Update locked deps for dev and docs

Otherwise the new setup.py dep on s3fs[boto3] is in conflict with the
locked deps.

.readthedocs-requirements.txt

@@ -6,69 +6,80 @@
 
 # Output of `pipenv run pip freeze`, with the git-based package spec for the
 # CLI removed in favor of the above local dir spec.
-aiobotocore==1.2.1
-aiohttp==3.7.4.post0
-aioitertools==0.7.1
+aiobotocore==1.4.2
+aiohttp==3.8.0
+aioitertools==0.8.0
+aiosignal==1.2.0
 alabaster==0.7.12
-async-timeout==3.0.1
-attrs==20.3.0
-Babel==2.9.0
+async-timeout==4.0.0
+asynctest==0.13.0
+attrs==21.2.0
+Babel==2.9.1
 boto3==1.16.52
-botocore==1.19.52
-certifi==2020.12.5
-chardet==4.0.0
+botocore==1.20.106
+certifi==2021.10.8
+cffi==1.15.0
+chardet==3.0.4
+charset-normalizer==2.0.7
 commonmark==0.9.1
+cryptography==35.0.0
 docutils==0.15.2
-filelock==3.0.12
-flake8==3.8.4
-fsspec==0.8.7
-idna==2.10
+fasteners==0.16.3
+filelock==3.3.2
+flake8==4.0.1
+frozenlist==1.2.0
+fsspec==2021.10.1
+idna==3.3
 idna-ssl==1.1.0
 imagesize==1.2.0
-importlib-metadata==3.7.2
+importlib-metadata==4.2.0
 iniconfig==1.1.1
-Jinja2==2.11.3
+Jinja2==3.0.2
 jmespath==0.10.0
 Markdown==3.3.4
-MarkupSafe==1.1.1
+MarkupSafe==2.0.1
 mccabe==0.6.1
-multidict==5.1.0
-mypy==0.812
+multidict==5.2.0
+mypy==0.910
 mypy-extensions==0.4.3
-netifaces==0.10.9
-nextstrain-sphinx-theme==2020.6
-packaging==20.9
-pluggy==0.13.1
+netifaces==0.11.0
+nextstrain-sphinx-theme==2021.3
+packaging==21.2
+pluggy==1.0.0
 py==1.10.0
-pycodestyle==2.6.0
-pyflakes==2.2.0
-Pygments==2.8.1
+pycodestyle==2.8.0
+pycparser==2.20
+pyflakes==2.4.0
+Pygments==2.10.0
+PyJWT==2.3.0
 pyparsing==2.4.7
-pytest==6.2.2
+pytest==6.2.5
 pytest-flake8==1.0.7
-pytest-mypy==0.8.0
-python-dateutil==2.8.1
-pytz==2021.1
+pytest-mypy==0.8.1
+python-dateutil==2.8.2
+pytz==2021.3
 recommonmark==0.7.1
-requests==2.25.1
-s3fs==0.5.1
+requests==2.26.0
+s3fs==2021.10.1
 s3transfer==0.3.4
-six==1.15.0
+six==1.16.0
 snowballstemmer==2.1.0
-Sphinx==3.5.2
+Sphinx==4.2.0
 sphinx-argparse @ https://github.com/alex-rudakov/sphinx-argparse/archive/b3b649743d4f8854349a2416ccdd770f41739c35.tar.gz
 sphinx-markdown-tables==0.0.15
-sphinx-rtd-theme==0.5.1
+sphinx-rtd-theme==1.0.0
 sphinxcontrib-applehelp==1.0.2
 sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==1.0.3
+sphinxcontrib-htmlhelp==2.0.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.4
+sphinxcontrib-serializinghtml==1.1.5
 toml==0.10.2
-typed-ast==1.4.2
-typing-extensions==3.7.4.3
-urllib3==1.26.3
-wrapt==1.12.1
-yarl==1.6.3
-zipp==3.4.1
+typed-ast==1.4.3
+types-requests==2.25.11
+types-setuptools==57.4.2
+typing-extensions==3.10.0.2
+urllib3==1.26.7
+wrapt==1.13.3
+yarl==1.7.2
+zipp==3.6.0