Bumps [apache-beam](https://github.com/apache/beam) from 2.9.0 to 2.11.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.9.0...v2.11.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.1 to 4.3.2.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.3.1...lxml-4.3.2

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.5 to 0.29.6.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.5...0.29.6

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.6 to 3.7.7.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.6...3.7.7

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.5 to 3.7.6.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.5...3.7.6

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.2.1 to 4.3.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.2.1...4.3.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.2.0 to 4.2.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.2.0...4.2.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.4 to 0.29.5.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.4...0.29.5

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.0 to 4.3.1.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.3.0...lxml-4.3.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.4 to 3.7.5.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.4...3.7.5

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [six](https://github.com/benjaminp/six) from 1.11.0 to 1.12.0.
- [Release notes](https://github.com/benjaminp/six/releases)
- [Changelog](https://github.com/benjaminp/six/blob/master/CHANGES)
- [Commits](https://github.com/benjaminp/six/compare/1.11.0...1.12.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 2.2.2 to 2.2.3.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v2.2.2...v2.2.3

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [tensorflow-transform]() from 0.6.0 to 0.11.0.

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.3 to 0.29.4.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.3...0.29.4

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [fuzzywuzzy](https://github.com/seatgeek/fuzzywuzzy) from 0.16.0 to 0.17.0.
- [Release notes](https://github.com/seatgeek/fuzzywuzzy/releases)
- [Changelog](https://github.com/seatgeek/fuzzywuzzy/blob/master/CHANGES.rst)
- [Commits](https://github.com/seatgeek/fuzzywuzzy/compare/0.16.0...0.17.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [numpy](https://www.numpy.org

) from 1.14.2 to 1.16.1.

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.3 to 3.7.4.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.3...3.7.4

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.2.0 to 4.3.0.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.2.0...lxml-4.3.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 3.4.2 to 4.2.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/3.4.2...4.2.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 1.6.0 to 1.12.0.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v1.6.0...v1.12.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pyqtree](https://github.com/karimbahgat/Pyqtree) from 0.24 to 1.0.0.
- [Release notes](https://github.com/karimbahgat/Pyqtree/releases)
- [Changelog](https://github.com/karimbahgat/Pyqtree/blob/master/CHANGES.txt)
- [Commits](https://github.com/karimbahgat/Pyqtree/commits

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [python-crfsuite](https://github.com/scrapinghub/python-crfsuite) from 0.9.5 to 0.9.6.
- [Release notes](https://github.com/scrapinghub/python-crfsuite/releases)
- [Changelog](https://github.com/scrapinghub/python-crfsuite/blob/master/CHANGES.rst)
- [Commits](https://github.com/scrapinghub/python-crfsuite/compare/0.9.5...0.9.6

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

* Bump apache-beam from 2.4.0 to 2.9.0

Bumps [apache-beam](https://beam.apache.org

) from 2.4.0 to 2.9.0.

Signed-off-by: dependabot[bot] <support@dependabot.com>

* removed outdated explicit dependency on protobuf

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.19.8 to 4.30.0.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.19.8...v4.30.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

* Bump flake8 from 3.5.0 to 3.7.3

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.5.0 to 3.7.3.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.5.0...3.7.3

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

* removed direct dependency on pycodestyle

* ignore W504 flake8 rule (changed recommendation)

* changed noqa comment (old one was ignored)

Bumps [pylint](https://github.com/PyCQA/pylint) from 1.8.3 to 1.9.4.
- [Release notes](https://github.com/PyCQA/pylint/releases)
- [Changelog](https://github.com/PyCQA/pylint/blob/pylint-1.9.4/ChangeLog)
- [Commits](https://github.com/PyCQA/pylint/compare/pylint-1.8.3...pylint-1.9.4

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest-watch](https://github.com/joeyespo/pytest-watch) from 4.1.0 to 4.2.0.
- [Release notes](https://github.com/joeyespo/pytest-watch/releases)
- [Changelog](https://github.com/joeyespo/pytest-watch/blob/master/CHANGES.md)
- [Commits](https://github.com/joeyespo/pytest-watch/compare/v4.1.0...v4.2.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [requests](https://github.com/requests/requests) from 2.20.0 to 2.21.0.
- [Release notes](https://github.com/requests/requests/releases)
- [Changelog](https://github.com/requests/requests/blob/master/HISTORY.md)
- [Commits](https://github.com/requests/requests/compare/v2.20.0...v2.21.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.28.1 to 0.29.3.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.28.1...0.29.3

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

* added pylint check

* added pylintrc to docker image

* reduced accessive apache beam debug logging

* configured pylint, addressed linting

* enabled flake8 checks

* downgrade pycodestyle to 2.3.1 due to error

* switch to 4 spaces indent

* autopep8

* more flake8

* added new line to .flake8

bumps requests to 2.20.0

* added sciencebeam-utils and sciencebeam-alignment dependency

* replaced local alignment module with sciencebeam-alignment

* replaced local beam_utils with sciencebeam-utils

* replaced local utils with sciencebeam-utils for modules that have moved

* removed tools that have been moved to sciencebeam-utils

* removed utility functions that have moved to sciencebeam-utils

* updated readme

* moved crf and cv conversion pipelines to sciencebeam-gym

* copied documentation from sciencebeam