Geoh5py

What's Changed
* Update release by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/563
* Support for python 3.11 and 3.12 [GEOPY-1494] by SamuelBradley in https://github.com/MiraGeoscience/geoh5py/pull/551
* GEOPY-1609: merge main to develop branch by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/569
* GEOPY-1620: geoh5py develop branch lost fixes around drillhole group by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/573
* GEOPY-1591: unstable test test_cell_from_part by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/575
* GEOPY-1380: Convert base forms to pydantic ui json class by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/571
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/MiraGeoscience/geoh5py/pull/546
* Bump jinja2 from 3.1.3 to 3.1.4 by dependabot in https://github.com/MiraGeoscience/geoh5py/pull/552
* GEOPY-1609: update with 0.9.1 by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/578
* image description by RichardScottOZ in https://github.com/MiraGeoscience/geoh5py/pull/582
* GEOPY-1602: Refactor input arguments of class instantiation by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/568
* GEOPY-1638: Convert mesh_type uuid to class type in ObjectForm by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/583
* GEOPY-1674: Fail reading Geometric data by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/585
* GEOPY-1637: Allow default state (empty string) for all forms by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/584
* GEOPY-1697: use pydantic plugin for mypy by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/581
* DEVOPS-452: Update package with python-poetry-template by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/587
* also run tests on Windows for Python 3.11 and 3.12 by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/588
* GEOPY-1656: Always check/closed EM loops and return warning by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/591
* DEVOPS-439: Switch from poetry to hatch by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/590
* GEOPY-1710: Find more efficient computation for DrapeModel centroids by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/592
* GEOPY-1664: Property group type validation is broken by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/594
* GEOPY-1645: Update for geoh5py refactor of class instantiation by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/593
* REVERT-590: Revert "DEVOPS-439: Switch from poetry to hatch" by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/596
* GEOPY-1668: Continue refactoring on Data classes. by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/597
* GEOPY-1718: allow dependency on not bool data by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/595
* DEVOPS-440: Fixup README by using regular double quotes by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/600
* GEOPY-1738: Crash handling GI queries by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/602
* GEOPY-1706: Add empty string to uid validator and flatten method in base class an… by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/603
* GEOPY-1720: Fix handling of geometric data from reference data table with user names by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/601
* GEOPY-1749: Point simpeg-driver to geoh5py feature 0.10.0 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/604
* GEOPY-1749: Point simpeg-driver to geoh5py feature 0.10.0 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/605
* GEOPY-1749: Point simpeg-driver to geoh5py feature 0.10.0 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/606
* GEOPY-1749: Point simpeg-driver to geoh5py feature 0.10.0 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/610
* GEOPY-1574: Modify UIJson to use pydantic structure with forms by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/609
* GEOPY-1624: loaddrillhole group table as a numpy array by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/608
* GEOPY-1738: _r2 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/614
* GEOPY-1760: Fix required based on logic dependent by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/612
* GEOPY-1758: define dtytpe in DataClass as a class attribute and use this attribute where it's needed by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/613
* GEOPY-1720: _r2 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/615
* GEOPY-1767: Support Value map with bytes by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/617
* GEOPY-1770: add a method to update metadata without rewriting everything by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/618
* GEOPY-1712: Exclude RUFF005 by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/620
* DEVOPS-471: Merge windows and unix python reusable workflow in one file by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/622
* GEOPY-1719: allow input active cells instead of topography by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/621
* GEOPY-1755: Property group refactor by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/623
* GEOPY-1755: create an object to access all the data of a property group in a recarray by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/619
* DEVOPS-466: Update input variable in shared workflows by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/616
* GEOPY-1774: Re-order the inversion inputs following users comments by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/626
* DEVOPS-466: rename python_ver input variable for consistency by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/628
* GEOPY-1669: Final clean up of Object class by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/625
* GEOPY-1774: Re-order the inversion inputs following users comments by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/631
* GEOPY-1333: geoh5py uijson documentation by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/630
* GEOPY-1670: change shutil move for copy by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/632
* GEOPY-1682: Add new data_type attributes by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/633
* GEOPY-1733: Block model centroids not computed correctly for negative cell delimiters by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/634
* GEOPY-1682: Add new data_type attributes by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/637
* GEOPY-1139: update the readme of geoh5py by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/636
* GEOPY-1798: fail to open workspace due to data_type mapping expected to be "cdf" by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/643
* GEOPY-1797: wrong minimum Python version in geoh5py doc by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/640
* GEOPY-1781: tests of las-goh5 fail with geoh5 0.10.0 by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/638
* GEOPY-1139: update the readme of geoh5py by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/644
* GEOPY-1739: add new InterpretationSection group by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/627
* DEVOPS-504: Add deployment workflows by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/629
* GEOPY-1802: Copying drillhole groups crashes by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/649
* DEVOPS-511: Update deploy workflows to release pip package on pypi by SophieCurinier in https://github.com/MiraGeoscience/geoh5py/pull/647
* DEVOPS-515: adjustments: update precommit and codecov publish by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/650
* GEOPY-1165: Check for properties for Property Group Type - Implement Property Group Type: Simple by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/645
* GEOPY-1165: b by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/651
* GEOPY-1811: Use latest "Tx ID tx property" on all EM surveys. by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/652
* GEOPY-1815: Can't read DrillholeGroup with Strike/dip property_group_type by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/654

New Contributors
* SamuelBradley made their first contribution in https://github.com/MiraGeoscience/geoh5py/pull/551
* SophieCurinier made their first contribution in https://github.com/MiraGeoscience/geoh5py/pull/587

**Full Changelog**: https://github.com/MiraGeoscience/geoh5py/compare/v0.9.1...v0.10.0-beta.1

What's Changed
* GEOPY-1559: Update docs for all release branches by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/566
* GEOPY-1619: allow python 3.11, 3.12, newer numpy and scipy by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/572

**Full Changelog**: https://github.com/MiraGeoscience/geoh5py/compare/v0.9.0...v0.9.1

What's Changed

* GEOPY-1062: Add merging utility for Points
* GEOPY-1092: Add collect_values method to collect values from property_groups.
* GEOPY-1045: Add merging of DrapeModel objects
* GEOPY-1102: Add merging of curve objects
* GEOPY-1144, GEOPY-1147: Increment property_group name if already exists.
* GEOPY-1287: Fix handling of byte strings.
* GEOPY-1297: Expose data tables from DrillholeGroup.
* GEOPY-1296: Allow access of Concatenated data in array form.
* GEOPY-1335: Improve drillholes tables memory and access.
* GEOPY-1332: Adapt geoh5py for drillhole group in ui.json form.
* GEOPY-1328: Issue loading Bool data in mode="r".
* GEOPY-1364: Facilitate metadata assignation to object.
* GEOPY-1351: Implement referenced data in depth_tables add_data.
* GEOPY-1349: Fix get_data() for ConcatenatedPropertyGroup.
* GEOPY-1441: Suppress unnecessary warnings triggered in set_enabled.
* GEOPY-1434: Fix DrillholeGroup exported for monitoring directory.
* GEOPY-532: Re-order curve parts for ANALYST efficiency.
* GEOPY-1440: Better handling of integer data.
* GEOPY-1418: Clean out empty property groups on drillhole objects after data removal.
* GEOPY-1439: Allow FileData associated to DrillholeGroup.
* GEOPY-1418: Avoid removing empty arrays.
* GEOPY-1460: Fix crash on remove_vertices of points object.
* GEOPY-1450: Handle Geoimage from tiff with float layers.
* GEOPY-1418: Clean out empty property groups on drillhole objects after data removal.
* GEOPY-1503: Octree mesh cell definition not update if record array.
* GEOPY-1539: Add a locations property to expose vertices or centroids on geoh5py.objects.ObjectBase.
* GEOPY-1032, GEOPY-1111, GEOPY-1217, GEOPY-1229, GEOPY-1230, GEOPY-1311, GEOPY-1321, GEOPY-1346, GEOPY-1349, GEOPY-1562: Better handling of Drillhole objects.

General maintenance
* GEOPY-1375, GEOPY-1456, GEOPY-1472, GEOPY-1481, GEOPY-1541, GEOPY-1548, GEOPY-1564

**Full Changelog**: https://github.com/MiraGeoscience/geoh5py/compare/v0.8.0...v0.9.0

What's Changed

New features
* GEOPY-516: Add group selection uijson, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/323
* GEOPY-785: EM: Data Filters, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/317
* GEOPY-720: Interface between uijson and inversion group metadata, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/325
* GEOPY-652: Input file: Handle multi select options uijson, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/326
* GEOPY-462: Flatten 2D array with warning, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/329
* GEOPY-741: Airborne FEM survey, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/334
* GEOPY-913: ui.json update list (most minor), by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/337
* GEOPY-747: Ground FEM, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/336
* GEOPY-747: Update uuids for large-loop surveys, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/338
* GEOPY-715: Prototype joint inversion driver (single property), by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/330
* GEOPY-919: Crop GeoImage on copy_from_extent, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/343
* GEOPY-915: Clip data on 2D grid after auto-cropping, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/342
* GEOPY-846: Support visual parameters, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/335
* GEOPY-262: geoh5 docs: improve navigation / show toctree level 3, by jamiefb in https://github.com/MiraGeoscience/geoh5py/pull/358
* GEOPY-241: Explicit creation of new workspace, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/361
* GEOPY-757: Add Ground TEM large-loop to geoapps, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/363
* GEOPY-846: Support visual parameters, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/360
* GEOPY-919: Crop GeoImage on copy_from_extent, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/353
* GEOPY-695: Expose Coordinate Reference System as property of objects, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/367
* GEOPY-1002: Have a dip property to geoimage: add dip to the conversion of geoimage and grid2d, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/372
* GEOPY-1002: Have a dip property to geoimage: changing the grid2d dip, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/371
* GEOPY-999: Raise ValueError for non-monotically increasing prism indices in drape model layers setter, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/373
* GEOPY-695: Expose Coordinate Reference System as property of objects, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/374
* GEOPY-1002: Have a dip property to geoimage, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/370
* GEOPY-1012: Store depth/from-to data depending on what is provided by user, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/378
* GEOPY-766: Creating a Boolean datatype, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/381
* GEOPY-766: better managing of potential no data values, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/382
* GEOPY-993: Creating a save_as function in workspace with path checking., by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/383
* GEOPY-776: Support masking attributes, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/384
* GEOPY-1025: Improve docs strings for drape_model object, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/385
* GEOPY-1008: address some type hint problems, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/390
* GEOPY-1014: Crop geoimage by extent yields large files. Look into compression format of PIL, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/388
* GEOPY-1013: Manage warnings on geoimage copy_from_extent, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/389
* GEOPY-438: Allow property_groups query from workspace.get_entity, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/394
* GEOPY-708: Add a dependency check before warning that parameter is non-optional, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/395
* GEOPY-1035: Crash on Airborne TEM selection, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/398
* GEOPY-438: Allow property_groups query from workspace.get_entity, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/397
* GEOPY-438: Update, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/391
* GEOPY-1017: specify write compression (in scope of converting large OMF), by jamiefb in https://github.com/MiraGeoscience/geoh5py/pull/401
* GEOPY-923: Add content for all EM loop configurations, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/403
* GEOPY-479: Add zenodo doi, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/404
* GEOPY-1050: Add user guide for drapemodel, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/405
* GEOPY-1039: add group type to monitory_directory_copy, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/406
* GEOPY-1024: Prepare release geoh5py-0.8.0, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/409
* GEOPY-1032: Allow passing property group as a string to return existing property, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/451

Fixes
* GEOPY-918: Nan showing up on clipped drillhole data, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/333
* GEOPY-987: Geoimage vertices not set by default when create the object with file, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/368
* GEOPY-992: Workspace creation from non-existent file should return deprecation warning, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/377
* GEOPY-1000: change uuid for all metadata on copy of EM objects, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/379
* GEOPY-1004: Test/fix UTF-8 in name and/or path, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/380
* GEOPY-1030: Concatenated drillhole data stored in property group can have different lengths when it should be collocated, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/392
* GEOPY-1042: cannot create several property groups, by MatthieuCMira in https://github.com/MiraGeoscience/geoh5py/pull/400
* GEOPY-1055: ConcatenatedDrillhole object from and to properties don't handle empty property list correctly, by benk-mira in https://github.com/MiraGeoscience/geoh5py/pull/402
* GEOPY-1067: Error reading concatenated property_groups, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/410
* GEOPY-1080: Value map not updated, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/415
* GEOPY-1127: Fix warnings about group optional, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/442

Technical changes
* GEOPY-893: Update develop with 0.7.0, by domfournier in https://github.com/MiraGeoscience/geoh5py/pull/327
* GEOPY-947: replace os.path by pathlib, by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/347
* GEOPY-976: update version of pip, by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/357
* GEOPY-985: remove obsolete setup.py, by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/362
* GEOPY-882: fix codecov report, by andrewg-mira in https://github.com/MiraGeoscience/geoh5py/pull/387
* GEOPY-116: set Pillow to at least 10.0.1, by sebhmg in https://github.com/MiraGeoscience/geoh5py/pull/446

**Full Changelog**: https://github.com/MiraGeoscience/geoh5py/compare/v0.7.1...v0.8.0

--------------------

GEOPY-967: Fix issue with copying drillholes from extent.

Main changes for geoh5py version 0.7.0 are:

New features:
- Add and improve function to copy entities from extent. (GEOPY-857, GEOPY-877)
- Handle geoh5 conversion from 4.2 (geoh5 v2.1) saved as 4.1 (geoh5 v2.0) format. (GEOPY-876)

Bug fixes:
- Throw user warning if change mode to "r+" to "r". (GEOPY-537)
- Fixes on drillhole copy and data selection. (GEOPY-667, GEOPY-668, GEOPY-723, GEOPY-848)
- Fix NDV not recognized on concatenated data. (GEOPY-851)

Technical issues:
- Add measure of maintainability with code climate. (GEOPY-862)