* 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 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

* 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

)

---
updated-dependencies:
- dependency-name: pylint
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

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

* 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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Daniel Ecer <de-code@users.noreply.github.com>

* added root user check in setup.py

* also check SCIENCEBEAM_GYM_NO_APT

* 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