* Bump pylint from 2.3.1 to 2.4.4

Bumps [pylint](https://github.com/PyCQA/pylint) from 2.3.1 to 2.4.4.
- [Release notes](https://github.com/PyCQA/pylint/releases)
- [Changelog](https://github.com/PyCQA/pylint/blob/master/ChangeLog)
- [Commits](https://github.com/PyCQA/pylint/compare/pylint-2.3.1...pylint-2.4.4

)

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

* removed explicit astroid dependency

* linting

* more flake8 linting

* explicit pylint dependency

Co-authored-by: Daniel Ecer <de-code@users.noreply.github.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.8 to 3.7.9.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.8...3.7.9

)

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

Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.1.2 to 5.3.2.
- [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/5.1.2...5.3.2

)

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

* Bump tensorflow from 1.14.0 to 1.15.0

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 1.14.0 to 1.15.0.
- [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/v1.14.0...v1.15.0

)

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

* bumps version of docker image from 3.6.9 to 3.6.10

* upgrades pip inside docker

* fixing astroid and pylint versions to avoid false positives

Co-authored-by: LSH <lsh-0@users.noreply.github.com>

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.35.0 to 4.36.1.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.35.0...v4.36.1

)

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

* ugraded to python 3

* upgrade pylint and pytest

* replaced StandardError

* exclude useless-object-inheritance

* python3 compatibilities uncovered by linting

* fixed tests

* fixed more python3 test incompatibilities

Bumps [numpy](https://github.com/numpy/numpy) from 1.16.4 to 1.16.5.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/master/doc/HOWTO_RELEASE.rst.txt)
- [Commits](https://github.com/numpy/numpy/compare/v1.16.4...v1.16.5

)

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

* refactored dev make targets

* added MatchingAnnotatorConfig

* extracted ratio constants

* added get_simple_fuzzy_match_filter

Bumps [sciencebeam-alignment](https://github.com/elifesciences/sciencebeam-alignment) from 0.0.3 to 0.0.4.
- [Release notes](https://github.com/elifesciences/sciencebeam-alignment/releases)
- [Commits](https://github.com/elifesciences/sciencebeam-alignment/compare/v0.0.3...v0.0.4

)

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

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.34.0 to 4.35.0.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.34.0...v4.35.0

)

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

Bumps [sciencebeam-alignment](https://github.com/elifesciences/sciencebeam-alignment) from 0.0.2 to 0.0.3.
- [Release notes](https://github.com/elifesciences/sciencebeam-alignment/releases)
- [Commits](https://github.com/elifesciences/sciencebeam-alignment/compare/v0.0.2...v0.0.3

)

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

Bumps [apache-beam](https://github.com/apache/beam) from 2.14.0 to 2.15.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.14.0...v2.15.0

)

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

* Bump sciencebeam-utils from 0.0.6 to 0.1.0

Bumps [sciencebeam-utils](https://github.com/elifesciences/sciencebeam-utils) from 0.0.6 to 0.1.0.
- [Release notes](https://github.com/elifesciences/sciencebeam-utils/releases)
- [Commits](https://github.com/elifesciences/sciencebeam-utils/compare/v0.0.6...v0.1.0

)

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

* removed call to process_sciencebeam_gym_dep_args

Bumps [nltk](https://github.com/nltk/nltk) from 3.4.4 to 3.4.5.
- [Release notes](https://github.com/nltk/nltk/releases)
- [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog)
- [Commits](https://github.com/nltk/nltk/compare/3.4.4...3.4.5

)

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

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.6.2 to 4.6.5.
- [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/4.6.2...4.6.5

)

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

Bumps [tensorflow-transform](https://github.com/tensorflow/transform) from 0.13.0 to 0.14.0.
- [Release notes](https://github.com/tensorflow/transform/releases)
- [Changelog](https://github.com/tensorflow/transform/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/transform/compare/v0.13.0...v0.14.0

)

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

Bumps [lxml](https://github.com/lxml/lxml) from 4.4.0 to 4.4.1.
- [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-4.4.0...lxml-4.4.1

)

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

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.32.2 to 4.34.0.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.32.2...v4.34.0

)

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

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 1.13.1 to 1.14.0.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/v1.14.0/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v1.13.1...v1.14.0

)

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

Bumps [nltk](https://github.com/nltk/nltk) from 3.4.3 to 3.4.4.
- [Release notes](https://github.com/nltk/nltk/releases)
- [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog)
- [Commits](https://github.com/nltk/nltk/commits

)

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

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.32.1 to 4.32.2.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.32.1...v4.32.2

)

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

Bumps [flask](https://github.com/pallets/flask) from 1.0.3 to 1.1.1.
- [Release notes](https://github.com/pallets/flask/releases)
- [Changelog](https://github.com/pallets/flask/blob/master/CHANGES.rst)
- [Commits](https://github.com/pallets/flask/compare/1.0.3...1.1.1

)

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

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.7 to 3.7.8.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.7...3.7.8

)

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

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.4 to 4.4.0.
- [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-4.3.4...lxml-4.4.0

)

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

Bumps [apache-beam](https://github.com/apache/beam) from 2.13.0 to 2.14.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.13.0...v2.14.0

)

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

Bumps [sciencebeam-utils](https://github.com/elifesciences/sciencebeam-utils) from 0.0.5 to 0.0.6.
- [Release notes](https://github.com/elifesciences/sciencebeam-utils/releases)
- [Commits](https://github.com/elifesciences/sciencebeam-utils/compare/v0.0.5...v0.0.6

)

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

* minor model training logging improvement

* make port configurable

* added autocut-start-cloud

Bumps [nltk](https://github.com/nltk/nltk) from 3.4.1 to 3.4.3.
- [Release notes](https://github.com/nltk/nltk/releases)
- [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog)
- [Commits](https://github.com/nltk/nltk/compare/3.4.1...3.4.3

)

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

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.3 to 4.3.4.
- [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-4.3.3...lxml-4.3.4

)

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

* move checkout and move to master into containers node

* use elifePipeline

* push unstable image

Bumps [numpy](https://www.numpy.org) from 1.16.2 to 1.16.4.

Bumps [apache-beam](https://github.com/apache/beam) from 2.12.0 to 2.13.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.12.0...v2.13.0)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.6.1 to 4.6.2.
- [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/4.6.1...4.6.2)

* added dev-venv target

* added subextract model

* added nltk dependency

* flake8 ignore line break before binary operator

* moved dev dependencies up

* added nltk punkt download

* added nltk download to dev-venv; pytest and pytest-not-slow target

* added subextract training pipeline

* added optional xpath namespaces

* log failed xml file

* use recover parser option

* added subextract app

* start subextract server

* renamed to autocut

* declare slow and very_slow pytest markers

* make autocut main test as slow

* fixed post data

* updated README

* also build non-dev image as part of ci

* added pytest.ini to dev image

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.5.0 to 4.6.1.
- [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/4.5.0...4.6.1)