BrainGlobe Atlas API - v2.3.0

What's Changed

• Improve core test coverage by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/535
• Update dependencies, add docstrings, fix url error handling by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/542
• Add tests for atlasgen annotationutils by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/537
• minor bug fix getstructureterminal_nodes by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/544
• Add tests for atlasgen metadata_utils by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/538
• minor bug fix atlasgen/meshutils by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/548
• fix minor bugs in atlasgen/structures by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/552
• Add tests for atlasgen structures by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/543
• Code coverage for brainglobe_atlasapi/config.py by @mxochicale in https://github.com/brainglobe/brainglobe-atlasapi/pull/549
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/brainglobe/brainglobe-atlasapi/pull/558
• Code coverage for brainglobe_atlasapi/core.py by @mxochicale in https://github.com/brainglobe/brainglobe-atlasapi/pull/551
• bug fixes atlasgen/mesh_utils by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/557
• remove xfail marker from atlasgen/test_structures by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/560
• Increase atlasgen mesh_utils coverage by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/556
• Add a note in the readme to link to the developer's guide by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/561
• Remove all references to the transformation to the BrainGlobe orientation by @thisisrick25 in https://github.com/brainglobe/brainglobe-atlasapi/pull/555
• Use correct directory for downloading atlases on CI by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/565
• Removed unreliable parallel running of mesh creation by @pranav33317 in https://github.com/brainglobe/brainglobe-atlasapi/pull/546
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/brainglobe/brainglobe-atlasapi/pull/567
• Allen bbp ccfv3a entire mouse brain, improve mesh utils, and add metadata filtering to wrapup by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/500
• add ccfv3a to table by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/575
• fix link to ccfv3a docs in readme by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/579
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/brainglobe/brainglobe-atlasapi/pull/580
• fix checkginstatus when GIN server is down by @carlocastoldi in https://github.com/brainglobe/brainglobe-atlasapi/pull/585
• Add additional_references keys on construction by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/586
• fix typo in kim dev p56 by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/590
• [588]: Removing function that doesnt exist, passing resolution directly for now by @Wolfffff in https://github.com/brainglobe/brainglobe-atlasapi/pull/594
• change from imsave to imwrite, updated version requirement for tifffi… by @Skxsmy in https://github.com/brainglobe/brainglobe-atlasapi/pull/597
• [586]: Improvements and refactoring to handle units in utils by @Wolfffff in https://github.com/brainglobe/brainglobe-atlasapi/pull/600
• [New Atlas]: Adding basic bumblebee atlas by @Wolfffff in https://github.com/brainglobe/brainglobe-atlasapi/pull/587
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/brainglobe/brainglobe-atlasapi/pull/610
• use unit consistently across conditionals in atlas_name_from_repr by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/609
• fix bee resolution in README list of atlases by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/611
• specify utf-8 explicitly when packaging atlases by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/605
• applying modal filter to wingdisc annotation before packing by @Skxsmy in https://github.com/brainglobe/brainglobe-atlasapi/pull/599
• Wing disc atlasapi script v0.1 by @Skxsmy in https://github.com/brainglobe/brainglobe-atlasapi/pull/595
• Wing disc script by @Skxsmy in https://github.com/brainglobe/brainglobe-atlasapi/pull/615
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/brainglobe/brainglobe-atlasapi/pull/618

New Contributors

• @thisisrick25 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/555
• @pranav33317 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/546
• @Wolfffff made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/594
• @Skxsmy made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/597

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.2.1...v2.3.0

Scientific Software - Peer-reviewed - Python
Published by alessandrofelder 10 months ago

BrainGlobe Atlas API - v2.2.1

What's Changed

• minor bug fix utils.atlasreprfrom_name by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/520
• minor bug fix utils.retrieveoverhttp by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/521
• Add Cuttlebase cuttlefish atlas by @kjungwoo5 in https://github.com/brainglobe/brainglobe-atlasapi/pull/338
• minor bug fix bgatlas.repr_ by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/523
• Improve coverage for bg_atlas.py by @mxochicale in https://github.com/brainglobe/brainglobe-atlasapi/pull/517
• Add blackcap atlas to readme by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/527
• add test_str by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/526
• Increase utils test coverage by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/518
• Increase atlas name validation stringency by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/529
• Increase update_atlases test coverage by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/531
• Validate metadata by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/530
• Increase cli test coverage by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/533
• Improve coverage list_atlases by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/532
• [ENH] Fix internet connection check for global accessibility by @samadpls in https://github.com/brainglobe/brainglobe-atlasapi/pull/536

New Contributors

• @mxochicale made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/517
• @samadpls made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/536

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.2.0...v2.2.1

Scientific Software - Peer-reviewed - Python
Published by adamltyson about 1 year ago

BrainGlobe Atlas API - v2.2.0

What's Changed

• Remove rich tracebacks by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/502
• Remove main script by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/504
• Remove inspectmeshesfolder function by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/505
• Standardise text formatting by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/507
• new atlas file added - for cat by @HenryCrosswell in https://github.com/brainglobe/brainglobe-atlasapi/pull/403
• Update Python versions to adhere to SPEC 0 and remove Intel testing on macOS by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/509
• add cat to readme table by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/508
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/513
• update setuptools dependency by @stellaprins in https://github.com/brainglobe/brainglobe-atlasapi/pull/516
• Add fn_update as an optional argument by @kira1228 in https://github.com/brainglobe/brainglobe-atlasapi/pull/519

New Contributors

• @HenryCrosswell made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/403
• @stellaprins made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/516
• @kira1228 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/519

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.1.0...v2.2.0

Scientific Software - Peer-reviewed - Python
Published by alessandrofelder about 1 year ago

BrainGlobe Atlas API - v2.1.0

What's Changed

• symmetrise mouselemur annotations by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/455
• Documents hemispheres behaviour for odd size templates by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/457
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/460
• update all script names to match api names by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/462
• correct version typo by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/493
• Australian mouse brain by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/409
• Ignore atlas packaging scripts in test coverage by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/494
• codecov-badge-to-main by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/495
• Add additional atlas validation functions. by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/453
• second version of perens lsfm atlas by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/458
• Table cleanup by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/496
• Integrating atlas validation in wrapup.py by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/445
• Adds fixture to download atlases for test_validation.py by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/498
• Adds fixture to mock home for local testing by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/499
• add support for custom offline atlases by @carlocastoldi in https://github.com/brainglobe/brainglobe-atlasapi/pull/497

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.13...v2.1.0

Scientific Software - Peer-reviewed - Python
Published by adamltyson over 1 year ago

BrainGlobe Atlas API - v2.0.13

What's Changed

• added nadkarnimrimouselemur by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/411
• add mouse lemur to docs by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/450
• update packaging script for new blackcap atlas name by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/452
• fix hemispheres being cut slightly off-centred by @carlocastoldi in https://github.com/brainglobe/brainglobe-atlasapi/pull/454
• Use pypa/gh-action-pypi-publish stable release v1 by @lochhh in https://github.com/brainglobe/brainglobe-atlasapi/pull/456

New Contributors

• @lochhh made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/456

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.12...v2.0.13

Scientific Software - Peer-reviewed - Python
Published by IgorTatarnikov over 1 year ago

BrainGlobe Atlas API - v2.0.12

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/436
• Hemisphere improvements to axolotl atlas by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/438
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/443
• first draft of symmetrical 25um blackcap atlas by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/314
• Add all Kim's DevCCFv1 atlases by @carlocastoldi in https://github.com/brainglobe/brainglobe-atlasapi/pull/441
• Perens stereotaxic mri by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/370
• document kim dev atlases in readme by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/444
• make kim dev atlas names lowercase by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/446
• Make atlas API more robust offline by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/448
• Replace NIU upload action with separate actions by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/449

New Contributors

• @carlocastoldi made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/441

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.11...v2.0.12

Scientific Software - Peer-reviewed - Python
Published by IgorTatarnikov over 1 year ago

BrainGlobe Atlas API - v2.0.11

What's Changed

• Add api name of atlases to readme by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/422
• Add Prairie Vole atlas to list by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/420
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/424
• Standardising atlas file downloading by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/351
• Notify slack on scheduled test failure by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/427
• Fix typo in atlas list by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/431
• Fail gracefully if cache directory is read only by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/430
• Add extra check for response code fetching last_versions by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/432

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.10...v2.0.11

Scientific Software - Peer-reviewed - Python
Published by IgorTatarnikov over 1 year ago

BrainGlobe Atlas API - v2.0.10

What's Changed

• Schedule tests to run weekly by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/412
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/414
• updated age of cavefish atlas based on correction by author by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/415
• Atlas packaging template by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/400
• Make list atlas function more robust by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/417
• Add praire vole atlas packaging script by @sacha091 in https://github.com/brainglobe/brainglobe-atlasapi/pull/336
• Deal with downloaded atlases with _v in the name by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/419

New Contributors

• @sacha091 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/336

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.9...v2.0.10

Scientific Software - Peer-reviewed - Python
Published by adamltyson over 1 year ago

BrainGlobe Atlas API - v2.0.9

What's Changed

• update waxholm to newest version by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/395
• Allen Human brain incorrectly listed as 100 micron by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/398
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/401
• Create .brainglobe dir if it doesn't exist when fetching atlas versions by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/402

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.8...v2.0.9

Scientific Software - Peer-reviewed - Python
Published by IgorTatarnikov over 1 year ago

BrainGlobe Atlas API - v2.0.8

What's Changed

• Add cavefish atlas :fish: by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/277
• add cavefish to readme by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/312
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/317
• Standardise contact information in readme by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/320
• Remove template script by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/325
• Ensure no allen_cord meshes are black by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/328
• Fix failing test by always using the same file from GIN by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-atlasapi/pull/329
• Script to generate Allen mouse brain atlas with barrel annotations by @abisi in https://github.com/brainglobe/brainglobe-atlasapi/pull/313
• Fixed spelling, grammatical and formatting errors, and removed empty code box. by @kjungwoo5 in https://github.com/brainglobe/brainglobe-atlasapi/pull/335
• initial Axolotl Atlas Implementation by @saimaabdus19 in https://github.com/brainglobe/brainglobe-atlasapi/pull/327
• use capital letter of each word for axolotl main structures by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/343
• Update atlas list by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/345
• Add Axolotl Pooch hash by @saimaabdus19 in https://github.com/brainglobe/brainglobe-atlasapi/pull/347
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/346
• Corrected orientation of the axolotl atlas by @saimaabdus19 in https://github.com/brainglobe/brainglobe-atlasapi/pull/348
• Fixing admba by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/322
• Removal of spurious pixels by @saimaabdus19 in https://github.com/brainglobe/brainglobe-atlasapi/pull/349
• modal-filter annotations before meshing by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/350
• merge atlaslink and atlasfile_url by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/352
• add axolotl to readme by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/353
• Standardise bullet formatting to remove extra whitespace by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/355
• created table for atlases by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/357
• fixed bug where progress bar didn't update properly by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/369
• Loading atlas with no Internet by @saarah815 in https://github.com/brainglobe/brainglobe-atlasapi/pull/358

New Contributors

• @abisi made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/313
• @kjungwoo5 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/335
• @saimaabdus19 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/327
• @saarah815 made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/358

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.7...v2.0.8

Scientific Software - Peer-reviewed - Python
Published by alessandrofelder almost 2 years ago

BrainGlobe Atlas API - v2.0.7

Dependency Slimming

Main purpose of this release is a number of small fixes to atlases, and slimming down of the dependencies of this package.

If you are only interested in the AtlasAPI, a default install will no longer fetch the dependencies that are required for generating a new atlas. If you were previously using this package to generate atlases, you will need to install it with the optional atlasgen dependency.

What's Changed

• Return brainglobe list in alphabetical order by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/298
• Return "Outside atlas" rather than key error by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/299
• Remove slow test marker by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/300
• Cache atlases to speed up CI by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/301
• Fixing human atlas script by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/290
• Fix AZBA by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/305
• fixing kim dev atlases by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/304
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/308
• Update supported Python versions by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/309
• Move pymcubes to an optional dependency. by @willGraham01 in https://github.com/brainglobe/brainglobe-atlasapi/pull/310

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.6...v2.0.7

Scientific Software - Peer-reviewed - Python
Published by willGraham01 almost 2 years ago

BrainGlobe Atlas API - v2.0.6

What's Changed

• add codecov token by @K-Meech in https://github.com/brainglobe/brainglobe-atlasapi/pull/269
• run CI on both types of Mac by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/272
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-atlasapi/pull/278
• Fixes to Perens and Kim mouse atlases by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/271
• Fix orientation issue in perens lsfm atlas by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/283
• Minor fixes to the atlas update workflow by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/287
• Update use of brainio to brainglobe-utils by @adamltyson in https://github.com/brainglobe/brainglobe-atlasapi/pull/288

New Contributors

• @K-Meech made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/269

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.5...v2.0.6

Scientific Software - Peer-reviewed - Python
Published by alessandrofelder about 2 years ago

BrainGlobe Atlas API - v2.0.5

What's Changed

• restore entrypoint by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/264
• add two simple additional validation functions by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/261

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.4...v2.0.5

Scientific Software - Peer-reviewed - Python
Published by alessandrofelder about 2 years ago

BrainGlobe Atlas API - v2.0.4

Dependency Updates

Removes unused brainio dependency and removes duplicate entries that are present in pyproject.toml.

What's Changed

• Remove duplicate dependencies in pyproject by @willGraham01 in https://github.com/brainglobe/brainglobe-atlasapi/pull/258

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.3...v2.0.4

Scientific Software - Peer-reviewed - Python
Published by willGraham01 about 2 years ago

BrainGlobe Atlas API - v2.0.3

Removes brainglobe-utils circular dependency

Removes this package's un-necessary dependency on brainglobe-utils by retiring a function that is no longer in use across the BrainGlobe tool-suite.

What's Changed

• remove loadlabelledvolume by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/257

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.2...v2.0.3

Scientific Software - Peer-reviewed - Python
Published by willGraham01 about 2 years ago

BrainGlobe Atlas API - v2.0.2

What's Changed

• testing and fixing outdated atlas generation scripts by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/249
• Fixed broken link in the add atlas readme. by @PolarBean in https://github.com/brainglobe/brainglobe-atlasapi/pull/252
• Fixing princeton_mouse atlas mesh by @viktorpm in https://github.com/brainglobe/brainglobe-atlasapi/pull/253
• fix metadata key by @alessandrofelder in https://github.com/brainglobe/brainglobe-atlasapi/pull/255

New Contributors

• @viktorpm made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/249
• @PolarBean made their first contribution in https://github.com/brainglobe/brainglobe-atlasapi/pull/252

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.1...v2.0.2

Scientific Software - Peer-reviewed - Python
Published by alessandrofelder about 2 years ago

BrainGlobe Atlas API - v2.0.1

Patch unnecessary brainglobe-utils dependency

The package metadata was fetching brainglobe-utils, however this package does not depend on it.

What's Changed

• Remove brainglobe-utils dependency that we don't need nor use by @willGraham01 in https://github.com/brainglobe/brainglobe-atlasapi/pull/248

Full Changelog: https://github.com/brainglobe/brainglobe-atlasapi/compare/v2.0.0...v2.0.1

Scientific Software - Peer-reviewed - Python
Published by willGraham01 over 2 years ago

BrainGlobe Atlas API - v1.0.4

Rename and merge with bg-atlasgen

This package will be merging with bg-atlasgen, and then renaming to brainglobe-atlasapi for consistency with other BrainGlobe tools. See https://github.com/brainglobe/BrainGlobe/issues/43 for details.

What's Changed

• Add CITATION.cff by @willGraham01 in https://github.com/brainglobe/bg-atlasapi/pull/192
• Update testanddeploy.yml by @alessandrofelder in https://github.com/brainglobe/bg-atlasapi/pull/194
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/195
• Add check manifest to CI by @willGraham01 in https://github.com/brainglobe/bg-atlasapi/pull/196
• Add PyArrow as dependency by @willGraham01 in https://github.com/brainglobe/bg-atlasapi/pull/197
• Prepare for merge and rename by @willGraham01 in https://github.com/brainglobe/bg-atlasapi/pull/198

New Contributors

• @alessandrofelder made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/194

Full Changelog: https://github.com/brainglobe/bg-atlasapi/compare/v1.0.3...v1.0.4

Scientific Software - Peer-reviewed - Python
Published by willGraham01 over 2 years ago

BrainGlobe Atlas API - v1.0.3

Bump to brainglobe-space dependency

What's Changed

• update travis by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/79
• Update testing by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/80
• Update readme by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/84
• Updating pbar and a couple other things by @FedeClaudi in https://github.com/brainglobe/bg-atlasapi/pull/87
• Remove auto-print upon BrainGlobeAtlas construction by @nickdelgrosso in https://github.com/brainglobe/bg-atlasapi/pull/89
• Atlas metadata print out by @FedeClaudi in https://github.com/brainglobe/bg-atlasapi/pull/91
• Add osten mouse atlas to readme by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/93
• Move to GitHub actions by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/95
• Create code of conduct by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/97
• List all available atlases and their versions in machine-readable format (2) by @nickdelgrosso in https://github.com/brainglobe/bg-atlasapi/pull/101
• Fix linting problems, and test on PR by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/102
• Fix NumPy future warning on get structure mask by @seankmartin in https://github.com/brainglobe/bg-atlasapi/pull/106
• moved print to BrainGlobeAtlas by @vigji in https://github.com/brainglobe/bg-atlasapi/pull/108
• Changes to config file location by @chrisroat in https://github.com/brainglobe/bg-atlasapi/pull/111
• Optimize get_structure_mask for structures with many children by @sdiebolt in https://github.com/brainglobe/bg-atlasapi/pull/120
• Lint setup fix by @vigji in https://github.com/brainglobe/bg-atlasapi/pull/122
• Fix the - in requirements by @paddyroddy in https://github.com/brainglobe/bg-atlasapi/pull/124
• Allow -h and --help for help by @paddyroddy in https://github.com/brainglobe/bg-atlasapi/pull/125
• Add an optional attribute to handle updates during atlas downloads by @yoda-vid in https://github.com/brainglobe/bg-atlasapi/pull/126
• Align with other BG packages by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/127
• Tutorial notebook improvements by @raacampbell in https://github.com/brainglobe/bg-atlasapi/pull/128
• Add new atlas by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/133
• Update supported Python versions by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/135
• Replace brainglobe with NI actions by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/137
• Use standard pre-commit config by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/138
• Switch to pyproject.toml by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/139
• Error on warnings raised in tests by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/140
• Turn off codecov comments by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/145
• Build wheel when building package by @dstansby in https://github.com/brainglobe/bg-atlasapi/pull/144
• Typo fixes by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/151
• Update links by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/152
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/153
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/154
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/155
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/156
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/158
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/159
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/160
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/162
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/164
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/165
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/166
• Set pre-commit autoupdate frequency to monthly by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/167
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/168
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/171
• Fix download progress bar by @IgorTatarnikov in https://github.com/brainglobe/bg-atlasapi/pull/178
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/181
• Remove banner image by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/185
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/186
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/bg-atlasapi/pull/188
• Add citation info by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/189
• Various housekeeping by @adamltyson in https://github.com/brainglobe/bg-atlasapi/pull/190
• Bump to brainglobe space by @willGraham01 in https://github.com/brainglobe/bg-atlasapi/pull/191

New Contributors

• @nickdelgrosso made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/89
• @seankmartin made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/106
• @chrisroat made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/111
• @sdiebolt made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/120
• @yoda-vid made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/126
• @raacampbell made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/128
• @dstansby made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/135
• @pre-commit-ci made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/153
• @IgorTatarnikov made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/178
• @willGraham01 made their first contribution in https://github.com/brainglobe/bg-atlasapi/pull/191

Full Changelog: https://github.com/brainglobe/bg-atlasapi/compare/v1.0.0...v1.0.3

Scientific Software - Peer-reviewed - Python
Published by willGraham01 over 2 years ago

BrainGlobe Atlas API - Version 1.0.0

Scientific Software - Peer-reviewed - Python
Published by adamltyson over 5 years ago

BrainGlobe Atlas API - Version 0.1.0

Initial public release.

Scientific Software - Peer-reviewed - Python
Published by adamltyson almost 6 years ago