From 8726bebfb678195e0d8185ec861fe4171c1c53de Mon Sep 17 00:00:00 2001
From: Alex Dewar <a.dewar@imperial.ac.uk>
Date: Mon, 14 Oct 2024 13:53:09 +0100
Subject: [PATCH 1/5] Bump all dependencies to latest version

I've also changed the supported range of Python versions: now the minimum is 3.10 (the minimum supported by the latest version of `networkx`) and the maximum is 3.12 (3.13 won't work for now: #55).

Fixes #35.
---
 poetry.lock    | 1106 ++++++++++++++++++++++++++----------------------
 pyproject.toml |   26 +-
 2 files changed, 615 insertions(+), 517 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d75e367..ce271c4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,20 +1,5 @@
 # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
-[[package]]
-name = "astunparse"
-version = "1.6.3"
-description = "An AST unparser for Python"
-optional = false
-python-versions = "*"
-files = [
-    {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"},
-    {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"},
-]
-
-[package.dependencies]
-six = ">=1.6.1,<2.0"
-wheel = ">=0.23.0,<1.0"
-
 [[package]]
 name = "attrs"
 version = "24.2.0"
@@ -45,45 +30,47 @@ files = [
     {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 = "beautifulsoup4"
-version = "4.9.3"
+version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.9.3-py2-none-any.whl", hash = "sha256:4c98143716ef1cb40bf7f39a8e3eec8f8b009509e74904ba3a7b315431577e35"},
-    {file = "beautifulsoup4-4.9.3-py3-none-any.whl", hash = "sha256:fff47e031e34ec82bf17e00da8f592fe7de69aeea38be00523c04623c04fb666"},
-    {file = "beautifulsoup4-4.9.3.tar.gz", hash = "sha256:84729e322ad1d5b4d25f805bfa05b902dd96450f43842c4e99067d5e1369eb25"},
+    {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
+    {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
 ]
 
 [package.dependencies]
-soupsieve = {version = ">1.2", markers = "python_version >= \"3.0\""}
+soupsieve = ">1.2"
 
 [package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
 [[package]]
 name = "bioc"
-version = "1.3.7"
-description = "BioC data structures and encoder/decoder for Python"
+version = "2.1"
+description = "bioc - Processing BioC, Brat, and PubTator with Python."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "bioc-1.3.7.tar.gz", hash = "sha256:278a4f6956b08c1297bfeae05958f5482a569104dd1a50c6abede17dfcfdbe10"},
+    {file = "bioc-2.1-py3-none-any.whl", hash = "sha256:f1730d26821330f9f625058841612d6cfb616efb906fc682297fe04dd5d9398a"},
+    {file = "bioc-2.1.tar.gz", hash = "sha256:7d9248198bdae291b0ebb218de2dc653c96d32a7eac2fa0ef4ed0c74ce45aaaa"},
 ]
 
 [package.dependencies]
-docutils = ">=0.15.2"
+docopt = "*"
+intervaltree = "*"
 jsonlines = ">=1.2.0"
 lxml = ">=4.6.3"
+tqdm = "*"
 
 [[package]]
 name = "certifi"
@@ -98,101 +85,116 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 [package.dependencies]
@@ -308,25 +300,13 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 toml = ["tomli"]
 
 [[package]]
-name = "decorator"
-version = "4.4.2"
-description = "Decorators for Humans"
+name = "docopt"
+version = "0.6.2"
+description = "Pythonic argument parser, that will make you smile"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*"
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-name = "docutils"
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-description = "Docutils -- Python Documentation Utilities"
-optional = false
-python-versions = ">=3.7"
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 ]
 
 [[package]]
@@ -376,17 +356,16 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "1.3.2"
+version = "1.4.1"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 ]
 
 [package.dependencies]
-astunparse = {version = ">=1.6", markers = "python_version < \"3.9\""}
 colorama = ">=0.4"
 
 [[package]]
@@ -403,29 +382,6 @@ files = [
 [package.extras]
 all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
 
-[[package]]
-name = "importlib-metadata"
-version = "8.5.0"
-description = "Read metadata from Python packages"
-optional = false
-python-versions = ">=3.8"
-files = [
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-]
-
-[package.dependencies]
-zipp = ">=3.20"
-
-[package.extras]
-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)"]
-perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
-type = ["pytest-mypy"]
-
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -437,6 +393,19 @@ files = [
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 ]
 
+[[package]]
+name = "intervaltree"
+version = "3.1.0"
+description = "Editable interval tree data structure for Python 2 and 3"
+optional = false
+python-versions = "*"
+files = [
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+]
+
+[package.dependencies]
+sortedcontainers = ">=2.0,<3.0"
+
 [[package]]
 name = "jinja2"
 version = "3.1.4"
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+]
+
+[package.dependencies]
+rapidfuzz = ">=3.9.0,<4.0.0"
+
 [[package]]
 name = "lxml"
 version = "5.3.0"
@@ -644,80 +706,78 @@ files = [
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 ]
 
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-
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 testing = ["coverage", "pyyaml"]
 
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 [[package]]
@@ -746,7 +806,6 @@ files = [
 click = ">=7.0"
 colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
 ghp-import = ">=1.0"
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 jinja2 = ">=2.11.1"
 markdown = ">=3.3.6"
 markupsafe = ">=2.0.1"
@@ -804,7 +863,6 @@ files = [
 ]
 
 [package.dependencies]
-importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
 mergedeep = ">=1.3.4"
 platformdirs = ">=2.2.0"
 pyyaml = ">=5.1"
@@ -825,13 +883,13 @@ mkdocs = ">=1.0.3"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.39"
+version = "9.5.40"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -890,7 +948,6 @@ files = [
 
 [package.dependencies]
 click = ">=7.0"
-importlib-metadata = {version = ">=4.6", markers = "python_version < \"3.10\""}
 Jinja2 = ">=2.11.1"
 Markdown = ">=3.3"
 MarkupSafe = ">=1.1"
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 mkdocs-autorefs = ">=0.3.1"
 platformdirs = ">=2.2.0"
 pymdown-extensions = ">=6.3"
-typing-extensions = {version = ">=4.1", markers = "python_version < \"3.10\""}
 
 [package.extras]
 crystal = ["mkdocstrings-crystal (>=0.3.4)"]
@@ -923,91 +979,108 @@ mkdocstrings = ">=0.25"
 
 [[package]]
 name = "networkx"
-version = "2.5.1"
+version = "3.4.1"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.10"
 files = [
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-decorator = ">=4.3,<5"
-
 [package.extras]
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-pydot = ["pydot"]
-pygraphviz = ["pygraphviz"]
-pytest = ["pytest"]
-pyyaml = ["pyyaml"]
-scipy = ["scipy"]
+default = ["matplotlib (>=3.7)", "numpy (>=1.24)", "pandas (>=2.0)", "scipy (>=1.10,!=1.11.0,!=1.11.1)"]
+developer = ["changelist (==0.5)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"]
+doc = ["intersphinx-registry", "myst-nb (>=1.1)", "numpydoc (>=1.8.0)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.15)", "sphinx (>=7.3)", "sphinx-gallery (>=0.16)", "texext (>=0.6.7)"]
+example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "momepy (>=0.7.2)", "osmnx (>=1.9)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
+extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
+test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "nltk"
-version = "3.6.2"
+version = "3.9.1"
 description = "Natural Language Toolkit"
 optional = false
-python-versions = ">=3.5.*"
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 files = [
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 ]
 
 [package.dependencies]
 click = "*"
 joblib = "*"
-regex = "*"
+regex = ">=2021.8.3"
 tqdm = "*"
 
 [package.extras]
-all = ["gensim (<4.0.0)", "matplotlib", "numpy", "pyparsing", "python-crfsuite", "requests", "scikit-learn", "scipy", "twython"]
+all = ["matplotlib", "numpy", "pyparsing", "python-crfsuite", "requests", "scikit-learn", "scipy", "twython"]
 corenlp = ["requests"]
-machine-learning = ["gensim (<4.0.0)", "numpy", "python-crfsuite", "scikit-learn", "scipy"]
+machine-learning = ["numpy", "python-crfsuite", "scikit-learn", "scipy"]
 plot = ["matplotlib"]
 tgrep = ["pyparsing"]
 twitter = ["twython"]
 
 [[package]]
 name = "numpy"
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 description = "Fundamental package for array computing in Python"
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 [[package]]
@@ -1234,16 +1306,18 @@ extra = ["pygments (>=2.12)"]
 
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+version = "0.3.13"
 description = "Python-tesseract is a python wrapper for Google's Tesseract-OCR"
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-python-versions = ">=3.6"
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 [package.dependencies]
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+Pillow = ">=8.0.0"
 
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 name = "pytest"
@@ -1318,27 +1392,17 @@ six = ">=1.5"
 
 [[package]]
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 [[package]]
 name = "pyyaml"
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 [package.dependencies]
 pyyaml = "*"
 
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+]
+
+[package.extras]
+all = ["numpy"]
+
 [[package]]
 name = "regex"
 version = "2024.9.11"
@@ -1540,26 +1704,6 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
-[[package]]
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-version = "75.1.0"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-optional = false
-python-versions = ">=3.8"
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-
-[package.extras]
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-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
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-type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.11.*)", "pytest-mypy"]
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -1571,6 +1715,17 @@ files = [
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 ]
 
+[[package]]
+name = "sortedcontainers"
+version = "2.4.0"
+description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
+optional = false
+python-versions = "*"
+files = [
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+]
+
 [[package]]
 name = "soupsieve"
 version = "2.6"
@@ -1584,13 +1739,13 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.0.2"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
 ]
 
 [[package]]
@@ -1613,17 +1768,6 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
-[[package]]
-name = "typing-extensions"
-version = "4.12.2"
-description = "Backported and Experimental Type Hints for Python 3.8+"
-optional = false
-python-versions = ">=3.8"
-files = [
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-]
-
 [[package]]
 name = "urllib3"
 version = "2.2.3"
@@ -1643,85 +1787,47 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "watchdog"
-version = "4.0.2"
+version = "5.0.3"
 description = "Filesystem events monitoring"
 optional = false
-python-versions = ">=3.8"
-files = [
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-    {file = "watchdog-4.0.2-py3-none-win_ia64.whl", hash = "sha256:baececaa8edff42cd16558a639a9b0ddf425f93d892e8392a56bf904f5eff22c"},
-    {file = "watchdog-4.0.2.tar.gz", hash = "sha256:b4dfbb6c49221be4535623ea4474a4d6ee0a9cef4a80b20c28db4d858b64e270"},
+python-versions = ">=3.9"
+files = [
+    {file = "watchdog-5.0.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:85527b882f3facda0579bce9d743ff7f10c3e1e0db0a0d0e28170a7d0e5ce2ea"},
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+    {file = "watchdog-5.0.3-pp39-pypy39_pp73-macosx_10_15_x86_64.whl", hash = "sha256:223160bb359281bb8e31c8f1068bf71a6b16a8ad3d9524ca6f523ac666bb6a1e"},
+    {file = "watchdog-5.0.3-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:560135542c91eaa74247a2e8430cf83c4342b29e8ad4f520ae14f0c8a19cfb5b"},
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+    {file = "watchdog-5.0.3-py3-none-manylinux2014_armv7l.whl", hash = "sha256:78864cc8f23dbee55be34cc1494632a7ba30263951b5b2e8fc8286b95845f82c"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_i686.whl", hash = "sha256:1e9679245e3ea6498494b3028b90c7b25dbb2abe65c7d07423ecfc2d6218ff7c"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_ppc64.whl", hash = "sha256:9413384f26b5d050b6978e6fcd0c1e7f0539be7a4f1a885061473c5deaa57221"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:294b7a598974b8e2c6123d19ef15de9abcd282b0fbbdbc4d23dfa812959a9e05"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_s390x.whl", hash = "sha256:26dd201857d702bdf9d78c273cafcab5871dd29343748524695cecffa44a8d97"},
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+    {file = "watchdog-5.0.3-py3-none-win_amd64.whl", hash = "sha256:f00b4cf737f568be9665563347a910f8bdc76f88c2970121c86243c8cfdf90e9"},
+    {file = "watchdog-5.0.3-py3-none-win_ia64.whl", hash = "sha256:49f4d36cb315c25ea0d946e018c01bb028048023b9e103d3d3943f58e109dd45"},
+    {file = "watchdog-5.0.3.tar.gz", hash = "sha256:108f42a7f0345042a854d4d0ad0834b741d421330d5f575b81cb27b883500176"},
 ]
 
 [package.extras]
 watchmedo = ["PyYAML (>=3.10)"]
 
-[[package]]
-name = "wheel"
-version = "0.44.0"
-description = "A built-package format for Python"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "wheel-0.44.0-py3-none-any.whl", hash = "sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f"},
-    {file = "wheel-0.44.0.tar.gz", hash = "sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49"},
-]
-
-[package.extras]
-test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
-
-[[package]]
-name = "zipp"
-version = "3.20.2"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
-    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
-]
-
-[package.extras]
-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"]
-
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.8,<3.11"
-content-hash = "3df738955122d7c19b8e1e06a93ac46d2f301b91d5fcb3a97fdc2a8adf286da9"
+python-versions = ">=3.10,<3.13"
+content-hash = "0626f222e6d16b0d89db4bb00230a59377f02b2110fe0ac4c41b5a1e0a3cd04a"
diff --git a/pyproject.toml b/pyproject.toml
index d347d9d..8836c58 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,25 +10,17 @@ license = "GPL-3.0-only"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-# This is an indirect dependency for bioc, but seemingly this version has been yanked.
-# Once we have updated bioc to the latest version, this line should be dropped.
-docutils = "!=0.21.post1"
-
-# Numpy is also an indirect dependency, but v2 isn't compatible with the version of
-# networkx we're using. This should also be dropped once we've upgraded.
-numpy = "<2"
-
-python = ">=3.8,<3.11"
-regex = "^2024.7.24"
-bioc = "1.3.7"
-beautifulsoup4 = "4.9.3"
-nltk = "3.6.2"
-fuzzywuzzy = "0.18.0"
-pytesseract = "0.3.8"
+python = ">=3.10,<3.13"
+regex = "^2024.9.11"
+bioc = "^2.1"
+beautifulsoup4 = "^4.12.3"
+nltk = "^3.9.1"
+fuzzywuzzy = "^0.18.0"
+pytesseract = "^0.3.13"
 lxml = "^5.3.0"
-networkx = "2.5.1"
+networkx = "^3.4.1"
 opencv-contrib-python = "^4.10.0.84"
-python-levenshtein = "0.12.2"
+python-levenshtein = "^0.26.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.2"

From b9104ecc28d04c7d8e1111ceb2e3a9080983c92d Mon Sep 17 00:00:00 2001
From: Alex Dewar <a.dewar@imperial.ac.uk>
Date: Mon, 14 Oct 2024 16:47:25 +0100
Subject: [PATCH 2/5] Fix: API changes in new version of bioc

---
 src/autoCORPus.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/autoCORPus.py b/src/autoCORPus.py
index c4a6e4b..ef60400 100644
--- a/src/autoCORPus.py
+++ b/src/autoCORPus.py
@@ -2,7 +2,7 @@
 import json
 import sys
 
-from bioc import loads, dumps, BioCFileType
+from bioc import loads, dumps, biocxml, biocjson
 from bs4 import BeautifulSoup
 
 from src.abbreviation import abbreviations
@@ -375,8 +375,8 @@ def main_text_to_bioc_json(self, indent=2):
         return BiocFormatter(self).to_json(indent)
 
     def main_text_to_bioc_xml(self):
-        collection = loads(BiocFormatter(self).to_json(2), BioCFileType.BIOC_JSON)
-        return dumps(collection, BioCFileType.BIOC_XML)
+        collection = biocjson.loads(BiocFormatter(self).to_json(2))
+        return biocxml.dumps(collection)
 
     def tables_to_bioc_json(self, indent=2):
         return json.dumps(self.tables, ensure_ascii=False, indent=indent)

From 86ee135c2de0c436bde7752824bf1f16a526cfda Mon Sep 17 00:00:00 2001
From: Alex Dewar <a.dewar@imperial.ac.uk>
Date: Mon, 14 Oct 2024 13:55:17 +0100
Subject: [PATCH 3/5] Add dependabot config

Closes #34.
---
 .github/dependabot.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..c030c0d
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: weekly
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly

From 9f6ecee0fdb8d6e90814714b4d386c71f0d61b71 Mon Sep 17 00:00:00 2001
From: Alex Dewar <a.dewar@imperial.ac.uk>
Date: Mon, 14 Oct 2024 13:58:08 +0100
Subject: [PATCH 4/5] CI: Check with all supported Python versions

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 688b78b..a37ed65 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,7 +16,7 @@ jobs:
         os:
           - ubuntu-latest
           - windows-latest
-        python-version: ['3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
       - uses: actions/checkout@v4
       - name: Install poetry

From 5a5d4ae257f65615298eeea12f169a532093ff1c Mon Sep 17 00:00:00 2001
From: Alex Dewar <a.dewar@imperial.ac.uk>
Date: Tue, 15 Oct 2024 09:47:04 +0100
Subject: [PATCH 5/5] Amend min version in README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 578caef..2c3f1d9 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 [![DOI:10.3389/fdgth.2022.788124](http://img.shields.io/badge/DOI-10.3389/fdgth.2022.788124-70286A.svg)](https://doi.org/10.3389/fdgth.2022.788124)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
-*Requires python 3.8+*
+*Requires Python 3.10+*
 
 The Automated pipeline for Consistent Outputs from Research Publications (Auto-CORPus) is a tool for the standardisation and conversion of publication HTML to three convenient machine-interpretable outputs to support biomedical text analytics. Firstly, Auto-CORPus can be configured to convert HTML from various publication sources to [BioC format](http://bioc.sourceforge.net/). Secondly, Auto-CORPus transforms publication tables to a JSON format to store, exchange and annotate table data between text analytics systems. Finally, Auto-CORPus extracts abbreviations declared within publication text and provides an abbreviations JSON output that relates an abbreviation with the full definition.