Refinegems

What's Changed
* Small improvement + Security Hot-Fixes by cb-Hades in https://github.com/draeger-lab/refinegems/pull/136
* Update version in pyproject.toml by GwennyGit in https://github.com/draeger-lab/refinegems/pull/137
* Update requirements.txt by GwennyGit in https://github.com/draeger-lab/refinegems/pull/138
* Update .readthedocs.yaml by GwennyGit in https://github.com/draeger-lab/refinegems/pull/139
* Patch 3 for read the docs by GwennyGit in https://github.com/draeger-lab/refinegems/pull/140
* Updated conf.py for docs by GwennyGit in https://github.com/draeger-lab/refinegems/pull/141
* Updated conf.py by GwennyGit in https://github.com/draeger-lab/refinegems/pull/142
* Updated conf.py by GwennyGit in https://github.com/draeger-lab/refinegems/pull/143
* Adjusted type hinting for Unions by GwennyGit in https://github.com/draeger-lab/refinegems/pull/144
* Updated regexes to raw strings by GwennyGit in https://github.com/draeger-lab/refinegems/pull/145
* Updated regexes to raw strings by GwennyGit in https://github.com/draeger-lab/refinegems/pull/146
* Updated regexes to raw strings by GwennyGit in https://github.com/draeger-lab/refinegems/pull/147
* Fixed documentation by GwennyGit in https://github.com/draeger-lab/refinegems/pull/148


**Full Changelog**: https://github.com/draeger-lab/refinegems/compare/v2.0.0a1...v2.0.0a2

What's Changed
- Fixed issues in `.classes.gapfill.GapFiller.fill_model` -> BioCycGapFiller is now usable.
- Fixed issues in `.analysis.growth.test_auxotrophies `-> Infeasible result from `model.optimize` is now handled as 0.0.
- Added a tutorial Python notebook
- Removed now obsolete deprecation warning from `index.html`
* Hot fixes for 2.0.0a0 pre-release by GwennyGit in https://github.com/draeger-lab/refinegems/pull/135


**Full Changelog**: https://github.com/draeger-lab/refinegems/compare/v2.0.0a0...v2.0.0a1

What's Changed
* For details see what cb-Hades + GwennyGit did in https://github.com/draeger-lab/refinegems/issues/121
* Polish update - Enable more GeneProduct annotations by GwennyGit in https://github.com/draeger-lab/refinegems/pull/88
* Refactoring of the complete program structure
* Move changes from structure update to dev-2 by GwennyGit in https://github.com/draeger-lab/refinegems/pull/119
* Merge dev-2 into dev to get refactoring ready for main by GwennyGit in https://github.com/draeger-lab/refinegems/pull/133
* Pre-release of version 2.0.0 by GwennyGit in https://github.com/draeger-lab/refinegems/pull/134


**Full Changelog**: https://github.com/draeger-lab/refinegems/compare/v1.5.0...v2.0.0a0

What's Changed
Due to changes in the planned-to-release version 2.0.0, which will lead to backward incompatibility for all functions, deprecation warnings for the end user were added to all modules and the documentation.
* Dev by GwennyGit in https://github.com/draeger-lab/refinegems/pull/132


**Full Changelog**: https://github.com/draeger-lab/refinegems/compare/v1.4.2...v1.5.0

The latest version did not import after it was downloaded from PyPI. This hotfix resolves the issue.

With this release, the following files are updated:
- README
- Makefile and make.bat
- requirements.txt
- main.py

For the documentation to work, a `requirements.in` file was created to automatically update the `requirements.txt` to make it more reproducible. Furthermore, the documentation for the ‘Notes for developers’ section is updated, and minor bugs in the `main.py` file are fixed.