Enable preprocessing of arXiv submission contents (#364)

* Enable preprocessing arXiv submission contents

* Document `preprocess_arxiv`

* Use copytree instead of copy

* Fix Path conversion

* Only copy upon preprocess

* Reduce preprocess option to a single param

* Rearrange cookiecutter comment

Enable preprocessing of arXiv submission contents (#364)

* Enable preprocessing arXiv submission contents

* Document `preprocess_arxiv`

* Use copytree instead of copy

* Fix Path conversion

* Only copy upon preprocess

* Reduce preprocess option to a single param

* Rearrange cookiecutter comment

remove conditional that removes hometemp (#363)

Enable custom root directory of build commands (#348)

* Add project flag to CLI

* Refactor `--project` to use contextmanager

* Refactor click options to avoid repetition

* Refactor click options to be set by common dicts

Fixed build warnings (#275) (#276)

* Using find_namespace_packages in setup to silence build warnings

* updating MANIFEST

Fixed build warnings (#275) (#276)

* Using find_namespace_packages in setup to silence build warnings

* updating MANIFEST

Protected the \nolinenumbers command (#251) (#274)

* Protected the \nolinenumbers command

The \nolinenumbers command is defined by the lineno package that isn't required, added the conditional check for the \numlines flag defined when lineno is imported

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: Christopher Lee <eelsirhc@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Update HISTORY.rst

update docs [skip ci]

Pin tabulate to fix snakemake AttributeError