From 54f82a8122b749c52e4b49349d60366fc5ac6caf Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 27 Jul 2023 09:46:46 +0200
Subject: [PATCH] Bump certifi from 2022.12.7 to 2023.7.22 (#311)

Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.12.7 to 2023.7.22.
- [Commits](https://github.com/certifi/python-certifi/compare/2022.12.07...2023.07.22)

---
updated-dependencies:
- dependency-name: certifi
  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 | 70 +++--------------------------------------------------
 1 file changed, 4 insertions(+), 66 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index b9469db..5b98971 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "attrs"
 version = "22.2.0"
 description = "Classes Without Boilerplate"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -23,7 +22,6 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy
 name = "bio"
 version = "1.5.9"
 description = "bio"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -43,7 +41,6 @@ tqdm = "*"
 name = "biopython"
 version = "1.81"
 description = "Freely available tools for computational molecular biology."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -80,7 +77,6 @@ numpy = "*"
 name = "biothings-client"
 version = "0.2.6"
 description = "Python Client for BioThings API services."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -98,21 +94,19 @@ jsonld = ["PyLD (>=0.7.2)"]
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
-    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
 name = "charset-normalizer"
 version = "3.0.1"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -210,7 +204,6 @@ files = [
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -222,7 +215,6 @@ files = [
 name = "contourpy"
 version = "1.0.7"
 description = "Python library for calculating contours of 2D quadrilateral grids"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -297,7 +289,6 @@ test-no-images = ["pytest"]
 name = "coverage"
 version = "7.2.7"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -373,7 +364,6 @@ toml = ["tomli"]
 name = "cycler"
 version = "0.11.0"
 description = "Composable style cycles"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -385,7 +375,6 @@ files = [
 name = "defusedxml"
 version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -397,7 +386,6 @@ files = [
 name = "et-xmlfile"
 version = "1.1.0"
 description = "An implementation of lxml.xmlfile for the standard library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -409,7 +397,6 @@ files = [
 name = "exceptiongroup"
 version = "1.1.0"
 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -424,7 +411,6 @@ test = ["pytest (>=6)"]
 name = "fasteners"
 version = "0.18"
 description = "A python package that provides useful locks"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -436,7 +422,6 @@ files = [
 name = "fonttools"
 version = "4.38.0"
 description = "Tools to manipulate font files"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -462,7 +447,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 name = "gprofiler-official"
 version = "1.0.0"
 description = "Functional enrichment analysis and more via the g:Profiler toolkit"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -477,7 +461,6 @@ requests = "*"
 name = "griddataformats"
 version = "1.0.1"
 description = "Reading and writing of data on regular grids in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -494,7 +477,6 @@ scipy = "*"
 name = "gsd"
 version = "2.7.0"
 description = "General simulation data file format."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -530,7 +512,6 @@ numpy = ">=1.9.3"
 name = "hypothesis"
 version = "6.82.0"
 description = "A library for property-based testing"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -563,7 +544,6 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2023.3)"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -575,7 +555,6 @@ files = [
 name = "importlib-resources"
 version = "5.12.0"
 description = "Read resources from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -594,7 +573,6 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -606,7 +584,6 @@ files = [
 name = "joblib"
 version = "1.2.0"
 description = "Lightweight pipelining with Python functions"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -618,7 +595,6 @@ files = [
 name = "jsonpickle"
 version = "3.0.1"
 description = "Python library for serializing any arbitrary object graph into JSON"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -635,7 +611,6 @@ testing-libs = ["simplejson", "ujson"]
 name = "kaleido"
 version = "0.2.1"
 description = "Static image export for web-based visualization libraries with zero dependencies"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -651,7 +626,6 @@ files = [
 name = "kiwisolver"
 version = "1.4.4"
 description = "A fast implementation of the Cassowary constraint solver"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -729,7 +703,6 @@ files = [
 name = "lxml"
 version = "4.9.3"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 files = [
@@ -837,7 +810,6 @@ source = ["Cython (>=0.29.35)"]
 name = "matplotlib"
 version = "3.7.2"
 description = "Python plotting package"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -900,7 +872,6 @@ python-dateutil = ">=2.7"
 name = "mdanalysis"
 version = "2.5.0"
 description = "An object-oriented toolkit to analyze molecular dynamics trajectories."
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -936,7 +907,6 @@ packaging = "*"
 scipy = ">=1.5.0"
 threadpoolctl = "*"
 tqdm = ">=4.43.0"
-kaleido = "0.2.1"
 
 [package.extras]
 analysis = ["scikit-learn", "seaborn", "tidynamics (>=1.0.0)"]
@@ -947,7 +917,6 @@ extra-formats = ["chemfiles (>=0.10)", "h5py (>=2.10)", "netCDF4 (>=1.0)", "pyed
 name = "mmtf-python"
 version = "1.1.3"
 description = "A decoding libary for the PDB mmtf format"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -966,7 +935,6 @@ test = ["coverage"]
 name = "mrcfile"
 version = "1.4.3"
 description = "MRC file I/O library"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -981,7 +949,6 @@ numpy = ">=1.16.0"
 name = "msgpack"
 version = "1.0.4"
 description = "MessagePack serializer"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1043,7 +1010,6 @@ files = [
 name = "mygene"
 version = "3.2.2"
 description = "Python Client for MyGene.Info services."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1058,7 +1024,6 @@ biothings-client = ">=0.2.6"
 name = "networkx"
 version = "3.0"
 description = "Python package for creating and manipulating graphs and networks"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1077,7 +1042,6 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
 name = "numpy"
 version = "1.24.2"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1115,7 +1079,6 @@ files = [
 name = "openpyxl"
 version = "3.1.2"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1130,7 +1093,6 @@ et-xmlfile = "*"
 name = "packaging"
 version = "23.0"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1142,7 +1104,6 @@ files = [
 name = "pandas"
 version = "2.0.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1210,7 +1171,6 @@ xml = ["lxml (>=4.6.3)"]
 name = "pdb-tools"
 version = "2.5.0"
 description = "A swiss army knife for PDB files."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1222,7 +1182,6 @@ files = [
 name = "pdbecif"
 version = "1.5"
 description = "A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1235,7 +1194,6 @@ files = [
 name = "pillow"
 version = "9.4.0"
 description = "Python Imaging Library (Fork)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1326,7 +1284,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 name = "platformdirs"
 version = "3.1.1"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1342,7 +1299,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytes
 name = "plotly"
 version = "5.15.0"
 description = "An open-source, interactive data visualization library for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1358,7 +1314,6 @@ tenacity = ">=6.2.0"
 name = "pluggy"
 version = "1.0.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1374,7 +1329,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "pooch"
 version = "1.7.0"
 description = "\"Pooch manages your Python library's sample data files: it automatically downloads and stores them in a local directory, with support for versioning and corruption checks.\""
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1396,7 +1350,6 @@ xxhash = ["xxhash (>=1.4.3)"]
 name = "pyparsing"
 version = "3.0.9"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
@@ -1411,7 +1364,6 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1434,7 +1386,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 name = "pytest-cov"
 version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1453,7 +1404,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1468,7 +1418,6 @@ six = ">=1.5"
 name = "pytz"
 version = "2022.7.1"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1480,7 +1429,6 @@ files = [
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1502,7 +1450,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "scipy"
 version = "1.11.1"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = "<3.13,>=3.9"
 files = [
@@ -1539,7 +1486,6 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1551,7 +1497,6 @@ files = [
 name = "sortedcontainers"
 version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1563,7 +1508,6 @@ files = [
 name = "tenacity"
 version = "8.1.0"
 description = "Retry code until it succeeds"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1578,7 +1522,6 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"]
 name = "threadpoolctl"
 version = "3.1.0"
 description = "threadpoolctl"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1590,7 +1533,6 @@ files = [
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1602,7 +1544,6 @@ files = [
 name = "tqdm"
 version = "4.64.1"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 files = [
@@ -1623,7 +1564,6 @@ telegram = ["requests"]
 name = "tzdata"
 version = "2023.3"
 description = "Provider of IANA time zone data"
-category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -1635,7 +1575,6 @@ files = [
 name = "urllib3"
 version = "1.26.14"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -1652,7 +1591,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "zipp"
 version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [