Ibridges

API:
- Add cwd to session and IrodsPath

CLI:
- Add metadata options
- Add cwd
- improve aliasing



What's Changed
* Add basic metadata options to CLI by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/293
* importlib-meta version by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/294
* CI: Fix Yoda integration tests by stsnel in https://github.com/iBridges-for-iRODS/iBridges/pull/298
* Add py.typed by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/295
* Move from Value -> fnf/nad error by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/297
* Workaround PRC different behavior file/dictionary by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/300
* Update the status of the project and the year by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/301
* Repl states by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/305
* Rework options by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/306
* Irods434 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/307
* Fix: setup no longer unintentionally overwrites existing env-file by maartenschermer in https://github.com/iBridges-for-iRODS/iBridges/pull/309
* Rework aliases to make them more user friendly by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/302
* v1.4.0 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/311


**Full Changelog**: https://github.com/iBridges-for-iRODS/iBridges/compare/v1.3.0...v1.4.0

- Metadata:
- one can now assign key, value and units separately to update a metadata entry
- When the Units of a metadata item are empty, then it will be displayed and treated in iBridges as `''`
- Search:
- The search now returns a list of `CachedIrodsPath`. This improves the performance when retrieving sizes and checksums.
- Data operations:
- New flag to disable the tqdm status bar when working with a lot of parallel transfers
- Bugfix
- Password field was not shown in Jupyter notebooks --> fixed

What's Changed
* Add documenation to main --> render RTD by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/186
* New minor release by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/190
* new version 0.2.2 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/193
* v0.2.3 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/211
* v0.2.4 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/215
* v1.0.0 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/219
* Update README.md by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/220
* v1.0.1 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/234
* V1.1.0 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/256
* Small updates for v1.1.1 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/271
* v1.2.0 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/280
* MetaData rework by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/281
* Search: Returning CachedIrodsPath for data objects by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/283
* Allow the tqdm progress bar to be disabled by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/284
* 285 metadata tutorial by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/286
* bug fix for ipython by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/288
* Add __setitem__ to metadata object and rename _rename method by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/289
* Improve error catching and message for add by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/290
* v1.3.0 by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/291


**Full Changelog**: https://github.com/iBridges-for-iRODS/iBridges/compare/v1.2.0...v1.3.0

- Cache scrambled non-pam passwords
- Add case sensitive search
- Protection of metadata wth keys starting with org_

What's Changed
* Change all the links to the new organization by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/272
* store actual password when no pam negotiation has happened by mmaschenk in https://github.com/iBridges-for-iRODS/iBridges/pull/274
* Update sphinx requirement from <8 to <9 by dependabot in https://github.com/iBridges-for-iRODS/iBridges/pull/273
* Cache packages and fix 3.12 issue by qubixes in https://github.com/iBridges-for-iRODS/iBridges/pull/276
* add param case_sensitive, by default False. by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/268
* Metadata blacklist by chStaiger in https://github.com/iBridges-for-iRODS/iBridges/pull/279

New Contributors
* mmaschenk made their first contribution in https://github.com/iBridges-for-iRODS/iBridges/pull/274

**Full Changelog**: https://github.com/iBridges-for-iRODS/iBridges/compare/v1.1.1...v1.2.0

Test pypi release from new github organisation.

What's Changed
* Bump pytest from 8.3.2 to 8.3.3 by dependabot in https://github.com/iBridges-for-iRods/iBridges-GUI/pull/265
* Bump pylint from 3.2.5 to 3.2.7 by dependabot in https://github.com/iBridges-for-iRods/iBridges-GUI/pull/260
* adjust size of meta and acls in browser by chStaiger in https://github.com/iBridges-for-iRods/iBridges-GUI/pull/270
* Bump pylint from 3.2.7 to 3.3.1 by dependabot in https://github.com/iBridges-for-iRods/iBridges-GUI/pull/271
* v.1.1.2 by chStaiger in https://github.com/iBridges-for-iRods/iBridges-GUI/pull/272


**Full Changelog**: https://github.com/iBridges-for-iRods/iBridges-GUI/compare/v1.1.1...v1.1.2

What's Changed
Move a to a new GitHub Organisation

* Update README.md by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/261
* Use older version of sphinx by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/262
* 263 timeout by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/264
* extending faqs by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/269
* Optimize the use of GitHub Actions resources by J535D165 in https://github.com/iBridges-for-iRods/iBridges/pull/266
* Small edits, code formatting and typos by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/270

-----
* Adding mkdir to CLI by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/137
* Move data objects and collections by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/136
* Create dependabot.yml by dometto in https://github.com/iBridges-for-iRods/iBridges/pull/143
* Check for host and port before checking network by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/139
* Update sphinx requirement from <7.0.0 to <8.0.0 by dependabot in https://github.com/iBridges-for-iRods/iBridges/pull/145
* Turning network_check into class method for GUI by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/146
* Install doc by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/147
* Fix docstring formatting error by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/140
* Add sync documentation. by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/148
* Ipath doc by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/149
* Ipath doc by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/153
* Move functions to utils by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/151
* Add missing search for data_name by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/161
* Rework API documentation by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/156
* Bugfix in search by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/162
* Don't use assert for control flow by dometto in https://github.com/iBridges-for-iRods/iBridges/pull/166
* Update iRODS path tutorial. by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/165
* Sync update by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/158
* Add tree for the iBridges CLI by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/159
* Fix spelling errors in the README by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/171
* Rewrite download/upload by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/169
* Cleanup tutorials. Create a First steps tutorial for the impatient. by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/174
* Fix behavior of parent property of IrodsPath by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/175
* Fix tutorials by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/177
* Turn None time into empty string in listing tickets. by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/178
* Add examples by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/180
* Docs cli by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/179
* Don't perform operations for files/dataobjects by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/182
* Rtd by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/183
* Update README.md by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/184
* Update README.md by dometto in https://github.com/iBridges-for-iRods/iBridges/pull/188
* Improve timeout situation with large files by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/189
* Fix operations with no up or download by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/192
* Add question if ibridges not in PATH by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/194
* Add 3.12 to classifiers by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/198
* Fix issue where root collection lists itself by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/205
* Treat path as string pattern by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/200
* Compute tutorial for streaming data by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/196
* Change default connection timeout to 25000 by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/204
* Easy connect to iRODS servers by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/207
* Fix did not work with cached passwords by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/214
* Add question for NetworkError by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/212
* Ignore symlinks creating operations by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/216
* Prep v1.0.0 by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/217
* Create v1.0.0 by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/218
* Update README.md by trel in https://github.com/iBridges-for-iRods/iBridges/pull/221
* Small change to be able to call the interactive auth from within R by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/222
* Update README.md by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/223
* 225 irods folder by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/226
* Implement aliases for the CLI by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/210
* Metadata up down by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/224
* Doc update for iBridges 1.1 by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/227
* Update docstrings across the board by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/232
* Update integration-tests-yoda.yml release-1.9 by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/235
* Update sphinx requirement from <8.0.0 to <9.0.0 by dependabot in https://github.com/iBridges-for-iRods/iBridges/pull/237
* Fix f-string issue in error message by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/240
* Main by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/244
* Modify progress bar to be updated during single files by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/242
* Fix obj_put not setting overwrite flag by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/247
* Make the iBridges search more easy to use by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/239
* Add feature to directly open files with IrodsPath by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/241
* Switch to IrodsPath, rename function by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/249
* Check for md5 checksums if remote uses that by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/248
* Fix overwrite / ignore_err flags in upload and download by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/254
* Notebooks by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/260
* Update README.md by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/261
* Use older version of sphinx by qubixes in https://github.com/iBridges-for-iRods/iBridges/pull/262
* 263 timeout by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/264
* extending faqs by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/269
* Optimize the use of GitHub Actions resources by J535D165 in https://github.com/iBridges-for-iRods/iBridges/pull/266
* Small edits, code formatting and typos by chStaiger in https://github.com/iBridges-for-iRods/iBridges/pull/270

New Contributors
* dependabot made their first contribution in https://github.com/iBridges-for-iRods/iBridges/pull/145
* trel made their first contribution in https://github.com/iBridges-for-iRods/iBridges/pull/221
* J535D165 made their first contribution in https://github.com/iBridges-for-iRods/iBridges/pull/266

**Full Changelog**: https://github.com/iBridges-for-iRods/iBridges/compare/v0.2.0...v1.1.1

API:

New progress bar taking the latest PRC development into account
Bugfix for data transfers: overwrite flag was not handled correctly
New search function: Path to search in, path pattern and metadata searches taking units into account
Open data objects from their IrodsPath
Support for md5 checksums in data transfers
CLI:

Search functionality

What's Changed
* Update sphinx requirement from <8.0.0 to <9.0.0 by dependabot in https://github.com/UtrechtUniversity/iBridges/pull/237
* Fix f-string issue in error message by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/240
* Main by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/244
* Modify progress bar to be updated during single files by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/242
* Fix obj_put not setting overwrite flag by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/247
* Make the iBridges search more easy to use by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/239
* Add feature to directly open files with IrodsPath by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/241
* Switch to IrodsPath, rename function by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/249
* Check for md5 checksums if remote uses that by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/248
* Fix overwrite / ignore_err flags in upload and download by qubixes in https://github.com/UtrechtUniversity/iBridges/pull/254
* V1.1.0 by chStaiger in https://github.com/UtrechtUniversity/iBridges/pull/256


**Full Changelog**: https://github.com/UtrechtUniversity/iBridges/compare/v1.0.1...v1.1.0