Bumps [types-requests](https://github.com/python/typeshed) from 2.25.6 to 2.25.9.
- [Release notes](https://github.com/python/typeshed/releases)
- [Commits](https://github.com/python/typeshed/commits

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Bumps [flask](https://github.com/pallets/flask) from 2.0.1 to 2.0.2.
- [Release notes](https://github.com/pallets/flask/releases)
- [Changelog](https://github.com/pallets/flask/blob/main/CHANGES.rst)
- [Commits](https://github.com/pallets/flask/compare/2.0.1...2.0.2

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* renamed --skip-errors to --ignore-unmatched-graphics

* implemented --skip-errors

* run test_should_annotate_using_jats_xml using beam

* fixed MapOrLog usage when skipping errors

* moved bbox main to separate module

* renamed test module to match main module under test

* conditionally write dummy copy of xml file

* renamed to output_json_path

* added coords attribute

* using namespace for coords attribute

* add namespace to nsmap

* process pdf and xml file lists

* allow sub directories in output path

* make output_annotated_images_path relative to output

* make sure that output directory is created

* use write_bytes in favour of explicit makedirs (cloud ready)

* make --pdf-base-path required

* added pipeline

* not extending ABC due to serialization errors

* log pipeline options

* added test to check serialization

* changed super import to avoid one of the serialization errors in Dataflow

* moved most functionality to separate module

* added libgl1 to setup.py

* added PreventFusion

* minor import grouping

* added TransformAndCount

* reverted super __init__ call

* use parse args, not ignoring unknown args

* expose all of the worker arguments

* added BoundingBoxScoreSummary

* added TestGetBoundingBoxMatchScoreSummary

* implemented algorithm to adjust final bounding box

* specify cache key for object keypoints

* made image id required for lower level functions

* added logging to find bounding boxes

* 2nd it to find bounding box without bounding box

* use fixed size when calculating image similarity

* calculate structural similarity using skimage

* fixed crop_image_to_bounding_box

* output score in JSON

* optionally output images with bounding boxes

* display bbox label inside if not enough space above

* sort by score, then key points

* fixed cache issue by using explicit cache key prefix

(otherwise ids may have been reused after memory being freed)

* raise GraphicImageNotFoundError

* allow skipping errors

* enable debug logging for tests

* added cli scaffolding

* extract images from pdf

* fixed type hint

* added bounding box to_list

* converted bounding box to named tuple

* added tests for validate

* implemented bounding box intersection

* implemented finding bounding boxes of single image

* added test for smaller partial image

* added libgl1 for open cv

* linting: use with statement for Popen

* added support for multiple image files

* added support for xml files

* join graphic href with xml dirname

* renamed cv2 to cv

* using ObjectDetectorMatcher

* moved funtions to image object matching module

* added TestGetObjectMatch

* added ImageObjectMarchResult

* added test_should_match_smaller_image

* added test_should_match_smaller_rotated_90_image

* fixed typo ImageObjectMatchResult

* moved object_detector_matcher parameter down

* added get_image_list_object_match

* added su...

Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.4 to 6.2.5.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/6.2.4...6.2.5

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* using single dockerfile

* updated docker compose config version

* refactored dockerfile

* calling dev tools via python module

* removed install_dev argument

* fixed DOCKER_DEV_RUN placeholder

* minor refactory of apt-get command

* using builder image

* updated nltk data directory

* added mypy dependency

* added dev-mypy

* added mypy make target

* declare EMPTY class prop

* removed incorrect tensors type hint

* added type hint to excluded_tokens

* removed unused ProcessedWrapper

* replacing backports.tempfile with builtin

* added T_ArgumentParserOrGroup

* fixed iter_tokenized_tokens return type hint

* added types-requests

* added type to DEFAULT_ANNOTATORS

* removed blank line

* ignore distutils import

* replaced T_Element with etree.ElementBase

* changed type check back to etree._Element

* replaced project_tests.sh

* removed second mypy make target dependency

Bumps [tensorflow-transform](https://github.com/tensorflow/transform) from 0.25.0 to 1.3.0.
- [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/v0.25.0...v1.3.0

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* Bump pylint from 2.8.3 to 2.10.2

Bumps [pylint](https://github.com/PyCQA/pylint) from 2.8.3 to 2.10.2.
- [Release notes](https://github.com/PyCQA/pylint/releases)
- [Changelog](https://github.com/PyCQA/pylint/blob/main/ChangeLog)
- [Commits](https://github.com/PyCQA/pylint/compare/v2.8.3...v2.10.2

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* make installing dependencies more predictable

* downgrade numpy due to conflict with apache beam

* downgraded numpy further due to conflict with tensorflow

* linting: use dict literal

* linting: pass in encoding to open function

* linting: pcoll renamed to input_or_inputs

* linting: iterate over list

* linting: use from .. import

* added pyarrow as explicit dependency

* downgrade google-cloud-bigquery

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Bumps [gevent](https://github.com/gevent/gevent) from 21.1.2 to 21.8.0.
- [Release notes](https://github.com/gevent/gevent/releases)
- [Changelog](https://github.com/gevent/gevent/blob/master/docs/changelog_pre.rst)
- [Commits](https://github.com/gevent/gevent/compare/21.1.2...21.8.0

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Bumps [apache-beam[gcp]](https://github.com/apache/beam) from 2.31.0 to 2.32.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Changelog](https://github.com/apache/beam/blob/master/CHANGES.md)
- [Commits](https://github.com/apache/beam/compare/v2.31.0...v2.32.0

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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.62.0 to 4.62.2.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.62.0...v4.62.2

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Bumps [numpy](https://github.com/numpy/numpy) from 1.21.1 to 1.21.2.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt)
- [Commits](https://github.com/numpy/numpy/compare/v1.21.1...v1.21.2

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Bumps [pip](https://github.com/pypa/pip) from 21.2.2 to 21.2.4.
- [Release notes](https://github.com/pypa/pip/releases)
- [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst)
- [Commits](https://github.com/pypa/pip/compare/21.2.2...21.2.4

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* initial create vocabulary utility

* extract vocabulary from embeddings

* renamed to --output-word-count-file

* added main call

* extracted iter_tokenized_tokens

* avoid empty tokens

* using tokenizer from delft

* optionally sort by count

* added file list support

* added support for remote files

* added limit argument

* added fsspec dependency

* optionally use multi threading or processing

* included full github link

* renamed to create_vocabulary

* moved to tools vocabulary

* filter embeddings

* renamed to embeddings

* using fsspec to open embeddings file when extracting

* use fsspec when filtering embeddings

* document tools

* added link to tools.md

* Bump apache-beam[gcp] from 2.28.0 to 2.29.0

Bumps [apache-beam[gcp]](https://github.com/apache/beam) from 2.28.0 to 2.29.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Changelog](https://github.com/apache/beam/blob/master/CHANGES.md)
- [Commits](https://github.com/apache/beam/compare/v2.28.0...v2.29.0

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* replaced mock with unittest.mock

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