Repository: HTTP-APIs/hydrus
Pull request #576 (2021-05-24 13:41:51)

Fix vulnerabilities. Set minimum Python version to 3.6.8


Patch:
diff --git a/hydrus/app_factory.py b/hydrus/app_factory.py
index a99436f..ac660c2 100644
--- a/hydrus/app_factory.py
+++ b/hydrus/app_factory.py
@@ -2,12 +2,9 @@ from flask import Flask, redirect, request
 import uuid
 from flask_cors import CORS
 from flask_restful import Api
-from hydrus_logger import HydrusLogger
 from hydrus.resources import (Index, Vocab, Contexts, Entrypoint,
                               ItemCollection, Item, Items, ItemMember)
 
-logger = HydrusLogger().get_logger()
-
 
 def app_factory(api_name: str = "api", vocab_route: str = "vocab") -> Flask:
     """
@@ -23,16 +20,6 @@ def app_factory(api_name: str = "api", vocab_route: str = "vocab") -> Flask:
     app.url_map.strict_slashes = False
     api = Api(app)
 
-    @app.after_request
-    def logging_request_response(response):
-        if response.location and response.status_code != 302:
-            logger.info(" {} {}:{} Object_created_at : {}, status_code : {} "
-                        .format(uuid.uuid4(), request.method, request.path, response.location, response.status))
-        else:
-            logger.info(" {} {}:{}  status_code : {} "
-                        .format(uuid.uuid4(), request.method, request.path, response.status))
-        return response
-
     # Redirecting root_path to root_path/api_name
     if api_name:
         @app.route("/")
diff --git a/hydrus/hydrus_logger.py b/hydrus/hydrus_logger.py
deleted file mode 100644
index d8b3ff9..0000000
--- a/hydrus/hydrus_logger.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import logging
-import logging.config
-import structlog
-import os
-
-class HydrusLogger:
-    def __init__(self):
-        logging.basicConfig(level = os.environ.get('LOGLEVEL', 'DEBUG'))
-        logging.config.fileConfig('LogConfig')
-        structlog.wrap_logger(logging.getLogger())
-        structlog.configure(logger_factory=structlog.stdlib.LoggerFactory())
-        self.logger = structlog.get_logger()
-
-    def get_logger(self):
-        return self.logger
diff --git a/poetry.lock b/poetry.lock
index 37b124f..d8b55b5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -49,21 +49,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "20.3.0"
+version = "21.2.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
-docs = ["furo", "sphinx", "zope.interface"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
-version = "2.9.0"
+version = "2.9.1"
 description = "Internationalization utilities"
 category = "main"
 optional = false
@@ -82,11 +82,11 @@ python-versions = "*"
 
 [[package]]
 name = "cachetools"
-version = "4.2.1"
+version = "3.1.1"
 description = "Extensible memoizing collections and decorators"
 category = "main"
 optional = false
-python-versions = "~=3.5"
+python-versions = "*"
 
 [[package]]
 name = "certifi"
@@ -155,17 +155,17 @@ pyflakes = ">=2.2.0,<2.3.0"
 
 [[package]]
 name = "flask"
-version = "1.1.2"
+version = "1.1.4"
 description = "A simple framework for building complex web applications."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
-click = ">=5.1"
-itsdangerous = ">=0.24"
-Jinja2 = ">=2.10.1"
-Werkzeug = ">=0.15"
+click = ">=5.1,<8.0"
+itsdangerous = ">=0.24,<2.0"
+Jinja2 = ">=2.10.1,<3.0"
+Werkzeug = ">=0.15,<2.0"
 
 [package.extras]
 dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
@@ -186,7 +186,7 @@ Six = "*"
 
 [[package]]
 name = "flask-restful"
-version = "0.3.8"
+version = "0.3.9"
 description = "Simple framework for creating REST APIs"
 category = "main"
 optional = false
@@ -215,11 +215,11 @@ python-socketio = ">=4.3.0"
 
 [[package]]
 name = "frozendict"
-version = "1.2"
-description = "An immutable dictionary"
+version = "2.0.2"
+description = "A simple immutable dictionary"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "gevent"
@@ -300,18 +300,19 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "2.1.1"
+version = "4.0.1"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.6"
 
 [package.dependencies]
+typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "rst.linker"]
-testing = ["packaging", "pep517", "unittest2", "importlib-resources (>=1.3)"]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "itsdangerous"
@@ -394,7 +395,7 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "8.7.0"
+version = "8.8.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "main"
 optional = false
@@ -411,17 +412,6 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 [package.dependencies]
 pyparsing = ">=2.0.2"
 
-[[package]]
-name = "pathlib2"
-version = "2.3.5"
-description = "Object-oriented filesystem paths"
-category = "main"
-optional = false
-python-versions = "*"
-
-[package.dependencies]
-six = "*"
-
 [[package]]
 name = "pep8"
 version = "1.7.1"
@@ -494,7 +484,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.8.1"
+version = "2.9.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = false
@@ -542,7 +532,6 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 more-itertools = ">=4.0.0"
 packaging = "*"
-pathlib2 = {version = ">=2.2.0", markers = "python_version < \"3.6\""}
 pluggy = ">=0.12,<1.0"
 py = ">=1.5.0"
 wcwidth = "*"
@@ -611,11 +600,11 @@ python-versions = "*"
 
 [[package]]
 name = "pyyaml"
-version = "5.3.1"
+version = "5.4.1"
 description = "YAML parser and emitter for Python"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
 [[package]]
 name = "requests"
@@ -708,11 +697,11 @@ test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "1.0.3"
+version = "2.0.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 
 [package.extras]
 lint = ["flake8", "mypy", "docutils-stubs"]
@@ -743,7 +732,7 @@ test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.4"
+version = "1.1.5"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
 category = "main"
 optional = false
@@ -773,6 +762,22 @@ postgresql_psycopg2binary = ["psycopg2-binary"]
 postgresql_psycopg2cffi = ["psycopg2cffi"]
 pymysql = ["pymysql (<1)", "pymysql"]
 
+[[package]]
+name = "structlog"
+version = "21.1.0"
+description = "Structured Logging for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+
+[package.extras]
+dev = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest-asyncio", "pytest-randomly", "pytest (>=6.0)", "simplejson", "furo", "sphinx", "sphinx-toolbox", "twisted", "pre-commit"]
+docs = ["furo", "sphinx", "sphinx-toolbox", "twisted"]
+tests = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest-asyncio", "pytest-randomly", "pytest (>=6.0)", "simplejson"]
+
 [[package]]
 name = "thespian"
 version = "3.9.11"
@@ -781,18 +786,25 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "typing-extensions"
+version = "3.10.0.0"
+description = "Backported and Experimental Type Hints for Python 3.5+"
+category = "main"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "urllib3"
-version = "1.26.4"
+version = "1.22"
 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.*, <4"
+python-versions = "*"
 
 [package.extras]
 secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
-brotli = ["brotlipy (>=0.6.0)"]
 
 [[package]]
 name = "wcwidth"
@@ -817,15 +829,15 @@ watchdog = ["watchdog"]
 
 [[package]]
 name = "zipp"
-version = "1.2.0"
+version = "3.4.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=2.7"
+python-versions = ">=3.6"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["pathlib2", "unittest2", "jaraco.itertools", "func-timeout"]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [[package]]
 name = "zope.event"
@@ -854,8 +866,8 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"]
 
 [metadata]
 lock-version = "1.1"
-python-versions = "^3.5.2"
-content-hash = "072ea29371ee77c5efda55dcae264d58e388f6d3d801de8c34fd0f4216b3742b"
+python-versions = ">=3.6.8"
+content-hash = "27edf8e86832fecb818625dac2a101b671f365deb30231247781187edb43a1a9"
 
 [metadata.files]
 alabaster = [
@@ -878,19 +890,19 @@ atomicwrites = [
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
 ]
 attrs = [
-    {file = "attrs-20.3.0-py2.py3-none-any.whl", hash = "sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6"},
-    {file = "attrs-20.3.0.tar.gz", hash = "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"},
+    {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
+    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
 ]
 babel = [
-    {file = "Babel-2.9.0-py2.py3-none-any.whl", hash = "sha256:9d35c22fcc79893c3ecc85ac4a56cde1ecf3f19c540bba0922308a6c06ca6fa5"},
-    {file = "Babel-2.9.0.tar.gz", hash = "sha256:da031ab54472314f210b0adcff1588ee5d1d1d0ba4dbd07b94dba82bde791e05"},
+    {file = "Babel-2.9.1-py2.py3-none-any.whl", hash = "sha256:ab49e12b91d937cd11f0b67cb259a57ab4ad2b59ac7a3b41d6c06c0ac5b0def9"},
+    {file = "Babel-2.9.1.tar.gz", hash = "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0"},
 ]
 blinker = [
     {file = "blinker-1.4.tar.gz", hash = "sha256:471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6"},
 ]
 cachetools = [
-    {file = "cachetools-4.2.1-py3-none-any.whl", hash = "sha256:1d9d5f567be80f7c07d765e21b814326d78c61eb0c3a637dffc0e5d1796cb2e2"},
-    {file = "cachetools-4.2.1.tar.gz", hash = "sha256:f469e29e7aa4cff64d8de4aad95ce76de8ea1125a16c68e0d93f65c3c3dc92e9"},
+    {file = "cachetools-3.1.1-py2.py3-none-any.whl", hash = "sha256:428266a1c0d36dc5aca63a2d7c5942e88c2c898d72139fca0e97fdd2380517ae"},
+    {file = "cachetools-3.1.1.tar.gz", hash = "sha256:8ea2d3ce97850f31e4a08b0e2b5e6c34997d7216a9d2c98e0f3978630d4da69a"},
 ]
 certifi = [
     {file = "certifi-2019.11.28-py2.py3-none-any.whl", hash = "sha256:017c25db2a153ce562900032d5bc68e9f191e44e9a0f762f373977de9df1fbb3"},
@@ -913,24 +925,36 @@ cffi = [
     {file = "cffi-1.14.5-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:48e1c69bbacfc3d932221851b39d49e81567a4d4aac3b21258d9c24578280058"},
     {file = "cffi-1.14.5-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:69e395c24fc60aad6bb4fa7e583698ea6cc684648e1ffb7fe85e3c1ca131a7d5"},
     {file = "cffi-1.14.5-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:9e93e79c2551ff263400e1e4be085a1210e12073a31c2011dbbda14bda0c6132"},
+    {file = "cffi-1.14.5-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:24ec4ff2c5c0c8f9c6b87d5bb53555bf267e1e6f70e52e5a9740d32861d36b6f"},
+    {file = "cffi-1.14.5-cp36-cp36m-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:3c3f39fa737542161d8b0d680df2ec249334cd70a8f420f71c9304bd83c3cbed"},
+    {file = "cffi-1.14.5-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:681d07b0d1e3c462dd15585ef5e33cb021321588bebd910124ef4f4fb71aef55"},
     {file = "cffi-1.14.5-cp36-cp36m-win32.whl", hash = "sha256:58e3f59d583d413809d60779492342801d6e82fefb89c86a38e040c16883be53"},
     {file = "cffi-1.14.5-cp36-cp36m-win_amd64.whl", hash = "sha256:005a36f41773e148deac64b08f233873a4d0c18b053d37da83f6af4d9087b813"},
     {file = "cffi-1.14.5-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:2894f2df484ff56d717bead0a5c2abb6b9d2bf26d6960c4604d5c48bbc30ee73"},
     {file = "cffi-1.14.5-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:0857f0ae312d855239a55c81ef453ee8fd24136eaba8e87a2eceba644c0d4c06"},
     {file = "cffi-1.14.5-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:cd2868886d547469123fadc46eac7ea5253ea7fcb139f12e1dfc2bbd406427d1"},
     {file = "cffi-1.14.5-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:35f27e6eb43380fa080dccf676dece30bef72e4a67617ffda586641cd4508d49"},
+    {file = "cffi-1.14.5-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:06d7cd1abac2ffd92e65c0609661866709b4b2d82dd15f611e602b9b188b0b69"},
+    {file = "cffi-1.14.5-cp37-cp37m-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:0f861a89e0043afec2a51fd177a567005847973be86f709bbb044d7f42fc4e05"},
+    {file = "cffi-1.14.5-cp37-cp37m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cc5a8e069b9ebfa22e26d0e6b97d6f9781302fe7f4f2b8776c3e1daea35f1adc"},
     {file = "cffi-1.14.5-cp37-cp37m-win32.whl", hash = "sha256:9ff227395193126d82e60319a673a037d5de84633f11279e336f9c0f189ecc62"},
     {file = "cffi-1.14.5-cp37-cp37m-win_amd64.whl", hash = "sha256:9cf8022fb8d07a97c178b02327b284521c7708d7c71a9c9c355c178ac4bbd3d4"},
     {file = "cffi-1.14.5-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:8b198cec6c72df5289c05b05b8b0969819783f9418e0409865dac47288d2a053"},
     {file = "cffi-1.14.5-cp38-cp38-manylinux1_i686.whl", hash = "sha256:ad17025d226ee5beec591b52800c11680fca3df50b8b29fe51d882576e039ee0"},
     {file = "cffi-1.14.5-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:6c97d7350133666fbb5cf4abdc1178c812cb205dc6f41d174a7b0f18fb93337e"},
     {file = "cffi-1.14.5-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:8ae6299f6c68de06f136f1f9e69458eae58f1dacf10af5c17353eae03aa0d827"},
+    {file = "cffi-1.14.5-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:04c468b622ed31d408fea2346bec5bbffba2cc44226302a0de1ade9f5ea3d373"},
+    {file = "cffi-1.14.5-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:06db6321b7a68b2bd6df96d08a5adadc1fa0e8f419226e25b2a5fbf6ccc7350f"},
+    {file = "cffi-1.14.5-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:293e7ea41280cb28c6fcaaa0b1aa1f533b8ce060b9e701d78511e1e6c4a1de76"},
     {file = "cffi-1.14.5-cp38-cp38-win32.whl", hash = "sha256:b85eb46a81787c50650f2392b9b4ef23e1f126313b9e0e9013b35c15e4288e2e"},
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@@ -1251,19 +1300,35 @@ pytz = [
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@@ -1290,8 +1355,8 @@ sphinxcontrib-devhelp = [
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 ]
 sphinxcontrib-htmlhelp = [
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@@ -1302,8 +1367,8 @@ sphinxcontrib-qthelp = [
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 sphinxcontrib-serializinghtml = [
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@@ -1341,12 +1406,21 @@ sqlalchemy = [
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 ]
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 urllib3 = [
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@@ -1357,8 +1431,8 @@ werkzeug = [
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 zipp = [
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diff --git a/pyproject.toml b/pyproject.toml
index 8de3d03..ffdce87 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,20 +1,21 @@
 [tool.poetry]
 name = "hydrus"
-version = "0.4.1"
+version = "0.4.2"
 description = "Hydra Ecosystem Flagship Server. Deploy REST data for Web 3.0"
 authors = ["Hydra Ecosystem"]
 license = "MIT License"
 
 [tool.poetry.dependencies]
-python = "^3.5.2"
+python = ">=3.6.8"
 alembic = "~1.0.10"
 aniso8601 = "~3.0.2"
 appdirs = "~1.4.3"
 blinker = "~1.4"
 click = "~7.1.2"
 certifi = "~2019.11.28"
+flake8 = "~3.8.3"
 Flask = "~1.1.1"
-Flask-Cors = "~3.0.8"
+Flask-Cors = ">=3.0.10"
 Flask-RESTful = "~0.3.7"
 Flask-SocketIO = "~4.2.1"
 gevent = "~20.12.0"
@@ -38,12 +39,12 @@ python-editor = "~1.0.4"
 python-engineio = "~3.11.2"
 python-socketio = "~4.4.0"
 pytz = "~2019.3"
-PyYAML = ">=5.3"
+PyYAML = ">=5.4"
 six = "~1.13.0"
 SQLAlchemy = "~1.3.12"
+structlog = ">=21.1.0"
 thespian = "~3.9.11"
 Werkzeug = "~0.16.0"
-flake8 = "~3.8.3"
 
 [tool.poetry.dev-dependencies]
 
diff --git a/requirements.txt b/requirements.txt
index 9017b63..495b6eb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,7 +6,7 @@ click==7.1.2
 certifi==2019.11.28
 flake8
 Flask==1.1.1
-Flask-Cors==3.0.8
+Flask-Cors==3.0.10
 Flask-RESTful==0.3.7
 Flask-SocketIO==4.2.1
 gevent==20.12.0
@@ -30,7 +30,7 @@ python-editor==1.0.4
 python-engineio==3.11.2
 python-socketio==4.4.0
 pytz==2019.3
-PyYAML==5.3
+PyYAML==5.4.1
 six==1.13.0
 SQLAlchemy==1.3.12
 thespian==3.9.11


Test patch:
diff --git a/tests/test_pep8.py b/tests/test_pep8.py
index 81a7c7c..e9eb853 100644
--- a/tests/test_pep8.py
+++ b/tests/test_pep8.py
@@ -1,24 +1,25 @@
 """Run PEP8 code format checker on all python files except samples directory."""
 
 import os
-from os.path import abspath, dirname
+from os.path import abspath, dirname, join
+import logging
 
 import pep8
 
 
 def test_pep8():
     """Test method to check PEP8 compliance over the entire project."""
-    file_structure = dirname(dirname(abspath(__file__)))
-    print(f"Testing for PEP8 compliance of python files in {file_structure}")
+    file_structure = join(dirname(dirname(__file__)), 'hydrus')
+    logging.info(f"Testing for PEP8 compliance of python files in {file_structure}")
     style = pep8.StyleGuide()
     style.options.max_line_length = 100  # Set this to desired maximum line length
     filenames = []
     # Set this to desired folder location
     for root, _, files in os.walk(file_structure):
-        python_files = [f for f in files if f.endswith('.py') and "examples" not in root]
+        exclude = ['samples', 'examples']
+        python_files = [f for f in files if f.endswith('.py') and all(e not in root for e in exclude)]
         for file in python_files:
-            if len(root.split('samples')) != 2:     # Ignore samples directory
-                filename = f'{root}/{file}'
-                filenames.append(filename)
+            filename = f'{root}/{file}'
+            filenames.append(filename)
     check = style.check_files(filenames)
     assert check.total_errors == 0, f'PEP8 style errors: check.total_errors'