From c343def1819eeff1152a2ec04aa166b1c016e49b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Oct 2023 09:55:39 +0200
Subject: [PATCH 01/16] Bump matplotlib from 3.7.3 to 3.8.0 (#349)

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.7.3 to 3.8.0.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v3.7.3...v3.8.0)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 83 +++++++++++++++++++-------------------------------
 pyproject.toml |  2 +-
 2 files changed, 33 insertions(+), 52 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5229b9e..7a45f5c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -765,58 +765,39 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "matplotlib"
-version = "3.7.3"
+version = "3.8.0"
 description = "Python plotting package"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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+    {file = "matplotlib-3.8.0.tar.gz", hash = "sha256:df8505e1c19d5c2c26aff3497a7cbd3ccfc2e97043d1e4db3e76afa399164b69"},
 ]
 
 [package.dependencies]
@@ -825,7 +806,7 @@ cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
 kiwisolver = ">=1.0.1"
-numpy = ">=1.20,<2"
+numpy = ">=1.21,<2"
 packaging = ">=20.0"
 pillow = ">=6.2.0"
 pyparsing = ">=2.3.1"
@@ -1622,4 +1603,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "83f3ec41867463b6f063ed5e01ce2e0f1764a6847b0d8086ac2cea90f20bdc9b"
+content-hash = "8b00977ead7b5b3eaf49d0faa76154db4d1bf2201b0cf9467ceb2b893ec5f01b"
diff --git a/pyproject.toml b/pyproject.toml
index 1510dbe..d121ac5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ mdanalysis = "2.6.1"
 requests = "2.31.0"
 biopython = "1.81"
 scipy = "1.11.2"
-matplotlib = "3.7.3"
+matplotlib = "3.8.0"
 pdb-tools = "2.5.0"
 pandas = "2.0.3"
 openpyxl = "3.1.2"

From 23e20b66cff0f86c36c14f9a535493fd02d4b23b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Oct 2023 10:03:17 +0200
Subject: [PATCH 02/16] Bump plotly from 5.16.1 to 5.17.0 (#353)

Bumps [plotly](https://github.com/plotly/plotly.py) from 5.16.1 to 5.17.0.
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md)
- [Commits](https://github.com/plotly/plotly.py/compare/v5.16.1...v5.17.0)

---
updated-dependencies:
- dependency-name: plotly
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 8 ++++----
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7a45f5c..fba87d5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1241,13 +1241,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytes
 
 [[package]]
 name = "plotly"
-version = "5.16.1"
+version = "5.17.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "plotly-5.16.1-py2.py3-none-any.whl", hash = "sha256:19cc34f339acd4e624177806c14df22f388f23fb70658b03aad959a0e650a0dc"},
-    {file = "plotly-5.16.1.tar.gz", hash = "sha256:295ac25edeb18c893abb71dcadcea075b78fd6fdf07cee4217a4e1009667925b"},
+    {file = "plotly-5.17.0-py2.py3-none-any.whl", hash = "sha256:7c84cdf11da162423da957bb093287134f2d6f170eb9a74f1459f825892247c3"},
+    {file = "plotly-5.17.0.tar.gz", hash = "sha256:290d796bf7bab87aad184fe24b86096234c4c95dcca6ecbca02d02bdf17d3d97"},
 ]
 
 [package.dependencies]
@@ -1603,4 +1603,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "8b00977ead7b5b3eaf49d0faa76154db4d1bf2201b0cf9467ceb2b893ec5f01b"
+content-hash = "78cde2fd0776674324f2507d5732de950c7f242cf68d13566840ab13f27c7dba"
diff --git a/pyproject.toml b/pyproject.toml
index d121ac5..582c4b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ matplotlib = "3.8.0"
 pdb-tools = "2.5.0"
 pandas = "2.0.3"
 openpyxl = "3.1.2"
-plotly = "5.16.1"
+plotly = "5.17.0"
 pdbecif = "1.5"
 jsonpickle = "3.0.2"
 kaleido = "0.2.1"

From 09688b8189572d72212246fd8eedef90ca16e309 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:23:45 +0200
Subject: [PATCH 03/16] Bump scipy from 1.11.2 to 1.11.3 (#351)

Bumps [scipy](https://github.com/scipy/scipy) from 1.11.2 to 1.11.3.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](https://github.com/scipy/scipy/compare/v1.11.2...v1.11.3)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 54 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index fba87d5..a1ae7fa 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1392,36 +1392,36 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "scipy"
-version = "1.11.2"
+version = "1.11.3"
 description = "Fundamental algorithms for scientific computing in Python"
 optional = false
 python-versions = "<3.13,>=3.9"
 files = [
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-    {file = "scipy-1.11.2-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:95763fbda1206bec41157582bea482f50eb3702c85fffcf6d24394b071c0e87a"},
-    {file = "scipy-1.11.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e367904a0fec76433bf3fbf3e85bf60dae8e9e585ffd21898ab1085a29a04d16"},
-    {file = "scipy-1.11.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d690e1ca993c8f7ede6d22e5637541217fc6a4d3f78b3672a6fe454dbb7eb9a7"},
-    {file = "scipy-1.11.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:d2b813bfbe8dec6a75164523de650bad41f4405d35b0fa24c2c28ae07fcefb20"},
-    {file = "scipy-1.11.2-cp310-cp310-win_amd64.whl", hash = "sha256:afdb0d983f6135d50770dd979df50bf1c7f58b5b33e0eb8cf5c73c70600eae1d"},
-    {file = "scipy-1.11.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:8d9886f44ef8c9e776cb7527fb01455bf4f4a46c455c4682edc2c2cc8cd78562"},
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-    {file = "scipy-1.11.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:90d3b1364e751d8214e325c371f0ee0dd38419268bf4888b2ae1040a6b266b2a"},
-    {file = "scipy-1.11.2-cp311-cp311-win_amd64.whl", hash = "sha256:f73102f769ee06041a3aa26b5841359b1a93cc364ce45609657751795e8f4a4a"},
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-    {file = "scipy-1.11.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b8425fa963a32936c9773ee3ce44a765d8ff67eed5f4ac81dc1e4a819a238ee9"},
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-    {file = "scipy-1.11.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:ea932570b1c2a30edafca922345854ff2cd20d43cd9123b6dacfdecebfc1a80b"},
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-    {file = "scipy-1.11.2-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:f28f1f6cfeb48339c192efc6275749b2a25a7e49c4d8369a28b6591da02fbc9a"},
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-    {file = "scipy-1.11.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:10eb6af2f751aa3424762948e5352f707b0dece77288206f227864ddf675aca0"},
-    {file = "scipy-1.11.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:0f3261f14b767b316d7137c66cc4f33a80ea05841b9c87ad83a726205b901423"},
-    {file = "scipy-1.11.2-cp39-cp39-win_amd64.whl", hash = "sha256:2c91cf049ffb5575917f2a01da1da082fd24ed48120d08a6e7297dfcac771dcd"},
-    {file = "scipy-1.11.2.tar.gz", hash = "sha256:b29318a5e39bd200ca4381d80b065cdf3076c7d7281c5e36569e99273867f61d"},
+    {file = "scipy-1.11.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:370f569c57e1d888304052c18e58f4a927338eafdaef78613c685ca2ea0d1fa0"},
+    {file = "scipy-1.11.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:9885e3e4f13b2bd44aaf2a1a6390a11add9f48d5295f7a592393ceb8991577a3"},
+    {file = "scipy-1.11.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e04aa19acc324a1a076abb4035dabe9b64badb19f76ad9c798bde39d41025cdc"},
+    {file = "scipy-1.11.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3e1a8a4657673bfae1e05e1e1d6e94b0cabe5ed0c7c144c8aa7b7dbb774ce5c1"},
+    {file = "scipy-1.11.3-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:7abda0e62ef00cde826d441485e2e32fe737bdddee3324e35c0e01dee65e2a88"},
+    {file = "scipy-1.11.3-cp310-cp310-win_amd64.whl", hash = "sha256:033c3fd95d55012dd1148b201b72ae854d5086d25e7c316ec9850de4fe776929"},
+    {file = "scipy-1.11.3-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:925c6f09d0053b1c0f90b2d92d03b261e889b20d1c9b08a3a51f61afc5f58165"},
+    {file = "scipy-1.11.3-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:5664e364f90be8219283eeb844323ff8cd79d7acbd64e15eb9c46b9bc7f6a42a"},
+    {file = "scipy-1.11.3-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:00f325434b6424952fbb636506f0567898dca7b0f7654d48f1c382ea338ce9a3"},
+    {file = "scipy-1.11.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5f290cf561a4b4edfe8d1001ee4be6da60c1c4ea712985b58bf6bc62badee221"},
+    {file = "scipy-1.11.3-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:91770cb3b1e81ae19463b3c235bf1e0e330767dca9eb4cd73ba3ded6c4151e4d"},
+    {file = "scipy-1.11.3-cp311-cp311-win_amd64.whl", hash = "sha256:e1f97cd89c0fe1a0685f8f89d85fa305deb3067d0668151571ba50913e445820"},
+    {file = "scipy-1.11.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:dfcc1552add7cb7c13fb70efcb2389d0624d571aaf2c80b04117e2755a0c5d15"},
+    {file = "scipy-1.11.3-cp312-cp312-macosx_12_0_arm64.whl", hash = "sha256:0d3a136ae1ff0883fffbb1b05b0b2fea251cb1046a5077d0b435a1839b3e52b7"},
+    {file = "scipy-1.11.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bae66a2d7d5768eaa33008fa5a974389f167183c87bf39160d3fefe6664f8ddc"},
+    {file = "scipy-1.11.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2f6dee6cbb0e263b8142ed587bc93e3ed5e777f1f75448d24fb923d9fd4dce6"},
+    {file = "scipy-1.11.3-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:74e89dc5e00201e71dd94f5f382ab1c6a9f3ff806c7d24e4e90928bb1aafb280"},
+    {file = "scipy-1.11.3-cp312-cp312-win_amd64.whl", hash = "sha256:90271dbde4be191522b3903fc97334e3956d7cfb9cce3f0718d0ab4fd7d8bfd6"},
+    {file = "scipy-1.11.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:a63d1ec9cadecce838467ce0631c17c15c7197ae61e49429434ba01d618caa83"},
+    {file = "scipy-1.11.3-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:5305792c7110e32ff155aed0df46aa60a60fc6e52cd4ee02cdeb67eaccd5356e"},
+    {file = "scipy-1.11.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9ea7f579182d83d00fed0e5c11a4aa5ffe01460444219dedc448a36adf0c3917"},
+    {file = "scipy-1.11.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c77da50c9a91e23beb63c2a711ef9e9ca9a2060442757dffee34ea41847d8156"},
+    {file = "scipy-1.11.3-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:15f237e890c24aef6891c7d008f9ff7e758c6ef39a2b5df264650eb7900403c0"},
+    {file = "scipy-1.11.3-cp39-cp39-win_amd64.whl", hash = "sha256:4b4bb134c7aa457e26cc6ea482b016fef45db71417d55cc6d8f43d799cdf9ef2"},
+    {file = "scipy-1.11.3.tar.gz", hash = "sha256:bba4d955f54edd61899776bad459bf7326e14b9fa1c552181f0479cc60a568cd"},
 ]
 
 [package.dependencies]
@@ -1603,4 +1603,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "78cde2fd0776674324f2507d5732de950c7f242cf68d13566840ab13f27c7dba"
+content-hash = "c3d0da3377b10e7088e432b5e38e13a9bb8eaf269cd50741d2ed17e90d1812a5"
diff --git a/pyproject.toml b/pyproject.toml
index 582c4b1..302af54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ lxml = "4.9.3"
 mdanalysis = "2.6.1"
 requests = "2.31.0"
 biopython = "1.81"
-scipy = "1.11.2"
+scipy = "1.11.3"
 matplotlib = "3.8.0"
 pdb-tools = "2.5.0"
 pandas = "2.0.3"

From 6e8dc4e028a1b5dce36c6b449c0b205b3fbdc395 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Oct 2023 14:04:27 +0200
Subject: [PATCH 04/16] Bump hypothesis from 6.84.3 to 6.87.1 (#350)

Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.84.3 to 6.87.1.
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.84.3...hypothesis-python-6.87.1)

---
updated-dependencies:
- dependency-name: hypothesis
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 8 ++++----
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a1ae7fa..5d9d42e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -467,13 +467,13 @@ scipy = "*"
 
 [[package]]
 name = "hypothesis"
-version = "6.84.3"
+version = "6.87.1"
 description = "A library for property-based testing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "hypothesis-6.84.3-py3-none-any.whl", hash = "sha256:4dd7de7a341a80c10d3e6beca12c084aab84c48ea270c1b9b8cee7e4aa5d7be2"},
-    {file = "hypothesis-6.84.3.tar.gz", hash = "sha256:b4117f4138e81986cf62ad4e1410a021adeaa52e4b0326419da626cd7d3b6250"},
+    {file = "hypothesis-6.87.1-py3-none-any.whl", hash = "sha256:6b03e774d7ddddc29810e58ba4c41b5c9a894427aaf336e6400c560655a7449b"},
+    {file = "hypothesis-6.87.1.tar.gz", hash = "sha256:13615a8f7fa27d102c43ab2f92eaef519988700f3ca8129bc6340d36dec372dd"},
 ]
 
 [package.dependencies]
@@ -1603,4 +1603,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "c3d0da3377b10e7088e432b5e38e13a9bb8eaf269cd50741d2ed17e90d1812a5"
+content-hash = "1dc4986ca1c5f2a3bc520f59139213e854fa2ce7a2e0e1f97217e98368165bfe"
diff --git a/pyproject.toml b/pyproject.toml
index 302af54..21a42fe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 pytest = "^7.4.2"
 pytest-cov = "^4.1.0"
 coverage = "^7.3.1"
-hypothesis = "^6.84.3"
+hypothesis = "^6.87.1"
 
 [tool.black]
 line-length = 79

From 37b1d0b287cb815a8c08f47e5c31f7e2b1e001a6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 3 Oct 2023 11:00:06 +0200
Subject: [PATCH 05/16] Bump pandas from 2.0.3 to 2.1.1 (#352)

Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.0.3 to 2.1.1.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](https://github.com/pandas-dev/pandas/compare/v2.0.3...v2.1.1)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 98 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 50 insertions(+), 50 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5d9d42e..a1c2e03 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1046,70 +1046,70 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.0.3"
+version = "2.1.1"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "pandas-2.0.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e4c7c9f27a4185304c7caf96dc7d91bc60bc162221152de697c98eb0b2648dd8"},
-    {file = "pandas-2.0.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f167beed68918d62bffb6ec64f2e1d8a7d297a038f86d4aed056b9493fca407f"},
-    {file = "pandas-2.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ce0c6f76a0f1ba361551f3e6dceaff06bde7514a374aa43e33b588ec10420183"},
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-    {file = "pandas-2.0.3-cp310-cp310-win32.whl", hash = "sha256:3ef285093b4fe5058eefd756100a367f27029913760773c8bf1d2d8bebe5d210"},
-    {file = "pandas-2.0.3-cp310-cp310-win_amd64.whl", hash = "sha256:9ee1a69328d5c36c98d8e74db06f4ad518a1840e8ccb94a4ba86920986bb617e"},
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 ]
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.20.3", markers = "python_version < \"3.10\""},
-    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
-    {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
+    {version = ">=1.22.4", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
 tzdata = ">=2022.1"
 
 [package.extras]
-all = ["PyQt5 (>=5.15.1)", "SQLAlchemy (>=1.4.16)", "beautifulsoup4 (>=4.9.3)", "bottleneck (>=1.3.2)", "brotlipy (>=0.7.0)", "fastparquet (>=0.6.3)", "fsspec (>=2021.07.0)", "gcsfs (>=2021.07.0)", "html5lib (>=1.1)", "hypothesis (>=6.34.2)", "jinja2 (>=3.0.0)", "lxml (>=4.6.3)", "matplotlib (>=3.6.1)", "numba (>=0.53.1)", "numexpr (>=2.7.3)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pandas-gbq (>=0.15.0)", "psycopg2 (>=2.8.6)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)", "python-snappy (>=0.6.0)", "pyxlsb (>=1.0.8)", "qtpy (>=2.2.0)", "s3fs (>=2021.08.0)", "scipy (>=1.7.1)", "tables (>=3.6.1)", "tabulate (>=0.8.9)", "xarray (>=0.21.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)", "zstandard (>=0.15.2)"]
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+aws = ["s3fs (>=2022.05.0)"]
+clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"]
+compression = ["zstandard (>=0.17.0)"]
+computation = ["scipy (>=1.8.1)", "xarray (>=2022.03.0)"]
+consortium-standard = ["dataframe-api-compat (>=0.1.7)"]
+excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pyxlsb (>=1.0.9)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)"]
 feather = ["pyarrow (>=7.0.0)"]
-fss = ["fsspec (>=2021.07.0)"]
-gcp = ["gcsfs (>=2021.07.0)", "pandas-gbq (>=0.15.0)"]
-hdf5 = ["tables (>=3.6.1)"]
-html = ["beautifulsoup4 (>=4.9.3)", "html5lib (>=1.1)", "lxml (>=4.6.3)"]
-mysql = ["SQLAlchemy (>=1.4.16)", "pymysql (>=1.0.2)"]
-output-formatting = ["jinja2 (>=3.0.0)", "tabulate (>=0.8.9)"]
+fss = ["fsspec (>=2022.05.0)"]
+gcp = ["gcsfs (>=2022.05.0)", "pandas-gbq (>=0.17.5)"]
+hdf5 = ["tables (>=3.7.0)"]
+html = ["beautifulsoup4 (>=4.11.1)", "html5lib (>=1.1)", "lxml (>=4.8.0)"]
+mysql = ["SQLAlchemy (>=1.4.36)", "pymysql (>=1.0.2)"]
+output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.8.10)"]
 parquet = ["pyarrow (>=7.0.0)"]
-performance = ["bottleneck (>=1.3.2)", "numba (>=0.53.1)", "numexpr (>=2.7.1)"]
+performance = ["bottleneck (>=1.3.4)", "numba (>=0.55.2)", "numexpr (>=2.8.0)"]
 plot = ["matplotlib (>=3.6.1)"]
-postgresql = ["SQLAlchemy (>=1.4.16)", "psycopg2 (>=2.8.6)"]
-spss = ["pyreadstat (>=1.1.2)"]
-sql-other = ["SQLAlchemy (>=1.4.16)"]
-test = ["hypothesis (>=6.34.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
-xml = ["lxml (>=4.6.3)"]
+postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"]
+spss = ["pyreadstat (>=1.1.5)"]
+sql-other = ["SQLAlchemy (>=1.4.36)"]
+test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
+xml = ["lxml (>=4.8.0)"]
 
 [[package]]
 name = "pdb-tools"
@@ -1603,4 +1603,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "1dc4986ca1c5f2a3bc520f59139213e854fa2ce7a2e0e1f97217e98368165bfe"
+content-hash = "a56c90a015520551f3e42362d147452b18e747143638910dc9bcebc8b76ee6ca"
diff --git a/pyproject.toml b/pyproject.toml
index 21a42fe..70df415 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ biopython = "1.81"
 scipy = "1.11.3"
 matplotlib = "3.8.0"
 pdb-tools = "2.5.0"
-pandas = "2.0.3"
+pandas = "2.1.1"
 openpyxl = "3.1.2"
 plotly = "5.17.0"
 pdbecif = "1.5"

From 2eaa75633c845c79fe8d435e50bef4998e546155 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 4 Oct 2023 10:23:21 +0100
Subject: [PATCH 06/16] Bump pillow from 9.4.0 to 10.0.1 (#355)

Bumps [pillow](https://github.com/python-pillow/Pillow) from 9.4.0 to 10.0.1.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](https://github.com/python-pillow/Pillow/compare/9.4.0...10.0.1)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock | 137 ++++++++++++++++++++++------------------------------
 1 file changed, 57 insertions(+), 80 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a1c2e03..739f9f5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1136,92 +1136,69 @@ files = [
 
 [[package]]
 name = "pillow"
-version = "9.4.0"
+version = "10.0.1"
 description = "Python Imaging Library (Fork)"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "Pillow-10.0.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:459307cacdd4138edee3875bbe22a2492519e060660eaf378ba3b405d1c66317"},
+    {file = "Pillow-10.0.1-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:b059ac2c4c7a97daafa7dc850b43b2d3667def858a4f112d1aa082e5c3d6cf7d"},
+    {file = "Pillow-10.0.1-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:d6caf3cd38449ec3cd8a68b375e0c6fe4b6fd04edb6c9766b55ef84a6e8ddf2d"},
+    {file = "Pillow-10.0.1.tar.gz", hash = "sha256:d72967b06be9300fed5cfbc8b5bafceec48bf7cdc7dab66b1d2549035287191d"},
 ]
 
 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
+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]]

From c48293c143ed5b147e9ebae72448b314dd3cd623 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 18 Oct 2023 09:37:54 +0200
Subject: [PATCH 07/16] Bump urllib3 from 1.26.14 to 1.26.18 (#356)

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.14 to 1.26.18.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/1.26.14...1.26.18)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 739f9f5..aed737d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1548,17 +1548,17 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.14"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-1.26.14-py2.py3-none-any.whl", hash = "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"},
-    {file = "urllib3-1.26.14.tar.gz", hash = "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72"},
+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+brotli = ["brotli (==1.0.9)", "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)"]
 

From 40005b7ca02819a625daac28cb6097f2a263a317 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 1 Nov 2023 16:37:05 +0100
Subject: [PATCH 08/16] Bump plotly from 5.17.0 to 5.18.0 (#361)

Bumps [plotly](https://github.com/plotly/plotly.py) from 5.17.0 to 5.18.0.
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md)
- [Commits](https://github.com/plotly/plotly.py/compare/v5.17.0...v5.18.0)

---
updated-dependencies:
- dependency-name: plotly
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 12 ++++++++----
 pyproject.toml |  2 +-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index aed737d..6bb8aeb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -52,6 +52,10 @@ files = [
     {file = "biopython-1.81-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a51d9c1d1b4b634447535da74a644fae59bc234fbbf9001e2dc6b6fbabb98019"},
     {file = "biopython-1.81-cp311-cp311-win32.whl", hash = "sha256:2f9cfaf16d55ab80d514e7aebe5710dabe4e4ff47ede851031202e33b3249da3"},
     {file = "biopython-1.81-cp311-cp311-win_amd64.whl", hash = "sha256:e41b55edcfd448630e77bf4de66a7235324a8a149621499891da6bd1d5085b9a"},
+    {file = "biopython-1.81-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:175fcddc9f22a070aa6db54755d60c4b31090cc39f5f5f4b0a9a5d1ae3b45cd7"},
+    {file = "biopython-1.81-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9ec149487f3d1e0cf2b52b6071641c161ed545b0855ff51a71506152e14fc5bb"},
+    {file = "biopython-1.81-cp312-cp312-win32.whl", hash = "sha256:daeab15274bbcc0455cbd378636e14f53bc7c5b1f383e77021d7222e72cc3418"},
+    {file = "biopython-1.81-cp312-cp312-win_amd64.whl", hash = "sha256:22f5741aca91af0a76c0d5617e58e554fd3374bbd16e0c0ac1facf45b107313b"},
     {file = "biopython-1.81-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de"},
     {file = "biopython-1.81-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7c5c07123ff5f44c9e6b5369df854a38afd3c0c50ef58498a0ae8f7eb799f3e8"},
     {file = "biopython-1.81-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6"},
@@ -1218,13 +1222,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytes
 
 [[package]]
 name = "plotly"
-version = "5.17.0"
+version = "5.18.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "plotly-5.17.0-py2.py3-none-any.whl", hash = "sha256:7c84cdf11da162423da957bb093287134f2d6f170eb9a74f1459f825892247c3"},
-    {file = "plotly-5.17.0.tar.gz", hash = "sha256:290d796bf7bab87aad184fe24b86096234c4c95dcca6ecbca02d02bdf17d3d97"},
+    {file = "plotly-5.18.0-py3-none-any.whl", hash = "sha256:23aa8ea2f4fb364a20d34ad38235524bd9d691bf5299e800bca608c31e8db8de"},
+    {file = "plotly-5.18.0.tar.gz", hash = "sha256:360a31e6fbb49d12b007036eb6929521343d6bee2236f8459915821baefa2cbb"},
 ]
 
 [package.dependencies]
@@ -1580,4 +1584,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "a56c90a015520551f3e42362d147452b18e747143638910dc9bcebc8b76ee6ca"
+content-hash = "2db07ae8465a426d942a8614e4580284d7b639980de0217fceb2ef04b5b9f719"
diff --git a/pyproject.toml b/pyproject.toml
index 70df415..1712a84 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ matplotlib = "3.8.0"
 pdb-tools = "2.5.0"
 pandas = "2.1.1"
 openpyxl = "3.1.2"
-plotly = "5.17.0"
+plotly = "5.18.0"
 pdbecif = "1.5"
 jsonpickle = "3.0.2"
 kaleido = "0.2.1"

From e317772d9903a8fefa2fcda70357a73e1f8a5fee Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 1 Nov 2023 17:05:44 +0100
Subject: [PATCH 09/16] Bump matplotlib from 3.8.0 to 3.8.1 (#360)

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.8.0 to 3.8.1.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v3.8.0...v3.8.1)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 113 ++++++++++++++-----------------------------------
 pyproject.toml |   2 +-
 2 files changed, 33 insertions(+), 82 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 6bb8aeb..9f94157 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -769,39 +769,39 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "matplotlib"
-version = "3.8.0"
+version = "3.8.1"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "matplotlib-3.8.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:c4940bad88a932ddc69734274f6fb047207e008389489f2b6f77d9ca485f0e7a"},
-    {file = "matplotlib-3.8.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a33bd3045c7452ca1fa65676d88ba940867880e13e2546abb143035fa9072a9d"},
-    {file = "matplotlib-3.8.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:2ea6886e93401c22e534bbfd39201ce8931b75502895cfb115cbdbbe2d31f287"},
-    {file = "matplotlib-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d670b9348e712ec176de225d425f150dc8e37b13010d85233c539b547da0be39"},
-    {file = "matplotlib-3.8.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:7b37b74f00c4cb6af908cb9a00779d97d294e89fd2145ad43f0cdc23f635760c"},
-    {file = "matplotlib-3.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:0e723f5b96f3cd4aad99103dc93e9e3cdc4f18afdcc76951f4857b46f8e39d2d"},
-    {file = "matplotlib-3.8.0-cp311-cp311-macosx_10_12_x86_64.whl", hash = "sha256:5dc945a9cb2deb7d197ba23eb4c210e591d52d77bf0ba27c35fc82dec9fa78d4"},
-    {file = "matplotlib-3.8.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:f8b5a1bf27d078453aa7b5b27f52580e16360d02df6d3dc9504f3d2ce11f6309"},
-    {file = "matplotlib-3.8.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6f25ffb6ad972cdffa7df8e5be4b1e3cadd2f8d43fc72085feb1518006178394"},
-    {file = "matplotlib-3.8.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eee482731c8c17d86d9ddb5194d38621f9b0f0d53c99006275a12523ab021732"},
-    {file = "matplotlib-3.8.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:36eafe2128772195b373e1242df28d1b7ec6c04c15b090b8d9e335d55a323900"},
-    {file = "matplotlib-3.8.0-cp311-cp311-win_amd64.whl", hash = "sha256:061ee58facb3580cd2d046a6d227fb77e9295599c5ec6ad069f06b5821ad1cfc"},
-    {file = "matplotlib-3.8.0-cp312-cp312-macosx_10_12_x86_64.whl", hash = "sha256:3cc3776836d0f4f22654a7f2d2ec2004618d5cf86b7185318381f73b80fd8a2d"},
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-    {file = "matplotlib-3.8.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dae97fdd6996b3a25da8ee43e3fc734fff502f396801063c6b76c20b56683196"},
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+    {file = "matplotlib-3.8.1.tar.gz", hash = "sha256:044df81c1f6f3a8e52d70c4cfcb44e77ea9632a10929932870dfaa90de94365d"},
 ]
 
 [package.dependencies]
@@ -809,13 +809,12 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
+kiwisolver = ">=1.3.1"
 numpy = ">=1.21,<2"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=7"
 
 [[package]]
 name = "mdanalysis"
@@ -1413,43 +1412,6 @@ dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyl
 doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
 test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
-[[package]]
-name = "setuptools"
-version = "68.2.2"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "setuptools-68.2.2-py3-none-any.whl", hash = "sha256:b454a35605876da60632df1a60f736524eb73cc47bbc9f3f1ef1b644de74fd2a"},
-    {file = "setuptools-68.2.2.tar.gz", hash = "sha256:4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-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 = "setuptools-scm"
-version = "7.1.0"
-description = "the blessed package to manage your versions by scm tags"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "setuptools_scm-7.1.0-py3-none-any.whl", hash = "sha256:73988b6d848709e2af142aa48c986ea29592bbcfca5375678064708205253d8e"},
-    {file = "setuptools_scm-7.1.0.tar.gz", hash = "sha256:6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27"},
-]
-
-[package.dependencies]
-packaging = ">=20.0"
-setuptools = "*"
-tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
-typing-extensions = "*"
-
-[package.extras]
-test = ["pytest (>=6.2)", "virtualenv (>20)"]
-toml = ["setuptools (>=42)"]
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -1528,17 +1490,6 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
-[[package]]
-name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {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 = "tzdata"
 version = "2023.3"
@@ -1584,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "2db07ae8465a426d942a8614e4580284d7b639980de0217fceb2ef04b5b9f719"
+content-hash = "231bbed190477e0e86c5faa20781da61f34796d7cf159026a1f1d681a5a41e49"
diff --git a/pyproject.toml b/pyproject.toml
index 1712a84..88be17d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ mdanalysis = "2.6.1"
 requests = "2.31.0"
 biopython = "1.81"
 scipy = "1.11.3"
-matplotlib = "3.8.0"
+matplotlib = "3.8.1"
 pdb-tools = "2.5.0"
 pandas = "2.1.1"
 openpyxl = "3.1.2"

From 1866f828a46e4a25f597ce0d389c6fb072b9ba46 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 1 Nov 2023 17:29:38 +0100
Subject: [PATCH 10/16] Bump coverage from 7.3.1 to 7.3.2 (#359)

Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.3.1 to 7.3.2.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](https://github.com/nedbat/coveragepy/compare/7.3.1...7.3.2)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 108 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   2 +-
 2 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9f94157..72dcff4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -291,63 +291,63 @@ test-no-images = ["pytest"]
 
 [[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]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "231bbed190477e0e86c5faa20781da61f34796d7cf159026a1f1d681a5a41e49"
+content-hash = "239216894cdd7c4e43d0407d5fb8d624d86ed52f3995d0a2ef905d54dbe00fa0"
diff --git a/pyproject.toml b/pyproject.toml
index 88be17d..1b9a487 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,7 @@ arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.2"
 pytest-cov = "^4.1.0"
-coverage = "^7.3.1"
+coverage = "^7.3.2"
 hypothesis = "^6.87.1"
 
 [tool.black]

From 07a758e551b95d0515fef25aec7def0dc9ed81f1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 1 Nov 2023 17:40:42 +0100
Subject: [PATCH 11/16] Bump pytest from 7.4.2 to 7.4.3 (#358)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.2 to 7.4.3.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.4.2...7.4.3)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 8 ++++----
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 72dcff4..d5052a9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1286,13 +1286,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
-    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
+    {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
+    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
 ]
 
 [package.dependencies]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "239216894cdd7c4e43d0407d5fb8d624d86ed52f3995d0a2ef905d54dbe00fa0"
+content-hash = "5dd45c3aa6b5b66540a3c7edab2f3b14ca901cd03ace06f0508bf93312a3931a"
diff --git a/pyproject.toml b/pyproject.toml
index 1b9a487..6c372f4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ arctic3d-localise = "arctic3d.cli_localise:maincli"
 arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4.2"
+pytest = "^7.4.3"
 pytest-cov = "^4.1.0"
 coverage = "^7.3.2"
 hypothesis = "^6.87.1"

From 1d978168d37ea0946e6e8c1eeece271a7cefa825 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 1 Nov 2023 17:53:52 +0100
Subject: [PATCH 12/16] Bump bio from 1.5.9 to 1.6.0 (#357)

Bumps [bio](https://github.com/ialbert/bio) from 1.5.9 to 1.6.0.
- [Commits](https://github.com/ialbert/bio/commits)

---
updated-dependencies:
- dependency-name: bio
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 6 +++---
 pyproject.toml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d5052a9..99e2eb2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -20,12 +20,12 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy
 
 [[package]]
 name = "bio"
-version = "1.5.9"
+version = "1.6.0"
 description = "bio"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "bio-1.5.9-py3-none-any.whl", hash = "sha256:b1c44e509922955a5d87de215f7d373796b278741735d86ce5663965d5cf386b"},
+    {file = "bio-1.6.0-py3-none-any.whl", hash = "sha256:38b14e11625ef233e1a3878c8b13253695e863bd997f94715c248b71612605d5"},
 ]
 
 [package.dependencies]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "5dd45c3aa6b5b66540a3c7edab2f3b14ca901cd03ace06f0508bf93312a3931a"
+content-hash = "67db31ff1707d1c479fe33fc2ae6ff9d02c56f56f43b72122eb0cf2181950a2e"
diff --git a/pyproject.toml b/pyproject.toml
index 6c372f4..2aad59b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bio = "1.5.9"
+bio = "1.6.0"
 defusedxml = "0.7.1"
 lxml = "4.9.3"
 mdanalysis = "2.6.1"

From 8a22513cbf9fc38959ad4ceae7f662efd3833f61 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Dec 2023 15:43:23 +0100
Subject: [PATCH 13/16] Bump scipy from 1.11.3 to 1.11.4 (#362)

Bumps [scipy](https://github.com/scipy/scipy) from 1.11.3 to 1.11.4.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](https://github.com/scipy/scipy/compare/v1.11.3...v1.11.4)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 58 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 99e2eb2..f4367ba 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "attrs"
@@ -1372,36 +1372,36 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "scipy"
-version = "1.11.3"
+version = "1.11.4"
 description = "Fundamental algorithms for scientific computing in Python"
 optional = false
-python-versions = "<3.13,>=3.9"
+python-versions = ">=3.9"
 files = [
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-    {file = "scipy-1.11.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:9885e3e4f13b2bd44aaf2a1a6390a11add9f48d5295f7a592393ceb8991577a3"},
-    {file = "scipy-1.11.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e04aa19acc324a1a076abb4035dabe9b64badb19f76ad9c798bde39d41025cdc"},
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-    {file = "scipy-1.11.3-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:7abda0e62ef00cde826d441485e2e32fe737bdddee3324e35c0e01dee65e2a88"},
-    {file = "scipy-1.11.3-cp310-cp310-win_amd64.whl", hash = "sha256:033c3fd95d55012dd1148b201b72ae854d5086d25e7c316ec9850de4fe776929"},
-    {file = "scipy-1.11.3-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:925c6f09d0053b1c0f90b2d92d03b261e889b20d1c9b08a3a51f61afc5f58165"},
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-    {file = "scipy-1.11.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5f290cf561a4b4edfe8d1001ee4be6da60c1c4ea712985b58bf6bc62badee221"},
-    {file = "scipy-1.11.3-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:91770cb3b1e81ae19463b3c235bf1e0e330767dca9eb4cd73ba3ded6c4151e4d"},
-    {file = "scipy-1.11.3-cp311-cp311-win_amd64.whl", hash = "sha256:e1f97cd89c0fe1a0685f8f89d85fa305deb3067d0668151571ba50913e445820"},
-    {file = "scipy-1.11.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:dfcc1552add7cb7c13fb70efcb2389d0624d571aaf2c80b04117e2755a0c5d15"},
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-    {file = "scipy-1.11.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c77da50c9a91e23beb63c2a711ef9e9ca9a2060442757dffee34ea41847d8156"},
-    {file = "scipy-1.11.3-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:15f237e890c24aef6891c7d008f9ff7e758c6ef39a2b5df264650eb7900403c0"},
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-    {file = "scipy-1.11.3.tar.gz", hash = "sha256:bba4d955f54edd61899776bad459bf7326e14b9fa1c552181f0479cc60a568cd"},
+    {file = "scipy-1.11.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bc9a714581f561af0848e6b69947fda0614915f072dfd14142ed1bfe1b806710"},
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+    {file = "scipy-1.11.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:933baf588daa8dc9a92c20a0be32f56d43faf3d1a60ab11b3f08c356430f6e56"},
+    {file = "scipy-1.11.4-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:8fce70f39076a5aa62e92e69a7f62349f9574d8405c0a5de6ed3ef72de07f446"},
+    {file = "scipy-1.11.4-cp310-cp310-win_amd64.whl", hash = "sha256:6550466fbeec7453d7465e74d4f4b19f905642c89a7525571ee91dd7adabb5a3"},
+    {file = "scipy-1.11.4-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:f313b39a7e94f296025e3cffc2c567618174c0b1dde173960cf23808f9fae4be"},
+    {file = "scipy-1.11.4-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:1b7c3dca977f30a739e0409fb001056484661cb2541a01aba0bb0029f7b68db8"},
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+    {file = "scipy-1.11.4-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:028eccd22e654b3ea01ee63705681ee79933652b2d8f873e7949898dda6d11b6"},
+    {file = "scipy-1.11.4-cp312-cp312-macosx_12_0_arm64.whl", hash = "sha256:2c6ff6ef9cc27f9b3db93a6f8b38f97387e6e0591600369a297a50a8e96e835d"},
+    {file = "scipy-1.11.4-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b030c6674b9230d37c5c60ab456e2cf12f6784596d15ce8da9365e70896effc4"},
+    {file = "scipy-1.11.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ad669df80528aeca5f557712102538f4f37e503f0c5b9541655016dd0932ca79"},
+    {file = "scipy-1.11.4-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:ce7fff2e23ab2cc81ff452a9444c215c28e6305f396b2ba88343a567feec9660"},
+    {file = "scipy-1.11.4-cp312-cp312-win_amd64.whl", hash = "sha256:36750b7733d960d7994888f0d148d31ea3017ac15eef664194b4ef68d36a4a97"},
+    {file = "scipy-1.11.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:6e619aba2df228a9b34718efb023966da781e89dd3d21637b27f2e54db0410d7"},
+    {file = "scipy-1.11.4-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:f3cd9e7b3c2c1ec26364856f9fbe78695fe631150f94cd1c22228456404cf1ec"},
+    {file = "scipy-1.11.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d10e45a6c50211fe256da61a11c34927c68f277e03138777bdebedd933712fea"},
+    {file = "scipy-1.11.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:91af76a68eeae0064887a48e25c4e616fa519fa0d38602eda7e0f97d65d57937"},
+    {file = "scipy-1.11.4-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:6df1468153a31cf55ed5ed39647279beb9cfb5d3f84369453b49e4b8502394fd"},
+    {file = "scipy-1.11.4-cp39-cp39-win_amd64.whl", hash = "sha256:ee410e6de8f88fd5cf6eadd73c135020bfbbbdfcd0f6162c36a7638a1ea8cc65"},
+    {file = "scipy-1.11.4.tar.gz", hash = "sha256:90a2b78e7f5733b9de748f589f09225013685f9b218275257f8a8168ededaeaa"},
 ]
 
 [package.dependencies]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "67db31ff1707d1c479fe33fc2ae6ff9d02c56f56f43b72122eb0cf2181950a2e"
+content-hash = "a86eda89dbcac4eb6e22e54ea7be79209868ee6da9cf7cae4dc2db6e994cf1f9"
diff --git a/pyproject.toml b/pyproject.toml
index 2aad59b..8a631bc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ lxml = "4.9.3"
 mdanalysis = "2.6.1"
 requests = "2.31.0"
 biopython = "1.81"
-scipy = "1.11.3"
+scipy = "1.11.4"
 matplotlib = "3.8.1"
 pdb-tools = "2.5.0"
 pandas = "2.1.1"

From b85b6d66081a79b50f6dac93c29300b4779be1e1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Dec 2023 16:05:33 +0100
Subject: [PATCH 14/16] Bump pandas from 2.1.1 to 2.1.3 (#364)

Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.1.1 to 2.1.3.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](https://github.com/pandas-dev/pandas/compare/v2.1.1...v2.1.3)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 62 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f4367ba..7aed1a1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1049,49 +1049,49 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.1.1"
+version = "2.1.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "pandas-2.1.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:58d997dbee0d4b64f3cb881a24f918b5f25dd64ddf31f467bb9b67ae4c63a1e4"},
-    {file = "pandas-2.1.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:02304e11582c5d090e5a52aec726f31fe3f42895d6bfc1f28738f9b64b6f0614"},
-    {file = "pandas-2.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ffa8f0966de2c22de408d0e322db2faed6f6e74265aa0856f3824813cf124363"},
-    {file = "pandas-2.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c1f84c144dee086fe4f04a472b5cd51e680f061adf75c1ae4fc3a9275560f8f4"},
-    {file = "pandas-2.1.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:75ce97667d06d69396d72be074f0556698c7f662029322027c226fd7a26965cb"},
-    {file = "pandas-2.1.1-cp310-cp310-win_amd64.whl", hash = "sha256:4c3f32fd7c4dccd035f71734df39231ac1a6ff95e8bdab8d891167197b7018d2"},
-    {file = "pandas-2.1.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:9e2959720b70e106bb1d8b6eadd8ecd7c8e99ccdbe03ee03260877184bb2877d"},
-    {file = "pandas-2.1.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:25e8474a8eb258e391e30c288eecec565bfed3e026f312b0cbd709a63906b6f8"},
-    {file = "pandas-2.1.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b8bd1685556f3374520466998929bade3076aeae77c3e67ada5ed2b90b4de7f0"},
-    {file = "pandas-2.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dc3657869c7902810f32bd072f0740487f9e030c1a3ab03e0af093db35a9d14e"},
-    {file = "pandas-2.1.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:05674536bd477af36aa2effd4ec8f71b92234ce0cc174de34fd21e2ee99adbc2"},
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 ]
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.22.4", markers = "python_version < \"3.11\""},
-    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
+    {version = ">=1.22.4,<2", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
 tzdata = ">=2022.1"
 
 [package.extras]
-all = ["PyQt5 (>=5.15.6)", "SQLAlchemy (>=1.4.36)", "beautifulsoup4 (>=4.11.1)", "bottleneck (>=1.3.4)", "dataframe-api-compat (>=0.1.7)", "fastparquet (>=0.8.1)", "fsspec (>=2022.05.0)", "gcsfs (>=2022.05.0)", "html5lib (>=1.1)", "hypothesis (>=6.46.1)", "jinja2 (>=3.1.2)", "lxml (>=4.8.0)", "matplotlib (>=3.6.1)", "numba (>=0.55.2)", "numexpr (>=2.8.0)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pandas-gbq (>=0.17.5)", "psycopg2 (>=2.9.3)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.5)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)", "pyxlsb (>=1.0.9)", "qtpy (>=2.2.0)", "s3fs (>=2022.05.0)", "scipy (>=1.8.1)", "tables (>=3.7.0)", "tabulate (>=0.8.10)", "xarray (>=2022.03.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)", "zstandard (>=0.17.0)"]
+all = ["PyQt5 (>=5.15.6)", "SQLAlchemy (>=1.4.36)", "beautifulsoup4 (>=4.11.1)", "bottleneck (>=1.3.4)", "dataframe-api-compat (>=0.1.7)", "fastparquet (>=0.8.1)", "fsspec (>=2022.05.0)", "gcsfs (>=2022.05.0)", "html5lib (>=1.1)", "hypothesis (>=6.46.1)", "jinja2 (>=3.1.2)", "lxml (>=4.8.0)", "matplotlib (>=3.6.1)", "numba (>=0.55.2)", "numexpr (>=2.8.0)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pandas-gbq (>=0.17.5)", "psycopg2 (>=2.9.3)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.5)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pyxlsb (>=1.0.9)", "qtpy (>=2.2.0)", "s3fs (>=2022.05.0)", "scipy (>=1.8.1)", "tables (>=3.7.0)", "tabulate (>=0.8.10)", "xarray (>=2022.03.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)", "zstandard (>=0.17.0)"]
 aws = ["s3fs (>=2022.05.0)"]
 clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"]
 compression = ["zstandard (>=0.17.0)"]
@@ -1111,7 +1111,7 @@ plot = ["matplotlib (>=3.6.1)"]
 postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"]
 spss = ["pyreadstat (>=1.1.5)"]
 sql-other = ["SQLAlchemy (>=1.4.36)"]
-test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
+test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
 xml = ["lxml (>=4.8.0)"]
 
 [[package]]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "a86eda89dbcac4eb6e22e54ea7be79209868ee6da9cf7cae4dc2db6e994cf1f9"
+content-hash = "b34e9272b3da6c82d9514358cae7a8f302c3578b826c226b45f3c99a20e7755e"
diff --git a/pyproject.toml b/pyproject.toml
index 8a631bc..f766e67 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ biopython = "1.81"
 scipy = "1.11.4"
 matplotlib = "3.8.1"
 pdb-tools = "2.5.0"
-pandas = "2.1.1"
+pandas = "2.1.3"
 openpyxl = "3.1.2"
 plotly = "5.18.0"
 pdbecif = "1.5"

From 0e5880785da25ddc164715ad2132fc66dce5f697 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Dec 2023 16:24:53 +0100
Subject: [PATCH 15/16] Bump matplotlib from 3.8.1 to 3.8.2 (#363)

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.8.1 to 3.8.2.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v3.8.1...v3.8.2)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 60 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7aed1a1..a5fd9ea 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -769,39 +769,39 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "matplotlib"
-version = "3.8.1"
+version = "3.8.2"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
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+    {file = "matplotlib-3.8.2.tar.gz", hash = "sha256:01a978b871b881ee76017152f1f1a0cbf6bd5f7b8ff8c96df0df1bd57d8755a1"},
 ]
 
 [package.dependencies]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "b34e9272b3da6c82d9514358cae7a8f302c3578b826c226b45f3c99a20e7755e"
+content-hash = "b5ef95243a2f8fdf231431760b1fa0e4f9e0108619d2b4f12ae9c069574ae584"
diff --git a/pyproject.toml b/pyproject.toml
index f766e67..5488073 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ mdanalysis = "2.6.1"
 requests = "2.31.0"
 biopython = "1.81"
 scipy = "1.11.4"
-matplotlib = "3.8.1"
+matplotlib = "3.8.2"
 pdb-tools = "2.5.0"
 pandas = "2.1.3"
 openpyxl = "3.1.2"

From 921a7b10ec304a8c788c6f3ebdf3cc3f4c97ec10 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Dec 2023 16:45:22 +0100
Subject: [PATCH 16/16] Bump hypothesis from 6.87.1 to 6.91.0 (#365)

Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.87.1 to 6.91.0.
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.87.1...hypothesis-python-6.91.0)

---
updated-dependencies:
- dependency-name: hypothesis
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 8 ++++----
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a5fd9ea..37c0126 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -471,13 +471,13 @@ scipy = "*"
 
 [[package]]
 name = "hypothesis"
-version = "6.87.1"
+version = "6.91.0"
 description = "A library for property-based testing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "hypothesis-6.87.1-py3-none-any.whl", hash = "sha256:6b03e774d7ddddc29810e58ba4c41b5c9a894427aaf336e6400c560655a7449b"},
-    {file = "hypothesis-6.87.1.tar.gz", hash = "sha256:13615a8f7fa27d102c43ab2f92eaef519988700f3ca8129bc6340d36dec372dd"},
+    {file = "hypothesis-6.91.0-py3-none-any.whl", hash = "sha256:316e06d6f7d5f8ab87bcc7417fca750a2b082ed3ce902b979816b413276680b3"},
+    {file = "hypothesis-6.91.0.tar.gz", hash = "sha256:a9f61a2bcfc342febcc1d04b80a99e789c57b700f91cbd43bbdb5d651af385cd"},
 ]
 
 [package.dependencies]
@@ -1535,4 +1535,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "b5ef95243a2f8fdf231431760b1fa0e4f9e0108619d2b4f12ae9c069574ae584"
+content-hash = "bc6d44dcd0b1a74f25d5a418c3c29d37155ebfebb6ac3b808cab541a51923df6"
diff --git a/pyproject.toml b/pyproject.toml
index 5488073..631469d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 pytest = "^7.4.3"
 pytest-cov = "^4.1.0"
 coverage = "^7.3.2"
-hypothesis = "^6.87.1"
+hypothesis = "^6.91.0"
 
 [tool.black]
 line-length = 79