Ibridges

Adding a commandline interface to the package.

What's Changed
* Python package uses latest PRC version by wurDevTim in https://github.com/UtrechtUniversity/iBridges/pull/108
* Reset CI/CD pipeline to do linting on all python versions by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/110
* Add user info to session, bugfix in session by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/114
* Add CLI to ibridges for sync/upload/download/init by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/109
* Adjust test setup with second resource for CLI by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/116

New Contributors
* wurDevTim made their first contribution in https://github.com/UtrechtUniversity/iBridges/pull/108

**Full Changelog**: https://github.com/UtrechtUniversity/iBridges/compare/v0.1.3...v0.1.4

- Bug fixes:
- checksum bug in sync_data
- README: bug in iRODS connection
- Quickstart tutuorial

- New feature: *Export metadata*
- Upload/Download: Introduce flag to turn exceptions into warnings when uploading collecions and folders

What's Changed
* Fix capitalization of tutorials by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/70
* Expand user home directory in `irods_env_path` by jpmcfarland in https://github.com/UtrechtUniversity/iBridges/pull/71
* 73 check tutorials by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/75
* Feature py37 types by maartenschermer in https://github.com/UtrechtUniversity/iBridges/pull/76
* 72 export metadata by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/83
* Add close method to session and remove __del__ by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/85
* Remove the keywords.py by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/86
* 84 simplify checksum in sync by maartenschermer in https://github.com/UtrechtUniversity/iBridges/pull/88
* Fix iBridges working in Python 3.8 by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/89
* Update integration-tests-irods.yml by dometto in https://github.com/UtrechtUniversity/iBridges/pull/91
* Fix ci by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/92
* Revert "Fix ci" by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/93
* Fixing typo in README by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/95
* Update integration-tests-irods.yml by dometto in https://github.com/UtrechtUniversity/iBridges/pull/97
* Improve errors by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/87
* sync: return dict of changed items by dometto in https://github.com/UtrechtUniversity/iBridges/pull/90
* fixed checksum-check NoneType error by maartenschermer in https://github.com/UtrechtUniversity/iBridges/pull/101
* Improving the error when upload or download fails by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/104
* Removing os module, tickets switched to demofile by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/106
* Bug fixes and tutorial updates by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/107

New Contributors
* jpmcfarland made their first contribution in https://github.com/UtrechtUniversity/iBridges/pull/71

**Full Changelog**: https://github.com/UtrechtUniversity/iBridges/compare/v0.1.2...v0.1.3

What's Changed
* Merge pull request 62 from UtrechtUniversity/develop by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/63
* iRODS integration tests by dometto in https://github.com/UtrechtUniversity/iBridges/pull/59
* Add tutorials and update README by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/65
* Polish off some small things by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/67
* New release with new license by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/68

New Contributors
* dometto made their first contribution in https://github.com/UtrechtUniversity/iBridges/pull/59

**Full Changelog**: https://github.com/UtrechtUniversity/iBridges/compare/v0.1.1...v0.1.2

What's Changed
* pypi release hook by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/61
* pypi release hook (61) by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/62


**Full Changelog**: https://github.com/UtrechtUniversity/iBridges/compare/v0.1.0...v0.1.1

- Using ibridges as backend
- Refactor tab views

- Refactoring of backend
- Configuration:
- Introducing new keys in ibridges_config.json: `check_free_space`, `force_transfers`, `amber_token`, `eln_token`
- All configuration is stored in a singleton `context` (utils.context.py); ibridges config is read in automatically; irods config can be set through offering the path to the irods_environment.json
- Logging: introduce log-levels, configurable in ibridges_config.json
- GUI:
- Improvements in frontend for ElabJournal and AmberScript tab
- Bundeling data: Check ACLs and respect `force_transfers` flag in configuration

- iBridgesCli.py:
- own config file is dropped and replaced by reading configuration from ibridges_config.json and irods_environment.json
- Elabjournal is moved to a plugin for Cli

What's Changed
* checking if the irods session is valid by wurDevTim in https://github.com/chStaiger/iBridges-Gui/pull/62
* Adding Amberscript connector to the merged code base. by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/66
* [65] Remove unneeded annotations by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/71
* Irods connector rewrite part 1 by wurDevTim in https://github.com/chStaiger/iBridges-Gui/pull/72
* Refactor cli new by maartenschermer in https://github.com/chStaiger/iBridges-Gui/pull/76
* Develop by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/77
* Ibridges context by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/78
* Test hooking by maartenschermer in https://github.com/chStaiger/iBridges-Gui/pull/79
* [73] Adjust session handling by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/80
* [85] Allow independent backend session by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/86
* Icommands refactor by maartenschermer in https://github.com/chStaiger/iBridges-Gui/pull/90
* [96] Fix print to logging bugs by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/97
* bugfix meta class not instantiated in manager by wurDevTim in https://github.com/chStaiger/iBridges-Gui/pull/104
* Cli integration by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/98
* Cli integration by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/106
* cli_improvements by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/112
* [108] Unify logging initialization by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/109
* [103] Connectors issues by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/105
* Cli session handling by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/114
* Feature request: 95 by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/116
* 115 gui elab and amber tabs hide tokens by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/117
* 40 how to integrate a new tab by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/118
* Updating user docs by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/119
* [121] Adjust Context workflow by jpmcfarland in https://github.com/chStaiger/iBridges-Gui/pull/122
* Check push by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/124
* CLI plugins compatible with Python 3.8 by maartenschermer in https://github.com/chStaiger/iBridges-Gui/pull/127
* Create iBridges-alpha-0.0.1 by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/120
* Fix bug in getting acls. by chStaiger in https://github.com/chStaiger/iBridges-Gui/pull/132

New Contributors
* maartenschermer made their first contribution in https://github.com/chStaiger/iBridges-Gui/pull/76

**Full Changelog**: https://github.com/chStaiger/iBridges-Gui/compare/v0.0.1-alpha...v0.0.2-alpha