From f84f16064b7fdb01412392a7295776430ce96e2c Mon Sep 17 00:00:00 2001
From: Ugur Bayindir <ubyndr@gmail.com>
Date: Wed, 11 Oct 2023 11:38:58 +0100
Subject: [PATCH] Updated poetry.lock and pyproject.toml

---
 poetry.lock    | 915 +++++++++++++++++++++++++++++++------------------
 pyproject.toml |   5 +-
 2 files changed, 583 insertions(+), 337 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 6d2f534..00c968d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -15,6 +15,17 @@ files = [
 dev = ["pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"]
 parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"]
 
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = true
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
 [[package]]
 name = "anndata"
 version = "0.9.2"
@@ -41,13 +52,13 @@ test = ["awkward (>=2.3)", "boltons", "dask[array]", "joblib", "loompy (>=3.0.5)
 
 [[package]]
 name = "annotated-types"
-version = "0.5.0"
+version = "0.6.0"
 description = "Reusable constraint types to use with typing.Annotated"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
-    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
+    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
+    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
 ]
 
 [[package]]
@@ -91,15 +102,18 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "babel"
-version = "2.12.1"
+version = "2.13.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
-    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+    {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"},
+    {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"},
 ]
 
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
 [[package]]
 name = "bcp47"
 version = "0.0.4"
@@ -507,63 +521,63 @@ test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
 
 [[package]]
 name = "coverage"
-version = "7.3.1"
+version = "7.3.2"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -598,13 +612,13 @@ tests = ["coverage", "pytest"]
 
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 [package.dependencies]
 packaging = "*"
 
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+description = "Docutils -- Python Documentation Utilities"
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 version = "0.12.3"
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 ]
 
 [package.dependencies]
@@ -1100,6 +1129,17 @@ files = [
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 ]
 
+[[package]]
+name = "imagesize"
+version = "1.4.1"
+description = "Getting image size from png/jpeg/jpeg2000/gif file"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+]
+
 [[package]]
 name = "importlib-metadata"
 version = "6.8.0"
@@ -1599,20 +1639,20 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "markdown"
-version = "3.4.4"
+version = "3.5"
 description = "Python implementation of John Gruber's Markdown."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
@@ -1789,13 +1829,13 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-material"
-version = "9.4.3"
+version = "9.4.5"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2309,13 +2349,13 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 
 [[package]]
 name = "platformdirs"
-version = "3.10.0"
+version = "3.11.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.extras]
@@ -2921,99 +2961,99 @@ rpds-py = ">=0.7.0"
 
 [[package]]
 name = "regex"
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+version = "2023.10.3"
 description = "Alternative regular expression module, to replace re."
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 ]
 
 [[package]]
@@ -3094,108 +3134,110 @@ files = [
 
 [[package]]
 name = "rpds-py"
-version = "0.10.3"
+version = "0.10.4"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
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+    {file = "rpds_py-0.10.4-pp39-pypy39_pp73-musllinux_1_2_x86_64.whl", hash = "sha256:ae8a32ab77a84cc870bbfb60645851ca0f7d58fd251085ad67464b1445d632ca"},
+    {file = "rpds_py-0.10.4.tar.gz", hash = "sha256:18d5ff7fbd305a1d564273e9eb22de83ae3cd9cd6329fddc8f12f6428a711a6a"},
 ]
 
 [[package]]
@@ -3314,25 +3356,25 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar
 
 [[package]]
 name = "setuptools-scm"
-version = "8.0.3"
+version = "8.0.4"
 description = "the blessed package to manage your versions by scm tags"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-scm-8.0.3.tar.gz", hash = "sha256:0169fd70197efda2f8c4d0b2a7a3d614431b488116f37b79d031e9e7ec884d8c"},
-    {file = "setuptools_scm-8.0.3-py3-none-any.whl", hash = "sha256:813822234453438a13c78d05c8af29918fbc06f88efb33d38f065340bbb48c39"},
+    {file = "setuptools-scm-8.0.4.tar.gz", hash = "sha256:b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7"},
+    {file = "setuptools_scm-8.0.4-py3-none-any.whl", hash = "sha256:b47844cd2a84b83b3187a5782c71128c28b4c94cad8bfb871da2784a5cb54c4f"},
 ]
 
 [package.dependencies]
 packaging = ">=20"
 setuptools = "*"
 tomli = {version = ">=1", markers = "python_version < \"3.11\""}
-typing-extensions = {version = "*", markers = "python_version < \"3.11\""}
+typing-extensions = "*"
 
 [package.extras]
 docs = ["entangled-cli[rich]", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings[python]", "pygments"]
 rich = ["rich"]
-test = ["pytest", "rich", "virtualenv (>20)"]
+test = ["build", "pytest", "rich", "wheel"]
 
 [[package]]
 name = "six"
@@ -3345,6 +3387,17 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
+[[package]]
+name = "snowballstemmer"
+version = "2.2.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+optional = true
+python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
+
 [[package]]
 name = "sortedcontainers"
 version = "2.4.0"
@@ -3387,6 +3440,196 @@ docs = ["sphinx (<5)", "sphinx-rtd-theme"]
 keepalive = ["keepalive (>=0.5)"]
 pandas = ["pandas (>=1.3.5)"]
 
+[[package]]
+name = "sphinx"
+version = "7.2.6"
+description = "Python documentation generator"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinx-7.2.6-py3-none-any.whl", hash = "sha256:1e09160a40b956dc623c910118fa636da93bd3ca0b9876a7b3df90f07d691560"},
+    {file = "sphinx-7.2.6.tar.gz", hash = "sha256:9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5"},
+]
+
+[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"
+imagesize = ">=1.3"
+importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.14"
+requests = ">=2.25.0"
+snowballstemmer = ">=2.0"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.9"
+
+[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 (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools (>=67.0)"]
+
+[[package]]
+name = "sphinx-copybutton"
+version = "0.5.2"
+description = "Add a copy button to each of your code cells."
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "sphinx-copybutton-0.5.2.tar.gz", hash = "sha256:4cf17c82fb9646d1bc9ca92ac280813a3b605d8c421225fd9913154103ee1fbd"},
+    {file = "sphinx_copybutton-0.5.2-py3-none-any.whl", hash = "sha256:fb543fd386d917746c9a2c50360c7905b605726b9355cd26e9974857afeae06e"},
+]
+
+[package.dependencies]
+sphinx = ">=1.8"
+
+[package.extras]
+code-style = ["pre-commit (==2.12.1)"]
+rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme", "sphinx-examples"]
+
+[[package]]
+name = "sphinx-rtd-theme"
+version = "1.3.0"
+description = "Read the Docs theme for Sphinx"
+optional = true
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+files = [
+    {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,<8"
+sphinxcontrib-jquery = ">=4,<5"
+
+[package.extras]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.7"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_applehelp-1.0.7-py3-none-any.whl", hash = "sha256:094c4d56209d1734e7d252f6e0b3ccc090bd52ee56807a5d9315b19c122ab15d"},
+    {file = "sphinxcontrib_applehelp-1.0.7.tar.gz", hash = "sha256:39fdc8d762d33b01a7d8f026a3b7d71563ea3b72787d5f00ad8465bd9d6dfbfa"},
+]
+
+[package.dependencies]
+Sphinx = ">=5"
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.5"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_devhelp-1.0.5-py3-none-any.whl", hash = "sha256:fe8009aed765188f08fcaadbb3ea0d90ce8ae2d76710b7e29ea7d047177dae2f"},
+    {file = "sphinxcontrib_devhelp-1.0.5.tar.gz", hash = "sha256:63b41e0d38207ca40ebbeabcf4d8e51f76c03e78cd61abe118cf4435c73d4212"},
+]
+
+[package.dependencies]
+Sphinx = ">=5"
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.4"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_htmlhelp-2.0.4-py3-none-any.whl", hash = "sha256:8001661c077a73c29beaf4a79968d0726103c5605e27db92b9ebed8bab1359e9"},
+    {file = "sphinxcontrib_htmlhelp-2.0.4.tar.gz", hash = "sha256:6c26a118a05b76000738429b724a0568dbde5b72391a688577da08f11891092a"},
+]
+
+[package.dependencies]
+Sphinx = ">=5"
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["html5lib", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-jquery"
+version = "4.1"
+description = "Extension to include jQuery on newer Sphinx releases"
+optional = true
+python-versions = ">=2.7"
+files = [
+    {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"},
+    {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"},
+]
+
+[package.dependencies]
+Sphinx = ">=1.8"
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+optional = true
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+
+[package.extras]
+test = ["flake8", "mypy", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-qthelp"
+version = "1.0.6"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_qthelp-1.0.6-py3-none-any.whl", hash = "sha256:bf76886ee7470b934e363da7a954ea2825650013d367728588732c7350f49ea4"},
+    {file = "sphinxcontrib_qthelp-1.0.6.tar.gz", hash = "sha256:62b9d1a186ab7f5ee3356d906f648cacb7a6bdb94d201ee7adf26db55092982d"},
+]
+
+[package.dependencies]
+Sphinx = ">=5"
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.9"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_serializinghtml-1.1.9-py3-none-any.whl", hash = "sha256:9b36e503703ff04f20e9675771df105e58aa029cfcbc23b8ed716019b7416ae1"},
+    {file = "sphinxcontrib_serializinghtml-1.1.9.tar.gz", hash = "sha256:0c64ff898339e1fac29abd2bf5f11078f3ec413cfe9c046d3120d7ca65530b54"},
+]
+
+[package.dependencies]
+Sphinx = ">=5"
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["pytest"]
+
 [[package]]
 name = "sqlalchemy"
 version = "2.0.21"
@@ -3604,13 +3847,13 @@ six = "*"
 
 [[package]]
 name = "urllib3"
-version = "2.0.5"
+version = "2.0.6"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "urllib3-2.0.5-py3-none-any.whl", hash = "sha256:ef16afa8ba34a1f989db38e1dbbe0c302e4289a47856990d0682e374563ce35e"},
-    {file = "urllib3-2.0.5.tar.gz", hash = "sha256:13abf37382ea2ce6fb744d4dad67838eec857c9f4f57009891805e0b5e123594"},
+    {file = "urllib3-2.0.6-py3-none-any.whl", hash = "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2"},
+    {file = "urllib3-2.0.6.tar.gz", hash = "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564"},
 ]
 
 [package.extras]
@@ -3785,4 +4028,4 @@ docs = []
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "1a19470460f2e43615132da17d54889368df4cd52aa952ff799fc00fc868d616"
+content-hash = "0490f677eb41eac66256b2e82d75373754b1af00ab061ce68e78a509b01ce86f"
diff --git a/pyproject.toml b/pyproject.toml
index 950f89b..2b4748a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,13 +26,16 @@ flake8-black = "^0.3.6"
 flake8-isort = "^6.0.0"
 pytest-cov = "^4.1.0"
 pytest-mock = "^3.10.0"
+sphinx = { version = "^7.2.6", optional = true }
+sphinx-rtd-theme = { version = "^1.3.0", optional = true }
+sphinx-copybutton = { version = "^0.5.2", optional = true }
 
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.extras]
-docs = ["Sphinx", "sphinx-rtd-theme", "sphinx-copybutton"]
+docs = ["sphinx", "sphinx-rtd-theme", "sphinx-copybutton"]
 
 [tool.black]
 line-length = 100