Commits · 85754f2d1bb9bd06926f9f76a2b00ee3bca46e53 · Sciencebeam / Sciencebeam Gym

Jun 05, 2019

Daniel Ecer authored 5 years ago

* 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

85754f2d

Jun 03, 2019

Bump pytest from 4.5.0 to 4.6.1 (#102) · be58236b

dependabot-preview[bot] authored 5 years ago

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)

be58236b

Bump cython from 0.29.9 to 0.29.10 (#101) · e3c09a89

dependabot-preview[bot] authored 5 years ago

Bumps [cython](https://github.com/cython/cython) from 0.29.9 to 0.29.10.
- [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/0.29.9...0.29.10)

e3c09a89

moved tests (#104) · 43fe414c
Daniel Ecer authored 5 years ago

43fe414c

refactor build (#103) · aae39c7a

Daniel Ecer authored 5 years ago

* added Makefile; optionally install dev requirements

* added ci-build-and-test

* use ci-build-and-test

* don't install dev dependencies as part of project_tests

* renamed to dev

* use PROJECT_FOLDER for consistency with other projects

* change order of tests run

aae39c7a

May 31, 2019

Bump requests from 2.21.0 to 2.22.0 (#98) · c6a4062f

dependabot-preview[bot] authored 5 years ago

Bumps [requests](https://github.com/requests/requests) from 2.21.0 to 2.22.0.
- [Release notes](https://github.com/requests/requests/releases)
- [Changelog](https://github.com/kennethreitz/requests/blob/master/HISTORY.md)
- [Commits](https://github.com/requests/requests/compare/v2.21.0...v2.22.0

)

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c6a4062f

Bump pytest from 4.4.1 to 4.5.0 (#96) · 2fe78aad

dependabot-preview[bot] authored 5 years ago

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.4.1 to 4.5.0.
- [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/4.4.1...4.5.0

)

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2fe78aad

Bump apache-beam from 2.11.0 to 2.12.0 (#93) · d321f5cb

dependabot-preview[bot] authored 5 years ago

Bumps [apache-beam](https://github.com/apache/beam) from 2.11.0 to 2.12.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.11.0...v2.12.0

)

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d321f5cb

Bump tqdm from 4.31.1 to 4.32.1 (#97) · 24893213

dependabot-preview[bot] authored 5 years ago

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.31.1 to 4.32.1.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.31.1...v4.32.1

)

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

24893213

Bump sciencebeam-utils from 0.0.1 to 0.0.5 (#95) · 85dae441

dependabot-preview[bot] authored 5 years ago

Bumps [sciencebeam-utils](https://github.com/elifesciences/sciencebeam-utils) from 0.0.1 to 0.0.5.
- [Release notes](https://github.com/elifesciences/sciencebeam-utils/releases)
- [Commits](https://github.com/elifesciences/sciencebeam-utils/compare/v0.0.1...v0.0.5

)

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

85dae441

Bump cython from 0.29.7 to 0.29.9 (#99) · cceabeaa

dependabot-preview[bot] authored 5 years ago

Bumps [cython](https://github.com/cython/cython) from 0.29.7 to 0.29.9.
- [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/0.29.7...0.29.9)

cceabeaa

May 06, 2019

[Security] Bump tensorflow from 1.12.0 to 1.13.1 (#79) · 83056093

dependabot[bot] authored 5 years ago

* Bump tensorflow from 1.12.0 to 1.13.1

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 1.12.0 to 1.13.1.
- [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/v1.12.0...v1.13.1

)

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

* disables two pylint warnings after security upgrade to tensorflow 1.13.1

* dropped 'futures' version requirement for python3

83056093

Apr 18, 2019

Bump pytest from 4.4.0 to 4.4.1 (#91) · bfbf89d0

dependabot[bot] authored 5 years ago

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

)

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

bfbf89d0

Apr 15, 2019

Bump cython from 0.29.6 to 0.29.7 (#90) · cff65d80

dependabot[bot] authored 5 years ago

Bumps [cython](https://github.com/cython/cython) from 0.29.6 to 0.29.7.
- [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/0.29.6...0.29.7

)

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cff65d80

Apr 02, 2019

added root user check in setup.py (#89) · 3cb81cfd
Daniel Ecer authored 6 years ago
```
* added root user check in setup.py

* also check SCIENCEBEAM_GYM_NO_APT
```
3cb81cfd

Bump matplotlib from 2.2.3 to 2.2.4 (#81) · e148b156

dependabot[bot] authored 6 years ago

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 2.2.3 to 2.2.4.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v2.2.3...v2.2.4

)

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

e148b156

Bump tqdm from 4.30.0 to 4.31.1 (#70) · c40b6386

dependabot[bot] authored 6 years ago

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.30.0 to 4.31.1.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.30.0...v4.31.1

)

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

c40b6386

Bump numpy from 1.16.1 to 1.16.2 (#78) · 96a3de1f

dependabot[bot] authored 6 years ago

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

) from 1.16.1 to 1.16.2.

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

96a3de1f

Bump lxml from 4.3.2 to 4.3.3 (#86) · e7e2138e

dependabot[bot] authored 6 years ago

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.2 to 4.3.3.
- [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-4.3.2...lxml-4.3.3

)

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

e7e2138e

Bump pytest from 4.3.0 to 4.4.0 (#87) · 941b2d5a

dependabot[bot] authored 6 years ago

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.3.0 to 4.4.0.
- [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/4.3.0...4.4.0

)

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

941b2d5a

Mar 07, 2019

Bump tensorflow-transform from 0.11.0 to 0.13.0 (#83) · 307a2cd6

dependabot[bot] authored 6 years ago

Bumps [tensorflow-transform](https://github.com/tensorflow/transform) from 0.11.0 to 0.13.0.
- [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/v0.11.0...v0.13.0

)

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

307a2cd6

Bump apache-beam from 2.9.0 to 2.11.0 (#84) · ebfdbfd5

dependabot[bot] authored 6 years ago

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>

ebfdbfd5

Mar 01, 2019

Bump lxml from 4.3.1 to 4.3.2 (#82) · ed35ecf6

dependabot[bot] authored 6 years ago

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>

ed35ecf6

Feb 28, 2019

Bump cython from 0.29.5 to 0.29.6 (#80) · 3fac73e4

dependabot[bot] authored 6 years ago

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>

3fac73e4

Feb 26, 2019

Bump flake8 from 3.7.6 to 3.7.7 (#77) · 00e0fa4a

dependabot[bot] authored 6 years ago

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>

00e0fa4a

Feb 19, 2019

Bump flake8 from 3.7.5 to 3.7.6 (#74) · e55897b0

dependabot[bot] authored 6 years ago

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>

e55897b0

Bump pytest from 4.2.1 to 4.3.0 (#75) · 28d9aaca

dependabot[bot] authored 6 years ago

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>

28d9aaca

Feb 14, 2019

Bump pytest from 4.2.0 to 4.2.1 (#73) · e0c04d3c

dependabot[bot] authored 6 years ago

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>

e0c04d3c

Feb 11, 2019

Bump cython from 0.29.4 to 0.29.5 (#71) · e7d95e9a

dependabot[bot] authored 6 years ago

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>

e7d95e9a

Bump lxml from 4.3.0 to 4.3.1 (#69) · 2d24d113

dependabot[bot] authored 6 years ago

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>

2d24d113

Feb 05, 2019

Bump flake8 from 3.7.4 to 3.7.5 (#68) · 2bd22b65

dependabot[bot] authored 6 years ago

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>

2bd22b65

Feb 04, 2019

Bump six from 1.11.0 to 1.12.0 (#65) · aff8622e

dependabot[bot] authored 6 years ago

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

)

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aff8622e

Bump matplotlib from 2.2.2 to 2.2.3 (#66) · 5b974685

dependabot[bot] authored 6 years ago

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

)

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5b974685

Bump tensorflow-transform from 0.6.0 to 0.11.0 (#64) · 4f551434

dependabot[bot] authored 6 years ago


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

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

4f551434

Bump cython from 0.29.3 to 0.29.4 (#67) · 1ce1b528

dependabot[bot] authored 6 years ago

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>

1ce1b528

Feb 01, 2019

Bump fuzzywuzzy from 0.16.0 to 0.17.0 (#60) · 523738b0

dependabot[bot] authored 6 years ago

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>

523738b0

Bump numpy from 1.14.2 to 1.16.1 (#59) · 83c4c588

dependabot[bot] authored 6 years ago

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

) from 1.14.2 to 1.16.1.

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

83c4c588

Bump flake8 from 3.7.3 to 3.7.4 (#61) · 06b4dfae

dependabot[bot] authored 6 years ago

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>

06b4dfae

Bump lxml from 4.2.0 to 4.3.0 (#62) · 86c7eaa0

dependabot[bot] authored 6 years ago

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

)

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86c7eaa0

Bump pytest from 3.4.2 to 4.2.0 (#63) · 231187e4

dependabot[bot] authored 6 years ago

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

)

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231187e4