b5394912eb1b108fcfd444dc78b7f1f3e16b16188054bd01cb9cb86f09"},
-    {file = "importlib_metadata-6.1.0.tar.gz", hash = "sha256:43ce9281e097583d758c2c708c4376371261a02c34682491a8e98352365aad20"},
+    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
+    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
 ]
 
 [package.dependencies]
@@ -753,30 +794,32 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "importlib-resources"
-version = "5.12.0"
+version = "6.0.1"
 description = "Read resources from Python packages"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
-    {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
+    {file = "importlib_resources-6.0.1-py3-none-any.whl", hash = "sha256:134832a506243891221b88b4ae1213327eea96ceb4e407a00d790bb0626f45cf"},
+    {file = "importlib_resources-6.0.1.tar.gz", hash = "sha256:4359457e42708462b9626a04657c6208ad799ceb41e5c58c57ffa0e6a098a5d4"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -788,6 +831,7 @@ files = [
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -803,19 +847,21 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "joblib"
-version = "1.2.0"
+version = "1.3.2"
 description = "Lightweight pipelining with Python functions"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "joblib-1.2.0-py3-none-any.whl", hash = "sha256:091138ed78f800342968c523bdde947e7a305b8594b910a0fea2ab83c3c6d385"},
-    {file = "joblib-1.2.0.tar.gz", hash = "sha256:e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018"},
+    {file = "joblib-1.3.2-py3-none-any.whl", hash = "sha256:ef4331c65f239985f3f2220ecc87db222f08fd22097a3dd5698f693875f8cbb9"},
+    {file = "joblib-1.3.2.tar.gz", hash = "sha256:92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1"},
 ]
 
 [[package]]
 name = "kallisto"
 version = "1.0.9"
 description = "The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented."
+category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -832,6 +878,7 @@ scipy = "1.9.2"
 name = "livereload"
 version = "2.6.3"
 description = "Python LiveReload is an awesome tool for web developers"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -847,6 +894,7 @@ tornado = {version = "*", markers = "python_version > \"2.7\""}
 name = "mako"
 version = "1.2.4"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -864,13 +912,14 @@ testing = ["pytest"]
 
 [[package]]
 name = "markdown-it-py"
-version = "2.2.0"
+version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "markdown-it-py-2.2.0.tar.gz", hash = "sha256:7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1"},
-    {file = "markdown_it_py-2.2.0-py3-none-any.whl", hash = "sha256:5a35f8d1870171d9acc47b99612dc146129b631baf04970128b568f190d0cc30"},
+    {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
+    {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
 ]
 
 [package.dependencies]
@@ -883,72 +932,84 @@ compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0
 linkify = ["linkify-it-py (>=1,<3)"]
 plugins = ["mdit-py-plugins"]
 profiling = ["gprof2dot"]
-rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.2"
+version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [[package]]
 name = "mccabe"
 version = "0.6.1"
 description = "McCabe checker, plugin for flake8"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -960,6 +1021,7 @@ files = [
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -969,37 +1031,39 @@ files = [
 
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+version = "1.5.1"
 description = "Optional static typing for Python"
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 optional = false
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@@ -1010,13 +1074,13 @@ typing-extensions = ">=4.1.0"
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
 install-types = ["pip"]
-python2 = ["typed-ast (>=1.4.0,<2)"]
 reports = ["lxml"]
 
 [[package]]
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 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1026,13 +1090,14 @@ files = [
 
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+version = "1.8.0"
 description = "Node.js virtual environment builder"
+category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
 files = [
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 ]
 
 [package.dependencies]
@@ -1042,6 +1107,7 @@ setuptools = "*"
 name = "numpy"
 version = "1.24.4"
 description = "Fundamental package for array computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 version = "2.3.0"
 description = "A hyperparameter optimization framework"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1113,6 +1180,7 @@ tests = ["fakeredis", "pytest"]
 name = "packaging"
 version = "21.3"
 description = "Core utilities for Python packages"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
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 description = "Utility library for gitignore style pattern matching of file paths."
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 name = "pbr"
 version = "5.11.1"
 description = "Python Build Reasonableness"
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 python-versions = ">=2.6"
 files = [
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 version = "0.13.2"
 description = "Check PEP-8 naming conventions, plugin for flake8"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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+docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "platformdirs"
-version = "3.2.0"
+version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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-    {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
@@ -1281,13 +1334,14 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
-version = "3.3.3"
+version = "3.4.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pre_commit-3.3.3-py2.py3-none-any.whl", hash = "sha256:10badb65d6a38caff29703362271d7dca483d01da88f9d7e05d0b97171c136cb"},
-    {file = "pre_commit-3.3.3.tar.gz", hash = "sha256:a2256f489cd913d575c145132ae196fe335da32d91a8294b7afe6622335dd023"},
+    {file = "pre_commit-3.4.0-py2.py3-none-any.whl", hash = "sha256:96d529a951f8b677f730a7212442027e8ba53f9b04d217c4c67dc56c393ad945"},
+    {file = "pre_commit-3.4.0.tar.gz", hash = "sha256:6bbd5129a64cad4c0dfaeeb12cd8f7ea7e15b77028d985341478c8af3c759522"},
 ]
 
 [package.dependencies]
@@ -1301,6 +1355,7 @@ virtualenv = ">=20.10.0"
 name = "pre-commit-hooks"
 version = "4.4.0"
 description = "Some out-of-the-box hooks for pre-commit."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1314,13 +1369,14 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "prettytable"
-version = "3.6.0"
+version = "3.9.0"
 description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "prettytable-3.6.0.tar.gz", hash = "sha256:2e0026af955b4ea67b22122f310b90eae890738c08cb0458693a49b6221530ac"},
+    {file = "prettytable-3.9.0-py3-none-any.whl", hash = "sha256:a71292ab7769a5de274b146b276ce938786f56c31cf7cea88b6f3775d82fe8c8"},
+    {file = "prettytable-3.9.0.tar.gz", hash = "sha256:f4ed94803c23073a90620b201965e5dc0bccf1760b7a7eaf3158cab8aaffdf34"},
 ]
 
 [package.dependencies]
@@ -1333,6 +1389,7 @@ tests = ["pytest", "pytest-cov", "pytest-lazy-fixture"]
 name = "pycodestyle"
 version = "2.8.0"
 description = "Python style guide checker"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1344,6 +1401,7 @@ files = [
 name = "pydocstyle"
 version = "6.3.0"
 description = "Python docstring style checker"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1361,6 +1419,7 @@ toml = ["tomli (>=1.2.3)"]
 name = "pyflakes"
 version = "2.4.0"
 description = "passive checker of Python programs"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1370,13 +1429,14 @@ files = [
 
 [[package]]
 name = "pygments"
-version = "2.14.0"
+version = "2.16.1"
 description = "Pygments is a syntax highlighting package written in Python."
+category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -1384,13 +1444,14 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.9"
+version = "3.1.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+category = "dev"
 optional = false
 python-versions = ">=3.6.8"
 files = [
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 ]
 
 [package.extras]
@@ -1400,6 +1461,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pyperclip"
 version = "1.8.2"
 description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1410,6 +1472,7 @@ files = [
 name = "pyreadline3"
 version = "3.4.1"
 description = "A python implementation of GNU readline."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1419,13 +1482,14 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1441,95 +1505,104 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "pyyaml"
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+version = "6.0.1"
 description = "YAML parser and emitter for Python"
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 python-versions = ">=3.6"
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+    {file = "rdkit-2023.3.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:7832a9da7b9be0652b1dfdf539b3d5c9a95be34c72681135757ac0767a6f8c38"},
+    {file = "rdkit-2023.3.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4b416727674d93c11a4576c7f7f6d40349c4f86fba03c094fdd4f6197ec71682"},
+    {file = "rdkit-2023.3.3-cp39-cp39-win_amd64.whl", hash = "sha256:870147c1966bc3938977986fb64c1516d11fbd08da7dfa37c0f3acdbaa141314"},
 ]
 
 [package.dependencies]
@@ -1540,6 +1613,7 @@ Pillow = "*"
 name = "reorder-python-imports"
 version = "3.10.0"
 description = "Tool for reordering python imports"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1554,6 +1628,7 @@ classify-imports = ">=4.1"
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1575,6 +1650,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "restructuredtext-lint"
 version = "1.4.0"
 description = "reStructuredText linter"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1586,17 +1662,18 @@ docutils = ">=0.11,<1.0"
 
 [[package]]
 name = "rich"
-version = "13.3.3"
+version = "13.5.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
+category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "rich-13.3.3-py3-none-any.whl", hash = "sha256:540c7d6d26a1178e8e8b37e9ba44573a3cd1464ff6348b99ee7061b95d1c6333"},
-    {file = "rich-13.3.3.tar.gz", hash = "sha256:dc84400a9d842b3a9c5ff74addd8eb798d155f36c1c91303888e0a66850d2a15"},
+    {file = "rich-13.5.2-py3-none-any.whl", hash = "sha256:146a90b3b6b47cac4a73c12866a499e9817426423f57c5a66949c086191a8808"},
+    {file = "rich-13.5.2.tar.gz", hash = "sha256:fb9d6c0a0f643c99eed3875b5377a184132ba9be4d61516a55273d3554d75a39"},
 ]
 
 [package.dependencies]
-markdown-it-py = ">=2.2.0,<3.0.0"
+markdown-it-py = ">=2.2.0"
 pygments = ">=2.13.0,<3.0.0"
 typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""}
 
@@ -1605,17 +1682,18 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "ruamel-yaml"
-version = "0.17.21"
+version = "0.17.32"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
+category = "dev"
 optional = false
 python-versions = ">=3"
 files = [
-    {file = "ruamel.yaml-0.17.21-py3-none-any.whl", hash = "sha256:742b35d3d665023981bd6d16b3d24248ce5df75fdb4e2924e93a05c1f8b61ca7"},
-    {file = "ruamel.yaml-0.17.21.tar.gz", hash = "sha256:8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af"},
+    {file = "ruamel.yaml-0.17.32-py3-none-any.whl", hash = "sha256:23cd2ed620231677564646b0c6a89d138b6822a0d78656df7abda5879ec4f447"},
+    {file = "ruamel.yaml-0.17.32.tar.gz", hash = "sha256:ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2"},
 ]
 
 [package.dependencies]
-"ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}
+"ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.12\""}
 
 [package.extras]
 docs = ["ryd"]
@@ -1625,6 +1703,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 name = "ruamel-yaml-clib"
 version = "0.2.7"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1635,8 +1714,7 @@ files = [
     {file = "ruamel.yaml.clib-0.2.7-cp310-cp310-win32.whl", hash = "sha256:763d65baa3b952479c4e972669f679fe490eee058d5aa85da483ebae2009d231"},
     {file = "ruamel.yaml.clib-0.2.7-cp310-cp310-win_amd64.whl", hash = "sha256:d000f258cf42fec2b1bbf2863c61d7b8918d31ffee905da62dede869254d3b8a"},
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:045e0626baf1c52e5527bd5db361bc83180faaba2ff586e763d3d5982a876a9e"},
-    {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_13_0_arm64.whl", hash = "sha256:1a6391a7cabb7641c32517539ca42cf84b87b667bad38b78d4d42dd23e957c81"},
-    {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-manylinux2014_aarch64.whl", hash = "sha256:9c7617df90c1365638916b98cdd9be833d31d337dbcd722485597b43c4a215bf"},
+    {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_12_6_arm64.whl", hash = "sha256:721bc4ba4525f53f6a611ec0967bdcee61b31df5a56801281027a3a6d1c2daf5"},
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:41d0f1fa4c6830176eef5b276af04c89320ea616655d01327d5ce65e50575c94"},
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-win32.whl", hash = "sha256:f6d3d39611ac2e4f62c3128a9eed45f19a6608670c5a2f4f07f24e8de3441d38"},
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-win_amd64.whl", hash = "sha256:da538167284de58a52109a9b89b8f6a53ff8437dd6dc26d33b57bf6699153122"},
@@ -1671,6 +1749,7 @@ files = [
 name = "safety"
 version = "2.3.5"
 description = "Checks installed dependencies for known vulnerabilities and licenses."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1694,6 +1773,7 @@ gitlab = ["python-gitlab (>=1.3.0)"]
 name = "scipy"
 version = "1.9.2"
 description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1730,24 +1810,26 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "67.6.1"
+version = "68.2.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "setuptools-67.6.1-py3-none-any.whl", hash = "sha256:e728ca814a823bf7bf60162daf9db95b93d532948c4c0bea762ce62f60189078"},
-    {file = "setuptools-67.6.1.tar.gz", hash = "sha256:257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a"},
+    {file = "setuptools-68.2.1-py3-none-any.whl", hash = "sha256:eff96148eb336377ab11beee0c73ed84f1709a40c0b870298b0d058828761bae"},
+    {file = "setuptools-68.2.1.tar.gz", hash = "sha256:56ee14884fd8d0cd015411f4a13f40b4356775a0aefd9ebc1d3bfb9a1acb32f1"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+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-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "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 (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1759,6 +1841,7 @@ files = [
 name = "smmap"
 version = "5.0.0"
 description = "A pure Python implementation of a sliding window memory map manager"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1770,6 +1853,7 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1781,6 +1865,7 @@ files = [
 name = "sphinx"
 version = "6.2.1"
 description = "Python documentation generator"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1816,6 +1901,7 @@ test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"]
 name = "sphinx-autobuild"
 version = "2021.3.14"
 description = "Rebuild Sphinx documentation on changes, with live-reload in the browser."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1835,6 +1921,7 @@ test = ["pytest", "pytest-cov"]
 name = "sphinx-click"
 version = "4.4.0"
 description = "Sphinx extension that automatically documents click applications"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1849,18 +1936,19 @@ sphinx = ">=2.0"
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.2.2"
+version = "1.3.0"
 description = "Read the Docs theme for Sphinx"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
-    {file = "sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl", hash = "sha256:6a7e7d8af34eb8fc57d52a09c6b6b9c46ff44aea5951bc831eeb9245378f3689"},
-    {file = "sphinx_rtd_theme-1.2.2.tar.gz", hash = "sha256:01c5c5a72e2d025bd23d1f06c59a4831b06e6ce6c01fdd5ebfe9986c0a880fc7"},
+    {file = "sphinx_rtd_theme-1.3.0-py2.py3-none-any.whl", hash = "sha256:46ddef89cc2416a81ecfbeaceab1881948c014b1b6e4450b815311a89fb977b0"},
+    {file = "sphinx_rtd_theme-1.3.0.tar.gz", hash = "sha256:590b030c7abb9cf038ec053b95e5380b5c70d61591eb0b552063fbe7c41f0931"},
 ]
 
 [package.dependencies]
 docutils = "<0.19"
-sphinx = ">=1.6,<7"
+sphinx = ">=1.6,<8"
 sphinxcontrib-jquery = ">=4,<5"
 
 [package.extras]
@@ -1870,6 +1958,7 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "1.0.4"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1885,6 +1974,7 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "1.0.2"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1900,6 +1990,7 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.0.1"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1915,6 +2006,7 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jquery"
 version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
+category = "dev"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -1929,6 +2021,7 @@ Sphinx = ">=1.8"
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1943,6 +2036,7 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "1.0.3"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1958,6 +2052,7 @@ test = ["pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "1.1.5"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1971,60 +2066,61 @@ test = ["pytest"]
 
 [[package]]
 name = "sqlalchemy"
-version = "2.0.7"
+version = "2.0.20"
 description = "Database Abstraction Library"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 typing-extensions = ">=4.2.0"
 
 [package.extras]
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 postgresql-psycopg = ["psycopg (>=3.0.7)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
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 pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
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+    {file = "tornado-6.3.3-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:71a8db65160a3c55d61839b7302a9a400074c9c753040455494e2af74e2501f2"},
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+    {file = "tornado-6.3.3-cp38-abi3-musllinux_1_1_i686.whl", hash = "sha256:7d01abc57ea0dbb51ddfed477dfe22719d376119844e33c661d873bf9c0e4a16"},
+    {file = "tornado-6.3.3-cp38-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:9dc4444c0defcd3929d5c1eb5706cbe1b116e762ff3e0deca8b715d14bf6ec17"},
+    {file = "tornado-6.3.3-cp38-abi3-win32.whl", hash = "sha256:65ceca9500383fbdf33a98c0087cb975b2ef3bfb874cb35b8de8740cf7f41bd3"},
+    {file = "tornado-6.3.3-cp38-abi3-win_amd64.whl", hash = "sha256:22d3c2fa10b5793da13c807e6fc38ff49a4f6e1e3868b0a6f4164768bb8e20f5"},
+    {file = "tornado-6.3.3.tar.gz", hash = "sha256:e7d8db41c0181c80d76c982aacc442c0783a2c54d6400fe028954201a2e032fe"},
 ]
 
 [[package]]
 name = "tqdm"
-version = "4.65.0"
+version = "4.66.1"
 description = "Fast, Extensible Progress Meter"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.65.0-py3-none-any.whl", hash = "sha256:c4f53a17fe37e132815abceec022631be8ffe1b9381c2e6e30aa70edc99e9671"},
-    {file = "tqdm-4.65.0.tar.gz", hash = "sha256:1871fb68a86b8fb3b59ca4cdd3dcccbc7e6d613eeed31f4c332531977b89beb5"},
+    {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
+    {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -2126,6 +2216,7 @@ telegram = ["requests"]
 name = "typeguard"
 version = "2.13.3"
 description = "Run-time type checker for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.5.3"
 files = [
@@ -2139,55 +2230,60 @@ test = ["mypy", "pytest", "typing-extensions"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.5.0"
+version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
-    {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
+    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "1.26.15"
+version = "2.0.4"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
-    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
+    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.21.0"
+version = "20.24.5"
 description = "Virtual Python Environment builder"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"},
-    {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"},
+    {file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"},
+    {file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"},
 ]
 
 [package.dependencies]
-distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<4"
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<4"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
 name = "wcwidth"
 version = "0.2.6"
 description = "Measures the displayed width of unicode strings in a terminal"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2199,6 +2295,7 @@ files = [
 name = "xdoctest"
 version = "1.1.1"
 description = "A rewrite of the builtin doctest module"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2226,20 +2323,21 @@ tests-strict = ["codecov (==2.0.15)", "pytest (==4.6.0)", "pytest (==4.6.0)", "p
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
+    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+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-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8.0"
-content-hash = "36bf14151034f1f4a87b116ea7453dc9550a272f537e6be5c62f25a063d2dc29"
+content-hash = "3eb9e2164764a36d6805dd89895c06cad4e8b0b08b041fd53a840e9068a33c10"
diff --git a/pyproject.toml b/pyproject.toml
index 589794b..dccbb59 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "jazzy"
-version = "0.0.11"
+version = "0.0.12"
 description = "Jazzy"
 authors = ["Gian Marco Ghiandoni <ghiandoni.g@gmail.com>", "Eike Caldeweyher <e.caldeweyher@gmail.com>"]
 license = "Apache-2.0"
@@ -20,8 +20,8 @@ Changelog = "https://github.com/AstraZeneca/jazzy/releases"
 
 [tool.poetry.dependencies]
 python = "^3.8.0"
-click = "8.0.4"
-rdkit = "<=2023.3.1"
+click = "^8.0.4"
+rdkit = "^2023.3.1"
 kallisto = "^1.0.9"
 
 [tool.poetry.group.optuna]
@@ -41,7 +41,7 @@ sphinx = "^6.2.1"
 sphinx-autobuild = "^2021.3.14"
 pre-commit = "^3.3.3"
 flake8 = "^4.0.1"
-black = "^21.12b0"
+black = "^22.1.0"
 flake8-bandit = "^3.0.0"
 flake8-bugbear = "^22.4.25"
 flake8-docstrings = "^1.6.0"
diff --git a/src/jazzy/core.py b/src/jazzy/core.py
index 3b2166f..eddad7c 100644
--- a/src/jazzy/core.py
+++ b/src/jazzy/core.py
@@ -227,12 +227,13 @@ def calculate_polar_strength_map(
 
             # distinguish between Carbon and other non-Hydrogen atoms
             nbr = atom.GetNeighbors()
-            # Carbon case
-            if nbr[0].GetAtomicNum() == 6:
-                sdc = sd
-            # other non-Hydrogen case
-            else:
-                sdx = sd
+            if nbr:
+                # Carbon case
+                if nbr[0].GetAtomicNum() == 6:
+                    sdc = sd
+                # other non-Hydrogen case
+                else:
+                    sdx = sd
         else:
             nlps = get_lone_pairs(atom)
             if nlps > 0:
@@ -354,7 +355,7 @@ def get_atom_and_nbrs_charges(
     q_gamma = get_charges_from_atom_list(gamma, charges)
 
     # equation 9
-    q_delta = t * sum(q_alpha) + (t ** 2) * sum(q_beta) + (t ** 3) * sum(q_gamma)
+    q_delta = t * sum(q_alpha) + (t**2) * sum(q_beta) + (t**3) * sum(q_gamma)
     return q, q_delta
 
 
@@ -506,8 +507,8 @@ def calculate_delta_polar(
         nlps = atom["num_lp"]
         sak = atom["sa"]
 
-        don += sdi * (nh ** expd)
-        acc += sak * (nlps ** expa)
+        don += sdi * (nh**expd)
+        acc += sak * (nlps**expa)
     # equation 14
     return float(gd * don + ga * acc)
 
@@ -536,7 +537,7 @@ def interaction_strength(idx: int, mol_map: dict, acceptor_exp: float) -> float:
     acceptor_strength = mol_map[idx]["sa"]
     num_lp = mol_map[idx]["num_lp"]
     if num_lp != 0:
-        return acceptor_strength * (num_lp ** acceptor_exp)
+        return acceptor_strength * (num_lp**acceptor_exp)
     return 0.0
 
 


Test patch:
diff --git a/tests/test_api.py b/tests/test_api.py
index c567845..10bae18 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -77,6 +77,16 @@ def test_deltag_from_smiles():
     assert np.isclose(scalar, 4.599630151706878)
 
 
+def test_deltag_from_smiles_hydrogen():
+    """Incorrect with successful calculation."""
+    # [H] has no neighbours but should not break the logic
+    smiles = "[H]"
+    # first only hydrogen bond strength
+    minimisation_method = "MMFF94"
+    scalar = deltag_from_smiles(smiles, minimisation_method)
+    assert np.isclose(scalar, 1.884)
+
+
 def test_api_deltag_from_smiles_fails_for_invalid_smiles():
     """Correcly fails for incorrect smiles."""
     smiles = "xxx"