* replace dagger html entity

* strip extra spaces at beginning of xml document

* 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

* 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...